From 4fa10119f1d94bcec34c289198ca2cebcb6f210a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= <lukas.krupcik@vsb.cz>
Date: Tue, 19 Jul 2016 14:58:33 +0200
Subject: [PATCH] update script
---
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+ <!-- TODO -->
+
+</div>
+</body>
+</html>
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation.md b/docs.it4i.cz/anselm-cluster-documentation.md
index 6ff741f5e..7d0f0258c 100644
--- a/docs.it4i.cz/anselm-cluster-documentation.md
+++ b/docs.it4i.cz/anselm-cluster-documentation.md
@@ -40,4 +40,3 @@ resources](get-started-with-it4innovations/applying-for-resources.html),
credentials,](get-started-with-it4innovations/obtaining-login-credentials.html)
and [access the
cluster](anselm-cluster-documentation/accessing-the-cluster.html).
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.html b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.html
new file mode 100644
index 000000000..f381892c7
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.html
@@ -0,0 +1,842 @@
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+
+
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+
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+ <dl class="portalMessage info" id="kssPortalMessage" style="display:none">
+ <dt>Info</dt>
+ <dd></dd>
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+ <div id="viewlet-above-content-title"></div>
+
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+
+ <h1 id="parent-fieldname-title" class="documentFirstHeading">
+ Shell access and data transfer
+ </h1>
+
+
+
+
+ <div id="viewlet-below-content-title">
+</div>
+
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+<dl id="document-toc" class="portlet toc" style="display: none">
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+ <div id="content-core">
+
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+
+ <div id="parent-fieldname-text-ceca9cfaad22488eaa73549210740832" class="">
+ <h2 class=" ">Interactive Login</h2>
+<p>The Anselm cluster is accessed by SSH protocol via login nodes login1 and login2 at address anselm.it4i.cz. The login nodes may be addressed specifically, by prepending the login node name to the address.</p>
+<table class="listing">
+<tbody>
+<tr><th>Login address</th><th>Port</th><th>Protocol</th><th>Login node</th></tr>
+<tr class="even">
+<td>anselm.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>round-robin DNS record for login1 and login2</td>
+</tr>
+<tr class="odd">
+<td>login1.anselm.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login1</td>
+</tr>
+<tr class="even">
+<td>login2.anselm.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login2</td>
+</tr>
+</tbody>
+</table>
+<p>The authentication is by the <a href="../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html" title="" target="_self" class="internal-link">private key</a></p>
+<p class="callout">Please verify SSH fingerprints during the first logon. They are identical on all login nodes:<span class="monospace"><br />29:b3:f4:64:b0:73:f5:6f:a7:85:0f:e0:0d:be:76:bf (DSA)<br />d4:6f:5c:18:f4:3f:70:ef:bc:fc:cc:2b:fd:13:36:b7 (RSA)</span></p>
+<p>Â </p>
+<p>Private keys authentication:</p>
+<p>On <strong>Linux</strong> or <strong>Mac</strong>, use</p>
+<pre class="prettyprint lang-sh">local $ ssh -i /path/to/id_rsa username@anselm.it4i.cz</pre>
+<p>If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this command to set lower permissions to private key file.</p>
+<pre class="prettyprint lang-sh">local $ chmod 600 /path/to/id_rsa</pre>
+<p>On <strong>Windows</strong>, use <a href="../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html" title="" target="_self" class="internal-link">PuTTY ssh client</a>.</p>
+<p>After logging in, you will see the command prompt:</p>
+<pre class=" "> _<br /> /\ | |<br /> / \ _ __ ___ ___| |_ __ ___<br /> / /\ \ | '_ \/ __|/ _ \ | '_ ` _ \<br /> / ____ \| | | \__ \ __/ | | | | | |<br /> /_/ \_\_| |_|___/\___|_|_| |_| |_|<br /><br /><br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http://www.it4i.cz/?lang=en<br /><br /><br />Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com<br />[username@login2.anselm ~]$</pre>
+<p class="callout">The environment is <strong>not</strong> shared between login nodes, except for <a href="accessing-the-cluster/storage-1.html#section-1" title="" target="_self" class="external-link">shared filesystems</a>.</p>
+<h2 class=" ">Data Transfer</h2>
+<p>Data in and out of the system may be transferred by the <a class="external-link" href="http://en.wikipedia.org/wiki/Secure_copy" target="_self" title="">scp</a> and sftp protocols. <span class="discreet">(Not available yet.) In case large volumes of data are transferred, use dedicated data mover node dm1.anselm.it4i.cz for increased performance.</span></p>
+<table class="listing">
+<tbody>
+<tr><th>Address</th><th>Port</th><th>Protocol</th></tr>
+<tr class="even">
+<td>anselm.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="odd">
+<td>login1.anselm.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="even">
+<td>login2.anselm.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="odd">
+<td><span class="discreet">dm1.anselm.it4i.cz</span></td>
+<td><span class="discreet">22</span></td>
+<td><span class="discreet">scp, sftp</span></td>
+</tr>
+</tbody>
+</table>
+<p>Â The authentication is by the <a href="../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html" title="" target="_self" class="internal-link">private key</a></p>
+<p class="callout">Data transfer rates up to <strong>160MB/s</strong> can be achieved with scp or sftp. 1TB may be transferred in 1:50h.</p>
+<p>To achieve 160MB/s transfer rates, the end user must be connected by 10G line all the way to IT4Innovations and use computer with fast processor for the transfer. Using Gigabit ethernet connection, up to 110MB/s may be expected. Fast cipher (aes128-ctr) should be used.</p>
+<p class="callout">If you experience degraded data transfer performance, consult your local network provider.</p>
+<p>On linux or Mac, use scp or sftp client to transfer the data to Anselm:</p>
+<pre class="prettyprint lang-sh">local $ scp -i /path/to/id_rsa my-local-file username@anselm.it4i.cz:directory/file</pre>
+<pre class="prettyprint lang-sh">local $ scp -i /path/to/id_rsa -r my-local-dir username@anselm.it4i.cz:directory</pre>
+<blockquote>or</blockquote>
+<pre class="prettyprint lang-sh">local $ sftp -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz</pre>
+<p>Very convenient way to transfer files in and out of the Anselm computer is via the fuse filesystem <a class="external-link" href="http://linux.die.net/man/1/sshfs" target="_self" title="">sshfs</a></p>
+<pre class="prettyprint lang-sh">local $ sshfs -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz:. mountpoint</pre>
+<p>Using sshfs, the users Anselm home directory will be mounted on your local computer, just like an external disk.</p>
+<p>Learn more on ssh, scp and sshfs by reading the manpages</p>
+<pre class="prettyprint lang-sh">$ man ssh<br />$ man scp<br />$ man sshfs</pre>
+<p>On Windows, use <a class="external-link" href="http://winscp.net/eng/download.php" target="_self" title="">WinSCP client</a> to transfer the data. The <a class="external-link" href="http://code.google.com/p/win-sshfs/" target="_self" title="">win-sshfs client</a> provides a way to mount the Anselm filesystems directly as an external disc.</p>
+<p>More information about the shared file systems is available <a href="storage.html" title="" target="_self" class="internal-link">here</a>.</p>
+
+ </div>
+
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.md b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.md
index ab6ec152f..93d7a7645 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.md
@@ -59,7 +59,7 @@ After logging in, you will see the command prompt:
                       http://www.it4i.cz/?lang=en
- Last loginTue Jul 9 15:57:38 2013 from your-host.example.com
+ Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com
[username@login2.anselm ~]$
The environment is **not** shared between login nodes, except for
@@ -139,4 +139,3 @@ way to mount the Anselm filesystems directly as an external disc.
More information about the shared file systems is available
[here](storage.html).
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.html b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.html
new file mode 100644
index 000000000..d2e958006
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.html
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+ Outgoing connections
+ </h1>
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+
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+ <div id="parent-fieldname-text-8909c73afd644ccdb3bb338f910a6285" class="">
+ <h2 class=" ">Connection restrictions</h2>
+<p>Outgoing connections, from Anselm Cluster login nodes to the outside world, are restricted to following ports:</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>Port</th><th>Protocol</th></tr>
+<tr class="even">
+<td>22</td>
+<td>ssh</td>
+</tr>
+<tr class="odd">
+<td>80</td>
+<td>http</td>
+</tr>
+<tr class="even">
+<td>443</td>
+<td>https</td>
+</tr>
+<tr class="odd">
+<td>9418</td>
+<td>git</td>
+</tr>
+</tbody>
+</table>
+<p class="callout">Please use<strong> ssh port forwarding</strong> and proxy servers to connect from Anselm to all other remote ports.</p>
+<p class=" ">Outgoing connections, from Anselm Cluster compute nodes are restricted to the internal network. Direct connections form compute nodes to outside world are cut.</p>
+<h2 class=" ">Port forwarding</h2>
+<h3 class=" "><a name="port-forwarding-from-login-nodes"></a>Port forwarding from login nodes</h3>
+<p class="callout">Port forwarding allows an application running on Anselm to connect to arbitrary remote host and port.</p>
+<p class=" ">It works by tunneling the connection from Anselm back to users workstation and forwarding from the workstation to the remote host.</p>
+<p>Pick some unused port on Anselm login node (for example 6000) and establish the port forwarding:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ ssh </span><span class="pun">-</span><span class="pln">R </span><span class="lit">6000</span><span class="pun">:</span><span class="pln">remote</span><span class="pun">.</span><span class="pln">host</span><span class="pun">.</span><span class="pln">com</span><span class="pun">:</span><span class="lit">1234</span><span class="pln"> anselm</span><span class="pun">.</span><span class="pln">it4i</span><span class="pun">.</span><span class="pln">cz</span></pre>
+<p>In this example, we establish port forwarding between port 6000 on Anselm and port 1234 on the remote.host.com. By accessing localhost:6000 on Anselm, an application will see response of remote.host.com:1234. The traffic will run via users local workstation.</p>
+<p class=" ">Port forwarding may be done<strong> using PuTTY</strong> as well. On the PuTTY Configuration screen, load your Anselm configuration first. Then go to Connection->SSH->Tunnels to set up the port forwarding. Click Remote radio button. Insert 6000 to Source port textbox. Insert remote.host.com:1234. Click Add button, then Open.</p>
+<p class=" ">Port forwarding may be established directly to the remote host. However, this requires that user has ssh access to remote.host.com</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ ssh </span><span class="pun">-</span><span class="pln">L </span><span class="lit">6000</span><span class="pun">:</span><span class="pln">localhost</span><span class="pun">:</span><span class="lit">1234</span><span class="pln"> remote</span><span class="pun">.</span><span class="pln">host</span><span class="pun">.</span><span class="pln">com</span></pre>
+<p class=" ">Note: Port number 6000 is chosen as an example only. Pick any free port.</p>
+<h3 class=" "><a name="port-forwarding-from-compute-nodes"></a>Port forwarding from compute nodes</h3>
+<p class=" ">Remote port forwarding from compute nodes allows applications running on the compute nodes to access hosts outside Anselm Cluster.</p>
+<p class=" ">First, establish the remote port forwarding form the login node, as <a class="anchor-link" href="outgoing-connections.html#port-forwarding-from-login-nodes" target="_self" title="">described above</a>.</p>
+<p class=" ">Second, invoke port forwarding from the compute node to the login node. Insert following line into your jobscript or interactive shell</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ ssh </span><span class="pun">-</span><span class="pln">TN </span><span class="pun">-</span><span class="pln">f </span><span class="pun">-</span><span class="pln">L </span><span class="lit">6000</span><span class="pun">:</span><span class="pln">localhost</span><span class="pun">:</span><span class="lit">6000</span><span class="pln"> login1</span></pre>
+<p>In this example, we assume that port forwarding from login1:6000 to remote.host.com:1234 has been established beforehand. By accessing localhost:6000, an application running on a compute node will see response of remote.host.com:1234</p>
+<h3 class=" ">Using proxy servers</h3>
+<p>Port forwarding is static, each single port is mapped to a particular port on remote host. Connection to other remote host, requires new forward.</p>
+<p class="callout">Applications with inbuilt proxy support, experience unlimited access to remote hosts, via single proxy server.</p>
+<p>To establish local proxy server on your workstation, install and run SOCKS proxy server software. On Linux, sshd demon provides the functionality. To establish SOCKS proxy server listening on port 1080 run:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ ssh </span><span class="pun">-</span><span class="pln">D </span><span class="lit">1080</span><span class="pln"> localhost</span></pre>
+<p>On Windows, install and run the free, open source <a class="external-link" href="http://sockspuppet.com/" target="_self" title="">Sock Puppet</a> server.</p>
+<p>Once the proxy server is running, establish ssh port forwarding from Anselm to the proxy server, port 1080, exactly as <a class="anchor-link" href="outgoing-connections.html#port-forwarding-from-login-nodes" target="_self" title="">described above</a>.</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ ssh </span><span class="pun">-</span><span class="pln">R </span><span class="lit">6000</span><span class="pun">:</span><span class="pln">localhost</span><span class="pun">:</span><span class="lit">1080</span><span class="pln"> anselm</span><span class="pun">.</span><span class="pln">it4i</span><span class="pun">.</span><span class="pln">cz</span></pre>
+<p>Now, configure the applications proxy settings to <strong>localhost:6000</strong>. Use port forwarding to access the <a class="anchor-link" href="outgoing-connections.html#port-forwarding-from-compute-nodes" target="_self" title="">proxy server from compute nodes</a> as well .</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
index 30f6a45a8..b18fe9a02 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
@@ -61,7 +61,7 @@ this requires that user has ssh access to remote.host.com
$ ssh -L 6000:localhost:1234 remote.host.com
```
-NotePort number 6000 is chosen as an example only. Pick any free port.
+Note: Port number 6000 is chosen as an example only. Pick any free port.
### []()Port forwarding from compute nodes
@@ -117,4 +117,3 @@ Now, configure the applications proxy settings to **localhost:6000**.
Use port forwarding to access the [proxy server from compute
nodes](outgoing-connections.html#port-forwarding-from-compute-nodes)
as well .
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html
new file mode 100644
index 000000000..7dea5f270
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html
@@ -0,0 +1,842 @@
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+</div>
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+ <dt>Info</dt>
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+ Shell access and data transfer
+ </h1>
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+</div>
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+ <div id="parent-fieldname-text-ceca9cfaad22488eaa73549210740832" class="">
+ <h2 class=" ">Interactive Login</h2>
+<p>The Anselm cluster is accessed by SSH protocol via login nodes login1 and login2 at address anselm.it4i.cz. The login nodes may be addressed specifically, by prepending the login node name to the address.</p>
+<table class="listing">
+<tbody>
+<tr><th>Login address</th><th>Port</th><th>Protocol</th><th>Login node</th></tr>
+<tr class="even">
+<td>anselm.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>round-robin DNS record for login1 and login2</td>
+</tr>
+<tr class="odd">
+<td>login1.anselm.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login1</td>
+</tr>
+<tr class="even">
+<td>login2.anselm.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login2</td>
+</tr>
+</tbody>
+</table>
+<p>The authentication is by the <a href="../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html" title="" target="_self" class="internal-link">private key</a></p>
+<p class="callout">Please verify SSH fingerprints during the first logon. They are identical on all login nodes:<span class="monospace"><br />29:b3:f4:64:b0:73:f5:6f:a7:85:0f:e0:0d:be:76:bf (DSA)<br />d4:6f:5c:18:f4:3f:70:ef:bc:fc:cc:2b:fd:13:36:b7 (RSA)</span></p>
+<p>Â </p>
+<p>Private keys authentication:</p>
+<p>On <strong>Linux</strong> or <strong>Mac</strong>, use</p>
+<pre class="prettyprint lang-sh">local $ ssh -i /path/to/id_rsa username@anselm.it4i.cz</pre>
+<p>If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this command to set lower permissions to private key file.</p>
+<pre class="prettyprint lang-sh">local $ chmod 600 /path/to/id_rsa</pre>
+<p>On <strong>Windows</strong>, use <a href="../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html" title="" target="_self" class="internal-link">PuTTY ssh client</a>.</p>
+<p>After logging in, you will see the command prompt:</p>
+<pre class=" "> _<br /> /\ | |<br /> / \ _ __ ___ ___| |_ __ ___<br /> / /\ \ | '_ \/ __|/ _ \ | '_ ` _ \<br /> / ____ \| | | \__ \ __/ | | | | | |<br /> /_/ \_\_| |_|___/\___|_|_| |_| |_|<br /><br /><br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http://www.it4i.cz/?lang=en<br /><br /><br />Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com<br />[username@login2.anselm ~]$</pre>
+<p class="callout">The environment is <strong>not</strong> shared between login nodes, except for <a href="../storage-1.html#section-1" title="" target="_self" class="external-link">shared filesystems</a>.</p>
+<h2 class=" ">Data Transfer</h2>
+<p>Data in and out of the system may be transferred by the <a class="external-link" href="http://en.wikipedia.org/wiki/Secure_copy" target="_self" title="">scp</a> and sftp protocols. <span class="discreet">(Not available yet.) In case large volumes of data are transferred, use dedicated data mover node dm1.anselm.it4i.cz for increased performance.</span></p>
+<table class="listing">
+<tbody>
+<tr><th>Address</th><th>Port</th><th>Protocol</th></tr>
+<tr class="even">
+<td>anselm.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="odd">
+<td>login1.anselm.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="even">
+<td>login2.anselm.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="odd">
+<td><span class="discreet">dm1.anselm.it4i.cz</span></td>
+<td><span class="discreet">22</span></td>
+<td><span class="discreet">scp, sftp</span></td>
+</tr>
+</tbody>
+</table>
+<p>Â The authentication is by the <a href="../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html" title="" target="_self" class="internal-link">private key</a></p>
+<p class="callout">Data transfer rates up to <strong>160MB/s</strong> can be achieved with scp or sftp. 1TB may be transferred in 1:50h.</p>
+<p>To achieve 160MB/s transfer rates, the end user must be connected by 10G line all the way to IT4Innovations and use computer with fast processor for the transfer. Using Gigabit ethernet connection, up to 110MB/s may be expected. Fast cipher (aes128-ctr) should be used.</p>
+<p class="callout">If you experience degraded data transfer performance, consult your local network provider.</p>
+<p>On linux or Mac, use scp or sftp client to transfer the data to Anselm:</p>
+<pre class="prettyprint lang-sh">local $ scp -i /path/to/id_rsa my-local-file username@anselm.it4i.cz:directory/file</pre>
+<pre class="prettyprint lang-sh">local $ scp -i /path/to/id_rsa -r my-local-dir username@anselm.it4i.cz:directory</pre>
+<blockquote>or</blockquote>
+<pre class="prettyprint lang-sh">local $ sftp -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz</pre>
+<p>Very convenient way to transfer files in and out of the Anselm computer is via the fuse filesystem <a class="external-link" href="http://linux.die.net/man/1/sshfs" target="_self" title="">sshfs</a></p>
+<pre class="prettyprint lang-sh">local $ sshfs -o IdentityFile=/path/to/id_rsa username@anselm.it4i.cz:. mountpoint</pre>
+<p>Using sshfs, the users Anselm home directory will be mounted on your local computer, just like an external disk.</p>
+<p>Learn more on ssh, scp and sshfs by reading the manpages</p>
+<pre class="prettyprint lang-sh">$ man ssh<br />$ man scp<br />$ man sshfs</pre>
+<p>On Windows, use <a class="external-link" href="http://winscp.net/eng/download.php" target="_self" title="">WinSCP client</a> to transfer the data. The <a class="external-link" href="http://code.google.com/p/win-sshfs/" target="_self" title="">win-sshfs client</a> provides a way to mount the Anselm filesystems directly as an external disc.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
index 46d22ec8e..6ca703c9f 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
@@ -59,7 +59,7 @@ After logging in, you will see the command prompt:
                       http://www.it4i.cz/?lang=en
- Last loginTue Jul 9 15:57:38 2013 from your-host.example.com
+ Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com
[username@login2.anselm ~]$
The environment is **not** shared between login nodes, except for
@@ -138,4 +138,3 @@ way to mount the Anselm filesystems directly as an external disc.
More information about the shared file systems is available
[here](../../storage.html).
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.html b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.html
new file mode 100644
index 000000000..1fb106c30
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.html
@@ -0,0 +1,991 @@
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+
+ <div id="parent-fieldname-text-1d1e813ad5694098ada90d35a6148610" class="">
+ <p>There are two main shared file systems on Anselm cluster, the <a class="anchor-link" href="../storage.html#home" target="_self" title="">HOME</a> and <a class="anchor-link" href="../storage.html#scratch" target="_self" title="">SCRATCH</a>. All login and compute nodes may access same data on shared filesystems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp filesystems.</p>
+<h2 class=" ">Archiving</h2>
+<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a href="../storage-1/cesnet-data-storage.html" title="" target="_self" class="internal-link">CESNET storage service</a>, which is available via SSHFS.</p>
+<h2 class=" ">Shared Filesystems</h2>
+<p class=" ">Anselm computer provides two main shared filesystems, the <a class="anchor-link" href="../storage.html#home" target="_self" title="">HOME filesystem</a> and the <a class="anchor-link" href="../storage.html#scratch" target="_self" title="">SCRATCH filesystem</a>. Both HOME and SCRATCH filesystems are realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both Lustre filesystems for the purpose of sharing data with other users using fine-grained control.</p>
+<h3 class=" ">Understanding the Lustre Filesystems</h3>
+<p>(source <a class="external-link" href="http://www.nas.nasa.gov" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
+<p>A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.</p>
+<p>When a client (a <span class="glossaryItem">compute <span class="glossaryItem">node</span></span> from your job) needs to create or access a file, the client queries the metadata server (<span class="glossaryItem">MDS</span>) and the metadata target (<span class="glossaryItem">MDT</span>) for the layout and location of the <a href="http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping">file's stripes</a>. Once the file is opened and the client obtains the striping information, the <span class="glossaryItem">MDS</span> is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.</p>
+<p>If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.</p>
+<p>There is default stripe configuration for Anselm Lustre filesystems. However, users can set the following stripe parameters for their own directories or files to get optimum I/O performance:</p>
+<ol><ol>
+<li>stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre filesystems</li>
+<li>stripe_count the number of OSTs to stripe across; default is 1 for Anselm Lustre filesystems one can specify -1 to use all OSTs in the filesystem.</li>
+<li>stripe_offset The index of the <span class="glossaryItem">OST</span> where the first stripe is to be placed; default is -1 which results in random selection; using a non-default value is NOT recommended.</li>
+</ol></ol>
+<p class=" ">Â </p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<p class=" ">Use the lfs getstripe for getting the stripe parameters. Use the lfs setstripe command for setting the stripe parameters to get optimal I/O performance The correct stripe setting depends on your needs and file access patterns. </p>
+<pre class="prettyprint lang-sh"><code>$ lfs getstripe dir|filename <br />$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename </code></pre>
+<p>Example:</p>
+<pre class="prettyprint lang-sh">$ lfs getstripe /scratch/username/<br />/scratch/username/<br />stripe_count: 1 stripe_size: 1048576 stripe_offset: -1<br /><br />$ lfs setstripe -c -1 /scratch/username/<br />$ lfs getstripe /scratch/username/<br />/scratch/username/<br />stripe_count: 10 stripe_size: 1048576 stripe_offset: -1</pre>
+<p>In this example, we view current stripe setting of the /scratch/username/ directory. The stripe count is changed to all OSTs, and verified. All files written to this directory will be striped over 10 OSTs</p>
+<p>Use lfs check OSTs to see the number and status of active OSTs for each filesystem on Anselm. Learn more by reading the man page</p>
+<pre class="prettyprint lang-sh">$ lfs check osts<br />$ man lfs</pre>
+<h3 class=" ">Hints on Lustre Stripping</h3>
+<p class="callout">Increase the stripe_count for parallel I/O to the same file.</p>
+<p>When multiple processes are writing blocks of data to the same file in parallel, the I/O performance for large files will improve when the stripe_count is set to a larger value. The stripe count sets the number of OSTs the file will be written to. By default, the stripe count is set to 1. While this default setting provides for efficient access of metadata (for example to support the ls -l command), large files should use stripe counts of greater than 1. This will increase the aggregate I/O bandwidth by using multiple OSTs in parallel instead of just one. A rule of thumb is to use a stripe count approximately equal to the number of gigabytes in the file.</p>
+<p>Another good practice is to make the stripe count be an integral factor of the number of processes performing the write in parallel, so that you achieve load balance among the OSTs. For example, set the stripe count to 16 instead of 15 when you have 64 processes performing the writes.</p>
+<p class="callout">Using a large stripe size can improve performance when accessing very large files</p>
+<p>Large stripe size allows each client to have exclusive access to its own part of a file. However, it can be counterproductive in some cases if it does not match your I/O pattern. The choice of stripe size has no effect on a single-stripe file.</p>
+<p>Read more on <a class="external-link" href="http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html" target="_self" title="">http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html</a></p>
+<h3 class=" ">Lustre on Anselm</h3>
+<p>The architecture of Lustre on Anselm is composed of two metadata servers (MDS) and four data/object storage servers (OSS). Two object storage servers are used for file system HOME and another two object storage servers are used for file system SCRATCH.</p>
+<p class=" "><span class="emphasis">Configuration of the storages</span></p>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem"><span class="emphasis">HOME Lustre object storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">One disk array NetApp E5400</li>
+<li class="listitem">22 OSTs</li>
+<li class="listitem">227 2TB NL-SAS 7.2krpm disks</li>
+<li class="listitem">22 groups of 10 disks in RAID6 (8+2)</li>
+<li class="listitem">7 hot-spare disks</li>
+</ul>
+</div>
+</li>
+<li class="listitem"><span class="emphasis">SCRATCH Lustre object storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">Two disk arrays NetApp E5400</li>
+<li class="listitem">10 OSTs</li>
+<li class="listitem">106 2TB NL-SAS 7.2krpm disks</li>
+<li class="listitem">10 groups of 10 disks in RAID6 (8+2)</li>
+<li class="listitem">6 hot-spare disks</li>
+</ul>
+</div>
+</li>
+<li class="listitem"><span class="emphasis">Lustre metadata storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">One disk array NetApp E2600</li>
+<li class="listitem">12 300GB SAS 15krpm disks</li>
+<li class="listitem">2 groups of 5 disks in RAID5</li>
+<li class="listitem">2 hot-spare disks</li>
+</ul>
+</div>
+</li>
+</ul>
+</div>
+<h3 class=" "><a name="home"></a><a name="home"></a>HOME</h3>
+<p>The HOME filesystem is mounted in directory /home. Users home directories /home/username reside on this filesystem. Accessible capacity is 320TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. <span>If 250GB should prove as insufficient for particular user, please contact</span>Â <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request.</p>
+<p class="callout">The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.</p>
+<p>The HOME filesystem should not be used to archive data of past Projects or other unrelated data.</p>
+<p>The files on HOME filesystem will not be deleted until end of the <a href="../../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html" title="" target="_self" class="internal-link">users lifecycle</a>.</p>
+<p class=" ">The filesystem is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files. </p>
+<p class=" ">The HOME filesystem is realized as Lustre parallel filesystem and is available on all login and computational nodes. <br />Default stripe size is 1MB, stripe count is 1. There are 22 OSTs dedicated for the HOME filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">HOME filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/home</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>320TB</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>2GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>250GB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>22</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><a name="scratch"></a><a name="scratch"></a>SCRATCH</h3>
+<p>The SCRATCH filesystem is mounted in directory /scratch. Users may freely create subdirectories and files on the filesystem. Accessible capacity is 146TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 100TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. <span>If 100TB should prove as insufficient for particular user, please contact <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request. </span></p>
+<p class="callout">The Scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the SCRATCH filesystem as their working directory.<br /><br />Users are advised to save the necessary data from the SCRATCH filesystem to HOME filesystem after the calculations and clean up the scratch files.<br /><br />Files on the SCRATCH filesystem that are <strong>not accessed for more than 90 days</strong> will be automatically <strong>deleted</strong>.</p>
+<p>The SCRATCH filesystem is realized as Lustre parallel filesystem and is available from all login and computational nodes. <br />Default stripe size is 1MB, stripe count is 1. There are 10 OSTs dedicated for the SCRATCH filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">SCRATCH filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/scratch</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>146TB</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>6GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>100TB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>10</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><span>Disk usage and quota commands</span></h3>
+<p><span>User quotas on the file systems can be checked and reviewed using following command:</span></p>
+<pre class="prettyprint lang-sh">$ lfs quota dir</pre>
+<p>Example for Lustre HOME directory:</p>
+<pre class="prettyprint lang-sh">$ lfs quota /home<br />Disk quotas for user user001 (uid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /home 300096 0 250000000 - 2102 0 500000 -<br />Disk quotas for group user001 (gid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /home 300096 0 0 - 2102 0 0 -</pre>
+<p>In this example, we view current quota size limit of 250GB and 300MB currently used by user001.</p>
+<p>Example for Lustre SCRATCH directory:</p>
+<pre class="prettyprint lang-sh">$ lfs quota /scratch<br />Disk quotas for user user001 (uid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br />  /scratch    8    0 100000000000    -    3    0    0    -<br />Disk quotas for gro<span>up user001 (gid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /scratch    8    0    0    -    3    0    0    -<br /></span></pre>
+<p>In this example, we view current quota size limit of 100TB and 8KB currently used by user001.</p>
+<p>Â </p>
+<p>To have a better understanding of where the space is exactly used, you can use following command to find out.</p>
+<pre class="prettyprint lang-sh">$ du -hs dir</pre>
+<p>Example for your HOME directory:</p>
+<pre class="prettyprint lang-sh">$ cd /home<br />$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr<br />258M cuda-samples<br />15M .cache<br />13M .mozilla<br />5,5M .eclipse<br />2,7M .idb_13.0_linux_intel64_app</pre>
+<p>This will list all directories which are having MegaBytes or GigaBytes of consumed space in your actual (in this example HOME) directory. List is sorted in descending order from largest to smallest files/directories.</p>
+<p><br /> <span>To have a better understanding of previous commands, you can read manpages.</span></p>
+<pre class="prettyprint lang-sh">$ man lfs</pre>
+<pre class="prettyprint lang-sh">$ man du </pre>
+<h3 class=" ">Extended ACLs</h3>
+<p class=" ">Extended ACLs provide another security mechanism beside the standard POSIX ACLs which are defined by three entries (for owner/group/others). Extended ACLs have more than the three basic entries. In addition, they also contain a mask entry and may contain any number of named user and named group entries.</p>
+<p class=" ">ACLs on a Lustre file system work exactly like ACLs on any Linux file system. They are manipulated with the standard tools in the standard manner. Below, we create a directory and allow a specific user access.</p>
+<pre class="prettyprint lang-sh">[vop999@login1.anselm ~]$ umask 027<br />[vop999@login1.anselm ~]$ mkdir test<br />[vop999@login1.anselm ~]$ ls -ld test<br />drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.anselm ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />group::r-x<br />other::---<br /><br />[vop999@login1.anselm ~]$ setfacl -m user:johnsm:rwx test<br />[vop999@login1.anselm ~]$ ls -ld test<br />drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.anselm ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />user:johnsm:rwx<br />group::r-x<br />mask::rwx<br />other::---</pre>
+<p class=" ">Default ACL mechanism can be used to replace setuid/setgid permissions on directories. Setting a default ACL on a directory (-d flag to setfacl) will cause the ACL permissions to be inherited by any newly created file or subdirectory within the directory. Refer to this page for more information on Linux ACL:</p>
+<p class=" "><a class="external-link" href="http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html" target="_self" title="">http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html </a></p>
+<h2 class=" ">Local Filesystems</h2>
+<h3 class=" ">Local Scratch</h3>
+<p>Every computational node is equipped with 330GB local scratch disk.</p>
+<p class="callout">Use local scratch in case you need to access large amount of small files during your calculation.</p>
+<p><a name="LocalScratch"></a>The local scratch disk is mounted as /lscratch and is accessible to user at /lscratch/$PBS_JOBID directory.</p>
+<p class=" ">The local scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs that access large number of small files within the calculation must use the local scratch filesystem as their working directory. This is required for performance reasons, as frequent access to number of small files may overload the metadata servers (MDS) of the Lustre filesystem.</p>
+<p class="callout">The local scratch directory /lscratch/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">local SCRATCH filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/lscratch</td>
+</tr>
+<tr class="odd">
+<td>Accesspoint</td>
+<td>/lscratch/$PBS_JOBID</td>
+</tr>
+<tr class="even">
+<td>Capacity</td>
+<td>330GB</td>
+</tr>
+<tr class="odd">
+<td>Throughput</td>
+<td>100MB/s</td>
+</tr>
+<tr class="even">
+<td>User quota</td>
+<td>none</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" ">RAM disk</h3>
+<p>Every computational node is equipped with filesystem realized in memory, so called RAM disk.</p>
+<p class="callout">Use RAM disk in case you need really fast access to your data of limited size during your calculation.<br />Be very careful, use of RAM disk filesystem is at the expense of operational memory.</p>
+<p><a name="LocalScratch"></a>The local RAM disk is mounted as /ramdisk and is accessible to user at /ramdisk/$PBS_JOBID directory.</p>
+<p class=" ">The local RAM disk filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. Size of RAM disk filesystem is limited. Be very careful, use of RAM disk filesystem is at the expense of operational memory. It is not recommended to allocate large amount of memory and use large amount of data in RAM disk filesystem at the same time.</p>
+<p class="callout">The local RAM disk directory /ramdisk/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">RAM disk</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td><span class="monospace">/ramdisk</span></td>
+</tr>
+<tr class="odd">
+<td>Accesspoint</td>
+<td><span class="monospace">/ramdisk/$PBS_JOBID</span></td>
+</tr>
+<tr class="even">
+<td>Capacity</td>
+<td>
+<p>60GB at compute nodes without accelerator</p>
+<p>90GB at compute nodes with accelerator</p>
+<p>500GB at fat nodes</p>
+</td>
+</tr>
+<tr class="odd">
+<td>Throughput</td>
+<td>
+<p>over 1.5 GB/s write, over 5 GB/s read, single thread<br />over 10 GB/s write, over 50 GB/s read, 16 threads</p>
+</td>
+</tr>
+<tr class="even">
+<td>User quota</td>
+<td>none</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" ">tmp</h3>
+<p>Each node is equipped with local /tmp directory of few GB capacity. The /tmp directory should be used to work with small temporary files. Old files in /tmp directory are automatically purged.</p>
+<div class="table">
+<h2 class=" "><strong>Summary<br /></strong></h2>
+<div class="table-contents">
+<table class="listing" summary="Best usage of the file systems"><colgroup><col><col><col><col><col><col><col><col></colgroup>
+<thead>
+<tr><th align="center" style="text-align: center; ">Mountpoint</th><th align="center" style="text-align: center; ">Usage</th><th align="center" style="text-align: center; ">Protocol</th><th align="center" style="text-align: center; ">Net Capacity</th><th align="center" style="text-align: center; ">Throughput</th><th align="center" style="text-align: center; ">Limitations</th><th align="center" style="text-align: center; ">Access</th><th align="center" style="text-align: center; ">Services</th></tr>
+</thead>
+<tbody>
+<tr class="even">
+<td><span class="monospace">/home</span></td>
+<td align="center">home directory</td>
+<td align="center">Lustre</td>
+<td align="center">320 TiB</td>
+<td align="center">2 GB/s</td>
+<td align="center">Quota 250GB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">backed up</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/scratch</span></td>
+<td align="center">cluster shared jobs' data</td>
+<td align="center">Lustre</td>
+<td align="center">146 TiB</td>
+<td align="center">6 GB/s</td>
+<td align="center">Quota 100TB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">files older 90 days removed</td>
+</tr>
+<tr class="even">
+<td><span class="monospace">/lscratch</span></td>
+<td align="center">node local jobs' data</td>
+<td align="center">local</td>
+<td align="center">330 GB</td>
+<td align="center">100 MB/s</td>
+<td align="center">none</td>
+<td align="center">Compute nodes</td>
+<td align="center">purged after job ends</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/ramdisk</span></td>
+<td align="center">node local jobs' data</td>
+<td align="center">local</td>
+<td align="center">60, 90, 500 GB</td>
+<td align="center">5-50 GB/s</td>
+<td align="center">none</td>
+<td align="center">Compute nodes</td>
+<td align="center">purged after job ends</td>
+</tr>
+<tr class="even">
+<td><span class="monospace">/tmp</span></td>
+<td align="center">local temporary files</td>
+<td align="center">local</td>
+<td align="center"></td>
+<td align="center">100 MB/s</td>
+<td align="center">none</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">auto purged</td>
+</tr>
+</tbody>
+</table>
+</div>
+</div>
+<p>Â </p>
+
+ </div>
+
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.md b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.md
index 7a0905bde..cb600cb94 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.md
@@ -61,7 +61,7 @@ There is default stripe configuration for Anselm Lustre filesystems.
However, users can set the following stripe parameters for their own
directories or files to get optimum I/O performance:
-1. stripe_sizethe size of the chunk in bytes; specify with k, m, or
+1. stripe_size: the size of the chunk in bytes; specify with k, m, or
g to use units of KB, MB, or GB, respectively; the size must be an
even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre
filesystems
@@ -93,12 +93,12 @@ Example:
```
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 1 stripe_size 1048576 stripe_offset -1
+stripe_count: 1 stripe_size: 1048576 stripe_offset: -1
$ lfs setstripe -c -1 /scratch/username/
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 10 stripe_size 1048576 stripe_offset -1
+stripe_count: 10 stripe_size: 1048576 stripe_offset: -1
```
In this example, we view current stripe setting of the
@@ -378,9 +378,9 @@ manner. Below, we create a directory and allow a specific user access.
[vop999@login1.anselm ~]$ ls -ld test
drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# filetest
-# ownervop999
-# groupvop999
+# file: test
+# owner: vop999
+# group: vop999
user::rwx
group::r-x
other::---
@@ -389,9 +389,9 @@ other::---
[vop999@login1.anselm ~]$ ls -ld test
drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# filetest
-# ownervop999
-# groupvop999
+# file: test
+# owner: vop999
+# group: vop999
user::rwx
user:johnsm:rwx
group::r-x
@@ -507,4 +507,3 @@ files in /tmp directory are automatically purged.
<span class="monospace">/tmp</span> local temporary files local 100 MB/s none Compute and login nodes auto purged
Â
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.html b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.html
new file mode 100644
index 000000000..90b52ad1c
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.html
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+ <span id="breadcrumbs-current">VPN Access</span>
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+ VPN Access
+ </h1>
+
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+
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+ <div id="viewlet-below-content-title">
+</div>
+
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+ <div id="content-core">
+
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+
+ <div id="parent-fieldname-text-2c3935b8355e4d8fbab23e10e8f9b474" class="">
+ <h2 class=" ">Accessing IT4Innovations internal resources via VPN</h2>
+<p class="callout"><strong>Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS patch</strong><br />Workaround can be found at <a class="external-link" href="../../vpn-connection-fail-in-win-8.1.html" target="_self" title="">https://docs.it4i.cz/vpn-connection-fail-in-win-8.1</a></p>
+<p class=" ">Â </p>
+<p class=" ">For using resources and licenses which are located at IT4Innovations local network, it is necessary to VPN connect to this network.<br />We use Cisco AnyConnect Secure Mobility Client, which is supported on the following operating systems:</p>
+<ul>
+<li><span>Windows XP</span></li>
+<li><span>Windows Vista</span></li>
+<li><span>Windows 7</span></li>
+<li><span>Windows 8</span></li>
+<li><span>Linux</span></li>
+<li><span>MacOS</span></li>
+</ul>
+<p class=" ">It is impossible to connect to VPN from other operating systems.</p>
+<h2 class=" "><span>VPN client installation</span></h2>
+<p class=" ">You can install VPN client from web interface after successful login with LDAP credentials on address <a href="https://vpn1.it4i.cz/anselm">https://vpn1.it4i.cz/anselm</a></p>
+<p class=" "><img alt="" src="../login.jpg/@@images/30271119-b392-4db9-a212-309fb41925d6.jpeg" title="" class="image-inline" /></p>
+<p class=" ">According to the Java settings after login, the client either automatically installs, or downloads installation file for your operating system. It is necessary to allow start of installation tool for automatic installation.</p>
+<p class=" "><img alt="Java detection" src="../java_detection.jpg/@@images/5498e1ba-2242-4b9c-a799-0377a73f779e.jpeg" title="Java detection" class="image-inline" /></p>
+<p class=" "><img alt="Execution access" src="../executionaccess.jpg/@@images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpeg" title="Execution access" class="image-inline" /><img alt="Execution access 2" src="../executionaccess2.jpg/@@images/bed3998c-4b82-4b40-83bd-c3528dde2425.jpeg" title="Execution access 2" class="image-inline" /></p>
+<p class=" ">After successful installation, VPN connection will be established and you can use available resources from IT4I network.</p>
+<p class=" "><img alt="Successfull instalation" src="../successfullinstalation.jpg/@@images/c6d69ffe-da75-4cb6-972a-0cf4c686b6e1.jpeg" title="Successfull instalation" class="image-inline" /></p>
+<p class=" ">If your Java setting doesn't allow automatic installation, you can download installation file and install VPN client manually.</p>
+<p class=" "><img alt="Installation file" src="../instalationfile.jpg/@@images/202d14e9-e2e1-450b-a584-e78c018d6b6a.jpeg" title="Installation file" class="image-inline" /></p>
+<p class=" ">After you click on the link, download of installation file will start.</p>
+<p class=" "><img alt="Download file successfull" src="../downloadfilesuccessfull.jpg/@@images/69842481-634a-484e-90cd-d65e0ddca1e8.jpeg" title="Download file successfull" class="image-inline" /></p>
+<p class=" ">After successful download of installation file, you have to execute this tool with administrator's rights and install VPN client manually.</p>
+<h2 class=" ">Working with VPN client</h2>
+<p class=" ">You can use graphical user interface or command line interface to run VPN client on all supported operating systems. We suggest using GUI.</p>
+<p class=" "><img alt="Icon" src="../icon.jpg" title="Icon" class="image-inline" /></p>
+<p>Before the first login to VPN, you have to fill URLÂ <strong>https://vpn1.it4i.cz/anselm</strong> into the text field.</p>
+<p><img alt="First run" src="../firstrun.jpg" title="First run" class="image-inline" /></p>
+<p>After you click on the Connect button, you must fill your login credentials.</p>
+<p><img alt="Login - GUI" src="../logingui.jpg" title="Login - GUI" class="image-inline" /></p>
+<p>After a successful login, the client will minimize to the system tray. If everything works, you can see a lock in the Cisco tray icon.</p>
+<p><img alt="Successfull connection" src="../anyconnecticon.jpg" title="Successfull connection" class="image-inline" /></p>
+<p>If you right-click on this icon, you will see a context menu in which you can control the VPN connection.</p>
+<p><img alt="Context menu" src="../anyconnectcontextmenu.jpg" title="Context menu" class="image-inline" /></p>
+<p>When you connect to the VPN for the first time, the client downloads the profile and creates a new item "ANSELM" in the connection list. For subsequent connections, it is not necessary to re-enter the URL address, but just select the corresponding item.</p>
+<p><img alt="Anselm profile" src="../Anselmprofile.jpg" title="Anselm profile" class="image-inline" /></p>
+<p>Then AnyConnect automatically proceeds like in the case of first logon.</p>
+<p><img alt="Login with profile" src="../loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpeg" title="Login with profile" class="image-inline" /></p>
+<p>After a successful logon, you can see a green circle with a tick mark on the lock icon.</p>
+<p><img alt="successful login" src="../successfullconnection.jpg" title="successful login" class="image-inline" /></p>
+<p>For disconnecting, right-click on the AnyConnect client icon in the system tray and select <strong>VPN Disconnect</strong>.</p>
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
index ac664a415..cfc7e40c0 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
@@ -120,4 +120,3 @@ login](../successfullconnection.jpg "successful login")
For disconnecting, right-click on the AnyConnect client icon in the
system tray and select **VPN Disconnect**.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.html b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.html
new file mode 100644
index 000000000..3a3d5475a
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.html
@@ -0,0 +1,662 @@
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+<p>Read more about configuring <a href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link"><b>X Window System</b></a>.</p>
+<h2>VNC</h2>
+<p>The <b>Virtual Network Computing</b> (<b>VNC</b>) is a graphical <span class="link-external"><a href="http://en.wikipedia.org/wiki/Desktop_sharing" title="Desktop sharing">desktop sharing</a></span> system that uses the <span class="link-external"><a href="http://en.wikipedia.org/wiki/RFB_protocol" title="RFB protocol">Remote Frame Buffer protocol (RFB)</a></span> to remotely control another <span class="link-external"><a href="http://en.wikipedia.org/wiki/Computer" title="Computer">computer</a></span>.</p>
+<p>Read more about configuring <strong><a href="../../salomon/accessing-the-cluster/graphical-user-interface/vnc.html" title="" target="_self" class="internal-link">VNC</a></strong>.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.md b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.md
index 25928db68..5e1cc315c 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.md
@@ -28,4 +28,3 @@ class="link-external">[computer](http://en.wikipedia.org/wiki/Computer "Computer
Read more about configuring
**[VNC](../../salomon/accessing-the-cluster/graphical-user-interface/vnc.html)**.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.html b/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.html
new file mode 100644
index 000000000..cb3a7e909
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.html
@@ -0,0 +1,970 @@
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+ <h2 class=" ">Nodes Configuration</h2>
+<p>Anselm is cluster of x86-64 Intel based nodes built on Bull Extreme Computing bullx technology. The cluster contains four types of compute nodes.<strong></strong></p>
+<h3 class=" "><strong>Compute Nodes Without Accelerator</strong></h3>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">
+<div class="itemizedlist">180 nodes</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">2880 cores in total</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">two Intel Sandy Bridge E5-2665, 8-core, 2.4GHz processors per node</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">64 GB of physical memory per node</div>
+</li>
+<li class="listitem">one 500GB SATA 2,5” 7,2 krpm HDD per node</li>
+<li class="listitem">
+<div class="itemizedlist">bullx B510 blade servers</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">cn[1-180]</div>
+</li>
+</ul>
+<h3 class=" "><strong>Compute Nodes With GPU Accelerator</strong></h3>
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">
+<div class="itemizedlist">23 nodes</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">368 cores in total</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">two Intel Sandy Bridge E5-2470, 8-core, 2.3GHz processors per node</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">96 GB of physical memory per node</div>
+</li>
+<li class="listitem">one 500GB SATA 2,5” 7,2 krpm HDD per node</li>
+<li class="listitem">
+<div class="itemizedlist">GPU accelerator 1x NVIDIA Tesla Kepler K20 per node</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">bullx B515 blade servers</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">cn[181-203]</div>
+</li>
+</ul>
+<h3 class=" "><strong>Compute Nodes With MIC Accelerator</strong></h3>
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">
+<div class="itemizedlist">4 nodes</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">64 cores in total</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">two Intel Sandy Bridge E5-2470, 8-core, 2.3GHz processors per node</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">96 GB of physical memory per node</div>
+</li>
+<li class="listitem">one 500GB SATA 2,5” 7,2 krpm HDD per node</li>
+<li class="listitem">
+<div class="itemizedlist">MIC accelerator 1x Intel Phi 5110P per node</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">bullx B515 blade servers</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">cn[204-207]</div>
+</li>
+</ul>
+<h3 class=" "><strong>Fat Compute Nodes</strong></h3>
+<ul>
+<li>
+<div>2 nodes</div>
+</li>
+<li>
+<div>32 cores in total</div>
+</li>
+<li>
+<div>2 Intel Sandy Bridge E5-2665, 8-core, 2.4GHz processors per node</div>
+</li>
+<li>
+<div>512 GB of physical memory per node</div>
+</li>
+<li>two 300GB SAS 3,5”15krpm HDD (RAID1) per node</li>
+<li>
+<div>two 100GB SLC SSD per node</div>
+</li>
+<li>
+<div>bullx R423-E3 servers</div>
+</li>
+<li>
+<div>cn[208-209]</div>
+</li>
+</ul>
+</div>
+<p>Â </p>
+<div class="figure">
+<p class="title"><strong><img alt="" src="bullxB510.png" title="" class="image-inline" /></strong></p>
+<p class="title"><strong><strong>Figure Anselm bullx B510 servers</strong></strong></p>
+<h3 class=" ">Compute Nodes Summary<strong><strong></strong></strong></h3>
+<table class="listing">
+<tbody>
+<tr><th>Node type</th><th>Count</th><th>Range</th><th>Memory</th><th>Cores</th><th><a href="resource-allocation-and-job-execution/resources-allocation-policy.html" title="" target="_self" class="internal-link">Access</a></th></tr>
+<tr class="even">
+<td>Nodes without accelerator</td>
+<td>180</td>
+<td>cn[1-180]</td>
+<td>64GB</td>
+<td>16 @ 2.4Ghz</td>
+<td>qexp, qprod, qlong, qfree</td>
+</tr>
+<tr class="odd">
+<td>Nodes with GPU accelerator</td>
+<td>23</td>
+<td>cn[181-203]</td>
+<td>96GB</td>
+<td>16 @ 2.3Ghz</td>
+<td>qgpu, qprod</td>
+</tr>
+<tr class="even">
+<td>Nodes with MIC accelerator</td>
+<td>4</td>
+<td>cn[204-207]</td>
+<td>96GB</td>
+<td>16 @ 2.3GHz</td>
+<td>qmic, qprod</td>
+</tr>
+<tr class="odd">
+<td>Fat compute nodes</td>
+<td>2</td>
+<td>cn[208-209]</td>
+<td>512GB</td>
+<td>16 @ 2.4GHz</td>
+<td>qfat, qprod</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="simplesect">
+<div class="titlepage">
+<div>
+<div>
+<h2 class=" ">Processor Architecture</h2>
+</div>
+</div>
+</div>
+<p>Anselm is equipped with Intel Sandy Bridge processors Intel Xeon E5-2665 (nodes without accelerator and fat nodes) and Intel Xeon E5-2470 (nodes with accelerator). Processors support Advanced Vector Extensions (AVX) 256-bit instruction set.</p>
+<div class="simplesect">
+<div class="titlepage">
+<div>
+<div>
+<h3 class=" ">Intel Sandy Bridge E5-2665 Processor</h3>
+</div>
+</div>
+</div>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">eight-core</li>
+<li class="listitem">speed: 2.4 GHz, up to 3.1 GHz using Turbo Boost Technology</li>
+<li class="listitem">peak performance: <span class="emphasis">19.2 Gflop/s</span> per core</li>
+<li class="listitem">caches:
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">L2: 256 KB per core</li>
+<li class="listitem">L3: 20 MB per processor</li>
+</ul>
+</div>
+</li>
+<li class="listitem">memory bandwidth at the level of the processor: 51.2 GB/s</li>
+</ul>
+</div>
+</div>
+<div class="simplesect">
+<div class="titlepage">
+<div>
+<div>
+<h3 class=" ">Intel Sandy Bridge E5-2470 Processor</h3>
+</div>
+</div>
+</div>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">eight-core</li>
+<li class="listitem">speed: 2.3 GHz, up to 3.1 GHz using Turbo Boost Technology</li>
+<li class="listitem">peak performance: <span class="emphasis">18.4 Gflop/s</span> per core</li>
+<li class="listitem">caches:
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">L2: 256 KB per core</li>
+<li class="listitem">L3: 20 MB per processor</li>
+</ul>
+</div>
+</li>
+<li class="listitem">memory bandwidth at the level of the processor: 38.4 GB/s</li>
+</ul>
+</div>
+<p>Â </p>
+<p>Nodes equipped with Intel Xeon E5-2665 CPU have set PBS resource attribute cpu_freq = 24, nodes equipped with Intel Xeon E5-2470 CPU have set PBS resource attribute cpu_freq = 23.</p>
+</div>
+<pre class="prettyprint lang-sh">$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16:cpu_freq=24 -I</pre>
+</div>
+<div class="section">
+<div class="titlepage">
+<div>In this example, we allocate 4 nodes, 16 cores at 2.4GHhz per node.</div>
+</div>
+<div></div>
+<div>Intel Turbo Boost Technology is used by default, you can disable it for all nodes of job by using resource attribute cpu_turbo_boost.</div>
+<pre class=" ">$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16 -l cpu_turbo_boost=0 -I</pre>
+<h2 class=" ">Memory Architecture</h2>
+<div class="simplesect">
+<div class="titlepage">
+<div>
+<div>
+<h3 class=" ">Compute Node Without Accelerator</h3>
+</div>
+</div>
+</div>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">2 sockets</li>
+<li class="listitem">Memory Controllers are integrated into processors.
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">8 DDR3 DIMMS per node</li>
+<li class="listitem">4 DDR3 DIMMS per CPU</li>
+<li class="listitem">1 DDR3 DIMMS per channel</li>
+<li class="listitem">Data rate support: up to 1600MT/s</li>
+</ul>
+</div>
+</li>
+<li class="listitem">Populated memory: 8x 8GB DDR3 DIMM 1600Mhz</li>
+</ul>
+</div>
+</div>
+<div class="simplesect">
+<div class="titlepage">
+<div>
+<div>
+<h3 class=" ">Compute Node With GPU or MIC Accelerator</h3>
+</div>
+</div>
+</div>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">2 sockets</li>
+<li class="listitem">Memory Controllers are integrated into processors.
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">6 DDR3 DIMMS per node</li>
+<li class="listitem">3 DDR3 DIMMS per CPU</li>
+<li class="listitem">1 DDR3 DIMMS per channel</li>
+<li class="listitem">Data rate support: up to 1600MT/s</li>
+</ul>
+</div>
+</li>
+<li class="listitem">Populated memory: 6x 16GB DDR3 DIMM 1600Mhz</li>
+</ul>
+</div>
+</div>
+<div class="simplesect">
+<div class="titlepage">
+<div>
+<div>
+<h3 class=" ">Fat Compute Node</h3>
+</div>
+</div>
+</div>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">2 sockets</li>
+<li class="listitem">Memory Controllers are integrated into processors.
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">16 DDR3 DIMMS per node</li>
+<li class="listitem">8 DDR3 DIMMS per CPU</li>
+<li class="listitem">2 DDR3 DIMMS per channel</li>
+<li class="listitem">Data rate support: up to 1600MT/s</li>
+</ul>
+</div>
+</li>
+<li class="listitem">Populated memory: 16x 32GB DDR3 DIMM 1600Mhz</li>
+</ul>
+</div>
+</div>
+</div>
+
+ </div>
+
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md b/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
index 6a013a209..5f8fe6273 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
@@ -219,33 +219,33 @@ with accelerator). Processors support Advanced Vector Extensions (AVX)
### Intel Sandy Bridge E5-2665 Processor
- eight-core
-- speed2.4 GHz, up to 3.1 GHz using Turbo Boost Technology
-- peak performance<span class="emphasis">19.2 Gflop/s</span> per
+- speed: 2.4 GHz, up to 3.1 GHz using Turbo Boost Technology
+- peak performance: <span class="emphasis">19.2 Gflop/s</span> per
core
- caches:
<div class="itemizedlist">
- - L2256 KB per core
- - L320 MB per processor
+ - L2: 256 KB per core
+ - L3: 20 MB per processor
-- memory bandwidth at the level of the processor51.2 GB/s
+- memory bandwidth at the level of the processor: 51.2 GB/s
### Intel Sandy Bridge E5-2470 Processor
- eight-core
-- speed2.3 GHz, up to 3.1 GHz using Turbo Boost Technology
-- peak performance<span class="emphasis">18.4 Gflop/s</span> per
+- speed: 2.3 GHz, up to 3.1 GHz using Turbo Boost Technology
+- peak performance: <span class="emphasis">18.4 Gflop/s</span> per
core
- caches:
<div class="itemizedlist">
- - L2256 KB per core
- - L320 MB per processor
+ - L2: 256 KB per core
+ - L3: 20 MB per processor
-- memory bandwidth at the level of the processor38.4 GB/s
+- memory bandwidth at the level of the processor: 38.4 GB/s
@@ -282,11 +282,11 @@ Memory Architecture
- 8 DDR3 DIMMS per node
- 4 DDR3 DIMMS per CPU
- 1 DDR3 DIMMS per channel
- - Data rate supportup to 1600MT/s
+ - Data rate support: up to 1600MT/s
-- Populated memory8x 8GB DDR3 DIMM 1600Mhz
+- Populated memory: 8x 8GB DDR3 DIMM 1600Mhz
### Compute Node With GPU or MIC Accelerator
- 2 sockets
@@ -296,11 +296,11 @@ Memory Architecture
- 6 DDR3 DIMMS per node
- 3 DDR3 DIMMS per CPU
- 1 DDR3 DIMMS per channel
- - Data rate supportup to 1600MT/s
+ - Data rate support: up to 1600MT/s
-- Populated memory6x 16GB DDR3 DIMM 1600Mhz
+- Populated memory: 6x 16GB DDR3 DIMM 1600Mhz
### Fat Compute Node
- 2 sockets
@@ -310,12 +310,11 @@ Memory Architecture
- 16 DDR3 DIMMS per node
- 8 DDR3 DIMMS per CPU
- 2 DDR3 DIMMS per channel
- - Data rate supportup to 1600MT/s
+ - Data rate support: up to 1600MT/s
-- Populated memory16x 32GB DDR3 DIMM 1600Mhz
-
+- Populated memory: 16x 32GB DDR3 DIMM 1600Mhz
diff --git a/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.html b/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.html
new file mode 100644
index 000000000..af226bf56
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.html
@@ -0,0 +1,706 @@
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+ <h3 class=" ">Environment Customization</h3>
+<p>After logging in, you may want to configure the environment. Write your preferred path definitions, aliases, functions and module loads in the .bashrc file</p>
+<pre class="prettyprint lang-sh"># ./bashrc<br /><br /># Source global definitions<br />if [ -f /etc/bashrc ]; then<br /> . /etc/bashrc<br />fi<br /><br /># User specific aliases and functions<br />alias qs='qstat -a'<br />module load PrgEnv-gnu<br /><br /># Display informations to standard output - only in interactive ssh session<br />if [ -n "$SSH_TTY" ]<br />then<br /> module list # Display loaded modules<br />fi</pre>
+<p class="callout">Do not run commands outputing to standard output (echo, module list, etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental functionality (scp, PBS) of your account! Take care for SSH session interactivity for such commands as <span class="short_text" id="result_box"><span class="hps alt-edited">stated</span> <span class="hps">in the previous example.</span></span></p>
+<h3 class=" ">Application Modules</h3>
+<p class=" ">In order to configure your shell for running particular application on Anselm we use Module package interface.</p>
+<p class="callout">The modules set up the application paths, library paths and environment variables for running particular application.</p>
+<p class="callout">We have also second modules repository. This modules repository is created using tool called EasyBuild. On Salomon cluster, all modules will be build by this tool. If you want to use software from this modules repository, please follow instructions in section <a class="anchor-link" href="environment-and-modules.html#EasyBuild" target="_self" title="">Application Modules Path Expansion</a>.</p>
+<p class=" ">The modules may be loaded, unloaded and switched, according to momentary needs.</p>
+<p class=" ">To check available modules use</p>
+<pre class="prettyprint lang-sh">$ module avail</pre>
+<p class=" ">To load a module, for example the octave module use</p>
+<pre class="prettyprint lang-sh">$ module load octave</pre>
+<p>loading the octave module will set up paths and environment variables of your active shell such that you are ready to run the octave software</p>
+<p class=" ">To check loaded modules use</p>
+<pre class="prettyprint lang-sh">$ module list</pre>
+<p>Â To unload a module, for example the octave module use</p>
+<pre class="prettyprint lang-sh">$ module unload octave</pre>
+<p class=" ">Learn more on modules by reading the module man page</p>
+<pre class="prettyprint lang-sh">$ man module</pre>
+<p class=" ">Following modules set up the development environment</p>
+<p class=" ">PrgEnv-gnu sets up the GNU development environment in conjunction with the bullx MPI library</p>
+<p class=" ">PrgEnv-intel sets up the INTEL development environment in conjunction with the Intel MPI library</p>
+<h3 class=" "><a name="EasyBuild"></a>Application Modules Path Expansion</h3>
+<p>All application modules on Salomon cluster (and further) will be build using tool called <a class="external-link" href="http://hpcugent.github.io/easybuild/" target="_self" title="EasyBuild">EasyBuild</a>. In case that you want to use some applications that are build by EasyBuild already, you have to modify your MODULEPATH environment variable.</p>
+<pre class="prettyprint lang-sh">export MODULEPATH=$MODULEPATH:/apps/easybuild/modules/all/</pre>
+<p class=" ">This command expands your searched paths to modules. You can also add this command to the .bashrc file to expand paths permanently. After this command, you can use same commands to list/add/remove modules as is described above.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md b/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
index b72a0f0b9..a4e9c7abc 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
@@ -113,4 +113,3 @@ This command expands your searched paths to modules. You can also add
this command to the .bashrc file to expand paths permanently. After this
command, you can use same commands to list/add/remove modules as is
described above.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.html b/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.html
new file mode 100644
index 000000000..a0fce7ec9
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.html
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+ Hardware Overview
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+ <div id="parent-fieldname-text-277179775b3c441a8b057e2eb7588b3a" class="">
+ <p>The Anselm cluster consists of 209 computational nodes named cn[1-209] of which 180 are regular compute nodes, 23 GPU Kepler K20 accelerated nodes, 4 MIC Xeon Phi 5110 accelerated nodes and 2 fat nodes. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 16 cores (two eight-core Intel Sandy Bridge processors), at least 64GB RAM, and local hard drive. The user access to the Anselm cluster is provided by two login nodes login[1,2]. The nodes are interlinked by high speed InfiniBand and Ethernet networks. All nodes share 320TB /home disk storage to store the user files. The 146TB shared /scratch storage is available for the scratch data.</p>
+<p>The Fat nodes are equipped with large amount (512GB) of memory. Virtualization infrastructure provides resources to run long term servers and services in virtual mode. Fat nodes and virtual servers may access 45 TB of dedicated block storage. Accelerated nodes, fat nodes, and virtualization infrastructure are available <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">upon request</a> made by a PI.</p>
+<p class="WYSIWYG_LINK">Schematic representation of the Anselm cluster. Each box represents a node (computer) or storage capacity:</p>
+<div class="wide-view-wrapper">
+<table class="plain" id="big-picture-of-cluster">
+<tbody>
+<tr><th colspan="3">User-oriented infrastructure</th><th>Storage</th><th>Management infrastructure</th></tr>
+<tr>
+<td title="Login nodes">
+<table class="filled">
+<tbody>
+<tr>
+<td>login1</td>
+</tr>
+<tr>
+<td>login2</td>
+</tr>
+<tr>
+<td>dm1</td>
+</tr>
+</tbody>
+</table>
+</td>
+<td title="Compute nodes">
+<p><strong>Rack 01, Switch isw5<br /></strong></p>
+<table class="filled" id="blade-chassis">
+<tbody>
+<tr>
+<td>cn186</td>
+<td>cn187</td>
+<td></td>
+<td>cn188</td>
+<td>cn189</td>
+</tr>
+<tr>
+<td>cn181</td>
+<td>cn182</td>
+<td>cn183</td>
+<td>cn184</td>
+<td>cn185</td>
+</tr>
+</tbody>
+</table>
+</td>
+<td title="Compute nodes">
+<p><strong>Rack 01, Switch isw4<br /></strong></p>
+<table class="filled" id="blade-chassis">
+<tbody>
+<tr>
+<td>cn29</td>
+<td>cn30</td>
+<td>cn31</td>
+<td>cn32</td>
+<td colspan="2"></td>
+<td>cn33</td>
+<td>cn34</td>
+<td>cn35</td>
+<td>cn36</td>
+</tr>
+<tr>
+<td>cn19</td>
+<td>cn20</td>
+<td>cn21</td>
+<td>cn22</td>
+<td>cn23</td>
+<td>cn24</td>
+<td>cn25</td>
+<td>cn26</td>
+<td>cn27</td>
+<td>cn28</td>
+</tr>
+</tbody>
+</table>
+</td>
+<td rowspan="5" title="Storage">
+<table class="filled">
+<tbody>
+<tr>
+<td>
+<p>Â </p>
+<p>Â </p>
+<p>Lustre FS</p>
+<p>/home<br />320TB</p>
+<p>Â </p>
+<p>Â </p>
+</td>
+</tr>
+<tr>
+<td>
+<p>Lustre FS</p>
+<p>/scratch<br />146TB</p>
+</td>
+</tr>
+</tbody>
+</table>
+</td>
+<td rowspan="5" title="Management infrastructure">
+<table class="filled">
+<tbody>
+<tr>
+<td>Management<br />nodes</td>
+<td rowspan="10">Block storage<br />45 TB</td>
+</tr>
+<tr>
+<td>Virtualization<br />infrastructure<br />servers</td>
+</tr>
+<tr></tr>
+<tr></tr>
+<tr></tr>
+<tr>
+<td>...</td>
+</tr>
+<tr>
+<td>Srv node</td>
+</tr>
+<tr>
+<td>Srv node</td>
+</tr>
+<tr>
+<td>Srv node</td>
+</tr>
+<tr>
+<td>...</td>
+</tr>
+</tbody>
+</table>
+</td>
+</tr>
+<tr>
+<td title="Compute nodes">
+<p><strong>Rack 01, Switch isw0<br /></strong></p>
+<table class="filled" id="blade-chassis">
+<tbody>
+<tr>
+<td>cn11</td>
+<td>cn12</td>
+<td>cn13</td>
+<td>cn14</td>
+<td colspan="2"></td>
+<td>cn15</td>
+<td>cn16</td>
+<td>cn17</td>
+<td>cn18</td>
+</tr>
+<tr>
+<td>cn1</td>
+<td>cn2</td>
+<td>cn3</td>
+<td>cn4</td>
+<td>cn5</td>
+<td>cn6</td>
+<td>cn7</td>
+<td>cn8</td>
+<td>cn9</td>
+<td>cn10</td>
+</tr>
+</tbody>
+</table>
+</td>
+<td title="Compute nodes">
+<p><strong>Rack 02, Switch isw10<br /></strong></p>
+<table class="filled" id="blade-chassis">
+<tbody>
+<tr>
+<td>cn73</td>
+<td>cn74</td>
+<td>cn75</td>
+<td>cn76</td>
+<td colspan="2"></td>
+<td>cn77</td>
+<td>cn78</td>
+<td>cn79</td>
+<td>cn80</td>
+</tr>
+<tr>
+<td colspan="2">cn190</td>
+<td colspan="2">cn191</td>
+<td colspan="2">cn192</td>
+<td colspan="2">cn205</td>
+<td colspan="2">cn206</td>
+</tr>
+</tbody>
+</table>
+</td>
+<td title="Compute nodes">
+<p><strong>Rack 02, Switch isw9<br /></strong></p>
+<table class="filled" id="blade-chassis">
+<tbody>
+<tr>
+<td>cn65</td>
+<td>cn66</td>
+<td>cn67</td>
+<td>cn68</td>
+<td colspan="2"></td>
+<td>cn69</td>
+<td>cn70</td>
+<td>cn71</td>
+<td>cn72</td>
+</tr>
+<tr>
+<td>cn55</td>
+<td>cn56</td>
+<td>cn57</td>
+<td>cn58</td>
+<td>cn59</td>
+<td>cn60</td>
+<td>cn61</td>
+<td>cn62</td>
+<td>cn63</td>
+<td>cn64</td>
+</tr>
+</tbody>
+</table>
+</td>
+</tr>
+<tr>
+<td title="Compute nodes">
+<p><strong>Rack 02, Switch isw6<br /></strong></p>
+<table class="filled" id="blade-chassis">
+<tbody>
+<tr>
+<td>cn47</td>
+<td>cn48</td>
+<td>cn49</td>
+<td>cn50</td>
+<td colspan="2"></td>
+<td>cn51</td>
+<td>cn52</td>
+<td>cn53</td>
+<td>cn54</td>
+</tr>
+<tr>
+<td>cn37</td>
+<td>cn38</td>
+<td>cn39</td>
+<td>cn40</td>
+<td>cn41</td>
+<td>cn42</td>
+<td>cn43</td>
+<td>cn44</td>
+<td>cn45</td>
+<td>cn46</td>
+</tr>
+</tbody>
+</table>
+</td>
+<td title="Compute nodes">
+<p><strong>Rack 03, Switch isw15<br /></strong></p>
+<table class="filled" id="blade-chassis">
+<tbody>
+<tr>
+<td colspan="2">cn193</td>
+<td colspan="2">cn194</td>
+<td colspan="2"></td>
+<td colspan="2">cn195</td>
+<td colspan="2">cn207</td>
+</tr>
+<tr>
+<td>cn117</td>
+<td>cn118</td>
+<td>cn119</td>
+<td>cn120</td>
+<td>cn121</td>
+<td>cn122</td>
+<td>cn123</td>
+<td>cn124</td>
+<td>cn125</td>
+<td>cn126</td>
+</tr>
+</tbody>
+</table>
+</td>
+<td title="Compute nodes">
+<p><strong>Rack 03, Switch isw14<br /></strong></p>
+<table class="filled" id="blade-chassis">
+<tbody>
+<tr>
+<td>cn109</td>
+<td>cn110</td>
+<td>cn111</td>
+<td>cn112</td>
+<td colspan="2"></td>
+<td>cn113</td>
+<td>cn114</td>
+<td>cn115</td>
+<td>cn116</td>
+</tr>
+<tr>
+<td>cn99</td>
+<td>cn100</td>
+<td>cn101</td>
+<td>cn102</td>
+<td>cn103</td>
+<td>cn104</td>
+<td>cn105</td>
+<td>cn106</td>
+<td>cn107</td>
+<td>cn108</td>
+</tr>
+</tbody>
+</table>
+</td>
+</tr>
+<tr>
+<td title="Compute nodes">
+<p><strong>Rack 03, Switch isw11<br /></strong></p>
+<table class="filled" id="blade-chassis">
+<tbody>
+<tr>
+<td>cn91</td>
+<td>cn92</td>
+<td>cn93</td>
+<td>cn94</td>
+<td colspan="2"></td>
+<td>cn95</td>
+<td>cn96</td>
+<td>cn97</td>
+<td>cn98</td>
+</tr>
+<tr>
+<td>cn81</td>
+<td>cn82</td>
+<td>cn83</td>
+<td>cn84</td>
+<td>cn85</td>
+<td>cn86</td>
+<td>cn87</td>
+<td>cn88</td>
+<td>cn89</td>
+<td>cn90</td>
+</tr>
+</tbody>
+</table>
+</td>
+<td title="Compute nodes">
+<p><strong>Rack 04, Switch isw20<br /></strong></p>
+<table class="filled" id="blade-chassis">
+<tbody>
+<tr>
+<td>cn173</td>
+<td>cn174</td>
+<td>cn175</td>
+<td>cn176</td>
+<td colspan="2"></td>
+<td>cn177</td>
+<td>cn178</td>
+<td>cn179</td>
+<td>cn180</td>
+</tr>
+<tr>
+<td>cn163</td>
+<td>cn164</td>
+<td>cn165</td>
+<td>cn166</td>
+<td>cn167</td>
+<td>cn168</td>
+<td>cn169</td>
+<td>cn170</td>
+<td>cn171</td>
+<td>cn172</td>
+</tr>
+</tbody>
+</table>
+</td>
+<td title="Compute nodes">
+<p><strong>Rack 04,<strong> Switch </strong>isw19<br /></strong></p>
+<table class="filled" id="blade-chassis">
+<tbody>
+<tr>
+<td>cn155</td>
+<td>cn156</td>
+<td>cn157</td>
+<td>cn158</td>
+<td colspan="2"></td>
+<td>cn159</td>
+<td>cn160</td>
+<td>cn161</td>
+<td>cn162</td>
+</tr>
+<tr>
+<td>cn145</td>
+<td>cn146</td>
+<td>cn147</td>
+<td>cn148</td>
+<td>cn149</td>
+<td>cn150</td>
+<td>cn151</td>
+<td>cn152</td>
+<td>cn153</td>
+<td>cn154</td>
+</tr>
+</tbody>
+</table>
+</td>
+</tr>
+<tr>
+<td title="Compute nodes">
+<p><strong>Rack 04, Switch isw16<br /></strong></p>
+<table class="filled" id="blade-chassis">
+<tbody>
+<tr>
+<td>cn137</td>
+<td>cn138</td>
+<td>cn139</td>
+<td>cn140</td>
+<td colspan="2"></td>
+<td>cn141</td>
+<td>cn142</td>
+<td>cn143</td>
+<td>cn144</td>
+</tr>
+<tr>
+<td>cn127</td>
+<td>cn128</td>
+<td>cn129</td>
+<td>cn130</td>
+<td>cn131</td>
+<td>cn132</td>
+<td>cn133</td>
+<td>cn134</td>
+<td>cn135</td>
+<td>cn136</td>
+</tr>
+</tbody>
+</table>
+</td>
+<td title="Compute nodes">
+<p><strong>Rack 05, Switch isw21<br /></strong></p>
+<table class="filled" id="blade-chassis">
+<tbody>
+<tr>
+<td>cn201</td>
+<td>cn202</td>
+<td></td>
+<td>cn203</td>
+<td>cn204</td>
+</tr>
+<tr>
+<td>cn196</td>
+<td>cn197</td>
+<td>cn198</td>
+<td>cn199</td>
+<td>cn200</td>
+</tr>
+</tbody>
+</table>
+</td>
+<td title="Fat nodes">
+<table class="filled">
+<tbody>
+<tr>
+<td>Fat node cn208</td>
+</tr>
+<tr>
+<td>Fat node cn209</td>
+</tr>
+<tr>
+<td>...</td>
+</tr>
+</tbody>
+</table>
+</td>
+</tr>
+</tbody>
+</table>
+</div>
+<p>The cluster compute nodes cn[1-207] are organized within 13 chassis. </p>
+<p>There are four types of compute nodes:</p>
+<ul>
+<li>180 compute nodes without the accelerator</li>
+<li>23 compute nodes with GPU accelerator - equipped with NVIDIA Tesla Kepler K20</li>
+<li>4Â compute nodes with MIC accelerator - equipped with Intel Xeon Phi 5110P</li>
+<li>2 fat nodes - equipped with 512GB RAM and two 100GB SSD drives</li>
+</ul>
+<p><a href="compute-nodes.html" title="" target="_self" class="internal-link">More about Compute nodes</a>.</p>
+<p>GPU and accelerated nodes are available upon request, see the <a href="resource-allocation-and-job-execution/resources-allocation-policy.html" title="" target="_self" class="internal-link">Resources Allocation Policy</a>.</p>
+<p class="WYSIWYG_LINK">All these nodes are interconnected by fast <span class="WYSIWYG_LINK">InfiniBand <span class="WYSIWYG_LINK">QDR</span> network</span> and Ethernet network. <a href="network.html" title="" target="_self" class="internal-link">More about the <span class="WYSIWYG_LINK">Network</span></a>. Every chassis provides Infiniband switch, marked <strong>isw</strong>, connecting all nodes in the chassis, as well as connecting the chassis to the upper level switches.</p>
+<p class="WYSIWYG_LINK">All nodes share 360TB /home disk storage to store user files. The 146TB shared /scratch storage is available for the scratch data. These file systems are provided by Lustre parallel file system. There is also local disk storage available on all compute nodes /lscratch. <a href="storage.html" title="" target="_self" class="internal-link">More about <span class="WYSIWYG_LINK">Storage</span></a>.</p>
+<p>The user access to the Anselm cluster is provided by two login nodes login1, login2, and data mover node dm1. <a href="accessing-the-cluster.html" title="" target="_self" class="internal-link">More about accessing cluster.</a></p>
+<p>Â The parameters are summarized in the following tables:</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2"><strong>In general</strong></th></tr>
+<tr class="even">
+<td>Primary purpose</td>
+<td>High Performance Computing</td>
+</tr>
+<tr class="odd">
+<td>Architecture of compute nodes</td>
+<td>x86-64</td>
+</tr>
+<tr class="even">
+<td>Operating system</td>
+<td>Linux</td>
+</tr>
+<tr><th colspan="2"><a href="compute-nodes.html" title="" target="_self" class="internal-link"><strong>Compute nodes</strong></a></th></tr>
+<tr class="even">
+<td>Totally</td>
+<td>209</td>
+</tr>
+<tr class="odd">
+<td>Processor cores</td>
+<td>16 (2x8 cores)</td>
+</tr>
+<tr class="even">
+<td>RAM</td>
+<td>min. 64 GB, min. 4 GB per core</td>
+</tr>
+<tr class="odd">
+<td>Local disk drive</td>
+<td>yes - usually 500 GB</td>
+</tr>
+<tr class="even">
+<td>Compute network</td>
+<td>InfiniBand QDR, fully non-blocking, fat-tree</td>
+</tr>
+<tr class="odd">
+<td>w/o accelerator</td>
+<td>180, cn[1-180]</td>
+</tr>
+<tr class="even">
+<td>GPU accelerated</td>
+<td>23, cn[181-203]</td>
+</tr>
+<tr class="odd">
+<td>MIC accelerated</td>
+<td>4, cn[204-207]</td>
+</tr>
+<tr class="even">
+<td>Fat compute nodes</td>
+<td>2, cn[208-209]</td>
+</tr>
+<tr><th colspan="2"><strong>In total</strong></th></tr>
+<tr class="even">
+<td>Total theoretical peak performance (Rpeak)</td>
+<td>94 Tflop/s</td>
+</tr>
+<tr class="odd">
+<td>Total max. LINPACK performance (Rmax)</td>
+<td>73 Tflop/s</td>
+</tr>
+<tr class="even">
+<td>Total amount of RAM</td>
+<td>15.136 TB</td>
+</tr>
+</tbody>
+</table>
+<table class="listing">
+<tbody>
+<tr><th>Node</th><th>Processor</th><th>Memory</th><th>Accelerator</th></tr>
+<tr class="even">
+<td>w/o accelerator</td>
+<td>2x Intel Sandy Bridge E5-2665, 2.4GHz</td>
+<td>64GB</td>
+<td>-</td>
+</tr>
+<tr class="odd">
+<td>GPU accelerated</td>
+<td>2x Intel Sandy Bridge E5-2470, 2.3GHz</td>
+<td>96GB</td>
+<td>NVIDIA Kepler K20</td>
+</tr>
+<tr class="even">
+<td>MIC accelerated</td>
+<td>2x Intel Sandy Bridge E5-2470, 2.3GHz</td>
+<td>96GB</td>
+<td>Intel Xeon Phi P5110</td>
+</tr>
+<tr class="odd">
+<td>Fat compute node</td>
+<td>2x Intel Sandy Bridge E5-2665, 2.4GHz</td>
+<td>512GB</td>
+<td>-</td>
+</tr>
+</tbody>
+</table>
+<p>Â For more details please refer to the <a href="compute-nodes.html" title="" target="_self" class="internal-link">Compute nodes</a>, <a href="storage.html" title="" target="_self" class="internal-link">Storage</a>, and <a href="network.html" title="" target="_self" class="internal-link">Network</a>.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md b/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
index 0986e4ceb..e996eddb1 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
@@ -398,4 +398,3 @@ Total amount of RAM
nodes](compute-nodes.html),
[Storage](storage.html), and
[Network](network.html).
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/introduction.html b/docs.it4i.cz/anselm-cluster-documentation/introduction.html
new file mode 100644
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+ <p>Welcome to Anselm supercomputer cluster. The Anselm cluster consists of 209 compute nodes, totaling 3344 compute cores with 15TB RAM and giving over 94 Tflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 16 cores, at least 64GB RAM, and 500GB harddrive. Nodes are interconnected by fully non-blocking fat-tree Infiniband network and equipped with Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in <a href="hardware-overview.html" title="" target="_self" class="internal-link">Hardware Overview</a>.</p>
+<p>The cluster runs bullx Linux <a class="external-link" href="http://www.bull.com/bullx-logiciels/systeme-exploitation.html" target="_self" title=""><span class="WYSIWYG_LINK"></span></a><a href="software/operating-system.html" title="" target="_self" class="internal-link">operating system</a>, which is compatible with the <span class="WYSIWYG_LINK">RedHat</span> <a class="external-link" href="http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg" target="_self" title=""><span class="WYSIWYG_LINK">Linux family.</span></a> We have installed a wide range of <a href="software.1.html" title="" target="_self" class="internal-link">software</a> packages targeted at different scientific domains. These packages are accessible via the <a href="environment-and-modules.html" title="" target="_self" class="internal-link">modules environment</a>.</p>
+<p>User data shared file-system (HOME, 320TB) and job data shared file-system (SCRATCH, 146TB) are available to users.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/introduction.md b/docs.it4i.cz/anselm-cluster-documentation/introduction.md
index c72b8f6f2..5be69738b 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/introduction.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/introduction.md
@@ -38,4 +38,3 @@ resources](../get-started-with-it4innovations/applying-for-resources.html),
[obtain login
credentials,](../get-started-with-it4innovations/obtaining-login-credentials.html)
and [access the cluster](accessing-the-cluster.html).
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/network.html b/docs.it4i.cz/anselm-cluster-documentation/network.html
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+ <p>All compute and login nodes of Anselm are interconnected by <a class="external-link" href="http://en.wikipedia.org/wiki/InfiniBand" target="_self" title="">Infiniband</a> QDR network and by Gigabit <a class="external-link" href="http://en.wikipedia.org/wiki/Ethernet" target="_self" title="">Ethernet</a> network. Both networks may be used to transfer user data.</p>
+<h2 class=" ">Infiniband Network</h2>
+<p>All compute and login nodes of Anselm are interconnected by a high-bandwidth, low-latency <a class="external-link" href="http://en.wikipedia.org/wiki/InfiniBand" target="_self" title="">Infiniband</a> QDR network (IB 4x QDR, 40 Gbps). The network topology is a fully non-blocking fat-tree.</p>
+<p>The compute nodes may be accessed via the Infiniband network using ib0 network interface, in address range 10.2.1.1-209. The MPI may be used to establish native Infiniband connection among the nodes.</p>
+<p class="callout">The network provides <strong>2170MB/s</strong> transfer rates via the TCP connection (single stream) and up to <strong>3600MB/s</strong> via native Infiniband protocol.</p>
+<p>The Fat tree topology ensures that peak transfer rates are achieved between any two nodes, independent of network traffic exchanged among other nodes concurrently.</p>
+<h2 class=" ">Ethernet Network</h2>
+<p>The compute nodes may be accessed via the regular Gigabit Ethernet network interface eth0, in address range 10.1.1.1-209, or by using aliases cn1-cn209. <br />The network provides<strong> 114MB/s</strong> transfer rates via the TCP connection.</p>
+<h2 class=" ">Example</h2>
+<pre class="prettyprint lang-sh">$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob<br />$ qstat -n -u username<br /> Req'd Req'd Elap<br />Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time<br />--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----<br />15209.srv11 username qexp Name0 5530 4 64 -- 01:00 R 00:00<br /> cn17/0*16+cn108/0*16+cn109/0*16+cn110/0*16<br /><br />$ ssh 10.2.1.110<br />$ ssh 10.1.1.108</pre>
+<p class=" ">In this example, we access the node cn110 by Infiniband network via the ib0 interface, then from cn110 to cn108 by Ethernet network.</p>
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/network.md b/docs.it4i.cz/anselm-cluster-documentation/network.md
index 416f594de..b18fe77e1 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/network.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/network.md
@@ -7,7 +7,7 @@ Network
All compute and login nodes of Anselm are interconnected by
[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
-DR network and by Gigabit
+QDR network and by Gigabit
[Ethernet](http://en.wikipedia.org/wiki/Ethernet)
network. Both networks may be used to transfer user data.
@@ -17,7 +17,7 @@ Infiniband Network
All compute and login nodes of Anselm are interconnected by a
high-bandwidth, low-latency
[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
-DR network (IB 4x QDR, 40 Gbps). The network topology is a fully
+QDR network (IB 4x QDR, 40 Gbps). The network topology is a fully
non-blocking fat-tree.
The compute nodes may be accessed via the Infiniband network using ib0
@@ -57,4 +57,3 @@ $ ssh 10.1.1.108
In this example, we access the node cn110 by Infiniband network via the
ib0 interface, then from cn110 to cn108 by Ethernet network.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/prace.html b/docs.it4i.cz/anselm-cluster-documentation/prace.html
new file mode 100644
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+ </h1>
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+</div>
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+ <h2 class=" ">Intro</h2>
+<p>PRACE users coming to Anselm as to TIER-1 system offered through the DECI calls are in general treated as standard users and so most of the general documentation applies to them as well. This section shows the main differences for quicker orientation, but often uses references to the original documentation. PRACE users who don't undergo the full procedure (including signing the IT4I AuP on top of the PRACE AuP) will not have a password and thus access to some services intended for regular users. This can lower their comfort, but otherwise they should be able to use the TIER-1 system as intended. Please see the <a href="../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html" title="" target="_self" class="internal-link">Obtaining Login Credentials section</a>, if the same level of access is required.</p>
+<p>All general <a class="external-link" href="http://www.prace-ri.eu/user-documentation/" target="_self" title="">PRACE User Documentation</a> should be read before continuing reading the local documentation here.</p>
+<h2 class=" "><a name="help-and-support"></a>Help and Support</h2>
+<p>If you have any troubles, need information, request support or want to install additional software, please use <a class="external-link" href="http://www.prace-ri.eu/helpdesk-guide264/" target="_self" title="">PRACE Helpdesk</a>.</p>
+<p>Information about the local services are provided in the <a href="introduction.html" title="" target="_self" class="internal-link">introduction of general user documentation</a>. Please keep in mind, that standard PRACE accounts don't have a password to access the web interface of the local (IT4Innovations) request tracker and thus a new ticket should be created by sending an e-mail to support[at]it4i.cz.</p>
+<h2 class=" ">Obtaining Login Credentials</h2>
+<p>In general PRACE users already have a PRACE account setup through their HOMESITE (institution from their country) as a result of rewarded PRACE project proposal. This includes signed PRACE AuP, generated and registered certificates, etc.</p>
+<p>If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on the Anselm cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so please see the corresponding <a href="../get-started-with-it4innovations/obtaining-login-credentials.html" title="" target="_self" class="internal-link">section of the general documentation here</a>.</p>
+<h2 class=" ">Accessing the cluster</h2>
+<h3 class=" ">Access with GSI-SSH</h3>
+<p>For all PRACE users the method for interactive access (login) and data transfer based on grid services from Globus Toolkit (GSI SSH and GridFTP) is supported.</p>
+<p>The user will need a valid certificate and to be present in the PRACE LDAP (please contact your HOME SITE or the primary investigator of your project for LDAP account creation).</p>
+<p>Most of the information needed by PRACE users accessing the Anselm TIER-1 system can be found here:</p>
+<ul>
+<li><a class="external-link" href="http://www.prace-ri.eu/Users-General-FAQs" target="_self" title="">General user's FAQ</a></li>
+<li><a class="external-link" href="http://www.prace-ri.eu/Certificates-FAQ" target="_self" title="">Certificates FAQ</a></li>
+<li><a class="external-link" href="http://www.prace-ri.eu/Interactive-Access-Using-gsissh" target="_self" title="">Interactive access using GSISSH</a></li>
+<li><a class="external-link" href="http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details" target="_self" title="">Data transfer with GridFTP</a></li>
+<li><a class="external-link" href="http://www.prace-ri.eu/Data-Transfer-with-gtransfer" target="_self" title="">Data transfer with gtransfer</a></li>
+</ul>
+<p class=" ">Â </p>
+<p class=" ">Before you start to use any of the services don't forget to create a proxy certificate from your certificate:</p>
+<pre class=" ">$ grid-proxy-init</pre>
+<p>To check whether your proxy certificate is still valid (by default it's valid 12 hours), use:</p>
+<pre class=" ">$ grid-proxy-info</pre>
+<p>Â </p>
+<p>To access Anselm cluster, two login nodes running GSI SSH service are available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).</p>
+<p><strong>Access from PRACE network:</strong></p>
+<p>It is recommended to use the single DNS name <span class="monospace">anselm-prace.it4i.cz</span> which is distributed between the two login nodes. If needed, user can login directly to one of the login nodes. The addresses are:</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>Login address</th><th>Port</th><th>Protocol</th><th>Login node</th></tr>
+<tr class="even">
+<td>anselm-prace.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login1 or login2</td>
+</tr>
+<tr class="odd">
+<td>login1-prace.anselm.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login1</td>
+</tr>
+<tr class="even">
+<td>login2-prace.anselm.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login2</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<pre class=" ">$ gsissh -p 2222 anselm-prace.it4i.cz</pre>
+<p>When logging from other PRACE system, the prace_service script can be used:</p>
+<pre class=" ">$ gsissh `prace_service -i -s anselm`</pre>
+<p>Â </p>
+<p><strong>Access from public Internet:</strong></p>
+<p>It is recommended to use the single DNS name <span class="monospace">anselm.it4i.cz</span> which is distributed between the two login nodes. If needed, user can login directly to one of the login nodes. The addresses are:</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>Login address</th><th>Port</th><th>Protocol</th><th>Login node</th></tr>
+<tr class="even">
+<td>anselm.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login1 or login2</td>
+</tr>
+<tr class="odd">
+<td>login1.anselm.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login1</td>
+</tr>
+<tr class="even">
+<td>login2.anselm.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login2</td>
+</tr>
+</tbody>
+</table>
+<pre class=" ">$ gsissh -p 2222 anselm.it4i.cz</pre>
+<p>When logging from other PRACE system, the <span class="monospace">prace_service</span> script can be used:</p>
+<pre class=" ">$ gsissh `prace_service -e -s anselm`</pre>
+<p>Â </p>
+<p>Although the preferred and recommended file transfer mechanism is <a class="anchor-link" href="prace.html#file-transfers" target="_self" title="">using GridFTP</a>, the GSI SSH implementation on Anselm supports also SCP, so for small files transfer gsiscp can be used:</p>
+<pre>$ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ anselm.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_</pre>
+<pre>$ gsiscp -P 2222 anselm.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_ </pre>
+<pre>$ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ anselm-prace.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_</pre>
+<pre>$ gsiscp -P 2222 anselm-prace.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_ </pre>
+<h3 class=" ">Access to X11 applications (VNC)</h3>
+<p>If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, please see the <a href="https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">section in general documentation</a>.</p>
+<p>If the user uses GSI SSH based access, then the procedure is similar to the SSH based access (<a href="https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">look here</a>), only the port forwarding must be done using GSI SSH:</p>
+<pre class=" ">$ gsissh -p 2222 anselm.it4i.cz -L 5961:localhost:5961</pre>
+<h3 class=" ">Access with SSH</h3>
+<p class=" ">After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information please see the <a href="https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/5d3d6f3d873a42e584cbf4365c4e251b" title="" target="_self" class="internal-link">section in general documentation</a>.</p>
+<h2 class=" "><a name="file-transfers"></a>File transfers</h2>
+<p>PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see <a href="https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/5d3d6f3d873a42e584cbf4365c4e251b" title="" target="_self" class="internal-link">the section in the general documentation</a>.</p>
+<p>Apart from the standard mechanisms, for PRACE users to transfer data to/from Anselm cluster, a GridFTP server running Globus Toolkit GridFTP service is available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).</p>
+<p>There's one control server and three backend servers for striping and/or backup in case one of them would fail.</p>
+<p><strong>Access from PRACE network:</strong></p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>Login address</th><th>Port</th><th>Node role</th></tr>
+<tr class="even">
+<td>gridftp-prace.anselm.it4i.cz</td>
+<td>2812</td>
+<td>Front end /control server</td>
+</tr>
+<tr class="odd">
+<td>login1-prace.anselm.it4i.cz</td>
+<td>2813</td>
+<td>Backend / data mover server</td>
+</tr>
+<tr class="even">
+<td>login2-prace.anselm.it4i.cz</td>
+<td>2813</td>
+<td>Backend / data mover server</td>
+</tr>
+<tr class="even">
+<td>dm1-prace.anselm.it4i.cz</td>
+<td>2813</td>
+<td>Backend / data mover server</td>
+</tr>
+</tbody>
+</table>
+<p>Copy files <strong>to</strong> Anselm by running the following commands on your local machine:</p>
+<pre>$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp-prace.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_</pre>
+<p>Or by using <span class="monospace">prace_service</span> script:</p>
+<pre>$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -i -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_</pre>
+<p>Copy files <strong>from</strong> Anselm:</p>
+<pre>$ globus-url-copy gsiftp://gridftp-prace.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_</pre>
+<p>Or by using <span class="monospace">prace_service</span> script:</p>
+<pre>$ globus-url-copy gsiftp://`prace_service -i -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_</pre>
+<p>Â </p>
+<p><strong>Access from public Internet:</strong></p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>Login address</th><th>Port</th><th>Node role</th></tr>
+<tr class="even">
+<td>gridftp.anselm.it4i.cz</td>
+<td>2812</td>
+<td>Front end /control server</td>
+</tr>
+<tr class="odd">
+<td>login1.anselm.it4i.cz</td>
+<td>2813</td>
+<td>Backend / data mover server</td>
+</tr>
+<tr class="even">
+<td>login2.anselm.it4i.cz</td>
+<td>2813</td>
+<td>Backend / data mover server</td>
+</tr>
+<tr class="even">
+<td>dm1.anselm.it4i.cz</td>
+<td>2813</td>
+<td>Backend / data mover server</td>
+</tr>
+</tbody>
+</table>
+<p>Copy files <strong>to</strong> Anselm by running the following commands on your local machine:</p>
+<pre>$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_</pre>
+<p>Or by using <span class="monospace">prace_service</span> script:</p>
+<pre>$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -e -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_</pre>
+<p>Copy files <strong>from</strong> Anselm:</p>
+<pre>$ globus-url-copy gsiftp://gridftp.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_</pre>
+<p>Or by using <span class="monospace">prace_service</span> script:</p>
+<pre>$ globus-url-copy gsiftp://`prace_service -e -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_</pre>
+<p>Â </p>
+<p>Generally both shared file systems are available through GridFTP:</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>File system mount point</th><th>Filesystem</th><th>Comment</th></tr>
+<tr class="even">
+<td>/home</td>
+<td>Lustre</td>
+<td>Default HOME directories of users in format /home/prace/login/</td>
+</tr>
+<tr class="odd">
+<td>/scratch</td>
+<td>Lustre</td>
+<td>Shared SCRATCH mounted on the whole cluster</td>
+</tr>
+</tbody>
+</table>
+<p class=" ">More information about the shared file systems is available <a href="storage.html" title="" target="_self" class="internal-link">here</a>.</p>
+<h2 class=" ">Usage of the cluster</h2>
+<p>There are some limitations for PRACE user when using the cluster. By default PRACE users aren't allowed to access special queues in the PBS Pro to have high priority or exclusive access to some special equipment like accelerated nodes and high memory (fat) nodes. There may be also restrictions obtaining a working license for the commercial software installed on the cluster, mostly because of the license agreement or because of insufficient amount of licenses.</p>
+<p>For production runs always use scratch file systems, either the global shared or the local ones. The available file systems are described <a href="hardware-overview.html" title="" target="_self" class="internal-link">here</a>.</p>
+<h3 class=" ">Software, Modules and PRACE Common Production Environment</h3>
+<p>All system wide installed software on the cluster is made available to the users via the modules. The information about the environment and modules usage is in this <a href="environment-and-modules.html" title="" target="_self" class="internal-link">section of general documentation</a>.</p>
+<p>PRACE users can use the "prace" module to use the <a class="external-link" href="http://www.prace-ri.eu/PRACE-common-production" target="_self" title="">PRACE Common Production Environment</a>.</p>
+<pre class=" ">$ module load prace</pre>
+<p>Â </p>
+<h3 class=" ">Resource Allocation and Job Execution</h3>
+<p>General information about the resource allocation, job queuing and job execution is in this <a href="resource-allocation-and-job-execution/introduction.html" title="" target="_self" class="internal-link">section of general documentation</a>.</p>
+<p>For PRACE users, the default production run queue is "qprace". PRACE users can also use two other queues "qexp" and "qfree".</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>queue</th><th>Active project</th><th>Project resources</th><th>Nodes</th><th>priority</th><th>authorization</th><th>walltime<br />default/max</th></tr>
+<tr class="even">
+<td><strong>qexp</strong><br />Express queue</td>
+<td>no</td>
+<td>none required</td>
+<td>2 reserved,<br />8 total</td>
+<td>high</td>
+<td>no</td>
+<td>1 / 1h</td>
+</tr>
+<tr class="odd">
+<td><strong>qprace</strong><br />Production queue</td>
+<td>yes<br /><br /></td>
+<td>> 0</td>
+<td>178 w/o accelerator</td>
+<td>medium</td>
+<td>no</td>
+<td>24 / 48h</td>
+</tr>
+<tr class="even">
+<td><strong>qfree</strong><br />Free resource queue</td>
+<td>yes</td>
+<td>none required</td>
+<td>178 w/o accelerator</td>
+<td>very low</td>
+<td>no</td>
+<td>12 / 12h</td>
+</tr>
+</tbody>
+</table>
+<p class=" "><strong>qprace</strong>, the PRACE Production queue<strong></strong>: This queue is intended for normal production runs. It is required that active project with nonzero remaining resources is specified to enter the qprace. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprace is 12 hours. If the job needs longer time, it must use checkpoint/restart functionality.</p>
+<h3 class=" ">Accounting & Quota</h3>
+<p>The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. See <a href="resource-allocation-and-job-execution/resources-allocation-policy.html" title="" target="_self" class="internal-link">example in the general documentation</a>.</p>
+<p>PRACE users should check their project accounting using the <a class="external-link" href="http://www.prace-ri.eu/accounting-report-tool/" target="_self" title="">PRACE Accounting Tool (DART)</a>.</p>
+<p>Users who have undergone the full local registration procedure (including signing the IT4Innovations Acceptable Use Policy) and who have received local password may check at any time, how many core-hours have been consumed by themselves and their projects using the command "it4ifree". Please note that you need to know your user password to use the command and that the displayed core hours are "system core hours" which differ from PRACE "standardized core hours".</p>
+<p class="callout">The <strong>it4ifree</strong> command is a part of it4i.portal.clients package, located here:<br /><a class="external-link" href="https://pypi.python.org/pypi/it4i.portal.clients" target="_self" title="">https://pypi.python.org/pypi/it4i.portal.clients</a></p>
+<pre class=" ">$ it4ifree<br />Password:<br />    PID  Total Used ...by me Free<br />  -------- ------- ------ -------- -------<br />  OPEN-0-0 1500000 400644  225265 1099356<br />  DD-13-1   10000 2606 2606 7394</pre>
+<p class=" ">Â </p>
+<p class=" ">By default file system quota is applied. To check the current status of the quota use</p>
+<pre>$ lfs quota -u USER_LOGIN /home<br />$ lfs quota -u USER_LOGIN /scratch</pre>
+<p class=" ">If the quota is insufficient, please contact the <a class="anchor-link" href="prace.html#help-and-support" target="_self" title="">support</a> and request an increase.</p>
+<p>Â </p>
+<p>Â </p>
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/prace.md b/docs.it4i.cz/anselm-cluster-documentation/prace.md
index bf274bdc1..a93c53a7a 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/prace.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/prace.md
@@ -318,7 +318,7 @@ users can also use two other queues "qexp" and "qfree".
Free resource queue
-------------------------------------------------------------------------------------------------------------------------
-**qprace**, the PRACE Production queue****This queue is intended for
+**qprace**, the PRACE Production queue****: This queue is intended for
normal production runs. It is required that active project with nonzero
remaining resources is specified to enter the qprace. The queue runs
with medium priority and no special authorization is required to use it.
@@ -373,4 +373,3 @@ increase.
Â
Â
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.html b/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.html
new file mode 100644
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+ <div id="parent-fieldname-text-a3341e86431f45c1b328facacf4a5232" class="">
+ <h2 id="schematic-overview">Introduction</h2>
+<p>The goal of this service is to provide the users a GPU accelerated use of OpenGL applications, especially for pre- and post- processing work, where not only the GPU performance is needed but also fast access to the shared file systems of the cluster and a reasonable amount of RAM.</p>
+<p>The service is based on integration of open source tools VirtualGL and TurboVNC together with the cluster's job scheduler PBS Professional.</p>
+<p>Currently two compute nodes are dedicated for this service with following configuration for each node:</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th colspan="2"><a href="compute-nodes.html" title="" target="_self" class="internal-link"><strong>Visualization node configuration</strong></a></th></tr>
+<tr class="even">
+<td>CPU</td>
+<td>2x Intel Sandy Bridge E5-2670, 2.6GHz</td>
+</tr>
+<tr class="odd">
+<td>Processor cores</td>
+<td>16 (2x8 cores)</td>
+</tr>
+<tr class="even">
+<td>RAM</td>
+<td>64 GB, min. 4 GB per core</td>
+</tr>
+<tr class="even">
+<td>GPU</td>
+<td>NVIDIA Quadro 4000, 2GB RAM</td>
+</tr>
+<tr class="odd">
+<td>Local disk drive</td>
+<td>yes - 500 GB</td>
+</tr>
+<tr class="even">
+<td>Compute network</td>
+<td>InfiniBand QDR</td>
+</tr>
+</tbody>
+</table>
+<h2>Schematic overview</h2>
+<p><img alt="rem_vis_scheme" src="scheme.png" title="rem_vis_scheme" class="image-inline" /></p>
+<p><img alt="rem_vis_legend" src="legend.png" title="rem_vis_legend" class="image-inline" /></p>
+<h2 class=" " id="setup-and-start-your-own-turbovnc-server">How to use the service</h2>
+<h3>Setup and start your own TurboVNC server.</h3>
+<p>TurboVNC is designed and implemented for cooperation with VirtualGL and available for free for all major platforms. For more information and download, please refer to: <a href="http://sourceforge.net/projects/turbovnc/">http://sourceforge.net/projects/turbovnc/</a></p>
+<p><strong>Always use TurboVNC on both sides</strong> (server and client) <strong>don't mix TurboVNC and other VNC implementations</strong> (TightVNC, TigerVNC, ...) as the VNC protocol implementation may slightly differ and diminish your user experience by introducing picture artifacts, etc.</p>
+<p>The procedure is:</p>
+<h4 id="1-connect-to-a-login-node">1. Connect to a login node.</h4>
+<p>Please <a href="https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/5d3d6f3d873a42e584cbf4365c4e251b" title="" target="_self" class="internal-link">follow the documentation</a>.</p>
+<h4 id="2-run-your-own-instance-of-turbovnc-server">2. Run your own instance of TurboVNC server.</h4>
+<p>To have the OpenGL acceleration, <strong>24 bit color depth must be used</strong>. Otherwise only the geometry (desktop size) definition is needed.</p>
+<p><em>At first VNC server run you need to define a password.</em></p>
+<p>This example defines desktop with dimensions 1200x700 pixels and 24 bit color depth.</p>
+<pre class="code highlight white shell"><code>$ module load turbovnc/1.2.2 <br />$ vncserver -geometry 1200x700 -depth 24 <br /><br />Desktop <span class="s1">'TurboVNC: login2:1 (username)'</span> started on display login2:1 <br /><br />Starting applications specified <span class="k">in</span> /home/username/.vnc/xstartup.turbovnc <br />Log file is /home/username/.vnc/login2:1.log </code></pre>
+<h4 id="3-remember-which-display-number-your-vnc-server-runs-you-will-need-it-in-the-future-to-stop-the-server">3. Remember which display number your VNC server runs (you will need it in the future to stop the server).</h4>
+<pre class="code highlight white shell"><code>$ vncserver -list <br /><br />TurboVNC server sessions: <br /><br />X DISPLAY <span class="c"># PROCESS ID</span> <br />:1 23269 </code></pre>
+<p>In this example the VNC server runs on display <strong>:1</strong>.</p>
+<h4 id="4-remember-the-exact-login-node-where-your-vnc-server-runs">4. Remember the exact login node, where your VNC server runs.</h4>
+<pre class="code highlight white shell"><code>$ uname -n<br />login2 </code></pre>
+<p>In this example the VNC server runs on <strong>login2</strong>.</p>
+<h4 id="5-remember-on-which-tcp-port-your-own-vnc-server-is-running">5. Remember on which TCP port your own VNC server is running.</h4>
+<p>To get the port you have to look to the log file of your VNC server.</p>
+<pre class="code highlight white shell"><code>$ grep -E <span class="s2">"VNC.*port"</span> /home/username/.vnc/login2:1.log <br />20/02/2015 14:46:41 Listening <span class="k">for </span>VNC connections on TCP port 5901 </code></pre>
+<p>In this example the VNC server listens on TCP port <strong>5901</strong>.</p>
+<h4 id="6-connect-to-the-login-node-where-your-vnc-server-runs-with-ssh-to-tunnel-your-vnc-session">6. Connect to the login node where your VNC server runs with SSH to tunnel your VNC session.</h4>
+<p>Tunnel the TCP port on which your VNC server is listenning.</p>
+<pre class="code highlight white shell"><code>$ ssh login2.anselm.it4i.cz -L 5901:localhost:5901 </code></pre>
+<p><em>If you use Windows and Putty, please refer to port forwarding setup <span class="internal-link">in the documentation</span>:</em> <a href="accessing-the-cluster/x-window-and-vnc.html#section-12">https://docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc#section-12</a></p>
+<h4 id="7-if-you-don-t-have-turbo-vnc-installed-on-your-workstation">7. If you don't have Turbo VNC installed on your workstation.</h4>
+<p>Get it from: <a href="http://sourceforge.net/projects/turbovnc/">http://sourceforge.net/projects/turbovnc/</a></p>
+<h4 id="8-run-turbovnc-viewer-from-your-workstation">8. Run TurboVNC Viewer from your workstation.</h4>
+<p>Mind that you should connect through the SSH tunneled port. In this example it is 5901 on your workstation (localhost).</p>
+<pre class="code highlight white shell"><code>$ vncviewer localhost:5901 </code></pre>
+<p><em>If you use Windows version of TurboVNC Viewer, just run the Viewer and use address *</em>localhost:5901*<em>.</em></p>
+<h4 id="9-proceed-to-the-chapter-access-the-visualization-node">9. Proceed to the chapter "Access the visualization node."</h4>
+<p><em>Now you should have working TurboVNC session connected to your workstation.</em></p>
+<h4 id="10-after-you-end-your-visualization-session">10. After you end your visualization session.</h4>
+<p><em>Don't forget to correctly shutdown your own VNC server on the login node!</em></p>
+<pre class="code highlight white shell"><code>$ vncserver -kill :1 </code></pre>
+<h2 id="access-the-visualization-node">Access the visualization node</h2>
+<p>To access the node use a dedicated PBS Professional scheduler queue <strong>qviz</strong>. The queue has following properties:</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>queue</th><th>active project</th><th>project resources</th><th>nodes</th><th>min ncpus*</th><th>priority</th><th>authorization</th><th>walltime<br />default/max</th></tr>
+<tr class="even">
+<td>
+<p><strong>qviz              </strong>Visualization queue</p>
+</td>
+<td>yes</td>
+<td>none required</td>
+<td>2</td>
+<td>4</td>
+<td><span><em>150</em></span></td>
+<td>no</td>
+<td>1 hour / 2 hours</td>
+</tr>
+</tbody>
+</table>
+<p>Currently when accessing the node, each user gets 4 cores of a CPU allocated, thus approximately 16 GB of RAM and 1/4 of the GPU capacity. <em>If more GPU power or RAM is required, it is recommended to allocate one whole node per user, so that all 16 cores, whole RAM and whole GPU is exclusive. This is currently also the maximum allowed allocation per one user. One hour of work is allocated by default, the user may ask for 2 hours maximum.</em></p>
+<p>To access the visualization node, follow these steps:</p>
+<h4 id="1-in-your-vnc-session-open-a-terminal-and-allocate-a-node-using-pbspro-qsub-command">1. In your VNC session, open a terminal and allocate a node using PBSPro qsub command.</h4>
+<p><em>This step is necessary to allow you to proceed with next steps.</em></p>
+<pre class="code highlight white shell"><code>$ qsub -I -q qviz -A PROJECT_ID </code></pre>
+<p>In this example the default values for CPU cores and usage time are used.</p>
+<pre class="code highlight white shell"><code>$ qsub -I -q qviz -A PROJECT_ID -l <span class="k">select</span><span class="o">=</span>1:ncpus<span class="o">=</span>16 -l <span class="nv">walltime</span><span class="o">=</span>02:00:00 </code></pre>
+<p><em>Substitute **PROJECT_ID</em>* with the assigned project identification string.*</p>
+<p>In this example a whole node for 2 hours is requested.</p>
+<p>If there are free resources for your request, you will have a shell running on an assigned node. Please remember the name of the node.</p>
+<pre class="code highlight white shell"><code>$ uname -n<br />srv8 </code></pre>
+<p>In this example the visualization session was assigned to node <strong>srv8</strong>.</p>
+<h4 id="2-in-your-vnc-session-open-another-terminal-keep-the-one-with-interactive-pbspro-job-open">2. In your VNC session open another terminal (keep the one with interactive PBSPro job open).</h4>
+<p>Setup the VirtualGL connection to the node, which PBSPro allocated for your job.</p>
+<pre class="code highlight white shell"><code>$ vglconnect srv8 </code></pre>
+<p>You will be connected with created VirtualGL tunnel to the visualization node, where you will have a shell.</p>
+<h4 id="3-load-the-virtualgl-module">3. Load the VirtualGL module.</h4>
+<pre class="code highlight white shell"><code>$ module load virtualgl/2.4 </code></pre>
+<h4 id="4-run-your-desired-opengl-accelerated-application-using-virtualgl-script-vglrun">4. Run your desired OpenGL accelerated application using VirtualGL script "vglrun".</h4>
+<pre class="code highlight white shell"><code>$ vglrun glxgears </code></pre>
+<p>Please note, that if you want to run an OpenGL application which is available through modules, you need at first load the respective module. E. g. to run the <strong>Mentat</strong> OpenGL application from <strong>MARC</strong> software package use:</p>
+<pre class="code highlight white shell"><code>$ module load marc/2013.1 <br />$ vglrun mentat </code></pre>
+<h4 id="5-after-you-end-your-work-with-the-opengl-application">5. After you end your work with the OpenGL application.</h4>
+<p>Just logout from the visualization node and exit both opened terminals and end your VNC server session as described above.</p>
+<h2 class=" ">Tips and Tricks</h2>
+<p>If you want to increase the responsibility of the visualization, please adjust your TurboVNC client settings in this way:</p>
+<p><img alt="rem_vis_settings" src="turbovncclientsetting.png" title="rem_vis_settings" class="image-inline" /></p>
+<p>To have an idea how the settings are affecting the resulting picture quality three levels of "JPEG image quality" are demonstrated:</p>
+<p>1. JPEG image quality = 30</p>
+<p><img alt="rem_vis_q3" src="quality3.png" title="rem_vis_q3" class="image-inline" /></p>
+<p>2. JPEG image quality = 15</p>
+<p><img alt="rem_vis_q2" src="quality2.png" title="rem_vis_q2" class="image-inline" /></p>
+<p>3. JPEG image quality = 10</p>
+<p><img alt="rem_vis_q1" src="quality1.png" title="rem_vis_q1" class="image-inline" /></p>
+<p><br /><br /></p>
+
+ </div>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md b/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
index 9cfd5efcd..9871e2aab 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
@@ -43,7 +43,7 @@ How to use the service
TurboVNC is designed and implemented for cooperation with VirtualGL and
available for free for all major platforms. For more information and
-download, please refer to<http://sourceforge.net/projects/turbovnc/>
+download, please refer to: <http://sourceforge.net/projects/turbovnc/>
**Always use TurboVNC on both sides** (server and client) **don't mix
TurboVNC and other VNC implementations** (TightVNC, TigerVNC, ...) as
@@ -71,7 +71,7 @@ color depth.
$ module load turbovnc/1.2.2
$ vncserver -geometry 1200x700 -depth 24
-Desktop 'TurboVNClogin2:1 (username)' started on display login2:1
+Desktop 'TurboVNC: login2:1 (username)' started on display login2:1
Starting applications specified in /home/username/.vnc/xstartup.turbovnc
Log file is /home/username/.vnc/login2:1.log
@@ -82,7 +82,7 @@ Log file is /home/username/.vnc/login2:1.log
```
$ vncserver -list
-TurboVNC server sessions
+TurboVNC server sessions:
X DISPLAY # PROCESS ID
:1 23269
@@ -124,7 +124,7 @@ $ ssh login2.anselm.it4i.cz -L 5901:localhost:5901
#### 7. If you don't have Turbo VNC installed on your workstation. {#7-if-you-don-t-have-turbo-vnc-installed-on-your-workstation}
-Get it from<http://sourceforge.net/projects/turbovnc/>
+Get it from: <http://sourceforge.net/projects/turbovnc/>
#### 8. Run TurboVNC Viewer from your workstation. {#8-run-turbovnc-viewer-from-your-workstation}
@@ -297,3 +297,7 @@ quality three levels of "JPEG image quality" are demonstrated:
3. JPEG image quality = 10
+
+
+
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.html b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.html
new file mode 100644
index 000000000..59eab7c76
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.html
@@ -0,0 +1,772 @@
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+ Resource Allocation and Job Execution
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+ <p>To run a <a href="introduction.html" title="" target="_self" class="internal-link">job</a>, <a href="introduction.html" title="" target="_self" class="internal-link">computational resources</a> for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive informations about PBS Pro can be found in the <a href="../pbspro-documentation.html" title="" target="_self" class="internal-link">official documentation here</a>, especially in the <a href="../pbspro-documentation/pbspro-users-guide.1" title="" target="_self" class="internal-link">PBS Pro User's Guide</a>.</p>
+<h2 class=" ">Resources Allocation Policy</h2>
+<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. <a href="resource-allocation-and-job-execution/job-priority.html" title="" target="_self" class="internal-link">The Fairshare</a> at Anselm ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:</p>
+<ul>
+<li><strong>qexp</strong>, the Express queue</li>
+<li><strong>qprod</strong>, the Production queue<strong></strong></li>
+<li><strong>qlong</strong>, the Long queue, regula</li>
+<li><strong>qnvidia, qmic, qfat</strong>, the Dedicated queues</li>
+<li><strong>qfree, </strong>the Free resource utilization queue</li>
+</ul>
+<p class="callout">Check the queue status at <a class="external-link" href="https://extranet.it4i.cz/anselm/" target="_self" title="">https://extranet.it4i.cz/anselm/</a></p>
+<p>Read more on the <a href="resource-allocation-and-job-execution/resources-allocation-policy.html" title="" target="_self" class="internal-link">Resource Allocation Policy</a> page.</p>
+<h2 class=" ">Job submission and execution</h2>
+<p class="callout">Use the <strong>qsub</strong> command to submit your jobs.</p>
+<p class=" ">The qsub submits the job into the queue. The qsub command creates a request to the PBS Job manager for allocation of specified resources. The <strong>smallest allocation unit is entire node, 16 cores</strong>, with exception of the qexp queue. The resources will be allocated when available, subject to allocation policies and constraints. <strong>After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.</strong></p>
+<p class=" ">Read more on the <a href="resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_self" class="internal-link">Job submission and execution</a> page.</p>
+<h2 class=" ">Capacity computing</h2>
+<p class="callout">Use Job arrays when running huge number of jobs.<br />Use GNU Parallel and/or Job arrays when running (many) single core jobs.</p>
+<p>In many cases, it is useful to submit huge (<span>100+</span>) number of computational jobs into the PBS queue system. Huge number of (small) jobs is one of the most effective ways to execute embarrassingly parallel calculations, achieving best runtime, throughput and computer utilization. In this chapter, we discuss the the recommended way to run huge number of jobs, including <strong>ways to run huge number of single core jobs</strong>.</p>
+<p>Read more on <a href="resource-allocation-and-job-execution/capacity-computing.html" title="" target="_self" class="internal-link">Capacity computing</a> page.</p>
+
+ </div>
+
+
+ <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.md b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.md
index d9b684756..83bd91c43 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.md
@@ -74,4 +74,3 @@ jobs**.
Read more on [Capacity
computing](resource-allocation-and-job-execution/capacity-computing.html)
page.
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.html b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.html
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+ <h2 class=" ">Introduction</h2>
+<p>In many cases, it is useful to submit huge (<span>100+</span>) number of computational jobs into the PBS queue system. Huge number of (small) jobs is one of the most effective ways to execute embarrassingly parallel calculations, achieving best runtime, throughput and computer utilization.</p>
+<p>However, executing huge number of jobs via the PBS queue may strain the system. This strain may result in slow response to commands, inefficient scheduling and overall degradation of performance and user experience, for all users. For this reason, the number of jobs is <strong>limited to 100 per user, 1000 per job array</strong></p>
+<p class="callout">Please follow one of the procedures below, in case you wish to schedule more than <span>100</span> jobs at a time.</p>
+<ul>
+<li class="anchor-link" title="">Use <a class="anchor-link" href="capacity-computing.html#job-arrays" target="_self" title="">Job arrays</a> when running huge number of <a class="anchor-link" href="capacity-computing.html#shared-jobscript-on-one-node" target="_self" title="">multithread</a> (bound to one node only) or multinode (multithread across several nodes) jobs</li>
+<li>Use <a class="anchor-link" href="capacity-computing.html#gnu-parallel" target="_self" title="">GNU parallel</a> when running single core jobs</li>
+<li>Combine<a class="anchor-link" href="capacity-computing.html#combining-job-arrays-and-gnu-parallel" target="_self" title=""> GNU parallel with Job arrays</a>Â when running huge number of single core jobs</li>
+</ul>
+<h2 class=" ">Policy</h2>
+<ol>
+<li>A user is allowed to submit at most 100 jobs. Each job may be <a class="anchor-link" href="capacity-computing.html#job-arrays" target="_self" title="">a job array</a>.</li>
+<li>The array size is at most 1000 subjobs.</li>
+</ol>
+<h2 class=" "><a name="job-arrays"></a>Job arrays</h2>
+<p class="callout">Huge number of jobs may be easily submitted and managed as a job array.</p>
+<p>A job array is a compact representation of many jobs, called subjobs. The subjobs share the same job script, and have the same values for all attributes and resources, with the following exceptions:</p>
+<ul>
+<li>each subjob has a unique index, $PBS_ARRAY_INDEX</li>
+<li>job Identifiers of subjobs only differ by their indices</li>
+<li>the state of subjobs can differ (R,Q,...etc.)</li>
+</ul>
+<p>All subjobs within a job array have the same scheduling priority and schedule as independent jobs.<br />Entire job array is submitted through a single qsub command and may be managed by qdel, qalter, qhold, qrls and qsig commands as a single job.</p>
+<h3 class=" "><a name="shared-jobscript-on-one-node"></a>Shared jobscript</h3>
+<p>All subjobs in job array use the very same, single jobscript. Each subjob runs its own instance of the jobscript. The instances execute different work controlled by $PBS_ARRAY_INDEX variable.</p>
+<p><a name="array_example"></a>Example:</p>
+<p>Assume we have 900 input files with name beginning with "file" (e. g. file001, ..., file900). Assume we would like to use each of these input files with program executable myprog.x, each as a separate job.</p>
+<p>First, we create a tasklist file (or subjobs list), listing all tasks (subjobs) - all input files in our example:</p>
+<pre class="prettyprint lang-sh">$ find . -name 'file*' > tasklist</pre>
+<p>Then we create jobscript:</p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -A PROJECT_ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=16,walltime=02:00:00<br /><br /># change to local scratch directory<br />SCR=/lscratch/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># get individual tasks from tasklist with index from PBS JOB ARRAY<br />TASK=$(sed -n "${PBS_ARRAY_INDEX}p" $PBS_O_WORKDIR/tasklist) <br /><br class=" " /># copy input file and executable to scratch <br />cp $PBS_O_WORKDIR/$TASK input ; cp $PBS_O_WORKDIR/myprog.x .<br /><br /># execute the calculation<br />./myprog.x < input > output<br /><br /># copy output file to submit directory<br />cp output $PBS_O_WORKDIR/$TASK.out</pre>
+<p class=" ">In this example, the submit directory holds the 900 input files, executable myprog.x and the jobscript file. As input for each run, we take the filename of input file from created tasklist file. We copy the input file to local scratch /lscratch/$PBS_JOBID, execute the myprog.x and copy the output file back to <span>the submit directory</span>, under the $TASK.out name. The myprog.x runs on one node only and must use threads to run in parallel. Be aware, that if the myprog.x <strong>is not multithreaded</strong>, then all the <strong>jobs are run as single thread programs in sequential</strong> manner. Due to allocation of the whole node, the <strong>accounted time is equal to the usage of whole node</strong>, while using only 1/16 of the node!</p>
+<p class=" ">If huge number of parallel multicore (in means of multinode multithread, e. g. MPI enabled) jobs is needed to run, then a job array approach should also be used. The main difference compared to previous example using one node is that the local scratch should not be used (as it's not shared between nodes) and MPI or other technique for parallel multinode run has to be used properly.</p>
+<h3 class=" ">Submit the job array</h3>
+<p>To submit the job array, use the qsub -J command. The 900 jobs of the <a class="anchor-link" href="capacity-computing.html#array_example" target="_self" title="">example above</a> may be submitted like this:</p>
+<pre class="prettyprint lang-sh">$ qsub -N JOBNAME -J 1-900 jobscript<br />12345[].dm2</pre>
+<p>In this example, we submit a job array of 900 subjobs. Each subjob will run on full node and is assumed to take less than 2 hours (please note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue).</p>
+<p>Sometimes for testing purposes, you may need to submit only one-element array. This is not allowed by PBSPro, but there's a workaround:</p>
+<pre class="prettyprint lang-sh">$ qsub -N JOBNAME -J 9-10:2 jobscript</pre>
+<p>This will only choose the lower index (9 in this example) for submitting/running your job.</p>
+<h3 class=" ">Manage the job array</h3>
+<p>Check status of the job array by the qstat command.</p>
+<pre class="prettyprint lang-sh">$ qstat -a 12345[].dm2<br /><br />dm2:<br /> Req'd Req'd Elap<br />Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time<br />--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----<br />12345[].dm2 user2 qprod xx 13516 1 16 -- 00:50 B 00:02</pre>
+<p>The status B means that some subjobs are already running.</p>
+<p>Check status of the first 100 subjobs by the qstat command.</p>
+<pre class="prettyprint lang-sh">$ qstat -a 12345[1-100].dm2<br /><br />dm2:<br /> Req'd Req'd Elap<br />Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time<br />--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----<br />12345[1].dm2 user2 qprod xx 13516 1 16 -- 00:50 R 00:02<br />12345[2].dm2 user2 qprod xx 13516 1 16 -- 00:50 R 00:02<br />12345[3].dm2 user2 qprod xx 13516 1 16 -- 00:50 R 00:01<br />12345[4].dm2 user2 qprod xx 13516 1 16 -- 00:50 Q --<br /> . . . . . . . . . . .<br /> , . . . . . . . . . . <br />12345[100].dm2 user2 qprod xx 13516 1 16 -- 00:50 Q --</pre>
+<p>Delete the entire job array. Running subjobs will be killed, queueing subjobs will be deleted.</p>
+<pre class="prettyprint lang-sh">$ qdel 12345[].dm2</pre>
+<p>Deleting large job arrays may take a while.</p>
+<p>Display status information for all user's jobs, job arrays, and subjobs.</p>
+<pre class="prettyprint lang-sh">$ qstat -u $USER -t</pre>
+<p>Display status information for all user's subjobs.</p>
+<pre class="prettyprint lang-sh">$ qstat -u $USER -tJ</pre>
+<p>Read more on job arrays in the <a href="../../pbspro-documentation.html" title="" target="_self" class="internal-link">PBSPro Users guide</a>.</p>
+<h2 class=" "><a name="gnu-parallel"></a>GNU parallel</h2>
+<p class="callout">Use GNU parallel to run many single core tasks on one node.</p>
+<p class=" ">GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. GNU parallel is most useful in running single core jobs via the queue system on Anselm.</p>
+<p class=" ">For more information and examples see the parallel man page:</p>
+<pre class="prettyprint lang-sh">$ module add parallel<br />$ man parallel</pre>
+<h3 class=" ">GNU parallel jobscript</h3>
+<p class=" ">The GNU parallel shell executes multiple instances of the jobscript using all cores on the node. The instances execute different work, controlled by the $PARALLEL_SEQ variable.</p>
+<p><a name="gp_example"></a>Example:</p>
+<p>Assume we have 101 input files with name beginning with "file" (e. g. file001, ..., file101). Assume we would like to use each of these input files with program executable myprog.x, each as a separate single core job. We call these single core jobs tasks.</p>
+<p>First, we create a tasklist file, listing all tasks - all input files in our example:</p>
+<pre class="prettyprint lang-sh">$ find . -name 'file*' > tasklist</pre>
+<p>Then we create jobscript:</p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -A PROJECT_ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=16,walltime=02:00:00<br /><br class="prettyprint lang-sh" />[ -z "$PARALLEL_SEQ" ] && \<br />{ module add parallel ; exec parallel -a $PBS_O_WORKDIR/tasklist $0 ; }<br /><br /># change to local scratch directory<br />SCR=/lscratch/$PBS_JOBID/$PARALLEL_SEQ<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># get individual task from tasklist<br />TASK=$1  <br /><br /># copy input file and executable to scratch <br />cp $PBS_O_WORKDIR/$TASK input <br /><br /># execute the calculation<br />cat input > output<br /><br /># copy output file to submit directory<br />cp output $PBS_O_WORKDIR/$TASK.out</pre>
+<p>In this example, tasks from tasklist are executed via the GNU parallel. The jobscript executes multiple instances of itself in parallel, on all cores of the node. Once an instace of jobscript is finished, new instance starts until all entries in tasklist are processed. Currently processed entry of the joblist may be retrieved via $1 variable. Variable $TASK expands to one of the input filenames from tasklist. We copy the input file to local scratch, execute the myprog.x and copy the output file back to the submit directory, under the $TASK.out name. </p>
+<h3 class=" ">Submit the job</h3>
+<p>To submit the job, use the qsub command. The 101 tasks' job of the <a class="anchor-link" href="capacity-computing.html#gp_example" target="_self" title="">example above</a> may be submitted like this:</p>
+<pre class="prettyprint lang-sh">$ qsub -N JOBNAME jobscript<br />12345.dm2</pre>
+<p>In this example, we submit a job of 101 tasks. 16 input files will be processed in parallel. The 101 tasks on 16 cores are assumed to complete in less than 2 hours.</p>
+<p>Please note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue.</p>
+<h2 class=" "><a name="combining-job-arrays-and-gnu-parallel"></a>Job arrays and GNU parallel</h2>
+<p class="callout">Combine the Job arrays and GNU parallel for best throughput of single core jobs</p>
+<p>While job arrays are able to utilize all available computational nodes, the GNU parallel can be used to efficiently run multiple single-core jobs on single node. The two approaches may be combined to utilize all available (current and future) resources to execute single core jobs.</p>
+<p class="callout">Every subjob in an array runs GNU parallel to utilize all cores on the node</p>
+<h3 class=" ">GNU parallel, shared jobscript</h3>
+<p class=" ">Combined approach, very similar to job arrays, can be taken. Job array is submitted to the queuing system. The subjobs run GNU parallel. The GNU parallel shell executes multiple instances of the jobscript using all cores on the node. The instances execute different work, controlled by the $PBS_JOB_ARRAY and $PARALLEL_SEQ variables.</p>
+<p><a name="combined_example"></a>Example:</p>
+<p>Assume we have 992 input files with name beginning with "file" (e. g. file001, ..., file992). Assume we would like to use each of these input files with program executable myprog.x, each as a separate single core job. We call these single core jobs tasks.</p>
+<p>First, we create a tasklist file, listing all tasks - all input files in our example:</p>
+<pre class="prettyprint lang-sh">$ find . -name 'file*' > tasklist</pre>
+<p>Next we create a file, controlling how many tasks will be executed in one subjob</p>
+<pre class="prettyprint lang-sh">$ seq 32 > numtasks</pre>
+<p>Then we create jobscript:</p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -A PROJECT_ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=16,walltime=02:00:00<br /><br />[ -z "$PARALLEL_SEQ" ] && \<br />{ module add parallel ; exec parallel -a $PBS_O_WORKDIR/numtasks $0 ; }<br /><br /># change to local scratch directory<br />SCR=/lscratch/$PBS_JOBID/$PARALLEL_SEQ<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># get individual task from tasklist with index from PBS JOB ARRAY and index form Parallel<br />IDX=$(($PBS_ARRAY_INDEX + $PARALLEL_SEQ - 1))<br />TASK=$(sed -n "${IDX}p" $PBS_O_WORKDIR/tasklist)<br />[ -z "$TASK" ] && exit<br /><br /># copy input file and executable to scratch <br />cp $PBS_O_WORKDIR/$TASK input <br /><br /># execute the calculation<br />cat input > output<br /><br /># copy output file to submit directory<br />cp output $PBS_O_WORKDIR/$TASK.out</pre>
+<p>In this example, the jobscript executes in multiple instances in parallel, on all cores of a computing node. Variable $TASK expands to one of the input filenames from tasklist. We copy the input file to local scratch, execute the myprog.x and copy the output file back to the submit directory, under the $TASK.out name. The numtasks file controls how many tasks will be run per subjob. Once an task is finished, new task starts, until the number of tasks in numtasks file is reached.</p>
+<p class="callout">Select subjob walltime and number of tasks per subjob carefully</p>
+<p>Â When deciding this values, think about following guiding rules :</p>
+<ol>
+<li>Let n=N/16. Inequality (n+1) * T < W should hold. The N is number of tasks per subjob, T is expected single task walltime and W is subjob walltime. Short subjob walltime improves scheduling and job throughput.</li>
+<li>Number of tasks should be modulo 16.</li>
+<li>These rules are valid only when all tasks have similar task walltimes T.</li>
+</ol>
+<h3 class=" ">Submit the job array</h3>
+<p>To submit the job array, use the qsub -J command. The 992 tasks' job of the <a class="anchor-link" href="capacity-computing.html#combined_example" target="_self" title="">example above</a> may be submitted like this:</p>
+<pre class="prettyprint lang-sh">$ qsub -N JOBNAME -J 1-992:32 jobscript<br />12345[].dm2</pre>
+<p>In this example, we submit a job array of 31 subjobs. Note the -J 1-992:<strong>32</strong>, this must be the same as the number sent to numtasks file. Each subjob will run on full node and process 16 input files in parallel, 32 in total per subjob. Every subjob is assumed to complete in less than 2 hours.</p>
+<p>Please note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue.</p>
+<h2 class=" ">Examples</h2>
+<p>Download the examples in <a href="capacity-computing-examples" title="" target="_self" class="internal-link">capacity.zip</a>, illustrating the above listed ways to run huge number of jobs. We recommend to try out the examples, before using this for running production jobs.</p>
+<p>Unzip the archive in an empty directory on Anselm and follow the instructions in the README file</p>
+<pre class="prettyprint lang-sh">$ unzip capacity.zip<br />$ cat README</pre>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
index e7b843484..bd2495e0d 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
@@ -432,3 +432,7 @@ $ cat README
```
Â
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.html b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.html
new file mode 100644
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--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.html
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+<h2 class=" ">Resources Allocation Policy</h2>
+<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. <a href="job-priority.html" title="" target="_self" class="internal-link">The Fairshare</a> at Anselm ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:</p>
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+<li><strong>qnvidia, qmic, qfat</strong>, the Dedicated queues</li>
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+<p class="callout">Use the <strong>qsub</strong> command to submit your jobs.</p>
+<p class=" ">The qsub submits the job into the queue. The qsub command creates a request to the PBS Job manager for allocation of specified resources. The <strong>smallest allocation unit is entire node, 16 cores</strong>, with exception of the qexp queue. The resources will be allocated when available, subject to allocation policies and constraints. <strong>After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.</strong></p>
+<p class=" ">Read more on the <a href="job-submission-and-execution.html" title="" target="_self" class="internal-link">Job submission and execution</a> page.</p>
+<h2 class=" ">Capacity computing</h2>
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+<p>In many cases, it is useful to submit huge (<span>100+</span>) number of computational jobs into the PBS queue system. Huge number of (small) jobs is one of the most effective ways to execute embarrassingly parallel calculations, achieving best runtime, throughput and computer utilization. In this chapter, we discuss the the recommended way to run huge number of jobs, including <strong>ways to run huge number of single core jobs</strong>.</p>
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computing](capacity-computing.html) page.
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+ <h2 class=" ">Job execution priority</h2>
+<p>Scheduler gives each job an execution priority and then uses this job execution priority to select which job(s) to run.</p>
+<p>Job execution priority on Anselm is determined by these job properties (in order of importance):</p>
+<ol>
+<li>queue priority</li>
+<li>fairshare priority</li>
+<li>eligible time</li>
+</ol>
+<h3 class=" ">Queue priority</h3>
+<p>Queue priority is priority of queue where job is queued before execution.</p>
+<p>Queue priority has the biggest impact on job execution priority. Execution priority of jobs in higher priority queues is always greater than execution priority of jobs in lower priority queues. Other properties of job used for determining job execution priority (fairshare priority, eligible time) cannot compete with queue priority.</p>
+<p>Queue priorities can be seen at <a class="external-link" href="https://extranet.it4i.cz/anselm/queues" target="_blank" title="">https://extranet.it4i.cz/anselm/queues</a></p>
+<h3 class=" ">Fairshare priority</h3>
+<p>Fairshare priority is priority calculated on recent usage of resources. Fairshare priority is calculated per project, all members of project share same fairshare priority. Projects with higher recent usage have lower fairshare priority than projects with lower or none recent usage.</p>
+<p>Fairshare priority is used for ranking jobs with equal queue priority.</p>
+<p>Fairshare priority is calculated as</p>
+<p class=" "><img alt="" src="fairshare_formula.png" title="" class="image-inline" /></p>
+<p class=" ">where MAX_FAIRSHARE has value 1E6,<br />usage<sub>Project</sub> is cumulated usage by all members of selected project,<br /> usage<sub>Total</sub> is total usage by all users, by all projects.</p>
+<p class=" ">Usage counts allocated corehours (ncpus*walltime). Usage is decayed, or cut in half periodically, at the interval 168 hours (one week).<br />Jobs queued in queue qexp are not calculated to project's usage.</p>
+<p class="callout"><span>Calculated usage and fairshare priority can be seen at <a class="external-link" href="https://extranet.it4i.cz/anselm/projects" target="_self" title="">https://extranet.it4i.cz/anselm/projects</a>.</span></p>
+<p class=" "><span><br /><span>Calculated fairshare priority can be also seen as Resource_List.fairshare attribute of a job.</span><br /></span></p>
+<h3 class=" "><span>Eligible time</span></h3>
+<p>Eligible time is amount (in seconds) of eligible time job accrued while waiting to run. Jobs with higher eligible time gains higher pri<span><span></span></span>ority.</p>
+<p>Eligible time has the least impact on execution priority. Eligible time is used for sorting jobs with equal queue priority and fairshare priority. It is very, very difficult for <span>eligible time</span> to compete with fairshare priority.</p>
+<p><span><span>Eligible time can be seen as eligible_time attribute of job.</span></span></p>
+<h3 class=" ">Formula</h3>
+<p class=" ">Job execution priority (job sort formula) is calculated as:</p>
+<p class=" "><img alt="" src="job_sort_formula.png" title="" class="image-inline" /></p>
+<h3 class=" ">Job backfilling</h3>
+<p><span>Anselm cluster uses job backfilling.</span></p>
+<p>Backfilling means fitting smaller jobs around the higher-priority jobs that the scheduler is going to run next, in such a way that the higher-priority jobs are not delayed. Backfilling allows us to keep resources from becoming idle when the top job (job with the highest execution priority) cannot run.</p>
+<p>The scheduler makes a list of jobs to run in order of execution priority. Scheduler looks for smaller jobs that can fit into the usage gaps<br />around the highest-priority jobs in the list. The scheduler looks in the prioritized list of jobs and chooses the highest-priority smaller jobs that fit. Filler jobs are run only if they will not delay the start time of top jobs.</p>
+<p>It means, that jobs with lower execution priority can be run before jobs with higher execution priority.</p>
+<p class="exclamation">It is <strong>very beneficial to specify the walltime</strong> when submitting jobs.</p>
+<p class=" ">Specifying more accurate walltime enables better schedulling, better execution times and better resource usage. Jobs with suitable (small) walltime could be backfilled - and overtake job(s) with higher priority.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
index 0bb5db050..5750dbfc6 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
@@ -16,16 +16,16 @@ Job execution priority on Anselm is determined by these job properties
### Queue priority
-ueue priority is priority of queue where job is queued before
+Queue priority is priority of queue where job is queued before
execution.
-ueue priority has the biggest impact on job execution priority.
+Queue priority has the biggest impact on job execution priority.
Execution priority of jobs in higher priority queues is always greater
than execution priority of jobs in lower priority queues. Other
properties of job used for determining job execution priority (fairshare
priority, eligible time) cannot compete with queue priority.
-ueue priorities can be seen at <https://extranet.it4i.cz/anselm/queues>
+Queue priorities can be seen at <https://extranet.it4i.cz/anselm/queues>
### Fairshare priority
@@ -104,4 +104,3 @@ execution times and better resource usage. Jobs with suitable (small)
walltime could be backfilled - and overtake job(s) with higher priority.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.html b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.html
new file mode 100644
index 000000000..a24f62ef9
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.html
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+ <h2 class=" ">Job Submission</h2>
+<p>When allocating computational resources for the job, please specify</p>
+<ol>
+<li>suitable queue for your job (default is qprod)</li>
+<li>number of computational nodes required</li>
+<li>number of cores per node required</li>
+<li>maximum wall time allocated to your calculation, note that jobs exceeding maximum wall time will be killed</li>
+<li>Project ID</li>
+<li>Jobscript or interactive switch</li>
+</ol>
+<p class="callout">Use the <strong>qsub</strong> command to submit your job to a queue for allocation of the computational resources.</p>
+<p>Submit the job using the qsub command:</p>
+<pre class="prettyprint lang-sh">$ qsub -A Project_ID -q queue -l select=x:ncpus=y,walltime=[[hh:]mm:]ss[.ms] jobscript</pre>
+<p>The qsub submits the job into the queue, in another words the qsub command creates a request to the PBS Job manager for allocation of specified resources. The resources will be allocated when available, subject to above described policies and constraints. <strong>After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.</strong></p>
+<h3 class=" ">Job Submission Examples</h3>
+<pre class="prettyprint lang-sh">$ qsub -A OPEN-0-0 -q qprod -l select=64:ncpus=16,walltime=03:00:00 ./myjob</pre>
+<p>In this example, we allocate 64 nodes, 16 cores per node, for 3 hours. We allocate these resources via the qprod queue, consumed resources will be accounted to the Project identified by Project ID OPEN-0-0. Jobscript myjob will be executed on the first node in the allocation.</p>
+<p>Â </p>
+<pre class="prettyprint lang-sh">$ qsub -q qexp -l select=4:ncpus=16 -I</pre>
+<p class=" ">In this example, we allocate 4 nodes, 16 cores per node, for 1 hour. We allocate these resources via the qexp queue. The resources will be available interactively</p>
+<p class=" ">Â </p>
+<pre class="prettyprint lang-sh">$ qsub -A OPEN-0-0 -q qnvidia -l select=10:ncpus=16 ./myjob</pre>
+<p class=" ">In this example, we allocate 10 nvidia accelerated nodes, 16 cores per node, for 24 hours. We allocate these resources via the qnvidia queue. Jobscript myjob will be executed on the first node in the allocation.</p>
+<p class=" ">Â </p>
+<pre class="prettyprint lang-sh">$ qsub -A OPEN-0-0 -q qfree -l select=10:ncpus=16 ./myjob</pre>
+<p class=" ">In this example, we allocate 10Â nodes, 16 cores per node, for 12 hours. We allocate these resources via the qfree queue. It is not required that the project OPEN-0-0 has any available resources left. Consumed resources are still accounted for. Jobscript myjob will be executed on the first node in the allocation.</p>
+<p class=" ">Â </p>
+<p class=" ">All qsub options may be <a class="anchor-link" href="job-submission-and-execution.html#PBSsaved" target="_self" title="">saved directly into the jobscript</a>. In such a case, no options to qsub are needed.</p>
+<pre class="prettyprint lang-sh">$ qsub ./myjob</pre>
+<p>Â </p>
+<p>By default, the PBS batch system sends an e-mail only when the job is aborted. Disabling mail events completely can be done like this:</p>
+<pre class="prettyprint lang-sh">$ qsub -m n</pre>
+<h2 class=" ">Advanced job placement</h2>
+<h3 class=" ">Placement by name</h3>
+<p>Specific nodes may be allocated via the PBS</p>
+<pre class="prettyprint lang-sh">qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16:host=cn171+1:ncpus=16:host=cn172 -I</pre>
+<p>In this example, we allocate nodes cn171 and cn172, all 16 cores per node, for 24 hours. Consumed resources will be accounted to the Project identified by Project ID OPEN-0-0. The resources will be available interactively.</p>
+<h3 class=" ">Placement by CPU type</h3>
+<p>Nodes equipped with Intel Xeon E5-2665 CPU have base clock frequency 2.4GHz, nodes equipped with Intel Xeon E5-2470 CPU have base frequency 2.3 GHz (see section Compute Nodes for details). Nodes may be selected via the PBS resource attribute <span class="highlightedSearchTerm">cpu_freq</span> .</p>
+<table class="listing">
+<tbody>
+<tr><th>CPU Type</th><th>base freq.</th><th>Nodes</th><th>cpu_freq attribute</th></tr>
+<tr class="odd">
+<td>Intel Xeon E5-2665</td>
+<td>2.4GHz</td>
+<td>cn[1-180], cn[208-209]</td>
+<td>24</td>
+</tr>
+<tr class="even">
+<td>Intel Xeon E5-2470</td>
+<td>2.3GHz</td>
+<td>cn[181-207]</td>
+<td>23</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ qsub </span><span class="pun">-</span><span class="pln">A OPEN</span><span class="pun">-</span><span class="lit">0</span><span class="pun">-</span><span class="lit">0</span><span class="pln"> </span><span class="pun">-</span><span class="pln">q qprod </span><span class="pun">-</span><span class="pln">l select</span><span class="pun">=</span><span class="lit">4</span><span class="pun">:</span><span class="pln">ncpus</span><span class="pun">=</span><span class="lit">16</span><span class="pun">:</span><span class="highlightedSearchTerm"><span class="pln">cpu_freq</span></span><span class="pun">=</span><span class="lit">24</span><span class="pln"> </span><span class="pun">-</span><span class="pln">I</span></pre>
+<div class="titlepage">
+<div>In this example, we allocate 4 nodes, 16 cores, selecting only the nodes with Intel Xeon E5-2665 CPU.</div>
+<h3 class=" ">Placement by IB switch</h3>
+<div>Groups of computational nodes are connected to chassis integrated Infiniband switches. These switches form the leaf switch layer of the <a href="../network.html" title="" target="_self" class="internal-link">Infiniband network</a> <span class="internal-link">fat</span> tree topology. Nodes sharing the leaf switch can communicate most efficiently. Sharing the same switch prevents hops in the network and provides for unbiased, most efficient network communication.<br /><br /></div>
+<div>Nodes sharing the same switch may be selected via the PBS resource attribute ibswitch. Values of this attribute are iswXX, where XX is the switch number. The node-switch mapping can be seen at <a href="../hardware-overview.html" title="" target="_self" class="internal-link">Hardware Overview</a> section.<br /><br /></div>
+<div>We recommend allocating compute nodes of a single switch when best possible computational network performance is required to run the job efficiently:</div>
+<pre class=" ">qsub -A OPEN-0-0 -q qprod -l select=18:ncpus=16:ibswitch=isw11 ./myjob</pre>
+<div>In this example, we request all the 18 nodes sharing the isw11 switch for 24 hours. Full chassis will be allocated.</div>
+<h2 class=" ">Advanced job handling</h2>
+<h3 class=" ">Selecting Turbo Boost off</h3>
+<div>Intel Turbo Boost Technology is on by default. We strongly recommend keeping the default. </div>
+<div>If necessary (such as in case of benchmarking) you can disable the Turbo for all nodes of the job by using the PBS resource attribute cpu_turbo_boost</div>
+</div>
+<div></div>
+<pre class=" ">$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16 -l cpu_turbo_boost=0 -I</pre>
+<p>More about the Intel Turbo Boost in the TurboBoost section</p>
+<h3 class=" ">Advanced examples</h3>
+<p>In the following example, we select an allocation for benchmarking a very special and demanding MPI program. We request Turbo off, 2 full chassis of compute nodes (nodes sharing the same IB switches) for 30 minutes:</p>
+<pre class=" ">$ qsub -A OPEN-0-0 -q qprod \<br />-l select=18:ncpus=16:ibswitch=isw10:mpiprocs=1:ompthreads=16+18:ncpus=16:ibswitch=isw20:mpiprocs=16:ompthreads=1 \<br />-l cpu_turbo_boost=0,walltime=00:30:00 \<br />-N Benchmark ./mybenchmark</pre>
+<p class=" ">The MPI processes will be distributed differently on the nodes connected to the two switches. On the isw10 nodes, we will run 1 MPI process per node 16 threads per process, on isw20Â nodes we will run 16 plain MPI processes.</p>
+<p class=" ">Although this example is somewhat artificial, it demonstrates the flexibility of the qsub command options.</p>
+<h2 class=" ">Job Management</h2>
+<p class="callout">Check status of your jobs using the <strong>qstat</strong> and <strong>check-pbs-jobs</strong> commands</p>
+<pre class="prettyprint lang-sh">$ qstat -a<br />$ qstat -a -u username<br />$ qstat -an -u username<br />$ qstat -f 12345.srv11</pre>
+<p class=" "><a name="Acc_example"></a>Example:</p>
+<pre class="prettyprint lang-sh">$ qstat -a<br /><br />srv11:<br /> Req'd Req'd Elap<br />Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time<br />--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----<br />16287.srv11 user1 qlong job1 6183 4 64 -- 144:0 R 38:25<br />16468.srv11 user1 qlong job2 8060 4 64 -- 144:0 R 17:44<br />16547.srv11 user2 qprod job3x 13516 2 32 -- 48:00 R 00:58</pre>
+<p class=" ">In this example user1 and user2 are running jobs named job1, job2 and job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each. The job1 already runs for 38 hours and 25 minutes, job2 for 17 hours 44 minutes. The job1 already consumed 64*38.41 = 2458.6 core hours. The job3x already consumed 0.96*32 = 30.93 core hours. These consumed core hours will be accounted on the respective project accounts, regardless of whether the allocated cores were actually used for computations.</p>
+<p class=" ">Check status of your jobs using check-pbs-jobs command. Check presence of user's PBS jobs' processes on execution hosts. Display load, processes. Display job standard and error output. Continuously display (tail -f) job standard or error output.</p>
+<pre class="prettyprint lang-sh">$ check-pbs-jobs --check-all<br />$ check-pbs-jobs --print-load --print-processes<br />$ check-pbs-jobs --print-job-out --print-job-err<br /><br />$ check-pbs-jobs --jobid JOBID --check-all --print-all<br /><br />$ check-pbs-jobs --jobid JOBID --tailf-job-out</pre>
+<p class=" ">Examples:</p>
+<pre class="prettyprint lang-sh">$ check-pbs-jobs --check-all<br />JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165<br />Check session id: OK<br />Check processes<br />cn164: OK<br />cn165: No process</pre>
+<p class=" ">In this example we see that job 35141.dm2 currently runs no process on allocated node cn165, which may indicate an execution error.</p>
+<pre class="prettyprint lang-sh">$ check-pbs-jobs --print-load --print-processes<br />JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165<br />Print load<br />cn164: LOAD: 16.01, 16.01, 16.00<br />cn165: LOAD: 0.01, 0.00, 0.01<br />Print processes<br /> %CPU CMD<br />cn164: 0.0 -bash<br />cn164: 0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC<br />cn164: 99.7 run-task<br />...</pre>
+<p class=" ">In this example we see that job 35141.dm2 currently runs process run-task on node cn164, using one thread only, while node cn165 is empty, which may indicate an execution error.</p>
+<pre class="prettyprint lang-sh">$ check-pbs-jobs --jobid 35141.dm2 --print-job-out<br />JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165<br />Print job standard output:<br />======================== Job start ==========================<br />Started at   : Fri Aug 30 02:47:53 CEST 2013<br />Script name  : script<br />Run loop 1<br />Run loop 2<br />Run loop 3</pre>
+<p class=" ">In this example, we see actual output (some iteration loops) of the job 35141.dm2</p>
+<p class="callout">Manage your queued or running jobs, using the <strong>qhold</strong>, <strong>qrls</strong>, <strong>qdel</strong><strong>,</strong> <strong>qsig</strong> or <strong>qalter</strong> commands</p>
+<p class=" ">You may release your allocation at any time, using qdel command</p>
+<pre class="prettyprint lang-sh">$ qdel 12345.srv11</pre>
+<p class=" ">You may kill a running job by force, using qsig command</p>
+<pre class="prettyprint lang-sh">$ qsig -s 9 12345.srv11</pre>
+<p class=" ">Learn more by reading the pbs man page</p>
+<pre class="prettyprint lang-sh">$ man pbs_professional</pre>
+<h2 class=" ">Job Execution</h2>
+<h3 class=" ">Jobscript</h3>
+<p class="callout">Prepare the jobscript to run batch jobs in the PBS queue system</p>
+<p>The Jobscript is a user made script, controlling sequence of commands for executing the calculation. It is often written in bash, other scripts may be used as well. The jobscript is supplied to PBS <strong>qsub</strong> command as an argument and executed by the PBS Professional workload manager.</p>
+<p class="callout">The jobscript or interactive shell is executed on first of the allocated nodes.</p>
+<pre class="prettyprint lang-sh">$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob<br />$ qstat -n -u username<br /><br />srv11:<br /> Req'd Req'd Elap<br />Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time<br />--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----<br />15209.srv11 username qexp Name0 5530 4 64 -- 01:00 R 00:00<br /> cn17/0*16+cn108/0*16+cn109/0*16+cn110/0*16</pre>
+<p>Â In this example, the nodes cn17, cn108, cn109 and cn110 were allocated for 1 hour via the qexp queue. The jobscript myjob will be executed on the node cn17, while the nodes cn108, cn109 and cn110 are available for use as well.</p>
+<p class="callout">The jobscript or interactive shell is by default executed in home directory</p>
+<pre class="prettyprint lang-sh">$ qsub -q qexp -l select=4:ncpus=16 -I<br />qsub: waiting for job 15210.srv11 to start<br />qsub: job 15210.srv11 ready<br /><br />$ pwd<br />/home/username</pre>
+<p class=" ">In this example, 4 nodes were allocated interactively for 1 hour via the qexp queue. The interactive shell is executed in the home directory.</p>
+<p class="callout">All nodes within the allocation may be accessed via ssh. Unallocated nodes are not accessible to user.</p>
+<p>The allocated nodes are accessible via ssh from login nodes. The nodes may access each other via ssh as well.</p>
+<p>Calculations on allocated nodes may be executed remotely via the MPI, ssh, pdsh or clush. You may find out which nodes belong to the allocation by reading the $PBS_NODEFILE file</p>
+<pre class="prettyprint lang-sh">qsub -q qexp -l select=4:ncpus=16 -I<br />qsub: waiting for job 15210.srv11 to start<br />qsub: job 15210.srv11 ready<br /><br />$ pwd<br />/home/username<br /><br />$ sort -u $PBS_NODEFILE<br />cn17.bullx<br />cn108.bullx<br />cn109.bullx<br />cn110.bullx<br /> <br />$ pdsh -w cn17,cn[108-110] hostname<br />cn17: cn17<br />cn108: cn108<br />cn109: cn109<br />cn110: cn110</pre>
+<p class=" ">In this example, the hostname program is executed via pdsh from the interactive shell. The execution runs on all four allocated nodes. The same result would be achieved if the pdsh is called from any of the allocated nodes or from the login nodes.</p>
+<h3 class=" ">Example Jobscript for MPI Calculation</h3>
+<p class="callout">Production jobs must use the /scratch directory for I/O</p>
+<p>The recommended way to run production jobs is to change to /scratch directory early in the jobscript, copy all inputs to /scratch, execute the calculations and copy outputs to home directory.</p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br /><br /># change to scratch directory, exit on failure<br />SCRDIR=/scratch/$USER/myjob<br />mkdir -p $SCRDIR<br />cd $SCRDIR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/input .<br />cp $PBS_O_WORKDIR/mympiprog.x .<br /><br /># load the mpi module<br />module load openmpi<br /><br /># execute the calculation<br />mpiexec -pernode ./mympiprog.x<br /><br /># copy output file to home<br />cp output $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
+<p class=" ">In this example, some directory on the /home holds the input file input and executable mympiprog.x . We create a directory myjob on the /scratch filesystem, copy input and executable files from the /home directory where the qsub was invoked ($PBS_O_WORKDIR) to /scratch, execute the MPI programm mympiprog.x and copy the output file back to the /home directory. The mympiprog.x is executed as one process per node, on all allocated nodes.</p>
+<p class="callout">Consider preloading inputs and executables onto <a href="../storage.html" title="" target="_self" class="internal-link">shared scratch</a> before the calculation starts.</p>
+<p>In some cases, it may be impractical to copy the inputs to scratch and outputs to home. This is especially true when very large input and output files are expected, or when the files should be reused by a subsequent calculation. In such a case, it is users responsibility to preload the input files on shared /scratch before the job submission and retrieve the outputs manually, after all calculations are finished.</p>
+<p class="callout"><a name="PBSsaved"></a>Store the qsub options within the jobscript. <br />Use <strong>mpiprocs</strong> and <strong>ompthreads</strong> qsub options to control the MPI job execution.</p>
+<p>Example jobscript for an MPI job with preloaded inputs and executables, options for qsub are stored within the script :</p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -q qprod<br />#PBS -N MYJOB<br />#PBS -l select=100:ncpus=16:mpiprocs=1:ompthreads=16<br />#PBS -A OPEN-0-0<br /><br /># change to scratch directory, exit on failure<br />SCRDIR=/scratch/$USER/myjob<br />cd $SCRDIR || exit<br /><br /><br /># load the mpi module<br />module load openmpi<br /><br /># execute the calculation<br />mpiexec ./mympiprog.x<br /><br /><br />#exit<br />exit</pre>
+<p class=" ">In this example, input and executable files are assumed preloaded manually in /scratch/$USER/myjob directory. Note the <strong>mpiprocs</strong> and <strong>ompthreads</strong> qsub options, controlling behavior of the MPI execution. The mympiprog.x is executed as one process per node, on all 100 allocated nodes. If mympiprog.x implements OpenMP threads, it will run 16 threads per node.</p>
+<p class=" ">More information is found in the <a href="../software/mpi-1/Running_OpenMPI.html" title="" target="_self" class="internal-link">Running OpenMPI</a> and <a href="../software/mpi-1/running-mpich2.html" title="" target="_self" class="internal-link">Running MPICH2</a> sections.</p>
+<h3 class=" ">Example Jobscript for Single Node Calculation<a name="JobscriptLocal"></a></h3>
+<p class="callout">Local scratch directory is often useful for single node jobs. Local scratch will be deleted immediately after the job ends.</p>
+<p>Example jobscript for single node calculation, using <a href="../storage.html" title="" target="_self" class="internal-link">local scratch</a> on the node:</p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br /><br /># change to local scratch directory<br />cd /lscratch/$PBS_JOBID || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/input .<br />cp $PBS_O_WORKDIR/myprog.x .<br /><br /># execute the calculation<br />./myprog.x<br /><br /># copy output file to home<br />cp output $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
+<p class=" ">In this example, some directory on the home holds the input file input and executable myprog.x . We copy input and executable files from the home directory where the qsub was invoked ($PBS_O_WORKDIR) to local scratch /lscratch/$PBS_JOBID, execute the myprog.x and copy the output file back to the /home directory. The myprog.x runs on one node only and may use threads.</p>
+<h3 class=" ">Other Jobscript Examples</h3>
+<p>Further jobscript examples may be found in the <a href="../software.1.html" title="" target="_self" class="internal-link">Software</a> section and the <a href="capacity-computing.html" title="" target="_self" class="internal-link">Capacity computing</a> section.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
index 7c7a3e6ac..9954980e4 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
@@ -258,10 +258,10 @@ Examples:
```
$ check-pbs-jobs --check-all
JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165
-Check session idOK
+Check session id: OK
Check processes
-cn164OK
-cn165No process
+cn164: OK
+cn165: No process
```
In this example we see that job 35141.dm2 currently runs no process on
@@ -271,13 +271,13 @@ allocated node cn165, which may indicate an execution error.
$ check-pbs-jobs --print-load --print-processes
JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165
Print load
-cn164LOAD16.01, 16.01, 16.00
-cn165LOAD 0.01, 0.00, 0.01
+cn164: LOAD: 16.01, 16.01, 16.00
+cn165: LOAD: 0.01, 0.00, 0.01
Print processes
%CPU CMD
-cn164 0.0 -bash
-cn164 0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC
-cn16499.7 run-task
+cn164: 0.0 -bash
+cn164: 0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC
+cn164: 99.7 run-task
...
```
@@ -290,8 +290,8 @@ $ check-pbs-jobs --jobid 35141.dm2 --print-job-out
JOB 35141.dm2, session_id 71995, user user2, nodes cn164,cn165
Print job standard output:
======================== Job start ==========================
-Started at   Fri Aug 30 02:47:53 CEST 2013
-Script name  script
+Started at   : Fri Aug 30 02:47:53 CEST 2013
+Script name  : script
Run loop 1
Run loop 2
Run loop 3
@@ -359,8 +359,8 @@ directory
```
$ qsub -q qexp -l select=4:ncpus=16 -I
-qsubwaiting for job 15210.srv11 to start
-qsubjob 15210.srv11 ready
+qsub: waiting for job 15210.srv11 to start
+qsub: job 15210.srv11 ready
$ pwd
/home/username
@@ -381,8 +381,8 @@ allocation by reading the $PBS_NODEFILE file
```
qsub -q qexp -l select=4:ncpus=16 -I
-qsubwaiting for job 15210.srv11 to start
-qsubjob 15210.srv11 ready
+qsub: waiting for job 15210.srv11 to start
+qsub: job 15210.srv11 ready
$ pwd
/home/username
@@ -394,10 +394,10 @@ cn109.bullx
cn110.bullx
$ pdsh -w cn17,cn[108-110] hostname
-cn17cn17
-cn108cn108
-cn109cn109
-cn110cn110
+cn17: cn17
+cn108: cn108
+cn109: cn109
+cn110: cn110
```
In this example, the hostname program is executed via pdsh from the
@@ -542,4 +542,3 @@ computing](capacity-computing.html) section.
Â
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.html b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.html
new file mode 100644
index 000000000..fd73df2fc
--- /dev/null
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+ <h2 class=" ">Resources Allocation Policy</h2>
+<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. The Fairshare at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the <a href="job-priority.html" title="" target="_self" class="internal-link">Job scheduling</a> section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:Â Â Â </p>
+<table class="listing">
+<tbody>
+<tr><th>queue</th><th>active project</th><th>project resources</th><th>nodes</th><th>min ncpus*</th><th>priority</th><th>authorization</th><th>walltime<br />default/max</th></tr>
+<tr class="even">
+<td><strong>qexp</strong><br />Express queue</td>
+<td>no</td>
+<td>none required</td>
+<td>2 reserved, 31 total<br />including MIC, GPU and FAT nodes</td>
+<td>1</td>
+<td><span><em>150</em></span></td>
+<td>no</td>
+<td>1h</td>
+</tr>
+<tr class="odd">
+<td><strong>qprod</strong><br />Production queue</td>
+<td>yes<br /><br /></td>
+<td>> 0</td>
+<td>
+<p><span><em>178 nodes w/o accelerator</em></span><br /><br /></p>
+</td>
+<td>16</td>
+<td>0</td>
+<td>no</td>
+<td>24/48h</td>
+</tr>
+<tr class="even">
+<td>
+<p><strong>qlong</strong><br />Long queue</p>
+</td>
+<td>yes</td>
+<td>> 0</td>
+<td>60 nodes w/o accelerator</td>
+<td>16</td>
+<td>0</td>
+<td>no</td>
+<td>72/144h</td>
+</tr>
+<tr class="odd">
+<td>
+<p><strong>qnvidia, qmic, qfat</strong><br />Dedicated queues</p>
+</td>
+<td>yes</td>
+<td>
+<p>> 0</p>
+</td>
+<td>23 total qnvidia<br />4 total qmic<br />2 total qfat</td>
+<td>16</td>
+<td><span><em>200</em></span></td>
+<td>yes</td>
+<td>24/48h</td>
+</tr>
+<tr class="even">
+<td><strong>qfree</strong><br />Free resource queue</td>
+<td>yes</td>
+<td>none required</td>
+<td>178 w/o accelerator</td>
+<td>16</td>
+<td>-1024</td>
+<td>no</td>
+<td>12h</td>
+</tr>
+</tbody>
+</table>
+<p class="callout"><strong>The qfree queue is not free of charge</strong>. <a class="anchor-link" href="resources-allocation-policy.html#resources-accounting-policy" target="_self" title="">Normal accounting</a> applies. However, it allows for utilization of free resources, once a Project exhausted all its allocated computational resources. This does not apply for Directors Discreation's projects (DD projects) by default. Usage of qfree after exhaustion of DD projects computational resources is allowed after request for this queue.</p>
+<p class="callout"><strong>The qexp queue is equipped with the nodes not having the very same CPU clock speed.</strong> Should you need the very same CPU speed, you have to select the proper nodes during the PSB job submission.<br /><strong></strong></p>
+<ul>
+<li><strong>qexp</strong>, the Express queue: This queue is dedicated for testing and running very small jobs. It is not required to specify a project to enter the qexp. <span><em><span>There are 2 nodes always reserved for this queue (w/o accelerator), maximum 8 nodes are available via the qexp for a particular user, from a pool of nodes containing <strong>Nvidia</strong> accelerated nodes (cn181-203), <strong>MIC</strong> accelerated nodes (cn204-207) and <strong>Fat</strong> nodes with 512GB RAM (cn208-209). This enables to test and tune also accelerated code or code with higher RAM requirements</span>.</em></span> The nodes may be allocated on per core basis. No special authorization is required to use it. The maximum runtime in qexp is 1 hour.</li>
+<li><strong>qprod</strong>, the Production queue<strong></strong>: This queue is intended for normal production runs. It is required that active project with nonzero remaining resources is specified to enter the qprod. All nodes may be accessed via the qprod queue, except the reserved ones. <span><em><span>178 nodes without accelerator are included</span>.</em></span>Â Full nodes, 16 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprod is 48 hours.</li>
+<li><strong>qlong</strong>, the Long queue<strong></strong>: This queue is intended for long production runs. It is required that active project with nonzero remaining resources is specified to enter the qlong. Only 60 nodes without acceleration may be accessed via the qlong queue. Full nodes, 16 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it.<span><em> The maximum runtime in qlong is 144 hours (three times of the standard qprod time - 3 * 48 h).</em></span></li>
+<li><strong>qnvidia, qmic, qfat</strong>, the Dedicated queues<strong></strong>: The queue qnvidia is dedicated to access the Nvidia accelerated nodes, the qmic to access MIC nodes and qfat the Fat nodes. It is required that active project with nonzero remaining resources is specified to enter these queues. 23 nvidia, 4 mic and 2 fat nodes are included. Full nodes, 16 cores per node are allocated. The queues run with<span><em> very high priority</em></span>, the jobs will be scheduled before the jobs coming from the<span> <em>qexp</em> </span>queue. An PI<span> <em>needs explicitly</em> </span>ask <a class="external-link" href="https://support.it4i.cz/rt/" target="_self" title="">support</a> for authorization to enter the dedicated queues for all users associated to her/his Project.</li>
+<li><strong>qfree</strong>, The Free resource queue<strong></strong>: The queue qfree is intended for utilization of free resources, after a Project exhausted all its allocated computational resources (Does not apply to DD projects by default. DD projects have to request for persmission on qfree after exhaustion of computational resources.). It is required that active project is specified to enter the queue, however no remaining resources are required. Consumed resources will be accounted to the Project. Only 178 nodes without accelerator may be accessed from this queue. Full nodes, 16 cores per node are allocated. The queue runs with very low priority and no special authorization is required to use it. The maximum runtime in qfree is 12 hours.</li>
+</ul>
+<h3 class=" ">Notes <strong><br /></strong></h3>
+<p>The job wall clock time defaults to<strong> half the maximum time</strong>, see table above. Longer wall time limits can be <a href="job-submission-and-execution.html" title="" target="_self" class="internal-link">set manually, see examples</a>. <br /><br />Jobs that exceed the reserved wall clock time (Req'd Time) get killed automatically. Wall clock time limit can be changed for queuing jobs (state Q) using the qalter command, however can not be changed for a running job (state R).</p>
+<p>Anselm users may check current queue configuration at <a class="external-link" href="https://extranet.it4i.cz/anselm/queues" target="_self" title="">https://extranet.it4i.cz/anselm/queues</a>.</p>
+<h3 class=" ">Queue status</h3>
+<p class="callout">Check the status of jobs, queues and compute nodes at <a class="external-link" href="https://extranet.it4i.cz/anselm/" target="_self" title="">https://extranet.it4i.cz/anselm/</a></p>
+<p class=" "><img alt="rspbs web interface" src="rsweb.png" title="" class="image-inline" /></p>
+<p>Display the queue status on Anselm:</p>
+<pre class="prettyprint lang-sh">$ qstat -q</pre>
+<p class=" ">The PBS allocation overview may be obtained also using the rspbs command.</p>
+<pre class="prettyprint lang-sh">$ rspbs<br />Usage: rspbs [options]<br /><br />Options:<br /> --version            show program's version number and exit<br /> -h, --help           show this help message and exit<br /> --get-node-ncpu-chart<br />                       Print chart of allocated ncpus per node<br /> --summary            Print summary<br /> --get-server-details Print server<br /> --get-queues         Print queues<br /> --get-queues-details Print queues details<br /> --get-reservations   Print reservations<br /> --get-reservations-details<br />                       Print reservations details<br /> --get-nodes          Print nodes of PBS complex<br /> --get-nodeset        Print nodeset of PBS complex<br /> --get-nodes-details  Print nodes details<br /> --get-jobs           Print jobs<br /> --get-jobs-details   Print jobs details<br /> --get-jobs-check-params<br />                       Print jobid, job state, session_id, user, nodes<br /> --get-users          Print users of jobs<br /> --get-allocated-nodes<br />                       Print allocated nodes of jobs<br /> --get-allocated-nodeset<br />                       Print allocated nodeset of jobs<br /> --get-node-users     Print node users<br /> --get-node-jobs      Print node jobs<br /> --get-node-ncpus     Print number of ncpus per node<br /> --get-node-allocated-ncpus<br />                       Print number of allocated ncpus per node<br /> --get-node-qlist     Print node qlist<br /> --get-node-ibswitch  Print node ibswitch<br /> --get-user-nodes     Print user nodes<br /> --get-user-nodeset   Print user nodeset<br /> --get-user-jobs      Print user jobs<br /> --get-user-jobc      Print number of jobs per user<br /> --get-user-nodec     Print number of allocated nodes per user<br /> --get-user-ncpus     Print number of allocated ncpus per user<br /> --get-qlist-nodes    Print qlist nodes<br /> --get-qlist-nodeset  Print qlist nodeset<br /> --get-ibswitch-nodes Print ibswitch nodes<br /> --get-ibswitch-nodeset<br />                       Print ibswitch nodeset<br /> --state=STATE        Only for given job state<br /> --jobid=JOBID        Only for given job ID<br /> --user=USER          Only for given user<br /> --node=NODE          Only for given node<br /> --nodestate=NODESTATE<br />                       Only for given node state (affects only --get-node*<br />                       --get-qlist-* --get-ibswitch-* actions)<br /> --incl-finished      Include finished jobs<br /><br /></pre>
+<h2 class=" "><a name="resources-accounting-policy"></a>Resources Accounting Policy</h2>
+<h3 class=" ">The Core-Hour</h3>
+<p>The resources that are currently subject to accounting are the core-hours. The core-hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. 1 core-hour is defined as 1 processor core allocated for 1 hour of wall clock time. Allocating a full node (16 cores) for 1 hour accounts to 16 core-hours. See example in the <a href="job-submission-and-execution.html" title="" target="_self" class="internal-link">Job submission and execution</a> section.</p>
+<h3 class=" ">Check consumed resources</h3>
+<p class="callout">The <strong>it4ifree</strong> command is a part of it4i.portal.clients package, located here:<br /><a class="external-link" href="https://pypi.python.org/pypi/it4i.portal.clients" target="_self" title="">https://pypi.python.org/pypi/it4i.portal.clients</a></p>
+<p>User may check at any time, how many core-hours have been consumed by himself/herself and his/her projects. The command is available on clusters' login nodes.</p>
+<pre class="prettyprint lang-sh">$ it4ifree<br />Password:<br />    PID  Total Used ...by me Free<br />  -------- ------- ------ -------- -------<br />  OPEN-0-0 1500000 400644  225265 1099356<br />  DD-13-1   10000 2606 2606 7394</pre>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
index 2e926808d..1e2bfd003 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -121,7 +121,7 @@ clock speed.** Should you need the very same CPU speed, you have to
select the proper nodes during the PSB job submission.
****
-- **qexp**, the Express queueThis queue is dedicated for testing and
+- **qexp**, the Express queue: This queue is dedicated for testing and
running very small jobs. It is not required to specify a project to
enter the qexp. <span>*<span>There are 2 nodes always reserved for
this queue (w/o accelerator), maximum 8 nodes are available via the
@@ -132,7 +132,7 @@ select the proper nodes during the PSB job submission.
RAM requirements</span>.*</span> The nodes may be allocated on per
core basis. No special authorization is required to use it. The
maximum runtime in qexp is 1 hour.
-- **qprod**, the Production queue****This queue is intended for
+- **qprod**, the Production queue****: This queue is intended for
normal production runs. It is required that active project with
nonzero remaining resources is specified to enter the qprod. All
nodes may be accessed via the qprod queue, except the reserved ones.
@@ -141,7 +141,7 @@ select the proper nodes during the PSB job submission.
are allocated. The queue runs with medium priority and no special
authorization is required to use it. The maximum runtime in qprod is
48 hours.
-- **qlong**, the Long queue****This queue is intended for long
+- **qlong**, the Long queue****: This queue is intended for long
production runs. It is required that active project with nonzero
remaining resources is specified to enter the qlong. Only 60 nodes
without acceleration may be accessed via the qlong queue. Full
@@ -149,7 +149,7 @@ select the proper nodes during the PSB job submission.
priority and no special authorization is required to use it.<span>
*The maximum runtime in qlong is 144 hours (three times of the
standard qprod time - 3 * 48 h).*</span>
-- **qnvidia, qmic, qfat**, the Dedicated queues****The queue qnvidia
+- **qnvidia, qmic, qfat**, the Dedicated queues****: The queue qnvidia
is dedicated to access the Nvidia accelerated nodes, the qmic to
access MIC nodes and qfat the Fat nodes. It is required that active
project with nonzero remaining resources is specified to enter
@@ -161,7 +161,7 @@ select the proper nodes during the PSB job submission.
[support](https://support.it4i.cz/rt/) for
authorization to enter the dedicated queues for all users associated
to her/his Project.
-- **qfree**, The Free resource queue****The queue qfree is intended
+- **qfree**, The Free resource queue****: The queue qfree is intended
for utilization of free resources, after a Project exhausted all its
allocated computational resources (Does not apply to DD projects
by default. DD projects have to request for persmission on qfree
@@ -206,7 +206,7 @@ command.
```
$ rspbs
-Usagerspbs [options]
+Usage: rspbs [options]
Options:
 --version            show program's version number and exit
@@ -297,4 +297,3 @@ Password:
Â
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software.1.html b/docs.it4i.cz/anselm-cluster-documentation/software.1.html
new file mode 100644
index 000000000..42285d5a0
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software.1.html
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.html b/docs.it4i.cz/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.html
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+ <h2 class=" ">MPICH2 program execution</h2>
+<p>The MPICH2 programs use mpd daemon or ssh connection to spawn processes, no PBS support is needed. However the PBS allocation is required to access compute nodes. On Anselm, the <strong>Intel MPI</strong> and <strong>mpich2 1.9</strong> are MPICH2 based MPI implementations.</p>
+<h3 class=" ">Basic usage</h3>
+<p class="callout">Use the mpirun to execute the MPICH2 code.</p>
+<p>Example:</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=16 -I<br />qsub: waiting for job 15210.srv11 to start<br />qsub: job 15210.srv11 ready<br /><br class=" " />$ module load impi<br /><br />$ mpirun -ppn 1 -hostfile $PBS_NODEFILE ./helloworld_mpi.x<br />Hello world! from rank 0 of 4 on host cn17<br />Hello world! from rank 1 of 4 on host cn108<br />Hello world! from rank 2 of 4 on host cn109<br />Hello world! from rank 3 of 4 on host cn110</pre>
+<p class=" ">In this example, we allocate 4 nodes via the express queue interactively. We set up the intel MPI environment and interactively run the helloworld_mpi.x program. We request MPI to spawn 1 process per node.<br />Note that the executable helloworld_mpi.x must be available within the same path on all nodes. This is automatically fulfilled on the /home and /scratch filesystem.</p>
+<p class=" ">You need to preload the executable, if running on the local scratch /lscratch filesystem</p>
+<pre class=" ">$ pwd<br />/lscratch/15210.srv11<br />$ mpirun -ppn 1 -hostfile $PBS_NODEFILE cp /home/username/helloworld_mpi.x .<br />$ mpirun -ppn 1 -hostfile $PBS_NODEFILE ./helloworld_mpi.x<br />Hello world! from rank 0 of 4 on host cn17<br />Hello world! from rank 1 of 4 on host cn108<br />Hello world! from rank 2 of 4 on host cn109<br />Hello world! from rank 3 of 4 on host cn110</pre>
+<p class=" ">In this example, we assume the executable helloworld_mpi.x is present on shared home directory. We run the cp command via mpirun, copying the executable from shared home to local scratch . Second mpirun will execute the binary in the /lscratch/15210.srv11 directory on nodes cn17, cn108, cn109 and cn110, one process per node.</p>
+<p class="callout">MPI process mapping may be controlled by PBS parameters.</p>
+<p class=" ">The mpiprocs and ompthreads parameters allow for selection of number of running MPI processes per node as well as number of OpenMP threads per MPI process.</p>
+<h3 class=" ">One MPI process per node</h3>
+<p class=" ">Follow this example to run one MPI process per node, 16 threads per process. Note that no options to mpirun are needed</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=16:mpiprocs=1:ompthreads=16 -I<br /><br />$ module load mvapich2<br /><br />$ mpirun ./helloworld_mpi.x</pre>
+<p class=" ">In this example, we demonstrate recommended way to run an MPI application, using 1 MPI processes per node and 16 threads per socket, on 4 nodes.</p>
+<h3 class=" ">Two MPI processes per node</h3>
+<p class=" ">Follow this example to run two MPI processes per node, 8 threads per process. Note the options to mpirun for mvapich2. No options are needed for impi.</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=16:mpiprocs=2:ompthreads=8 -I<br /><br />$ module load mvapich2<br /><br />$ mpirun -bind-to numa ./helloworld_mpi.x</pre>
+<p>In this example, we demonstrate recommended way to run an MPI application, using 2 MPI processes per node and 8 threads per socket, each process and its threads bound to a separate processor socket of the node, on 4 nodes</p>
+<h3 class=" ">16 MPI processes per node</h3>
+<p class=" ">Follow this example to run 16 MPI processes per node, 1 thread per process. Note the options to mpirun for mvapich2. No options are needed for impi.</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=16:mpiprocs=16:ompthreads=1 -I<br /><br />$ module load mvapich2<br /><br />$ mpirun -bind-to core ./helloworld_mpi.x</pre>
+<p>In this example, we demonstrate recommended way to run an MPI application, using 16 MPI processes per node, single threaded. Each process is bound to separate processor core, on 4 nodes.</p>
+<h3 class=" ">OpenMP thread affinity</h3>
+<p class="callout">Important! Bind every OpenMP thread to a core!</p>
+<p>In the previous two examples with one or two MPI processes per node, the operating system might still migrate OpenMP threads between cores. You might want to avoid this by setting these environment variable for GCC OpenMP:</p>
+<pre class=" "><span class="s1">$ export GOMP_CPU_AFFINITY="0-15"</span></pre>
+<p>or this one for Intel OpenMP:</p>
+<pre class=" ">$ export KMP_AFFINITY=granularity=fine,compact,1,0</pre>
+<p class=" ">As of OpenMP 4.0 (supported by GCC 4.9 and later and Intel 14.0 and later) the following variables may be used for Intel or GCC:</p>
+<pre class=" ">$ export OMP_PROC_BIND=true<br />$ export OMP_PLACES=cores </pre>
+<p>Â </p>
+<h2 class=" ">MPICH2 Process Mapping and Binding</h2>
+<p>The mpirun allows for precise selection of how the MPI processes will be mapped to the computational nodes and how these processes will bind to particular processor sockets and cores.</p>
+<h3 class=" ">Machinefile</h3>
+<p>Process mapping may be controlled by specifying a machinefile input to the mpirun program. Altough all implementations of MPI provide means for process mapping and binding, following examples are valid for the impi and mvapich2 only.</p>
+<p>Example machinefile</p>
+<pre class=" ">cn110.bullx<br />cn109.bullx<br />cn108.bullx<br />cn17.bullx<br />cn108.bullx</pre>
+<p class=" ">Use the machinefile to control process placement</p>
+<pre class=" ">$ mpirun -machinefile machinefile helloworld_mpi.x<br />Hello world! from rank 0 of 5 on host cn110<br />Hello world! from rank 1 of 5 on host cn109<br />Hello world! from rank 2 of 5 on host cn108<br />Hello world! from rank 3 of 5 on host cn17<br />Hello world! from rank 4 of 5 on host cn108</pre>
+<p>In this example, we see that ranks have been mapped on nodes according to the order in which nodes show in the machinefile</p>
+<h3 class=" ">Process Binding</h3>
+<p>The Intel MPI automatically binds each process and its threads to the corresponding portion of cores on the processor socket of the node, no options needed. The binding is primarily controlled by environment variables. Read more about mpi process binding on <a class="external-link" href="https://software.intel.com/sites/products/documentation/hpc/ics/impi/41/lin/Reference_Manual/Environment_Variables_Process_Pinning.htm" target="_self" title="">Intel website</a>. The MPICH2 uses the -bind-to option Use -bind-to numa or -bind-to core to bind the process on single core or entire socket.</p>
+<h3 class=" ">Bindings verification</h3>
+<p>In all cases, binding and threading may be verified by executing</p>
+<pre class=" ">$ mpirun -bindto numa numactl --show<br />$ mpirun -bindto numa echo $OMP_NUM_THREADS</pre>
+<h2 class=" ">Intel MPI on Xeon Phi</h2>
+<p>The<a href="../../../intel-xeon-phi.html" title="" target="_self" class="internal-link"> MPI section of Intel Xeon Phi chapter</a> provides details on how to run Intel MPI code on Xeon Phi architecture.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.md b/docs.it4i.cz/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
index 8e3ef76ab..59b1c5bfd 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
@@ -20,8 +20,8 @@ Use the mpirun to execute the MPICH2 code.
Example:
$ qsub -q qexp -l select=4:ncpus=16 -I
- qsubwaiting for job 15210.srv11 to start
- qsubjob 15210.srv11 ready
+ qsub: waiting for job 15210.srv11 to start
+ qsub: job 15210.srv11 ready
$ module load impi
@@ -193,4 +193,3 @@ chapter](../../../intel-xeon-phi.html) provides details
on how to run Intel MPI code on Xeon Phi architecture.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys.html
new file mode 100644
index 000000000..55af2d64b
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys.html
@@ -0,0 +1,1173 @@
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+<p>Anselm provides as commercial as academic variants. Academic variants are distinguished by "<strong>Academic...</strong>" word in the name of  license or by two letter preposition "<strong>aa_</strong>" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). <a href="ansys/licensing.html" title="" target="_self" class="internal-link"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> <span class="hps">here</span></span></a></p>
+<p>To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module:</p>
+<pre class=" ">$ module load ansys</pre>
+<p>ANSYS supports interactive regime, but due to assumed solution of extremely difficult tasks it is not recommended.</p>
+<p>If user needs to work in interactive regime we recommend to configure the RSM service on the client machine which allows to forward the solution to the Anselm directly from the client's Workbench project (see ANSYS RSM service).</p>
+
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+<li class="navTreeItem visualNoMarker section-ansys-ls-dyna">
+
+
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+ <a href="ansys/ansys-ls-dyna.html" title="" class="state-published contenttype-document">
+
+ <span>ANSYS LS-DYNA</span>
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+
+
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+
+</li>
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+<li class="navTreeItem visualNoMarker section-ls-dyna">
+
+
+
+
+ <a href="ansys/ls-dyna.html" title="" class="state-published contenttype-document">
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+ <span>LS-DYNA</span>
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+
+
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+</li>
+
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+<li class="navTreeItem visualNoMarker section-ansys-mapdl-pbs-file">
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+<li class="navTreeItem visualNoMarker section-ansys-cfx-pbs-file">
+
+
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+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
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+<li class="navTreeItem visualNoMarker section-ansys-fluent-pbs-file">
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+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
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+<li class="navTreeItem visualNoMarker section-ansys-ls-dyna-pbs-file">
+
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+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>ANSYS LS-DYNA PBS file</span>
+ </a>
+
+
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+
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+<li class="navTreeItem visualNoMarker section-ls-dyna-pbs-file">
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+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
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+ </ul>
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+ <a href="comsol.html" title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder">
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
index 7709b2a16..b8d91d70e 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
@@ -32,4 +32,3 @@ solution to the Anselm directly from the client's Workbench project
(see ANSYS RSM service).
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view.html
new file mode 100644
index 000000000..9c3e88cfb
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx-pbs-file/view.html
@@ -0,0 +1,1170 @@
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+ <p><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX" target="_blank" title="">ANSYS CFX</a> software is a high-performance, general purpose fluid dynamics program that has been applied to solve wide-ranging fluid flow problems for over 20 years. At the heart of ANSYS CFX is its advanced solver technology, the key to achieving reliable and accurate solutions quickly and robustly. The modern, highly parallelized solver is the foundation for an abundant choice of physical models to capture virtually any type of phenomena related to fluid flow. The solver and its many physical models are wrapped in a modern, intuitive, and flexible GUI and user environment, with extensive capabilities for customization and automation using session files, scripting and a powerful expression language.</p>
+<p><span>To run ANSYS CFX in batch mode you can utilize/modify the default cfx.pbs script and execute it via the qsub command.</span></p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l nodes=2:ppn=16<br />#PBS -q qprod<br />#PBS -N $USER-CFX-Project<br />#PBS -A XX-YY-ZZ<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/$USER/work"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />module load ansys<br /><br />#### Set number of processors per host listing<br />#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)<br />procs_per_host=1<br />#### Create host list<br />hl=""<br />for host in `cat $PBS_NODEFILE`<br />do<br /> if [ "$hl" = "" ]<br /> then hl="$host:$procs_per_host"<br /> else hl="${hl}:$host:$procs_per_host"<br /> fi<br />done<br /><br />echo Machines: $hl<br /><br />#-dev input.def includes the input of CFX analysis in DEF format<br />#-P the name of prefered license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial))<br />/ansys_inc/v145/CFX/bin/cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r</pre>
+<p>Header of the pbs file (above) is common and description can be find on <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_blank" class="internal-link">this site</a>. SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. <span>Input file has to be defined by common CFX def file which is attached to the cfx solver via parameter -def</span></p>
+<p><strong>License</strong>Â should be selected by parameter -P (Big letter <strong>P</strong>). Licensed products are the following: aa_r (ANSYSÂ <strong>Academic</strong>Â Research), ane3fl (ANSYS Multiphysics)-<strong>Commercial.</strong> <br /><a href="licensing.html" title="" target="_self" class="internal-link"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> <span class="hps">here</span></span></a></p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
index fa6e2d1fa..e12ff1575 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
@@ -54,7 +54,7 @@ do
fi
done
-echo Machines$hl
+echo Machines: $hl
#-dev input.def includes the input of CFX analysis in DEF format
#-P the name of prefered license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial))
@@ -64,7 +64,7 @@ echo Machines$hl
Header of the pbs file (above) is common and description can be find
on [this
site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
-SVS FEM recommends to utilize sources by keywordsnodes, ppn. These
+SVS FEM recommends to utilize sources by keywords: nodes, ppn. These
keywords allows to address directly the number of nodes (computers) and
cores (ppn) which will be utilized in the job. Also the rest of code
assumes such structure of allocated resources.
@@ -76,7 +76,7 @@ CFX def file which is attached to the cfx solver via parameter
-def</span>
**License**Â should be selected by parameter -P (Big letter **P**).
-Licensed products are the followingaa_r
+Licensed products are the following: aa_r
(ANSYSÂ **Academic**Â Research), ane3fl (ANSYS
Multiphysics)-**Commercial.**
[<span id="result_box" class="short_text"><span class="hps">More</span>
@@ -84,3 +84,7 @@ Multiphysics)-**Commercial.**
class="hps">here</span></span>](licensing.html)
Â
+
+
+
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view.html
new file mode 100644
index 000000000..fc0721ffe
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent-pbs-file/view.html
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+ <p><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent" target="_blank" title="">ANSYS Fluent</a> software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. Special models that give the software the ability to model in-cylinder combustion, aeroacoustics, turbomachinery, and multiphase systems have served to broaden its reach.</p>
+<h2 class=" "><span>1. Common way to run Fluent over pbs file</span></h2>
+<p><span>To run ANSYS Fluent in batch mode you can utilize/modify the default fluent.pbs script and execute it via the qsub command.</span></p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -S /bin/bash<br />#PBS -l nodes=2:ppn=16<br />#PBS -q qprod<br />#PBS -N $USER-Fluent-Project<br />#PBS -A XX-YY-ZZ<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/$USER/work"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />#### Load ansys module so that we find the cfx5solve command<br />module load ansys<br /><br /># Use following line to specify MPI for message-passing instead<br />NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`<br /><br />/ansys_inc/v145/fluent/bin/fluent 3d -t$NCORES -cnf=$PBS_NODEFILE -g -i fluent.jou</pre>
+<p>Header of the pbs file (above) is common and description can be find on <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_blank" class="internal-link">this site</a>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common Fluent journal file which is attached to the Fluent solver via parameter -i fluent.jou</p>
+<p>Journal file with definition of the input geometry and boundary conditions and defined process of solution has e.g. the following structure:</p>
+<pre class=" ">/file/read-case aircraft_2m.cas.gz<br />/solve/init<br />init<br />/solve/iterate<br />10<br />/file/write-case-dat aircraft_2m-solution<br />/exit yes</pre>
+<p><span>The appropriate dimension of the problem has to be set by parameter (2d/3d). </span></p>
+<h2 class=" "><span>2. Fast way to run Fluent from command line</span></h2>
+<div class="section" title="3.1.2. Usage">
+<pre class="prettyprint lang-sh"><code class="systemitem">fluent</code> <span class="emphasis"><em>solver_version</em></span> <code class="systemitem">[</code><span class="emphasis"><em>FLUENT_options</em></span><code class="systemitem">] -i</code> <span class="emphasis"><em>journal_file</em></span> <code class="systemitem">-pbs</code></pre>
+<div class="section" title="3.1.2. Usage">
+<p>This syntax will start the ANSYS FLUENT job under PBS Professional using the <span class="monospace">qsub</span>Â command in a batch manner. When resources are available, PBS Professional will start the job and return a job ID, usually in the form of <span class="emphasis"><em>job_ID.hostname</em></span>. This job ID can then be used to query, control, or stop the job using standard PBS Professional commands, such as <span class="monospace">qstat</span>Â or <span class="monospace">qdel</span>. The job will be run out of the current working directory, and all output will be written to the file <span class="monospace">fluent.o</span><span>Â </span><span class="emphasis"><em>job_ID</em></span>. Â Â Â Â </p>
+<h2 class=" ">3. Running Fluent via user's config file</h2>
+<div class="section" title="3.3.1. Configuration File Example">
+<p>The sample script uses a configuration file called <span class="monospace">pbs_fluent.conf</span> Â if no command line arguments are present. This configuration file should be present in the directory from which the jobs are submitted (which is also the directory in which the jobs are executed). The following is an example of what the content of <span class="monospace">pbs_fluent.conf</span>Â can be:</p>
+<pre class="screen">input="example_small.flin"
+case="Small-1.65m.cas"
+fluent_args="3d -pmyrinet"
+outfile="fluent_test.out"
+mpp="true"</pre>
+<p>The following is an explanation of the parameters:</p>
+<div>
+<div class="variablelist">
+<p class=" " style="padding-left: 30px; "><span><span class="monospace">input</span> is the name of the input file.</span></p>
+<p class=" " style="padding-left: 30px; "><span class="monospace">case</span> is the name of the <span class="monospace">.cas</span>Â file that the input file will utilize.</p>
+<p class=" " style="padding-left: 30px; "><span class="monospace">fluent_args</span> are extra ANSYS FLUENT arguments. As shown in the previous example, you can specify the interconnect by using the <span class="monospace">-p</span>Â interconnect command. The available interconnects include <span class="monospace">ethernet</span>Â (the default), <span class="monospace">myrinet</span>,<span class="monospace"> infiniband</span>, <span class="monospace">vendor</span>, <span class="monospace">altix</span><span>,</span> and <span class="monospace">crayx</span>. The MPI is selected automatically, based on the specified interconnect.</p>
+<p class=" " style="padding-left: 30px; "><span class="monospace">outfile</span> is the name of the file to which the standard output will be sent.</p>
+<p class=" " style="padding-left: 30px; "><span class="monospace">mpp="true"</span> will tell the job script to execute the job across multiple processors. Â Â Â Â Â Â Â Â </p>
+</div>
+</div>
+</div>
+</div>
+</div>
+<p><span>To run ANSYS Fluent in batch mode with user's config file you can utilize/modify the following script and execute it via the qsub command.</span></p>
+<div class="section" title="3.3.2. Altair’s Sample Script">
+<pre class="prettyprint lang-sh">#!/bin/sh<br />#PBS -l nodes=2:ppn=4<br />#PBS -1 qprod<br />#PBS -N $USE-Fluent-Project<br />#PBS -A XX-YY-ZZ<br />
+ cd $PBS_O_WORKDIR
+
+ #We assume that if they didn’t specify arguments then they should use the
+ #config file if [ "xx${input}${case}${mpp}${fluent_args}zz" = "xxzz" ]; then
+ if [ -f pbs_fluent.conf ]; then
+ . pbs_fluent.conf
+ else
+ printf "No command line arguments specified, "
+ printf "and no configuration file found. Exiting \n"
+ fi
+ fi
+
+
+ #Augment the ANSYS FLUENT command line arguments case "$mpp" in
+ true)
+ #MPI job execution scenario
+ num_nodes=â€cat $PBS_NODEFILE | sort -u | wc -lâ€
+ cpus=â€expr $num_nodes \* $NCPUSâ€
+ #Default arguments for mpp jobs, these should be changed to suit your
+ #needs.
+ fluent_args="-t${cpus} $fluent_args -cnf=$PBS_NODEFILE"
+ ;;
+ *)
+ #SMP case
+ #Default arguments for smp jobs, should be adjusted to suit your
+ #needs.
+ fluent_args="-t$NCPUS $fluent_args"
+ ;;
+ esac
+ #Default arguments for all jobs
+ fluent_args="-ssh -g -i $input $fluent_args"
+
+ echo "---------- Going to start a fluent job with the following settings:
+ Input: $input
+ Case: $case
+ Output: $outfile
+ Fluent arguments: $fluent_args"
+
+ #run the solver
+ /ansys_inc/v145/fluent/bin/fluent $fluent_args > $outfile</pre>
+</div>
+<p><span>It runs the jobs out of the directory from which they are submitted (PBS_O_WORKDIR).</span></p>
+<h2 class=" ">4. Running Fluent in parralel</h2>
+<p>Fluent could be run in parallel only under Academic Research license. To do so this ANSYS Academic Research license must be placed before ANSYS CFD license in user preferences. To make this change anslic_admin utility should be run</p>
+<pre class="prettyprint lang-sh">/ansys_inc/shared_ les/licensing/lic_admin/anslic_admin</pre>
+<p>ANSLIC_ADMIN Utility will be run</p>
+<p><img alt="" src="Fluent_Licence_1.jpg" title="" class="image-inline" /></p>
+<p><img alt="" src="Fluent_Licence_2.jpg" title="" class="image-inline" /></p>
+<p><img alt="" src="Fluent_Licence_3.jpg" title="" class="image-inline" /></p>
+<p>Â </p>
+<p>ANSYS Academic Research license should be moved up to the top of the list.</p>
+<p>Â </p>
+<p><img alt="" src="Fluent_Licence_4.jpg" title="" class="image-inline" /></p>
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
index b30190d27..e43a8033c 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
@@ -53,7 +53,7 @@ Header of the pbs file (above) is common and description can be find
on [this
site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
[SVS FEM](http://www.svsfem.cz) recommends to utilize
-sources by keywordsnodes, ppn. These keywords allows to address
+sources by keywords: nodes, ppn. These keywords allows to address
directly the number of nodes (computers) and cores (ppn) which will be
utilized in the job. Also the rest of code assumes such structure of
allocated resources.
@@ -193,10 +193,10 @@ command.</span>
fluent_args="-ssh -g -i $input $fluent_args"
echo "---------- Going to start a fluent job with the following settings:
- Input$input
- Case$case
- Output$outfile
- Fluent arguments$fluent_args"
+ Input: $input
+ Case: $case
+ Output: $outfile
+ Fluent arguments: $fluent_args"
#run the solver
/ansys_inc/v145/fluent/bin/fluent $fluent_args > $outfile
@@ -235,3 +235,7 @@ list.
Â
+
+
+
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view.html
new file mode 100644
index 000000000..78d790b6b
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna-pbs-file/view.html
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+ <p><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA" target="_blank" title="">ANSYS LS-DYNA</a> software provides convenient and easy-to-use access to the technology-rich, time-tested explicit solver without the need to contend with the complex input requirements of this sophisticated program. Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in numerous industries to resolve highly intricate design issues. <span>ANSYS Mechanical users have been able take advantage of complex explicit solutions for a long time utilizing the traditional ANSYS Parametric Design Language (APDL) environment. <span>These explicit capabilities are available to ANSYS Workbench users as well. The Workbench platform is a powerful, comprehensive, easy-to-use environment for engineering simulation. CAD import from all sources, geometry cleanup, automatic meshing, solution, parametric optimization, result visualization and comprehensive report generation are all available within a single fully interactive modern graphical user environment.</span></span></p>
+<p><span>To run ANSYS LS-DYNA in batch mode you can utilize/modify the default ansysdyna.pbs script and execute it via the qsub command.</span></p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l nodes=2:ppn=16<br />#PBS -q qprod<br />#PBS -N $USER-DYNA-Project<br />#PBS -A XX-YY-ZZ<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory><br />WORK_DIR="/scratch/$USER/work"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />#! Counts the number of processors<br />NPROCS=`wc -l < $PBS_NODEFILE`<br /><br />echo This job has allocated $NPROCS nodes<br /><br />module load ansys<br /><br />#### Set number of processors per host listing<br />#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)<br />procs_per_host=1<br />#### Create host list<br />hl=""<br />for host in `cat $PBS_NODEFILE`<br />do<br /> if [ "$hl" = "" ]<br /> then hl="$host:$procs_per_host"<br /> else hl="${hl}:$host:$procs_per_host"<br /> fi<br />done<br /><br />echo Machines: $hl<br /><br />/ansys_inc/v145/ansys/bin/ansys145 -dis -lsdynampp i=input.k -machines $hl</pre>
+<p><span>Header of the pbs file (above) is common and description can be find on </span><a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_blank" class="internal-link">this site</a><span>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</span></p>
+<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA .<strong>k</strong> file which is attached to the ansys solver via parameter i=</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
index 38c83e918..4f27959d5 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
@@ -63,7 +63,7 @@ do
fi
done
-echo Machines$hl
+echo Machines: $hl
/ansys_inc/v145/ansys/bin/ansys145 -dis -lsdynampp i=input.k -machines $hl
```
@@ -72,7 +72,7 @@ echo Machines$hl
find on </span>[this
site](../../resource-allocation-and-job-execution/job-submission-and-execution.html)<span>.
[SVS FEM](http://www.svsfem.cz) recommends to utilize
-sources by keywordsnodes, ppn. These keywords allows to address
+sources by keywords: nodes, ppn. These keywords allows to address
directly the number of nodes (computers) and cores (ppn) which will be
utilized in the job. Also the rest of code assumes such structure of
allocated resources.</span>
@@ -83,3 +83,7 @@ file has to be specified. Input file has to be defined by common LS-DYNA
.**k** file which is attached to the ansys solver via parameter i=
<span><span>Â </span></span>
+
+
+
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view.html
new file mode 100644
index 000000000..9d7964651
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mapdl-pbs-file/view.html
@@ -0,0 +1,1170 @@
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+ <p><span><strong><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics" target="_blank" title="">ANSYS Multiphysics</a></strong> software offers a comprehensive product solution for both multiphysics and single-physics analysis. The product includes structural, thermal, fluid and both high- and low-frequency electromagnetic analysis. The product also contains solutions for both direct and sequentially coupled physics problems including direct coupled-field elements and the ANSYS multi-field solver.</span></p>
+<p><span>To run ANSYS MAPDL in batch mode you can utilize/modify the default mapdl.pbs script and execute it via the qsub command.</span></p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l nodes=2:ppn=16<br />#PBS -q qprod<br />#PBS -N $USER-ANSYS-Project<br />#PBS -A XX-YY-ZZ<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/$USER/work"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />module load ansys<br /><br />#### Set number of processors per host listing<br />#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)<br />procs_per_host=1<br />#### Create host list<br />hl=""<br />for host in `cat $PBS_NODEFILE`<br />do<br /> if [ "$hl" = "" ]<br /> then hl="$host:$procs_per_host"<br /> else hl="${hl}:$host:$procs_per_host"<br /> fi<br />done<br /><br />echo Machines: $hl<br /><br />#-i input.dat includes the input of analysis in APDL format<br />#-o file.out is output file from ansys where all text outputs will be redirected <br />#-p the name of license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial), aa_r_dy=Academic AUTODYN)<br />/ansys_inc/v145/ansys/bin/ansys145 -b -dis -p aa_r -i input.dat -o file.out -machines $hl -dir $WORK_DIR</pre>
+<p>Header of the pbs file (above) is common and description can be find on <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_blank" class="internal-link">this site</a>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common APDL file which is attached to the ansys solver via parameter -i</p>
+<p><strong>License</strong> should be selected by parameter -p. Licensed products are the following: aa_r (ANSYS <strong>Academic</strong> Research), ane3fl (ANSYS Multiphysics)-<strong>Commercial</strong>, aa_r_dy (ANSYS <strong>Academic</strong> AUTODYN)<span> <br /><a href="licensing.html" title="" target="_self" class="internal-link"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> <span class="hps">here</span></span></a><br /></span></p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
index c344de564..285f909a4 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
@@ -49,7 +49,7 @@ do
fi
done
-echo Machines$hl
+echo Machines: $hl
#-i input.dat includes the input of analysis in APDL format
#-o file.out is output file from ansys where all text outputs will be redirected
@@ -61,7 +61,7 @@ Header of the pbs file (above) is common and description can be find on
[this
site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
[SVS FEM](http://www.svsfem.cz) recommends to utilize
-sources by keywordsnodes, ppn. These keywords allows to address
+sources by keywords: nodes, ppn. These keywords allows to address
directly the number of nodes (computers) and cores (ppn) which will be
utilized in the job. Also the rest of code assumes such structure of
allocated resources.
@@ -72,10 +72,14 @@ file has to be specified. Input file has to be defined by common APDL
file which is attached to the ansys solver via parameter -i
**License** should be selected by parameter -p. Licensed products are
-the followingaa_r (ANSYS **Academic** Research), ane3fl (ANSYS
+the following: aa_r (ANSYS **Academic** Research), ane3fl (ANSYS
Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic**
AUTODYN)<span>
[<span id="result_box" class="short_text"><span class="hps">More</span>
<span class="hps">about licensing</span> <span
class="hps">here</span></span>](licensing.html)
</span>
+
+
+
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.html
new file mode 100644
index 000000000..cdcfaebec
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.html
@@ -0,0 +1,1173 @@
+
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+
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+
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+ <p><strong><a class="external-link" href="http://www.svsfem.cz/" target="_blank" title="">SVS FEM</a></strong> as <em><strong><a class="external-link" href="http://www.ansys.com/" target="_self" title="">ANSYS Channel partner</a></strong></em> for Czech Republic provided all ANSYS licenses for ANSELM cluster and supports of all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent, Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging to problem of ANSYS functionality contact please <a class="email-link" href="mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM" target="_self" title="">hotline@svsfem.cz</a></p>
+<p>Anselm provides as commercial as academic variants. Academic variants are distinguished by "<strong>Academic...</strong>" word in the name of  license or by two letter preposition "<strong>aa_</strong>" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). <a href="licensing.html" title="" target="_self" class="internal-link"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> <span class="hps">here</span></span></a></p>
+<p>To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module:</p>
+<pre class=" ">$ module load ansys</pre>
+<p>ANSYS supports interactive regime, but due to assumed solution of extremely difficult tasks it is not recommended.</p>
+<p>If user needs to work in interactive regime we recommend to configure the RSM service on the client machine which allows to forward the solution to the Anselm directly from the client's Workbench project (see ANSYS RSM service).</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
index 58f64de2c..ea369b7a8 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
@@ -30,3 +30,7 @@ If user needs to work in interactive regime we recommend to configure
the RSM service on the client machine which allows to forward the
solution to the Anselm directly from the client's Workbench project
(see ANSYS RSM service).
+
+
+
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing.html
new file mode 100644
index 000000000..c168c66fd
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/licensing.html
@@ -0,0 +1,351 @@
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+ <!-- nagios_check_http_expect_string -->
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view.html
new file mode 100644
index 000000000..78a316289
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna-pbs-file/view.html
@@ -0,0 +1,1170 @@
+
+<!DOCTYPE html>
+
+<html xmlns="http://www.w3.org/1999/xhtml" lang="cs">
+
+
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+
+
+<title>LS-DYNA PBS file — IT4I Docs</title>
+
+ <link rel="canonical" href="../ls-dyna-pbs-file.1" />
+
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+ <meta name="generator" content="Plone - http://plone.org" />
+
+</head>
+
+<body dir="ltr" class="template-file_view portaltype-file site-docs section-anselm-cluster-documentation subsection-software subsection-software-ansys subsection-software-ansys-ls-dyna-pbs-file icons-on userrole-anonymous">
+
+<div id="visual-portal-wrapper">
+
+ <div id="portal-top" class="row">
+<div class="cell width-full position-0">
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+ <p class="hiddenStructure">
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+ <p><a class="external-link" href="http://www.lstc.com/" target="_blank" title="">LS-DYNA</a> is a multi-purpose, explicit and implicit finite element program used to analyze the nonlinear dynamic response of structures. Its fully automated contact analysis capability, a wide range of constitutive models to simulate a whole range of engineering materials (steels, composites, foams, concrete, etc.), error-checking features and the high scalability have enabled users worldwide to solve successfully many complex problems. <span>Additionally LS-DYNA is extensively used to simulate impacts on structures from drop tests, underwater shock, explosions or high-velocity impacts. Explosive forming, process engineering, accident reconstruction, vehicle dynamics, thermal brake disc analysis or nuclear safety are further areas in the broad range of possible applications. In leading-edge research LS-DYNA is used to investigate the behaviour of materials like composites, ceramics, concrete, or wood. Moreover, it is used in biomechanics, human modelling, molecular structures, casting, forging, or virtual testing.</span></p>
+<p><span>Anselm provides <strong>1 commercial license of LS-DYNA without HPC</strong> support now. </span></p>
+<p><span><span>To run LS-DYNA in batch mode you can utilize/modify the default lsdyna.pbs script and execute it via the qsub command.</span></span></p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l nodes=1:ppn=16<br />#PBS -q qprod<br />#PBS -N $USER-LSDYNA-Project<br />#PBS -A XX-YY-ZZ<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/$USER/work"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br /><br />module load lsdyna<br /><br />/apps/engineering/lsdyna/lsdyna700s i=input.k</pre>
+<p>Header of the pbs file (above) is common and description can be find on <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_blank" class="internal-link">this site</a>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA <strong>.k</strong> file which is attached to the LS-DYNA solver via parameter i=</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
index 8113ddac5..51443a473 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
@@ -53,7 +53,7 @@ Header of the pbs file (above) is common and description can be find
on [this
site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
[SVS FEM](http://www.svsfem.cz) recommends to utilize
-sources by keywordsnodes, ppn. These keywords allows to address
+sources by keywords: nodes, ppn. These keywords allows to address
directly the number of nodes (computers) and cores (ppn) which will be
utilized in the job. Also the rest of code assumes such structure of
allocated resources.
@@ -62,3 +62,7 @@ Working directory has to be created before sending pbs job into the
queue. Input file should be in working directory or full path to input
file has to be specified. Input file has to be defined by common LS-DYNA
**.k** file which is attached to the LS-DYNA solver via parameter i=
+
+
+
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/chemistry.html b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry.html
new file mode 100644
index 000000000..b3cb364a2
--- /dev/null
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+ <h2 class=" ">About Molpro</h2>
+<p>Molpro is a software package used for accurate ab-initio quantum chemistry calculations. More information can be found at the <a class="external-link" href="http://www.molpro.net/" target="_self" title="">official webpage</a>.</p>
+<h2 class=" ">License</h2>
+<p>Molpro software package is available only to users that have a valid license. Please contact support to enable access to Molpro if you have a valid license appropriate for running on our cluster (eg. <span>academic research group licence, parallel execution).</span></p>
+<p class=" "><span>To run Molpro, you need to have a valid license token present in "<span class="monospace">$HOME/.molpro/token"</span></span>. You can download the token from <a class="external-link" href="https://www.molpro.net/licensee/?portal=licensee" target="_self" title="">Molpro website</a>.</p>
+<h2 class=" ">Installed version</h2>
+<p>Currently on Anselm is installed version 2010.1, patch level 45, parallel version compiled with Intel compilers and Intel MPI.</p>
+<p>Compilation parameters are default :</p>
+<table class="plain">
+<tbody>
+<tr><th>Parameter</th><th>Value</th></tr>
+<tr>
+<td><span>max number of atoms</span></td>
+<td>200</td>
+</tr>
+<tr>
+<td><span>max number of valence orbitals</span></td>
+<td>300</td>
+</tr>
+<tr>
+<td><span>max number of basis functions</span></td>
+<td>4095</td>
+</tr>
+<tr>
+<td><span>max number of states per symmmetry</span></td>
+<td>20</td>
+</tr>
+<tr>
+<td><span>max number of state symmetries</span></td>
+<td>16</td>
+</tr>
+<tr>
+<td><span>max number of records</span></td>
+<td>200</td>
+</tr>
+<tr>
+<td><span>max number of primitives</span></td>
+<td><span>maxbfn x [2]</span></td>
+</tr>
+</tbody>
+</table>
+<p class="p1">Â </p>
+<h2 class=" ">Running</h2>
+<p>Molpro is compiled for parallel execution using MPI and OpenMP. By default, Molpro reads the number of allocated nodes from PBS and launches a data server on one node. On the remaining allocated nodes, compute processes are launched, one process per node, each with 16 threads. You can modify this behavior by using -n, -t and helper-server options. Please refer to the <a class="external-link" href="http://www.molpro.net/info/2010.1/doc/manual/node9.html" target="_self" title="">Molpro documentation</a> for more details. </p>
+<p class="exclamation">The OpenMP parallelization in Molpro is limited and has been observed to produce limited scaling. We therefore recommend to use MPI parallelization only. This can be achieved by passing option <span class="monospace">mpiprocs=16:ompthreads=1</span> to PBS.</p>
+<p>You are advised to use the -d option to point to a directory in <a href="../../storage.html" title="" target="_self" class="internal-link">SCRATCH filesystem</a>. Molpro can produce a large amount of temporary data during its run, and it is important that these are placed in the fast scratch filesystem.</p>
+<h3 class=" ">Example jobscript</h3>
+<pre class=" ">#PBS -A IT4I-0-0<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1<br /><br />cd $PBS_O_WORKDIR<br /><br /># load Molpro module<br />module add molpro<br /><br /># create a directory in the SCRATCH filesystem<br />mkdir -p /scratch/$USER/$PBS_JOBID<br /><br /># copy an example input<br />cp /apps/chem/molpro/2010.1/molprop_2010_1_Linux_x86_64_i8/examples/caffeine_opt_diis.com .<br /><br /># run Molpro with default options<br /><span>molpro -d /scratch/$USER/$PBS_JOBID caffeine_opt_diis.com<br /><br /># delete scratch directory<br />rm -rf /scratch/$USER/$PBS_JOBIDÂ </span></pre>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
index 965b37aab..878debb79 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
@@ -89,4 +89,3 @@ these are placed in the fast scratch filesystem.
rm -rf /scratch/$USER/$PBS_JOBIDÂ
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.html b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.html
new file mode 100644
index 000000000..9dc29e6b4
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.html
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+ <h2 class=" "><span>Introduction</span></h2>
+<p><span>NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.</span></p>
+<p><a class="external-link" href="http://www.nwchem-sw.org/index.php/Main_Page" target="_blank" title="">Homepage</a></p>
+<h2 class=" ">Installed versions</h2>
+<p>The following versions are currently installed :Â </p>
+<ul>
+<li>
+<p class="p1">6.1.1, not recommended, problems have been observed with this version</p>
+</li>
+<li>
+<p class="p1">6.3-rev2-patch1, current release with QMD patch applied. Compiled with Intel compilers, MKL and Intel MPI</p>
+</li>
+<li>
+<p class="p1">6.3-rev2-patch1-openmpi, same as above, but compiled with OpenMPI and NWChem provided BLAS instead of MKL. This version is expected to be slower</p>
+</li>
+<li>
+<p class="p1">6.3-rev2-patch1-venus, this version contains only libraries for VENUS interface linking. Does not provide standalone NWChem executable</p>
+</li>
+</ul>
+<p>For a current list of installed versions, execute :Â </p>
+<pre class=" ">module avail nwchem</pre>
+<h2 class=" ">Running</h2>
+<p>NWChem is compiled for parallel MPI execution. Normal procedure for MPI jobs applies. Sample jobscript :</p>
+<pre class=" ">#PBS -A IT4I-0-0<br />#PBS -q qprod<br /><span>#PBS -l select=1:ncpus=16<br /></span><span><br />module add nwchem/6.3-rev2-patch1<br /></span><span>mpirun -np 16 nwchem h2o.nw</span></pre>
+<h2 class=" "><span>Options</span></h2>
+<p>Please refer to <a class="external-link" href="http://www.nwchem-sw.org/index.php/Release62:Top-level" target="_self" title="">the documentation</a>Â and in the input file set the following directives :</p>
+<ul>
+<li><span>MEMORY : controls the amount of memory NWChem will use</span></li>
+<li><span>SCRATCH_DIR : set this to a directory in <a href="../../storage.html#scratch" title="" target="_self" class="internal-link">SCRATCH filesystem</a> (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"</span></li>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
index ab0bfe2bb..588e90ee2 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
@@ -56,12 +56,11 @@ Please refer to [the
documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level)Â and
in the input file set the following directives :
-- <span>MEMORY controls the amount of memory NWChem will use</span>
-- <span>SCRATCH_DIR set this to a directory in [SCRATCH
+- <span>MEMORY : controls the amount of memory NWChem will use</span>
+- <span>SCRATCH_DIR : set this to a directory in [SCRATCH
filesystem](../../storage.html#scratch)Â (or run the
calculation completely in a scratch directory). For certain
calculations, it might be advisable to reduce I/O by forcing
"direct" mode, eg. "scf direct"</span>
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/compilers.html b/docs.it4i.cz/anselm-cluster-documentation/software/compilers.html
new file mode 100644
index 000000000..66b44baca
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/compilers.html
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+ Compilers
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+
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+</div>
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+ Available compilers, including GNU, INTEL and UPC compilers
+ </div>
+
+
+
+
+
+ <div id="viewlet-above-content-body">
+<dl id="document-toc" class="portlet toc" style="display: none">
+ <dt class="portletHeader">Obsah</dt>
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+ <div id="content-core">
+
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+ <div id="parent-fieldname-text-e5dff595c7ca4fd3b1e298b3e08b1ee2" class="">
+ <p>Currently there are several compilers for different programming languages available on the Anselm cluster:</p>
+<ul>
+<li>C/C++</li>
+<li>Fortran 77/90/95</li>
+<li>Unified Parallel C</li>
+<li>Java</li>
+<li>nVidia CUDA</li>
+</ul>
+<p>Â </p>
+<p class=" ">The C/C++ and Fortran compilers are divided into two main groups GNU and Intel.</p>
+<h2 class=" ">Intel Compilers</h2>
+<p class=" ">For information about the usage of Intel Compilers and other Intel products, please read the <a href="intel-suite.html" title="" target="_self" class="internal-link">Intel Parallel studio</a> page.</p>
+<h2 class=" ">GNU C/C++ and Fortran Compilers</h2>
+<p>For compatibility reasons there are still available the original (old 4.4.6-4) versions of GNU compilers as part of the OS. These are accessible in the search path by default.</p>
+<p>It is strongly recommended to use the up to date version (4.8.1) which comes with the module gcc:</p>
+<pre class=" ">$ module load gcc<br />$ gcc -v<br />$ g++ -v<br />$ gfortran -v</pre>
+<p class=" ">With the module loaded two environment variables are predefined. One for maximum optimizations on the Anselm cluster architecture, and the other for debugging purposes:</p>
+<pre class=" ">$ echo $OPTFLAGS<br />-O3 -march=corei7-avx</pre>
+<pre class=" ">$ echo $DEBUGFLAGS<br />-O0 -g</pre>
+<p class=" ">For more informations about the possibilities of the compilers, please see the man pages.</p>
+<h2 class=" ">Unified Parallel C</h2>
+<p class=" ">UPC is supported by two compiler/runtime implementations:</p>
+<ul>
+<li>GNU - SMP/multi-threading support only</li>
+<li>Berkley - multi-node support as well as SMP/multi-threading support</li>
+</ul>
+<h3 class=" ">GNU UPC Compiler</h3>
+<p>To use the GNU UPC compiler and run the compiled binaries use the module gupc</p>
+<pre class=" ">$ module add gupc<br />$ gupc -v<br />$ g++ -v</pre>
+<p>Simple program to test the compiler</p>
+<pre class=" ">$ cat count.upc <br /><br />/* hello.upc - a simple UPC example */<br />#include <upc.h><br />#include <stdio.h><br /><br />int main() {<br />Â if (MYTHREAD == 0) {<br />Â Â Â printf("Welcome to GNU UPC!!!\n");<br />Â }<br />Â upc_barrier;<br />Â printf(" - Hello from thread %i\n", MYTHREAD);<br />Â return 0;<br />} </pre>
+<p>To compile the example use</p>
+<pre class=" ">$ gupc -o count.upc.x count.upc</pre>
+<p>To run the example with 5 threads issue</p>
+<pre class=" ">$ ./count.upc.x -fupc-threads-5</pre>
+<p class=" ">For more informations see the man pages.</p>
+<h3 class=" ">Berkley UPC Compiler</h3>
+<p>To use the Berkley UPC compiler and runtime environment to run the binaries use the module bupc</p>
+<pre class=" ">$ module add bupc<br />$ upcc -version</pre>
+<p>As default UPC network the "smp" is used. This is very quick and easy way for testing/debugging, but limited to one node only.</p>
+<p>For production runs, it is recommended to use the native Infiband implementation of UPC network "ibv". For testing/debugging using multiple nodes, the "mpi" UPC network is recommended. Please note, that <strong>the selection of the network is done at the compile time</strong> and not at runtime (as expected)!</p>
+<p>Example UPC code:</p>
+<pre class=" ">$ cat hello.upc <br /><br />/* hello.upc - a simple UPC example */<br />#include <upc.h><br />#include <stdio.h><br /><br />int main() {<br />Â if (MYTHREAD == 0) {<br />Â Â Â printf("Welcome to Berkeley UPC!!!\n");<br />Â }<br />Â upc_barrier;<br />Â printf(" - Hello from thread %i\n", MYTHREAD);<br />Â return 0;<br />} </pre>
+<p class=" ">To compile the example with the "ibv" UPC network use</p>
+<pre class=" ">$ upcc -network=ibv -o hello.upc.x hello.upc </pre>
+<p class=" ">To run the example with 5 threads issue</p>
+<pre class=" ">$ upcrun -n 5 ./hello.upc.x</pre>
+<p class=" ">To run the example on two compute nodes using all 32 cores, with 32 threads, issue</p>
+<pre class=" ">$ qsub -I -q qprod -A PROJECT_ID -l select=2:ncpus=16 <br />$ module add bupc<br />$ upcrun -n 32 ./hello.upc.x</pre>
+<p class=" ">Â For more informations see the man pages.</p>
+<h2 class=" ">Java</h2>
+<p>For information how to use Java (runtime and/or compiler), please read the <a href="java.html" title="" target="_self" class="internal-link">Java page</a>.</p>
+<h2 class=" ">nVidia CUDA</h2>
+<p>For information how to work with nVidia CUDA, please read the <a href="nvidia-cuda.html" title="" target="_self" class="internal-link">nVidia CUDA page</a>.</p>
+
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CUDA page](nvidia-cuda.html).
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+ COMSOL Multiphysics®
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+ <div id="parent-fieldname-text-2aad5f03c8db4ea2bac6df527ebbed80" class="">
+ <h2 class=" "><span><span>Introduction<br /></span></span></h2>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com" target="_self" title="">COMSOL</a></span></span><span><span> is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.</span></span></p>
+<ul>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/structural-mechanics-module" target="_self" title="">Structural Mechanics Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/heat-transfer-module" target="_self" title="">Heat Transfer Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/cfd-module" target="_self" title="">CFD Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/acoustics-module" target="_self" title="">Acoustics Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span>and <a class="external-link" href="http://www.comsol.com/products" target="_self" title="">many others</a></span></span></p>
+</li>
+</ul>
+<p align="JUSTIFY"><span><span>COMSOL also allows an </span></span><span><span><span><span>interface support for equation-based modelling of </span></span></span></span><span><span>partial differential equations.</span></span></p>
+<h2 class=" "><span><span>Execution<br /></span></span></h2>
+<p align="JUSTIFY"><span><span>On the Anselm cluster COMSOL is available in the latest stable version. There are two variants of the release:</span></span></p>
+<ul>
+<li>
+<p align="JUSTIFY"><span><span><b>Non commercial</b></span></span><span><span> or so called </span></span><span><span><b>EDU variant</b></span></span><span><span>, which can be used for research and educational purposes.</span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><b>Commercial</b></span></span><span><span> or so called </span></span><span><span><b>COM variant</b></span></span><span><span>, which can used also for commercial activities. </span></span><span><span><b>COM variant</b></span></span><span><span> has only subset of features compared to the </span></span><span><span><b>EDU variant</b></span></span><span><span> available. <span class="internal-link"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> will be posted <span class="hps">here soon</span>.</span></span><br /></span></span></p>
+</li>
+</ul>
+<p align="JUSTIFY"><span><span>To load the of COMSOL load the module</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>$ module load comsol</span></span></pre>
+<p align="JUSTIFY"><span><span>By default the </span></span><span><span><b>EDU variant</b></span></span><span><span> will be loaded. If user needs other version or variant, load the particular version. To obtain the list of available versions use</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>$ module avail comsol</span></span></pre>
+<p align="JUSTIFY"><span><span>If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">Virtual Network Computing (VNC)</a>.</span></span></p>
+<pre class="prettyprint lang-sh"><span><span><span>$ xhost +<br />$ qsub -I -X</span></span></span><span><span><span><span> </span></span></span></span><span><span><span>-A</span></span></span><span><span> </span></span><span><span><span><span>PROJECT_ID </span></span></span></span><span><span><span>-q </span></span></span><span><span><span><span>qprod</span></span></span></span><span><span><span> -l </span></span></span><span><span><span><span>select=1:ncpus=16</span><br />$ module load </span></span></span><span><span>comsol<span><br />$ </span></span></span><span><span>comsol<br /></span></span></pre>
+<p align="JUSTIFY"><span><span>To run COMSOL in batch mode, without the COMSOL Desktop GUI environment, user can utilized the default (comsol.pbs) job script and execute it via the qsub command.</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>#!/bin/bash<br />#PBS -l select=3:ncpus=16<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -A PROJECT_ID<br /><br />cd /scratch/$USER/ || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load comsol<br /># module load comsol/43b-COM<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log<br /><br /></span></span></pre>
+<p align="JUSTIFY"><span><span>Working directory has to be created before sending the (comsol.pbs) job script into the queue. Input file (name_input_f.mph) has to be in working directory or full path to input file has to be specified. The appropriate path to the temp directory of the job has to be set by command option (-tmpdir).</span></span></p>
+<h2 class=" ">LiveLink™<i> </i>for MATLAB<sup>®</sup></h2>
+<p align="JUSTIFY"><span><span>COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL</span></span><span><span><sup><span><span><span><span><span><span><span><b>®</b></span></span></span></span></span></span></span></sup></span></span><span><span> API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB. </span></span></p>
+<p align="JUSTIFY"><span><span>LiveLink for MATLAB is available in both </span></span><span><span><b>EDU</b></span></span><span><span> and </span></span><span><span><b>COM</b></span></span><span><span> </span></span><span><span><b>variant</b></span></span><span><span> of the COMSOL release. On Anselm 1 commercial (</span></span><span><span><b>COM</b></span></span><span><span>) license and the 5 educational (</span></span><span><span><b>EDU</b></span></span><span><span>) licenses of LiveLink for MATLAB (please see the <a href="isv_licenses.html" title="" target="_self" class="internal-link">ISV Licenses</a>) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.</span></span></p>
+<pre class="prettyprint lang-sh">$ xhost +<br />$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ncpus=16<br />$ module load matlab<br />$ module load comsol<br />$ comsol server matlab</pre>
+<p align="JUSTIFY"><span><span>At the first time to launch the LiveLink for MATLAB (client-MATLAB/server-COMSOL connection) the login and password is requested and this information is not requested again.</span></span></p>
+<p align="JUSTIFY"><span><span>To run LiveLink for MATLAB in batch mode with (comsol_matlab.pbs) job script you can utilize/modify the following script and execute it via the qsub command.</span></span></p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l select=3:ncpus=16<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -AÂ PROJECT_ID<br /><br />cd /scratch/$USER || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load matlab<br />module load comsol/43b-EDU<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/$USER &<br />cd /apps/engineering/comsol/comsol43b/mli<br />matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/$USER; test_job"</pre>
+<p>This example shows how to run Livelink for MATLAB with following configuration: 3 nodes and 16 cores per node. Working directory has to be created before submitting (comsol_matlab.pbs) job script into the queue. Input file (test_job.m) has to be in working directory or full path to input file has to be specified. The Matlab command option (-r ”mphstart”) created a connection with a COMSOL server using the default port number.<br /><br /></p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/comsol.md b/docs.it4i.cz/anselm-cluster-documentation/software/comsol.md
index ee91edf62..2b71e4fe6 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/comsol.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/comsol.md
@@ -198,11 +198,10 @@ matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/$USER; test_job"
```
This example shows how to run Livelink for MATLAB with following
-configuration3 nodes and 16 cores per node. Working directory has to
+configuration: 3 nodes and 16 cores per node. Working directory has to
be created before submitting (comsol_matlab.pbs) job script into the
queue. Input file (test_job.m) has to be in working directory or full
path to input file has to be specified. The Matlab command option (-r
”mphstart”) created a connection with a COMSOL server using the default
port number.
-
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+ COMSOL Multiphysics®
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+ <h2 class=" "><span><span>Introduction<br /></span></span></h2>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com" target="_self" title="">COMSOL</a></span></span><span><span> is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.</span></span></p>
+<ul>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/structural-mechanics-module" target="_self" title="">Structural Mechanics Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/heat-transfer-module" target="_self" title="">Heat Transfer Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/cfd-module" target="_self" title="">CFD Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/acoustics-module" target="_self" title="">Acoustics Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span>and <a class="external-link" href="http://www.comsol.com/products" target="_self" title="">many others</a></span></span></p>
+</li>
+</ul>
+<p align="JUSTIFY"><span><span>COMSOL also allows an </span></span><span><span><span><span>interface support for equation-based modelling of </span></span></span></span><span><span>partial differential equations.</span></span></p>
+<h2 class=" "><span><span>Execution<br /></span></span></h2>
+<p align="JUSTIFY"><span><span>On the Anselm cluster COMSOL is available in the latest stable version. There are two variants of the release:</span></span></p>
+<ul>
+<li>
+<p align="JUSTIFY"><span><span><b>Non commercial</b></span></span><span><span> or so called </span></span><span><span><b>EDU variant</b></span></span><span><span>, which can be used for research and educational purposes.</span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><b>Commercial</b></span></span><span><span> or so called </span></span><span><span><b>COM variant</b></span></span><span><span>, which can used also for commercial activities. </span></span><span><span><b>COM variant</b></span></span><span><span> has only subset of features compared to the </span></span><span><span><b>EDU variant</b></span></span><span><span> available. <span class="internal-link"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> will be posted <span class="hps">here soon</span>.</span></span><br /></span></span></p>
+</li>
+</ul>
+<p align="JUSTIFY"><span><span>To load the of COMSOL load the module</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>$ module load comsol</span></span></pre>
+<p align="JUSTIFY"><span><span>By default the </span></span><span><span><b>EDU variant</b></span></span><span><span> will be loaded. If user needs other version or variant, load the particular version. To obtain the list of available versions use</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>$ module avail comsol</span></span></pre>
+<p align="JUSTIFY"><span><span>If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/comsol/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">Virtual Network Computing (VNC)</a>.</span></span></p>
+<pre class="prettyprint lang-sh"><span><span><span>$ xhost +<br />$ qsub -I -X</span></span></span><span><span><span><span> </span></span></span></span><span><span><span>-A</span></span></span><span><span> </span></span><span><span><span><span>PROJECT_ID </span></span></span></span><span><span><span>-q </span></span></span><span><span><span><span>qprod</span></span></span></span><span><span><span> -l </span></span></span><span><span><span><span>select=1:ncpus=16</span><br />$ module load </span></span></span><span><span>comsol<span><br />$ </span></span></span><span><span>comsol<br /></span></span></pre>
+<p align="JUSTIFY"><span><span>To run COMSOL in batch mode, without the COMSOL Desktop GUI environment, user can utilized the default (comsol.pbs) job script and execute it via the qsub command.</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>#!/bin/bash<br />#PBS -l select=3:ncpus=16<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -A PROJECT_ID<br /><br />cd /scratch/$USER/ || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load comsol<br /># module load comsol/43b-COM<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log<br /><br /></span></span></pre>
+<p align="JUSTIFY"><span><span>Working directory has to be created before sending the (comsol.pbs) job script into the queue. Input file (name_input_f.mph) has to be in working directory or full path to input file has to be specified. The appropriate path to the temp directory of the job has to be set by command option (-tmpdir).</span></span></p>
+<h2 class=" ">LiveLink™<i> </i>for MATLAB<sup>®</sup></h2>
+<p align="JUSTIFY"><span><span>COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL</span></span><span><span><sup><span><span><span><span><span><span><span><b>®</b></span></span></span></span></span></span></span></sup></span></span><span><span> API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB. </span></span></p>
+<p align="JUSTIFY"><span><span>LiveLink for MATLAB is available in both </span></span><span><span><b>EDU</b></span></span><span><span> and </span></span><span><span><b>COM</b></span></span><span><span> </span></span><span><span><b>variant</b></span></span><span><span> of the COMSOL release. On Anselm 1 commercial (</span></span><span><span><b>COM</b></span></span><span><span>) license and the 5 educational (</span></span><span><span><b>EDU</b></span></span><span><span>) licenses of LiveLink for MATLAB (please see the <a href="../isv_licenses.html" title="" target="_self" class="internal-link">ISV Licenses</a>) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.</span></span></p>
+<pre class="prettyprint lang-sh">$ xhost +<br />$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ncpus=16<br />$ module load matlab<br />$ module load comsol<br />$ comsol server matlab</pre>
+<p align="JUSTIFY"><span><span>At the first time to launch the LiveLink for MATLAB (client-MATLAB/server-COMSOL connection) the login and password is requested and this information is not requested again.</span></span></p>
+<p align="JUSTIFY"><span><span>To run LiveLink for MATLAB in batch mode with (comsol_matlab.pbs) job script you can utilize/modify the following script and execute it via the qsub command.</span></span></p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l select=3:ncpus=16<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -AÂ PROJECT_ID<br /><br />cd /scratch/$USER || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load matlab<br />module load comsol/43b-EDU<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/$USER &<br />cd /apps/engineering/comsol/comsol43b/mli<br />matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/$USER; test_job"</pre>
+<p>This example shows how to run Livelink for MATLAB with following configuration: 3 nodes and 16 cores per node. Working directory has to be created before submitting (comsol_matlab.pbs) job script into the queue. Input file (test_job.m) has to be in working directory or full path to input file has to be specified. The Matlab command option (-r ”mphstart”) created a connection with a COMSOL server using the default port number.<br /><br /></p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md b/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
index 0968326e9..e6729427d 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
@@ -198,11 +198,10 @@ matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/$USER; test_job"
```
This example shows how to run Livelink for MATLAB with following
-configuration3 nodes and 16 cores per node. Working directory has to
+configuration: 3 nodes and 16 cores per node. Working directory has to
be created before submitting (comsol_matlab.pbs) job script into the
queue. Input file (test_job.m) has to be in working directory or full
path to input file has to be specified. The Matlab command option (-r
”mphstart”) created a connection with a COMSOL server using the default
port number.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.1.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.1.html
new file mode 100644
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+ <div id="parent-fieldname-text-e5c6c8364e82439f88e2de1434687fba" class="">
+ <h2 class=" ">Introduction</h2>
+<p>We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations.<br />On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.</p>
+<h2 class=" ">Intel debugger</h2>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">X display</a> for running the GUI.</p>
+<pre class=" ">$ module load intel<br />$ idb</pre>
+<p>Read more at the <a href="intel-suite/intel-debugger.html" title="" target="_self" class="internal-link">Intel Debugger</a> page.</p>
+<h2 class=" ">Allinea Forge (DDT/MAP)</h2>
+<p>Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
+<pre class=" ">$ module load Forge<br />$ forge</pre>
+<p>Read more at the <a href="debuggers/allinea-ddt.html" title="" target="_self" class="internal-link">Allinea DDT</a> page.</p>
+<h2 class=" ">Allinea Performance Reports</h2>
+<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.</p>
+<pre class=" ">$ module load PerformanceReports/6.0 <br />$ perf-report mpirun -n 64 ./my_application argument01 argument02</pre>
+<p class=" ">Read more at the <a href="debuggers/allinea-performance-reports.html" title="" target="_self" class="internal-link">Allinea Performance Reports</a> page.</p>
+<h2 class=" ">RougeWave Totalview</h2>
+<p>TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.</p>
+<pre class=" ">$ module load totalview<br />$ totalview</pre>
+<p>Read more at the <a href="debuggers/total-view.html" title="" target="_self" class="internal-link">Totalview</a> page.</p>
+<h2 class=" ">Vampir trace analyzer</h2>
+<p>Vampir is a GUI trace analyzer for traces in OTF format.</p>
+<pre>$ module load Vampir/8.5.0<br />$ vampir</pre>
+<p>Read more at the <a href="../../salomon/software/debuggers/vampir.html" title="" target="_self" class="internal-link">Vampir</a> page.</p>
+
+ </div>
+
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.1.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.1.md
index da1f6c8fd..8649c1741 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.1.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.1.md
@@ -88,3 +88,7 @@ Vampir is a GUI trace analyzer for traces in OTF format.
Read more at
the [Vampir](../../salomon/software/debuggers/vampir.html) page.
+
+
+
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.html
new file mode 100644
index 000000000..c6e6e8a8f
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.html
@@ -0,0 +1,1244 @@
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+ <span id="breadcrumbs-current">Allinea Forge (DDT,MAP)</span>
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+ Allinea Forge (DDT,MAP)
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+ <p class=" ">Allinea Forge consist of two tools - debugger DDT and profiler MAP.</p>
+<p class=" ">Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
+<p class=" ">Allinea MAP is a profiler for C/C++/Fortran HPC codes. It is designed for profiling parallel code, which uses pthreads, OpenMP or MPI.</p>
+<h2 class=" ">License and Limitations for Anselm Users</h2>
+<p class=" ">On Anselm users can debug OpenMP or MPI code that runs up to 64 parallel processes. In case of debugging GPU or Xeon Phi accelerated codes the limit is 8 accelerators. These limitation means that:</p>
+<ul>
+<li>1 user can debug up 64 processes, or</li>
+<li>32 users can debug 2 processes, etc.</li>
+</ul>
+<p class=" ">In case of debugging on accelerators:</p>
+<ul>
+<li>1 user can debug on up to 8 accelerators, or </li>
+<li>8 users can debug on single accelerator. </li>
+</ul>
+<h2 class=" ">Compiling Code to run with DDT</h2>
+<h3 class=" ">Modules</h3>
+<p>Load all necessary modules to compile the code. For example:Â </p>
+<pre class=" ">$ module load intel<br />$ module load impi ... or ... module load openmpi/X.X.X-icc </pre>
+<p class=" ">Load the Allinea DDT module:</p>
+<pre class=" ">$ module load Forge</pre>
+<p>Compile the code:</p>
+<pre class="code-basic" style="text-align: start; ">$ mpicc -g -O0 -o test_debug test.c<br /><br />$ mpif90 -g -O0 -o test_debug test.f</pre>
+<p>Â </p>
+<h3 class=" ">Compiler flags</h3>
+<p>Before debugging, you need to compile your code with theses flags:</p>
+<p class="callout"><strong>-g</strong> : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.<br /><br /><strong>-O0</strong> : Suppress all optimizations.</p>
+<p>Â </p>
+<h2 class=" ">Starting a Job with DDT</h2>
+<p class=" ">Be sure to log in with an <span class="internal-link">X window forwarding</span> enabled. This could mean using the -X in the ssh: Â </p>
+<pre class=" ">$ ssh -X username@anselm.it4i.cz </pre>
+<p class=" ">Other options is to access login node using VNC. Please see the detailed information on how to <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">use graphic user interface on Anselm</a><span class="internal-link"></span>.</p>
+<p class=" ">From the login node an interactive session <strong>with X windows forwarding</strong> (-X option) can be started by following command:Â </p>
+<pre class=" ">$ qsub -I -X -A NONE-0-0 -q qexp -lselect=1:ncpus=16:mpiprocs=16,walltime=01:00:00Â </pre>
+<p class=" ">Then launch the debugger with the ddt command followed by the name of the executable to debug:</p>
+<pre class=" ">$ ddt test_debug</pre>
+<p class=" ">A<span style="text-align: start; "> submission window that appears have a prefilled path to the executable to debug. You can select the number of MPI processors and/or OpenMP threads on which to run and press run. Command line arguments to a program can be entered to the</span> "Arguments<span class="Apple-converted-space">" </span><span style="text-align: start; ">box.</span></p>
+<p class=" "><img src="ddt1.png" width="451" title="" class="image-inline" alt="" height="513" />Â </p>
+<p class=" ">To start the debugging directly without the submission window, user can specify the debugging and execution parameters from the command line. For example the number of MPI processes is set by option "-np 4". Skipping the dialog is done by "-start" option. To see the list of the "ddt" command line parameters, run "ddt --help". Â </p>
+<pre class=" ">ddt -start -np 4 ./hello_debug_impi</pre>
+<p class=" ">Â </p>
+<h2 class=" ">Documentation</h2>
+<p>Users can find original User Guide after loading the DDT module:Â </p>
+<pre class=" ">$DDTPATH/doc/userguide.pdf</pre>
+<p class=" ">Â </p>
+<p class=" ">Â </p>
+<p class=" ">Â [1] Discipline, Magic, Inspiration and Science: Best Practice Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May 10, 2013, <a class="external-link" href="https://computing.llnl.gov/tutorials/allineaDDT/index.html" target="_self" title="">link </a></p>
+<p class=" ">Â </p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
index bd376cfb2..1d1fbd6ce 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
@@ -49,7 +49,7 @@ Load the Allinea DDT module:
Compile the code:
-``` {.code-basic style="text-alignstart; "}
+```
$ mpicc -g -O0 -o test_debug test.c
$ mpif90 -g -O0 -o test_debug test.f
@@ -61,11 +61,11 @@ $ mpif90 -g -O0 -o test_debug test.f
Before debugging, you need to compile your code with theses flags:
-**-g** Generates extra debugging information usable by GDB. -g3
+**-g** : Generates extra debugging information usable by GDB. -g3
includes even more debugging information. This option is available for
GNU and INTEL C/C++ and Fortran compilers.
-**-O0** Suppress all optimizations.
+**-O0** : Suppress all optimizations.
Â
@@ -73,7 +73,7 @@ Starting a Job with DDT
-----------------------
Be sure to log in with an <span class="internal-link">X window
-forwarding</span> enabled. This could mean using the -X in the sshÂ
+forwarding</span> enabled. This could mean using the -X in the ssh: Â
$ ssh -X username@anselm.it4i.cz
@@ -92,12 +92,12 @@ the executable to debug:
$ ddt test_debug
-A<span style="text-alignstart; "> submission window that appears have
+A<span style="text-align: start; "> submission window that appears have
a prefilled path to the executable to debug. You can select the number
of MPI processors and/or OpenMP threads on which to run and press run.
Command line arguments to a program can be entered to the</span>
"Arguments<span class="Apple-converted-space">" </span><span
-style="text-alignstart; ">box.</span>
+style="text-align: start; ">box.</span>
Â
@@ -122,7 +122,7 @@ Users can find original User Guide after loading the DDT module:Â
Â
-Â [1] Discipline, Magic, Inspiration and ScienceBest Practice
+Â [1] Discipline, Magic, Inspiration and Science: Best Practice
Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May
10, 2013,
[link](https://computing.llnl.gov/tutorials/allineaDDT/index.html)
@@ -130,4 +130,3 @@ Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May
Â
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.html
new file mode 100644
index 000000000..46e2466e6
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.html
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+</div>
+ <div id="content-core">
+
+
+
+ <div id="parent-fieldname-text-3030efea5b9143d29ba7d053d7d94120" class="">
+ <h2 class=" ">Introduction</h2>
+<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs.</p>
+<p>The Allinea Performance Reports is most useful in profiling MPI programs.</p>
+<p>Our license is limited to 64 MPI processes.</p>
+<h2 class=" ">Modules</h2>
+<p>Allinea Performance Reports version 6.0 is available</p>
+<pre class=" ">$ module load PerformanceReports/6.0</pre>
+<p class=" ">The module sets up environment variables, required for using the Allinea Performance Reports. This particular command loads the default module, which is performance reports version 4.2.</p>
+<h2 class=" ">Usage</h2>
+<p class="callout">Use the the perf-report wrapper on your (MPI) program.</p>
+<p>Instead of <a href="../mpi-1.html" title="" target="_self" class="internal-link">running your MPI program the usual way</a>, use the the perf report wrapper:</p>
+<pre class=" ">$ perf-report mpirun ./mympiprog.x</pre>
+<p class=" ">The mpi program will run as usual. The perf-report creates two additional files, in *.txt and *.html format, containing the performance report. Note that <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_self" class="internal-link">demanding MPI codes should be run within the queue system</a>.</p>
+<h2 class=" ">Example</h2>
+<p class=" ">In this example, we will be profiling the mympiprog.x MPI program, using Allinea performance reports. Assume that the code is compiled with intel compilers and linked against intel MPI library:</p>
+<p class=" ">First, we allocate some nodes via the express queue:</p>
+<pre class=" ">$ qsub -q qexp -l select=2:ncpus=16:mpiprocs=16:ompthreads=1 -I<br />qsub: waiting for job 262197.dm2 to start<br />qsub: job 262197.dm2 ready</pre>
+<p class=" ">Then we load the modules and run the program the usual way:</p>
+<pre class=" ">$ module load intel impi allinea-perf-report/4.2<br />$ mpirun ./mympiprog.x</pre>
+<p class=" ">Now lets profile the code:</p>
+<pre class=" ">$ perf-report mpirun ./mympiprog.x</pre>
+<p class=" ">Performance report files <a href="mympiprog_32p_2014-10-15_16-56.txt" title="" target="_self" class="internal-link">mympiprog_32p*.txt</a> and <a href="mympiprog_32p_2014-10-15_16-56.html" title="" target="_self" class="internal-link">mympiprog_32p*.html</a> were created. We can see that the code is very efficient on MPI and is CPU bounded.</p>
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
index 68d752e51..5ea3709fa 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
@@ -57,8 +57,8 @@ compilers and linked against intel MPI library:
First, we allocate some nodes via the express queue:
$ qsub -q qexp -l select=2:ncpus=16:mpiprocs=16:ompthreads=1 -I
- qsubwaiting for job 262197.dm2 to start
- qsubjob 262197.dm2 ready
+ qsub: waiting for job 262197.dm2 to start
+ qsub: job 262197.dm2 ready
Then we load the modules and run the program the usual way:
@@ -75,4 +75,3 @@ and
[mympiprog_32p*.html](mympiprog_32p_2014-10-15_16-56.html)
were created. We can see that the code is very efficient on MPI and is
CPU bounded.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.html
new file mode 100644
index 000000000..f51111c95
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.html
@@ -0,0 +1,1223 @@
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+ <h2 class=" ">Introduction</h2>
+<p class=" ">CUBE is a graphical performance report explorer for displaying data from Score-P and Scalasca (and other compatible tools). The name comes from the fact that it displays performance data in a three-dimensions :</p>
+<ul>
+<li><strong>performance metric</strong>, where a number of metrics are available, such as communication time or cache misses,</li>
+<li><strong>call path</strong>, which contains the call tree of your program</li>
+<li>s<strong>ystem resource</strong>, which contains system's nodes, processes and threads, depending on the parallel programming model.</li>
+</ul>
+<div>Each dimension is organized in a tree, for example the time performance metric is divided into Execution time and Overhead time, call path dimension is organized by files and routines in your source code etc.</div>
+<div></div>
+<div><img alt="CUBE Screenshot" src="Snmekobrazovky20141204v12.56.36.png" title="CUBE Screenshot" class="image-inline" /></div>
+<p class=" " style="text-align: center; "><em>Figure 1. Screenshot of CUBE displaying data from Scalasca.</em></p>
+<p class=" " style="text-align: left; "><em><br /></em>Each node in the tree is colored by severity (the color scheme is displayed at the bottom of the window, ranging from the least severe blue to the most severe being red). For example in Figure 1, we can see that most of the point-to-point MPI communication happens in routine exch_qbc, colored red.</p>
+<h2 class=" ">Installed versions</h2>
+<p>Currently, there are two versions of CUBE 4.2.3 available as <a href="../../environment-and-modules.html" title="" target="_self" class="internal-link">modules</a> :</p>
+<ul>
+<li>
+<p class="p1"><span class="s1"><span class="monospace">cube/4.2.3-gcc</span>, compiled with GCC</span></p>
+</li>
+<li>
+<p class="p1"><span class="s1"><span class="monospace">cube/4.2.3-icc</span>, compiled with Intel compiler</span></p>
+</li>
+</ul>
+<h2 class=" ">Usage</h2>
+<p>CUBE is a graphical application. Refer to <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">Graphical User Interface documentation</a> for a list of methods to launch graphical applications on Anselm.</p>
+<p class="exclamation">Analyzing large data sets can consume large amount of CPU and RAM. Do not perform large analysis on login nodes.</p>
+<p class=" ">After loading the apropriate module, simply launch <span class="monospace">cube</span> command, or alternatively you can use <span class="monospace">scalasca -examine</span> command to launch the GUI. Note that for Scalasca datasets, if you do not analyze the data with <span><span class="monospace">scalasca -examine </span></span>before to opening them with CUBE, not all performance data will be available.</p>
+<p class=" ">Â <span>References</span></p>
+<ol>
+<li><a class="external-link" href="http://www.scalasca.org/software/cube-4.x/download.html" target="_self" title="">http://www.scalasca.org/software/cube-4.x/download.html</a></li>
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1. <http://www.scalasca.org/software/cube-4.x/download.html>
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+ <h2 class=" ">Introduction</h2>
+<p>Intel PCM (Performance Counter Monitor) is a tool to monitor performance hardware counters on Intel<span>®</span> processors, similar to <a href="papi.html" title="" target="_self" class="internal-link">PAPI</a>. The difference between PCM and PAPI is that PCM supports only Intel hardware, but PCM can monitor also uncore metrics, like memory controllers and <span>QuickPath Interconnect links.</span></p>
+<h2 class=" "><span>Installed version</span></h2>
+<p>Currently installed version 2.6. To load the <a href="../../environment-and-modules.html" title="" target="_self" class="internal-link">module</a>, issue :</p>
+<pre class=" ">$ module load intelpcm</pre>
+<h2 class=" ">Command line tools</h2>
+<p>PCM provides a set of tools to monitor system/or application. </p>
+<h3 class=" ">pcm-memory</h3>
+<p>Measures memory bandwidth of your application or the whole system. Usage:</p>
+<pre class=" "><span class="s1">$ pcm-memory.x <delay>|[external_program parameters]</span></pre>
+<p>Specify either a delay of updates in seconds or an external program to monitor. If you get an error about PMU in use, respond "y" and relaunch the program.</p>
+<p>Sample output:</p>
+<pre>---------------------------------------||---------------------------------------
+-- Socket 0 --||-- Socket 1 --
+---------------------------------------||---------------------------------------
+---------------------------------------||---------------------------------------
+---------------------------------------||---------------------------------------
+-- Memory Performance Monitoring --||-- Memory Performance Monitoring --
+---------------------------------------||---------------------------------------
+-- Mem Ch 0: Reads (MB/s): 2.44 --||-- Mem Ch 0: Reads (MB/s): 0.26 --
+-- Writes(MB/s): 2.16 --||-- Writes(MB/s): 0.08 --
+-- Mem Ch 1: Reads (MB/s): 0.35 --||-- Mem Ch 1: Reads (MB/s): 0.78 --
+-- Writes(MB/s): 0.13 --||-- Writes(MB/s): 0.65 --
+-- Mem Ch 2: Reads (MB/s): 0.32 --||-- Mem Ch 2: Reads (MB/s): 0.21 --
+-- Writes(MB/s): 0.12 --||-- Writes(MB/s): 0.07 --
+-- Mem Ch 3: Reads (MB/s): 0.36 --||-- Mem Ch 3: Reads (MB/s): 0.20 --
+-- Writes(MB/s): 0.13 --||-- Writes(MB/s): 0.07 --
+-- NODE0 Mem Read (MB/s): 3.47 --||-- NODE1 Mem Read (MB/s): 1.45 --
+-- NODE0 Mem Write (MB/s): 2.55 --||-- NODE1 Mem Write (MB/s): 0.88 --
+-- NODE0 P. Write (T/s) : 31506 --||-- NODE1 P. Write (T/s): 9099 --
+-- NODE0 Memory (MB/s): 6.02 --||-- NODE1 Memory (MB/s): 2.33 --
+---------------------------------------||---------------------------------------
+-- System Read Throughput(MB/s): 4.93 --
+-- System Write Throughput(MB/s): 3.43 --
+-- System Memory Throughput(MB/s): 8.35 --
+---------------------------------------||---------------------------------------Â </pre>
+<h3 class=" ">pcm-msr</h3>
+<p>Command <span class="monospace">pcm-msr.x</span> can be used to read/write model specific registers of the CPU.</p>
+<h3 class=" ">pcm-numa</h3>
+<p>NUMA monitoring utility does not work on Anselm.</p>
+<h3 class=" ">pcm-pcie</h3>
+<p>Can be used to monitor PCI Express bandwith. Usage: <span class="monospace">pcm-pcie.x <delay></span></p>
+<h3>pcm-power</h3>
+<p>Displays energy usage and thermal headroom for CPU and DRAM sockets. Usage:Â <span>Â </span><span class="monospace">pcm-power.x <delay> | <external program></span></p>
+<h3 class=" ">pcm</h3>
+<p>This command provides an overview of performance counters and memory usage. <span>Usage: </span><span> </span><span class="monospace">pcm.x <delay> | <external program></span></p>
+<p class=" ">Sample output :</p>
+<pre>$ pcm.x ./matrix
+
+ Intel(r) Performance Counter Monitor V2.6 (2013-11-04 13:43:31 +0100 ID=db05e43)
+
+ Copyright (c) 2009-2013 Intel Corporation
+
+Number of physical cores: 16
+Number of logical cores: 16
+Threads (logical cores) per physical core: 1
+Num sockets: 2
+Core PMU (perfmon) version: 3
+Number of core PMU generic (programmable) counters: 8
+Width of generic (programmable) counters: 48 bits
+Number of core PMU fixed counters: 3
+Width of fixed counters: 48 bits
+Nominal core frequency: 2400000000 Hz
+Package thermal spec power: 115 Watt; Package minimum power: 51 Watt; Package maximum power: 180 Watt;
+Socket 0: 1 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
+Socket 1: 1 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
+Number of PCM instances: 2
+Max QPI link speed: 16.0 GBytes/second (8.0 GT/second)
+
+Detected Intel(R) Xeon(R) CPU E5-2665 0 @ 2.40GHz "Intel(r) microarchitecture codename Sandy Bridge-EP/Jaketown"
+
+ Executing "./matrix" command:
+
+Exit code: 0
+
+
+ EXEC : instructions per nominal CPU cycle
+ IPC : instructions per CPU cycle
+ FREQ : relation to nominal CPU frequency='unhalted clock ticks'/'invariant timer ticks' (includes Intel Turbo Boost)
+ AFREQ : relation to nominal CPU frequency while in active state (not in power-saving C state)='unhalted clock ticks'/'invariant timer ticks while in C0-state' (includes Intel Turbo Boost)
+ L3MISS: L3 cache misses
+ L2MISS: L2 cache misses (including other core's L2 cache *hits*)
+ L3HIT : L3 cache hit ratio (0.00-1.00)
+ L2HIT : L2 cache hit ratio (0.00-1.00)
+ L3CLK : ratio of CPU cycles lost due to L3 cache misses (0.00-1.00), in some cases could be >1.0 due to a higher memory latency
+ L2CLK : ratio of CPU cycles lost due to missing L2 cache but still hitting L3 cache (0.00-1.00)
+ READ : bytes read from memory controller (in GBytes)
+ WRITE : bytes written to memory controller (in GBytes)
+ TEMP : Temperature reading in 1 degree Celsius relative to the TjMax temperature (thermal headroom): 0 corresponds to the max temperature
+
+
+ Core (SKT) | EXEC | IPC | FREQ | AFREQ | L3MISS | L2MISS | L3HIT | L2HIT | L3CLK | L2CLK | READ | WRITE | TEMP
+
+ 0 0 0.00 0.64 0.01 0.80 5592 11 K 0.49 0.13 0.32 0.06 N/A N/A 67
+ 1 0 0.00 0.18 0.00 0.69 3086 5552 0.44 0.07 0.48 0.08 N/A N/A 68
+ 2 0 0.00 0.23 0.00 0.81 300 562 0.47 0.06 0.43 0.08 N/A N/A 67
+ 3 0 0.00 0.21 0.00 0.99 437 862 0.49 0.06 0.44 0.09 N/A N/A 73
+ 4 0 0.00 0.23 0.00 0.93 293 559 0.48 0.07 0.42 0.09 N/A N/A 73
+ 5 0 0.00 0.21 0.00 1.00 423 849 0.50 0.06 0.43 0.10 N/A N/A 69
+ 6 0 0.00 0.23 0.00 0.94 285 558 0.49 0.06 0.41 0.09 N/A N/A 71
+ 7 0 0.00 0.18 0.00 0.81 674 1130 0.40 0.05 0.53 0.08 N/A N/A 65
+ 8 1 0.00 0.47 0.01 1.26 6371 13 K 0.51 0.35 0.31 0.07 N/A N/A 64
+ 9 1 2.30 1.80 1.28 1.29 179 K 15 M 0.99 0.59 0.04 0.71 N/A N/A 60
+ 10 1 0.00 0.22 0.00 1.26 315 570 0.45 0.06 0.43 0.08 N/A N/A 67
+ 11 1 0.00 0.23 0.00 0.74 321 579 0.45 0.05 0.45 0.07 N/A N/A 66
+ 12 1 0.00 0.22 0.00 1.25 305 570 0.46 0.05 0.42 0.07 N/A N/A 68
+ 13 1 0.00 0.22 0.00 1.26 336 581 0.42 0.04 0.44 0.06 N/A N/A 69
+ 14 1 0.00 0.22 0.00 1.25 314 565 0.44 0.06 0.43 0.07 N/A N/A 69
+ 15 1 0.00 0.29 0.00 1.19 2815 6926 0.59 0.39 0.29 0.08 N/A N/A 69
+-------------------------------------------------------------------------------------------------------------------
+ SKT 0 0.00 0.46 0.00 0.79 11 K 21 K 0.47 0.10 0.38 0.07 0.00 0.00 65
+ SKT 1 0.29 1.79 0.16 1.29 190 K 15 M 0.99 0.59 0.05 0.70 0.01 0.01 61
+-------------------------------------------------------------------------------------------------------------------
+ TOTAL * 0.14 1.78 0.08 1.28 201 K 15 M 0.99 0.59 0.05 0.70 0.01 0.01 N/A
+
+ Instructions retired: 1345 M ; Active cycles: 755 M ; Time (TSC): 582 Mticks ; C0 (active,non-halted) core residency: 6.30 %
+
+ C1 core residency: 0.14 %; C3 core residency: 0.20 %; C6 core residency: 0.00 %; C7 core residency: 93.36 %;
+ C2 package residency: 48.81 %; C3 package residency: 0.00 %; C6 package residency: 0.00 %; C7 package residency: 0.00 %;
+
+ PHYSICAL CORE IPC : 1.78 => corresponds to 44.50 % utilization for cores in active state
+ Instructions per nominal CPU cycle: 0.14 => corresponds to 3.60 % core utilization over time interval
+
+Intel(r) QPI data traffic estimation in bytes (data traffic coming to CPU/socket through QPI links):
+
+ QPI0 QPI1 | QPI0 QPI1
+----------------------------------------------------------------------------------------------
+ SKT 0 0 0 | 0% 0%
+ SKT 1 0 0 | 0% 0%
+----------------------------------------------------------------------------------------------
+Total QPI incoming data traffic: 0 QPI data traffic/Memory controller traffic: 0.00
+
+Intel(r) QPI traffic estimation in bytes (data and non-data traffic outgoing from CPU/socket through QPI links):
+
+ QPI0 QPI1 | QPI0 QPI1
+----------------------------------------------------------------------------------------------
+ SKT 0 0 0 | 0% 0%
+ SKT 1 0 0 | 0% 0%
+----------------------------------------------------------------------------------------------
+Total QPI outgoing data and non-data traffic: 0
+
+----------------------------------------------------------------------------------------------
+ SKT 0 package consumed 4.06 Joules
+ SKT 1 package consumed 9.40 Joules
+----------------------------------------------------------------------------------------------
+ TOTAL: 13.46 Joules
+
+----------------------------------------------------------------------------------------------
+ SKT 0 DIMMs consumed 4.18 Joules
+ SKT 1 DIMMs consumed 4.28 Joules
+----------------------------------------------------------------------------------------------
+ TOTAL: 8.47 Joules
+Cleaning up
+</pre>
+<p class=" ">Â </p>
+<h3 class=" ">pcm-sensor</h3>
+<p>Can be used as a sensor for ksysguard GUI, which is currently not installed on Anselm. </p>
+<h2 class=" ">API</h2>
+<p>In a similar fashion to PAPI, PCM provides a C++ API to access the performance counter from within your application. Refer to the <a class="external-link" href="http://intel-pcm-api-documentation.github.io/classPCM.html" target="_self" title="">doxygen documentation</a> for details of the API.</p>
+<p class="exclamation">Due to security limitations, using PCM API to monitor your applications is currently not possible on Anselm. (The application must be run as root user)</p>
+<p class=" ">Sample program using the API :</p>
+<pre>#include <stdlib.h>
+#include <stdio.h>
+#include "cpucounters.h"
+
+#define SIZE 1000
+
+using namespace std;
+
+int main(int argc, char **argv) {
+ float matrixa[SIZE][SIZE], matrixb[SIZE][SIZE], mresult[SIZE][SIZE];
+ float real_time, proc_time, mflops;
+ long long flpins;
+ int retval;
+ int i,j,k;
+
+ PCM * m = PCM::getInstance();
+
+ if (m->program() != PCM::Success) return 1;
+
+ SystemCounterState before_sstate = getSystemCounterState();
+
+ /* Initialize the Matrix arrays */
+ for ( i=0; i<SIZE*SIZE; i++ ){
+ mresult[0][i] = 0.0;
+ matrixa[0][i] = matrixb[0][i] = rand()*(float)1.1; }
+
+ /* A naive Matrix-Matrix multiplication */
+ for (i=0;i<SIZE;i++)
+ for(j=0;j<SIZE;j++)
+ for(k=0;k<SIZE;k++)
+ mresult[i][j]=mresult[i][j] + matrixa[i][k]*matrixb[k][j];
+
+ SystemCounterState after_sstate = getSystemCounterState();
+
+ cout << "Instructions per clock:" << getIPC(before_sstate,after_sstate)
+ << "L3 cache hit ratio:" << getL3CacheHitRatio(before_sstate,after_sstate)
+ << "Bytes read:" << getBytesReadFromMC(before_sstate,after_sstate);
+
+ for (i=0; i<SIZE;i++)
+ for (j=0; j<SIZE; j++)
+ if (mresult[i][j] == -1) printf("x");
+
+ return 0;
+}
+
+</pre>
+<p class=" ">Compile it with :</p>
+<pre class=" "><span class="s1">$ icc matrix.cpp -o matrix -lpthread -lpcm</span></pre>
+<p class=" ">Sample output :Â </p>
+<pre class=" ">$ ./matrix<br />Number of physical cores: 16
+Number of logical cores: 16
+Threads (logical cores) per physical core: 1
+Num sockets: 2
+Core PMU (perfmon) version: 3
+Number of core PMU generic (programmable) counters: 8
+Width of generic (programmable) counters: 48 bits
+Number of core PMU fixed counters: 3
+Width of fixed counters: 48 bits
+Nominal core frequency: 2400000000 Hz
+Package thermal spec power: 115 Watt; Package minimum power: 51 Watt; Package maximum power: 180 Watt;
+Socket 0: 1 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
+Socket 1: 1 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
+Number of PCM instances: 2
+Max QPI link speed: 16.0 GBytes/second (8.0 GT/second)
+Instructions per clock:1.7<br />L3 cache hit ratio:1.0<br />Bytes read:12513408</pre>
+<h2 class=" ">References</h2>
+<ol>
+<li><a class="external-link" href="https://software.intel.com/en-us/articles/intel-performance-counter-monitor-a-better-way-to-measure-cpu-utilization" target="_self" title="">https://software.intel.com/en-us/articles/intel-performance-counter-monitor-a-better-way-to-measure-cpu-utilization</a></li>
+<li><a class="external-link" href="https://software.intel.com/sites/default/files/m/3/2/2/xeon-e5-2600-uncore-guide.pdf" target="_self" title="">https://software.intel.com/sites/default/files/m/3/2/2/xeon-e5-2600-uncore-guide.pdf</a> Intel® Xeon® Processor E5-2600 Product Family Uncore Performance Monitoring Guide.</li>
+<li><a class="external-link" href="http://intel-pcm-api-documentation.github.io/classPCM.html" target="_self" title="">http://intel-pcm-api-documentation.github.io/classPCM.html</a>Â API Documentation</li>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
index 008ec7ceb..8e1e391a1 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
@@ -44,22 +44,22 @@ Sample output:
---------------------------------------||---------------------------------------
-- Memory Performance Monitoring --||-- Memory Performance Monitoring --
---------------------------------------||---------------------------------------
- -- Mem Ch 0Reads (MB/s) 2.44 --||-- Mem Ch 0Reads (MB/s) 0.26 --
- -- Writes(MB/s) 2.16 --||-- Writes(MB/s) 0.08 --
- -- Mem Ch 1Reads (MB/s) 0.35 --||-- Mem Ch 1Reads (MB/s) 0.78 --
- -- Writes(MB/s) 0.13 --||-- Writes(MB/s) 0.65 --
- -- Mem Ch 2Reads (MB/s) 0.32 --||-- Mem Ch 2Reads (MB/s) 0.21 --
- -- Writes(MB/s) 0.12 --||-- Writes(MB/s) 0.07 --
- -- Mem Ch 3Reads (MB/s) 0.36 --||-- Mem Ch 3Reads (MB/s) 0.20 --
- -- Writes(MB/s) 0.13 --||-- Writes(MB/s) 0.07 --
- -- NODE0 Mem Read (MB/s) 3.47 --||-- NODE1 Mem Read (MB/s) 1.45 --
- -- NODE0 Mem Write (MB/s) 2.55 --||-- NODE1 Mem Write (MB/s) 0.88 --
- -- NODE0 P. Write (T/s) 31506 --||-- NODE1 P. Write (T/s) 9099 --
- -- NODE0 Memory (MB/s) 6.02 --||-- NODE1 Memory (MB/s) 2.33 --
+ -- Mem Ch 0: Reads (MB/s): 2.44 --||-- Mem Ch 0: Reads (MB/s): 0.26 --
+ -- Writes(MB/s): 2.16 --||-- Writes(MB/s): 0.08 --
+ -- Mem Ch 1: Reads (MB/s): 0.35 --||-- Mem Ch 1: Reads (MB/s): 0.78 --
+ -- Writes(MB/s): 0.13 --||-- Writes(MB/s): 0.65 --
+ -- Mem Ch 2: Reads (MB/s): 0.32 --||-- Mem Ch 2: Reads (MB/s): 0.21 --
+ -- Writes(MB/s): 0.12 --||-- Writes(MB/s): 0.07 --
+ -- Mem Ch 3: Reads (MB/s): 0.36 --||-- Mem Ch 3: Reads (MB/s): 0.20 --
+ -- Writes(MB/s): 0.13 --||-- Writes(MB/s): 0.07 --
+ -- NODE0 Mem Read (MB/s): 3.47 --||-- NODE1 Mem Read (MB/s): 1.45 --
+ -- NODE0 Mem Write (MB/s): 2.55 --||-- NODE1 Mem Write (MB/s): 0.88 --
+ -- NODE0 P. Write (T/s) : 31506 --||-- NODE1 P. Write (T/s): 9099 --
+ -- NODE0 Memory (MB/s): 6.02 --||-- NODE1 Memory (MB/s): 2.33 --
---------------------------------------||---------------------------------------
- -- System Read Throughput(MB/s) 4.93 --
- -- System Write Throughput(MB/s) 3.43 --
- -- System Memory Throughput(MB/s) 8.35 --
+ -- System Read Throughput(MB/s): 4.93 --
+ -- System Write Throughput(MB/s): 3.43 --
+ -- System Memory Throughput(MB/s): 8.35 --
---------------------------------------||---------------------------------------Â
### pcm-msr
@@ -73,7 +73,7 @@ NUMA monitoring utility does not work on Anselm.
### pcm-pcie
-Can be used to monitor PCI Express bandwith. Usage<span
+Can be used to monitor PCI Express bandwith. Usage: <span
class="monospace">pcm-pcie.x <delay></span>
### pcm-power
@@ -96,42 +96,42 @@ Sample output :
Copyright (c) 2009-2013 Intel Corporation
- Number of physical cores16
- Number of logical cores16
- Threads (logical cores) per physical core1
- Num sockets2
- Core PMU (perfmon) version3
- Number of core PMU generic (programmable) counters8
- Width of generic (programmable) counters48 bits
- Number of core PMU fixed counters3
- Width of fixed counters48 bits
- Nominal core frequency2400000000 Hz
- Package thermal spec power115 Watt; Package minimum power51 Watt; Package maximum power180 Watt;
- Socket 01 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
- Socket 11 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
- Number of PCM instances2
- Max QPI link speed16.0 GBytes/second (8.0 GT/second)
+ Number of physical cores: 16
+ Number of logical cores: 16
+ Threads (logical cores) per physical core: 1
+ Num sockets: 2
+ Core PMU (perfmon) version: 3
+ Number of core PMU generic (programmable) counters: 8
+ Width of generic (programmable) counters: 48 bits
+ Number of core PMU fixed counters: 3
+ Width of fixed counters: 48 bits
+ Nominal core frequency: 2400000000 Hz
+ Package thermal spec power: 115 Watt; Package minimum power: 51 Watt; Package maximum power: 180 Watt;
+ Socket 0: 1 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
+ Socket 1: 1 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
+ Number of PCM instances: 2
+ Max QPI link speed: 16.0 GBytes/second (8.0 GT/second)
Detected Intel(R) Xeon(R) CPU E5-2665 0 @ 2.40GHz "Intel(r) microarchitecture codename Sandy Bridge-EP/Jaketown"
Executing "./matrix" command:
- Exit code0
+ Exit code: 0
- EXEC instructions per nominal CPU cycle
- IPC instructions per CPU cycle
- FREQ relation to nominal CPU frequency='unhalted clock ticks'/'invariant timer ticks' (includes Intel Turbo Boost)
- AFREQ relation to nominal CPU frequency while in active state (not in power-saving C state)='unhalted clock ticks'/'invariant timer ticks while in C0-state' (includes Intel Turbo Boost)
- L3MISSL3 cache misses
- L2MISSL2 cache misses (including other core's L2 cache *hits*)
- L3HIT L3 cache hit ratio (0.00-1.00)
- L2HIT L2 cache hit ratio (0.00-1.00)
- L3CLK ratio of CPU cycles lost due to L3 cache misses (0.00-1.00), in some cases could be >1.0 due to a higher memory latency
- L2CLK ratio of CPU cycles lost due to missing L2 cache but still hitting L3 cache (0.00-1.00)
- READ bytes read from memory controller (in GBytes)
- WRITE bytes written to memory controller (in GBytes)
- TEMP Temperature reading in 1 degree Celsius relative to the TjMax temperature (thermal headroom)0 corresponds to the max temperature
+ EXEC : instructions per nominal CPU cycle
+ IPC : instructions per CPU cycle
+ FREQ : relation to nominal CPU frequency='unhalted clock ticks'/'invariant timer ticks' (includes Intel Turbo Boost)
+ AFREQ : relation to nominal CPU frequency while in active state (not in power-saving C state)='unhalted clock ticks'/'invariant timer ticks while in C0-state' (includes Intel Turbo Boost)
+ L3MISS: L3 cache misses
+ L2MISS: L2 cache misses (including other core's L2 cache *hits*)
+ L3HIT : L3 cache hit ratio (0.00-1.00)
+ L2HIT : L2 cache hit ratio (0.00-1.00)
+ L3CLK : ratio of CPU cycles lost due to L3 cache misses (0.00-1.00), in some cases could be >1.0 due to a higher memory latency
+ L2CLK : ratio of CPU cycles lost due to missing L2 cache but still hitting L3 cache (0.00-1.00)
+ READ : bytes read from memory controller (in GBytes)
+ WRITE : bytes written to memory controller (in GBytes)
+ TEMP : Temperature reading in 1 degree Celsius relative to the TjMax temperature (thermal headroom): 0 corresponds to the max temperature
Core (SKT) | EXEC | IPC | FREQ | AFREQ | L3MISS | L2MISS | L3HIT | L2HIT | L3CLK | L2CLK | READ | WRITE | TEMP
@@ -158,13 +158,13 @@ Sample output :
-------------------------------------------------------------------------------------------------------------------
TOTAL * 0.14 1.78 0.08 1.28 201 K 15 M 0.99 0.59 0.05 0.70 0.01 0.01 N/A
- Instructions retired1345 M ; Active cycles 755 M ; Time (TSC) 582 Mticks ; C0 (active,non-halted) core residency6.30 %
+ Instructions retired: 1345 M ; Active cycles: 755 M ; Time (TSC): 582 Mticks ; C0 (active,non-halted) core residency: 6.30 %
- C1 core residency0.14 %; C3 core residency0.20 %; C6 core residency0.00 %; C7 core residency93.36 %;
- C2 package residency48.81 %; C3 package residency0.00 %; C6 package residency0.00 %; C7 package residency0.00 %;
+ C1 core residency: 0.14 %; C3 core residency: 0.20 %; C6 core residency: 0.00 %; C7 core residency: 93.36 %;
+ C2 package residency: 48.81 %; C3 package residency: 0.00 %; C6 package residency: 0.00 %; C7 package residency: 0.00 %;
- PHYSICAL CORE IPC 1.78 => corresponds to 44.50 % utilization for cores in active state
- Instructions per nominal CPU cycle0.14 => corresponds to 3.60 % core utilization over time interval
+ PHYSICAL CORE IPC : 1.78 => corresponds to 44.50 % utilization for cores in active state
+ Instructions per nominal CPU cycle: 0.14 => corresponds to 3.60 % core utilization over time interval
Intel(r) QPI data traffic estimation in bytes (data traffic coming to CPU/socket through QPI links):
@@ -173,7 +173,7 @@ Sample output :
SKT 0 0 0 | 0% 0%
SKT 1 0 0 | 0% 0%
----------------------------------------------------------------------------------------------
- Total QPI incoming data traffic 0 QPI data traffic/Memory controller traffic0.00
+ Total QPI incoming data traffic: 0 QPI data traffic/Memory controller traffic: 0.00
Intel(r) QPI traffic estimation in bytes (data and non-data traffic outgoing from CPU/socket through QPI links):
@@ -182,19 +182,19 @@ Sample output :
SKT 0 0 0 | 0% 0%
SKT 1 0 0 | 0% 0%
----------------------------------------------------------------------------------------------
- Total QPI outgoing data and non-data traffic 0
+ Total QPI outgoing data and non-data traffic: 0
----------------------------------------------------------------------------------------------
SKT 0 package consumed 4.06 Joules
SKT 1 package consumed 9.40 Joules
----------------------------------------------------------------------------------------------
- TOTAL 13.46 Joules
+ TOTAL: 13.46 Joules
----------------------------------------------------------------------------------------------
SKT 0 DIMMs consumed 4.18 Joules
SKT 1 DIMMs consumed 4.28 Joules
----------------------------------------------------------------------------------------------
- TOTAL 8.47 Joules
+ TOTAL: 8.47 Joules
Cleaning up
Â
@@ -270,21 +270,21 @@ Compile it with :
Sample output :Â
$ ./matrix
- Number of physical cores16
- Number of logical cores16
- Threads (logical cores) per physical core1
- Num sockets2
- Core PMU (perfmon) version3
- Number of core PMU generic (programmable) counters8
- Width of generic (programmable) counters48 bits
- Number of core PMU fixed counters3
- Width of fixed counters48 bits
- Nominal core frequency2400000000 Hz
- Package thermal spec power115 Watt; Package minimum power51 Watt; Package maximum power180 Watt;
- Socket 01 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
- Socket 11 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
- Number of PCM instances2
- Max QPI link speed16.0 GBytes/second (8.0 GT/second)
+ Number of physical cores: 16
+ Number of logical cores: 16
+ Threads (logical cores) per physical core: 1
+ Num sockets: 2
+ Core PMU (perfmon) version: 3
+ Number of core PMU generic (programmable) counters: 8
+ Width of generic (programmable) counters: 48 bits
+ Number of core PMU fixed counters: 3
+ Width of fixed counters: 48 bits
+ Nominal core frequency: 2400000000 Hz
+ Package thermal spec power: 115 Watt; Package minimum power: 51 Watt; Package maximum power: 180 Watt;
+ Socket 0: 1 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
+ Socket 1: 1 memory controllers detected with total number of 4 channels. 2 QPI ports detected.
+ Number of PCM instances: 2
+ Max QPI link speed: 16.0 GBytes/second (8.0 GT/second)
Instructions per clock:1.7
L3 cache hit ratio:1.0
Bytes read:12513408
@@ -300,4 +300,3 @@ References
Documentation
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.html
new file mode 100644
index 000000000..1e1370329
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.html
@@ -0,0 +1,1233 @@
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+ Intel VTune Amplifier
+ </h1>
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+ <h2 class=" ">Introduction</h2>
+<p>Intel<em>® </em>VTune™ <span>Amplifier, part of Intel Parallel studio, is a GUI profiling tool designed for Intel processors. It offers a graphical performance analysis of single core and multithreaded applications. A highlight of the features:</span></p>
+<ul>
+<li>Hotspot analysis</li>
+<li>Locks and waits analysis</li>
+<li>Low level specific counters, such as branch analysis and memory bandwidth</li>
+<li>Power usage analysis - frequency and sleep states.</li>
+</ul>
+<div></div>
+<div><img alt="screenshot" src="vtune-amplifier/@@images/3d4533af-8ce5-4aed-9bac-09fbbcd2650a.png" title="VTune Amplifier" class="image-inline" /></div>
+<h2 class=" ">Usage</h2>
+<p>To launch the GUI, first load the module:</p>
+<pre class=" "><span class="s1">$ module add VTune/2016_update1</span></pre>
+<p class=" "><span class="s1">and launch the GUI :</span></p>
+<pre class=" "><span class="s1">$Â </span><span>amplxe-gui</span></pre>
+<p class="exclamation"><span>To profile an application with VTune Amplifier, special kernel modules need to be loaded. The modules are not loaded on Anselm login nodes, thus direct profiling on login nodes is not possible. Use VTune on compute nodes and refer to the documentation on <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">using GUI applications</a>.</span></p>
+<p class=" "><span>The GUI will open in new window. Click on "<em>New Project...</em>" to create a new project. After clicking <em>OK</em>, a new window with project properties will appear. Â At "<em>Application:</em>", select the bath to your binary you want to profile (the binary should be compiled with -g flag). Some additional options such as command line arguments can be selected. At "<em>Managed code profiling mode:</em>" select "<em>Native</em>" (unless you want to profile managed mode .NET/Mono applications). After clicking <em>OK</em>, your project is created.</span></p>
+<p class=" ">To run a new analysis, click "<em>New analysis...</em>". You will see a list of possible analysis. Some of them will not be possible on the current CPU (eg. Intel Atom analysis is not possible on Sandy Bridge CPU), the GUI will show an error box if you select the wrong analysis. For example, select "<em>Advanced Hotspots</em>". Clicking on <em>Start </em>will start profiling of the application.</p>
+<h2 class=" ">Remote Analysis</h2>
+<p>VTune Amplifier also allows a form of remote analysis. In this mode, data for analysis is collected from the command line without GUI, and the results are then loaded to GUI on another machine. This allows profiling without interactive graphical jobs. To perform a remote analysis, launch a GUI somewhere, open the new analysis window and then click the button "<em>Command line</em>" in bottom right corner. It will show the command line needed to perform the selected analysis.</p>
+<p>The command line will look like this:</p>
+<pre class=" ">/apps/all/VTune/2016_update1/vtune_amplifier_xe_2016.1.1.434111/bin64/amplxe-cl -collect advanced-hotspots -knob collection-detail=stack-and-callcount -mrte-mode=native -target-duration-type=veryshort -app-working-dir /home/sta545/test -- /home/sta545/test_pgsesv</pre>
+<p>Copy the line to clipboard and then you can paste it in your jobscript or in command line. After the collection is run, open the GUI once again, click the menu button in the upper right corner, and select "<em>Open > Result...</em>". The GUI will load the results from the run.</p>
+<h2 class=" ">Xeon Phi</h2>
+<p class="exclamation">This section is outdated. It will be updated with new information soon.</p>
+<p>It is possible to analyze both native and offload Xeon Phi applications. For offload mode, just specify the path to the binary. For native mode, you need to specify in project properties:</p>
+<p>Application: <span class="monospace">ssh</span></p>
+<p>Application parameters: <span class="monospace">mic0 source ~/.profile && /path/to/your/bin</span></p>
+<p class=" ">Note that we include <span class="monospace">source ~/.profile </span>in the command to setup environment paths <a href="../intel-xeon-phi.html" title="" target="_self" class="internal-link">as described here</a>. </p>
+<p class="exclamation">If the analysis is interrupted or aborted, further analysis on the card might be impossible and you will get errors like "ERROR connecting to MIC card". In this case please contact our support to reboot the MIC card.</p>
+<p class=" ">You may also use remote analysis to collect data from the MIC and then analyze it in the GUI later :</p>
+<pre class=" ">$ amplxe-cl -collect knc-hotspots -no-auto-finalize -- ssh mic0<br />"export LD_LIBRARY_PATH=/apps/intel/composer_xe_2015.2.164/compiler/lib/mic/:/apps/intel/composer_xe_2015.2.164/mkl/lib/mic/; export KMP_AFFINITY=compact; /tmp/app.mic"</pre>
+<h2 class=" ">References</h2>
+<ol>
+<li><span><a class="external-link" href="https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf" target="_self" title="">https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf</a> Performance Tuning for Intel® Xeon Phi™ Coprocessors</span></li>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
index 954b8fdaf..488513eab 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
@@ -85,9 +85,9 @@ It is possible to analyze both native and offload Xeon Phi applications.
For offload mode, just specify the path to the binary. For native mode,
you need to specify in project properties:
-Application<span class="monospace">ssh</span>
+Application: <span class="monospace">ssh</span>
-Application parameters<span class="monospace">mic0 source ~/.profile
+Application parameters: <span class="monospace">mic0 source ~/.profile
&& /path/to/your/bin</span>
Note that we include <span class="monospace">source ~/.profile
@@ -110,4 +110,3 @@ References
1. <span><https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf>Â Performance
Tuning for Intel® Xeon Phi™ Coprocessors</span>
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56.html
new file mode 100644
index 000000000..ce60070a9
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/mympiprog_32p_2014-10-15_16-56.html
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+ return (p < 0.4) ? "start" : ((p > 0.6) ? "end" : "middle");
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+ .style("fill", function(j, i){return cfg.color(series)})
+ .style("fill-opacity", cfg.opacityArea)
+ .on('mouseover', function (d){
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+ g.selectAll("polygon").transition(200).style("fill-opacity", 0.1);
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+ .on('mouseout', function(){
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+
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+ .data(y).enter()
+ .append("svg:circle").attr("class", "radar-chart-serie"+series)
+ .attr('r', cfg.radius)
+ .attr("alt", function(j){return Math.max(j.value, 0)})
+ .attr("cx", function(j, i){
+ dataValues.push([
+ getHorizontalPosition(i, cfg.w/2, (parseFloat(Math.max(j.value, 0))/cfg.maxValue)*cfg.factor),
+ getVerticalPosition(i, cfg.h/2, (parseFloat(Math.max(j.value, 0))/cfg.maxValue)*cfg.factor)
+ ]);
+ return getHorizontalPosition(i, cfg.w/2, (Math.max(j.value, 0)/cfg.maxValue)*cfg.factor);
+ })
+ .attr("cy", function(j, i){
+ return getVerticalPosition(i, cfg.h/2, (Math.max(j.value, 0)/cfg.maxValue)*cfg.factor);
+ })
+ .attr("data-id", function(j){return j.axis})
+ .style("fill", cfg.color(series)).style("fill-opacity", .9)
+ .on('mouseover', function (d){
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+ //Tooltip
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+}
+
+</script>
+<script type="text/javascript">window.onload = function() {
+ var cpu = 88.6;
+ var mpi = 11.4;
+ var io = 0.0;
+
+ // Draw radar chart, choose its color based on application classification
+ var radar_data = [[ { axis: "CPU", value: cpu },
+ { axis: "MPI", value: mpi },
+ { axis: "I/O", value: io } ]];
+ var radar_options = { w: 200, h: 200, factor: 0.7, fontSize: 16, radius: 0,
+ opacityArea: 0.64, maxValue: 100,
+ color: function() {
+ if ("cpu" == "io") return "#ed8140";
+ if ("cpu" == "cpu") return "#4fd32e";
+ if ("cpu" == "mpi") return "#409ded";
+ else return "#bb58d6";
+ }
+ };
+ RadarChart.draw("#time_radar", radar_data, radar_options);
+
+ // Wrap the exe path on slashes if necessary
+ var exe_path = document.getElementById("exe_path");
+ exe_path.innerHTML = exe_path.innerHTML.replace(/\//g, '/​'); // insert a zero width space after slashes as a word wrap hint
+
+ // Format our byte value numbers to show at most 2 decimal places, but only if required to attain 3 digits of precision
+ // 1234.56 -> "1234"
+ // 12.3456 -> "12.3"
+ // 1.23456 -> "1.23"
+ // 0.00000 -> "0.00"
+ var formatNumber = function(num) {
+ if (num > 100) return new Number(num).toFixed(0); // 1234.56 -> 1234
+ if (num > 10) return new Number(num).toFixed(1); // 12.3456 -> 12.3
+ else return new Number(num).toFixed(2); // 1.23456 -> 1.23 and 0 -> 0.00
+ }
+
+ // Parse a number, but return 0 for invalid numbers, not NaN
+ var toNumber = function(num_str) {
+ var num = Number(num_str)
+ return isNaN(num) ? 0 : num;
+ }
+
+ // Scale byte values to bytes, kB, MB or GB as appropriate
+ var fillBytes = function(base_name, bytes_str, per_second) {
+ var units = "bytes";
+ var scale = 1.0;
+ var bytes = Number(bytes_str)
+ if (isNaN(bytes) ) { units = "" ; }
+ else if (bytes > 1000000000) { units = "GB"; scale = 1*1000*1000*1000; }
+ else if (bytes > 1000000 ) { units = "MB"; scale = 1*1000*1000 }
+ else if (bytes > 1000 ) { units = "kB"; scale = 1*1000 }
+ var num = isNaN(bytes) ? bytes_str : formatNumber(bytes / scale);
+ var elementNum = document.getElementById(base_name + "_num");
+ elementNum.innerHTML = num;
+ var elementUnits = document.getElementById(base_name + "_units");
+ elementUnits.innerHTML = units + (per_second && !isNaN(bytes) ? "/s" : "");
+ };
+
+ // Fill all the byte numbers and their units with the scaled values
+ fillBytes("mpi_colrate", "1.65e+02", true);
+ fillBytes("mpi_p2prate", "0.00e+00", true);
+ fillBytes("io_readrate", "0.00e+00", true);
+ fillBytes("io_writerate", "0.00e+00", true);
+ fillBytes("ram_mean", "2.33e+07", false);
+ fillBytes("ram_peak", "2.35e+07", false);
+
+ // Set widths for all graphs
+ var bar = function(name, width) {
+ var rounded = Math.round(width);
+ if (!isFinite(rounded) || rounded < 1)
+ document.getElementById(name).style.width = "1px"
+ else
+ document.getElementById(name).style.width = rounded + "px";
+ };
+ bar("cpu_bar", cpu * 2);
+ bar("mpi_bar", mpi * 2);
+ bar("io_bar", io * 2);
+
+ bar("cpu_num_bar", toNumber("50.0") / 2);
+ bar("cpu_vec_bar", toNumber("50.0") / 2);
+ bar("cpu_mem_bar", toNumber("0.0") / 2);
+ bar("cpu_other_bar", toNumber("0.0") / 2);
+
+ bar("mpi_col_bar", toNumber("100.0") / 2);
+ bar("mpi_p2p_bar", toNumber("0.0") / 2);
+ var mpi_scale = Math.max(toNumber("1.65e+02"), toNumber("0.00e+00"));
+ bar("mpi_colrate_bar", 50 * toNumber("1.65e+02") / mpi_scale);
+ bar("mpi_p2prate_bar", 50 * toNumber("0.00e+00") / mpi_scale);
+
+ bar("io_read_bar", toNumber("0.0") / 2);
+ bar("io_write_bar", toNumber("0.0") / 2);
+ var io_scale = Math.max(toNumber("0.00e+00"), toNumber("0.00e+00"));
+ bar("io_readrate_bar", 50 * toNumber("0.00e+00") / io_scale);
+ bar("io_writerate_bar", 50 * toNumber("0.00e+00") / io_scale);
+
+ bar("ram_mean_bar", 50 * toNumber("2.33e+07") / toNumber("2.35e+07"));
+ bar("ram_peak_bar", 50);
+ bar("ram_node_bar", toNumber("2.8") / 2);
+
+ // Formatting replacement helper function
+ var replaceIn = function(elementId, re, new_text) {
+ element = document.getElementById(elementId);
+ element.innerHTML = element.innerHTML.replace(re, new_text);
+ };
+
+ // Add formatting for the overview advice section
+ replaceIn('overview_advice', /CPU/g, '<span class="cpu_span">CPU</span>');
+ replaceIn('overview_advice', /MPI/g, '<span class="mpi_span">MPI</span>');
+ replaceIn('overview_advice', /I\/O/g, '<span class="io_span">I\/O</span>');
+
+ // Add formatting for the CPU advice section
+ if ( 88.6 < 0.05 )
+ replaceIn('cpu_explanation', /application code/g, '<span class="cpu_span">application code</span>');
+ replaceIn('cpu_explanation', /vectorized instructions/g, '<span class="cpu_vec_span">vectorized instructions</span>');
+ replaceIn('cpu_explanation', /memory accesses/g, '<span class="cpu_mem_span">memory accesses</span>');
+ replaceIn('cpu_explanation', /memory-bound/g, '<span class="cpu_mem_span">memory-bound</span>');
+ replaceIn('cpu_explanation', /arithmetic-bound/g, '<span class="cpu_num_span">arithmetic-bound</span>');
+ replaceIn('cpu_explanation', /numerical computation/g, '<span class="cpu_num_span">numerical computation</span>');
+
+ // Add formatting for the MPI advice section
+ if ( 11.4 < 0.05 )
+ replaceIn('mpi_explanation', /MPI/g, '<span class="mpi_span">MPI</span>');
+ replaceIn('mpi_explanation', /collective calls/g, '<span class="mpi_col_span">collective calls</span>');
+ replaceIn('mpi_explanation', /point-to-point calls/g, '<span class="mpi_p2p_span">point-to-point calls</span>');
+ replaceIn('mpi_explanation', / very low/g, ' <span class="mpi_colrate_span">very low</span>');
+ replaceIn('mpi_explanation', / low/g, ' <span class="mpi_colrate_span">low</span>');
+ replaceIn('mpi_explanation', / average/g, ' <span class="mpi_colrate_span">average</span>');
+ replaceIn('mpi_explanation', / very high/g, ' <span class="mpi_colrate_span">very high</span>');
+ replaceIn('mpi_explanation', / high/g, ' <span class="mpi_colrate_span">high</span>');
+
+ // Add formatting for the I/O advice section
+ if ( 0.0 < 0.05 )
+ replaceIn('io_explanation', /I\/O/g, '<span class="io_span">I/O</span>');
+ replaceIn('io_explanation', /read operations/g, '<span class="io_read_span">read operations</span>');
+ replaceIn('io_explanation', /write operations/g, '<span class="io_write_span">write operations</span>');
+ replaceIn('io_explanation', / very low/g, ' <span class="io_readrate_span">very low</span>');
+ replaceIn('io_explanation', / low/g, ' <span class="io_readrate_span">low</span>');
+ replaceIn('io_explanation', / average/g, ' <span class="io_readrate_span">average</span>');
+ replaceIn('io_explanation', / very high/g, ' <span class="io_readrate_span">very high</span>');
+ replaceIn('io_explanation', / high/g, ' <span class="io_readrate_span">high</span>');
+
+ // Add formatting for the RAM advice section
+ replaceIn('ram_explanation', /high/g, ' <span class="ram_node_span">high</span>');
+ replaceIn('ram_explanation', /well-balanced/g, '<span class="ram_peak_span">well-balanced</span>');
+ replaceIn('ram_explanation', /significant variation/g, '<span class="ram_peak_span">significant variation</span>');
+ replaceIn('ram_explanation', /peak node memory usage/g, '<span class="ram_node_span">peak node memory usage</span>');
+
+ // Hide the error warning if the script got this far
+ document.getElementById('error').style.display = 'none';
+};
+</script>
+</head>
+
+<body>
+<div id="content">
+
+<div class="header">
+ <div class="logo"><img src="http://content.allinea.com/downloads/performance-report-logo.png" alt="Allinea Performance Reports" /></div>
+ <div class="header_left">
+ <div class="application_details">
+ <table>
+ <tr><td class="details_key">Executable:</td><td id="exe_name">mympiprog.x</td></tr>
+ <tr><td class="details_key">Resources:</td><td id="num_procs">32 processes, 2 nodes</td></tr>
+ <tr><td class="details_key">Machine:</td><td id="machine_name">cn182</td></tr>
+ <tr><td class="details_key">Start time:</td><td id="start_date">Wed Oct 15 16:56:23 2014</td></tr>
+ <tr><td class="details_key">Total time:</td><td id="time_string">7 seconds (0 minutes)</td></tr>
+ <tr><td class="details_key">Full path:</td><td id="exe_path">/home/user</td></tr>
+ <tr><td class="details_key">Notes:</td><td id="notes"></td></tr>
+ </table>
+ </div>
+ </div>
+ <div id="time_radar"></div>
+ <div class="clear"></div>
+</div>
+<hr />
+<div id="error">
+<p><strong>Error: javascript is not running</strong></p>
+<p>The graphs in this Performance Report require <strong>javascript</strong>, which is disabled or not working.</p>
+<p>Check whether your javascript support is enabled or try another browser.<p>
+<p>Remember, you can always contact <a href="mailto:support@allinea.com">support@allinea.com</a>, we're very nice!</p>
+</div>
+<div class="summary">
+ <div class="heading">Summary: mympiprog.x is <span class="cpu_span">CPU-bound</span> in this configuration</div>
+ <div>The total wallclock time was spent as follows:</div>
+ <table class="summary_table">
+ <tr><td class="heading_cpu">CPU</td><td class="percent">88.6%</td><td class="bar_graph"><div id="cpu_bar" /></td>
+ <td class="details"><p>Time spent running application code. High values are usually good.</p><p>This is <span id="summary_cpu_class">high</span>; check the CPU performance section for optimization advice.</p></td></tr>
+ <tr><td class="heading_mpi">MPI</td><td class="percent">11.4%</td><td class="bar_graph"><div id="mpi_bar" /></td>
+ <td class="details"><p>Time spent in MPI calls. High values are usually bad.</p><p>This is <span id="summary_mpi_class">very low</span>; this code may benefit from increasing the process count.</p></td></tr>
+ <tr><td class="heading_io">I/O</td><td class="percent">0.0%</td><td class="bar_graph"><div id="io_bar" /></td>
+ <td class="details"><p>Time spent in filesystem I/O. High values are usually bad.</p><p>This is <span id="summary_io_class">negligible</span>; there's no need to investigate I/O performance.</p></td></tr>
+ </table>
+ <div class="overview_general_advice"><p>This application run was <span class="cpu_span">CPU-bound</span>. A breakdown of this time and advice for investigating further is in the <span class="cpu_span">CPU</span> section below.</p><p id="overview_advice">As very little time is spent in MPI calls, this code may also benefit from running at larger scales.</p></div>
+</div>
+<hr />
+<div class="subsections">
+ <div class="ltcol">
+ <div class="heading_cpu">CPU</div>
+ <div>A breakdown of how the <span class="cpu_span">88.6</span>% total CPU time was spent:</div>
+ <table id="cpu_chart">
+ <tr><td>Scalar numeric ops</td><td class="right_cell"><span class="cpu_num_span">50.0</span>%</td><td class="mini_bar_graph"><div id="cpu_num_bar" /></td></tr>
+ <tr><td>Vector numeric ops</td><td class="right_cell"><span class="cpu_vec_span">50.0</span>%</td><td class="mini_bar_graph"><div id="cpu_vec_bar" /></td></tr>
+ <tr><td>Memory accesses</td><td class="right_cell"><span class="cpu_mem_span">0.0</span>%</td><td class="mini_bar_graph"><div id="cpu_mem_bar" /></td></tr>
+ <tr><td>Other</td><td class="right_cell"><span class="cpu_other_span">0.0</span>%</td><td class="mini_bar_graph"><div id="cpu_other_bar" /></td></tr>
+ </table>
+ <div id="cpu_explanation">
+ <div class="explanation">The per-core performance is arithmetic-bound. Try to increase the amount of time spent in vectorized instructions by analyzing the compiler's vectorization reports.</div>
+ <div class="explanation"></div>
+ </div>
+ </div>
+ <div class="rtcol">
+ <div class="heading_mpi">MPI</div>
+ <div>Of the <span class="mpi_span">11.4</span>% total time spent in MPI calls:</div>
+ <table id="mpi_chart">
+ <tr><td>Time in collective calls</td><td class="right_cell"><span class="mpi_col_span">100.0</span>%</td><td class="mini_bar_graph"><div id="mpi_col_bar" /></td></tr>
+ <tr><td>Time in point-to-point calls</td><td class="right_cell"><span class="mpi_p2p_span">0.0</span>%</td><td class="mini_bar_graph"><div id="mpi_p2p_bar" /></td></tr>
+ <tr><td>Effective process collective rate</td><td class="right_cell"><span class="mpi_colrate_span"><span id="mpi_colrate_num">1.65e+02</span></span> <span id="mpi_colrate_units"></span></td><td class="mini_bar_graph"><div id="mpi_colrate_bar" /></td></tr>
+ <tr><td>Effective process point-to-point rate</td><td class="right_cell"><span class="mpi_p2prate_span"><span id="mpi_p2prate_num">0.00e+00</span></span> <span id="mpi_p2prate_units"></span></td><td class="mini_bar_graph"><div id="mpi_p2prate_bar" /></td></tr>
+ </table>
+ <div id="mpi_explanation">
+ <div class="explanation">Most of the time is spent in collective calls with a very low transfer rate. This suggests load imbalance is causing synchonization overhead; use an MPI profiler to investigate further.</div>
+ <div class="explanation"></div>
+ </div>
+ </div>
+ <div class="clear"></div>
+</div>
+<div class="subsections">
+ <div class="ltcol">
+ <div class="heading_io">I/O</div>
+ <div>A breakdown of how the <span class="io_span">0.0</span>% total I/O time was spent:</div>
+ <table id="io_chart">
+ <tr><td>Time in reads</td><td class="right_cell"><span class="io_read_span">0.0</span>%</td><td class="mini_bar_graph"><div id="io_read_bar" /></td></tr>
+ <tr><td>Time in writes</td><td class="right_cell"><span class="io_write_span">0.0</span>%</td><td class="mini_bar_graph"><div id="io_write_bar" /></td></tr>
+ <tr><td>Effective process read rate</td><td class="right_cell"><span class="io_readrate_span"><span id="io_readrate_num">0.00e+00</span></span> <span id="io_readrate_units"></span></td><td class="mini_bar_graph"><div id="io_readrate_bar" /></td></tr>
+ <tr><td>Effective process write rate</td><td class="right_cell"><span class="io_writerate_span"><span id="io_writerate_num">0.00e+00</span></span> <span id="io_writerate_units"></span></td><td class="mini_bar_graph"><div id="io_writerate_bar" /></td></tr>
+ </table>
+ <div id="io_explanation">
+ <div class="explanation">No time is spent in I/O operations. There's nothing to optimize here!</div>
+ <div class="explanation"></div>
+ </div>
+ </div>
+ <div class="rtcol">
+ <div class="heading_ram">Memory</div>
+ <div>Per-process memory usage may also affect scaling:</div>
+ <table id="ram_chart">
+ <tr><td>Mean process memory usage</td><td class="right_cell"><span class="ram_mean_span"><span id="ram_mean_num">2.33e+07</span></span> <span id="ram_mean_units"></span></td><td class="mini_bar_graph"><div id="ram_mean_bar" /></td></tr>
+ <tr><td>Peak process memory usage</td><td class="right_cell"><span class="ram_peak_span"><span id="ram_peak_num">2.35e+07</span></span> <span id="ram_peak_units"></span></td><td class="mini_bar_graph"><div id="ram_peak_bar" /></td></tr>
+ <tr><td>Peak node memory usage</td><td class="right_cell"><span class="ram_node_span">2.8</span>%</td><td class="mini_bar_graph"><div id="ram_node_bar" /></td></tr>
+ </table>
+ <div id="ram_explanation">
+ <div class="explanation">The peak node memory usage is very low. You may be able to reduce the amount of allocation time used by running with fewer MPI processes and more data on each process.</div>
+ <div class="explanation"></div>
+ </div>
+ </div>
+ <div class="clear"></div>
+</div>
+</div> <!-- content -->
+</body>
+</html>
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.html
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+ PAPI
+ </h1>
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+</div>
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+
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+ <div id="parent-fieldname-text-14189656124845798b0b4b2b718568ba" class="">
+ <h2 class=" ">Introduction</h2>
+<p class=" "><span dir="auto">Performance Application Programming Interface </span><span>(PAPI)  is a portable interface to access hardware performance counters (such as instruction counts and cache misses) found in most modern architectures. With the new component framework, PAPI is not limited only to CPU counters, but offers also components for CUDA, network, Infiniband etc.</span></p>
+<p class=" "><span>PAPI provides two levels of interface - a simpler, high level interface and more detailed low level interface.</span></p>
+<p class=" "><span>PAPI can be used with parallel as well as serial programs.</span></p>
+<h2 class=" ">Usage</h2>
+<p>To use PAPI, load <a href="../../environment-and-modules.html" title="" target="_self" class="internal-link">module</a> <span class="monospace">papi</span> :</p>
+<pre class=" ">$ module load papi</pre>
+<p class=" ">This will load the default version. Execute <span class="monospace">module avail papi</span> for a list of installed versions.</p>
+<h2 class=" ">Utilites</h2>
+<p>The <span class="monospace">bin</span> directory of PAPI (which is automatically added to <span class="monospace">$PATH</span> upon loading the module) contains various utilites.</p>
+<h3 class=" ">papi_avail</h3>
+<p>Prints which preset events are available on the current CPU. The third column indicated whether the preset event is available on the current CPU.</p>
+<pre class=" ">$ papi_avail<br /><span>Available events and hardware information.<br /></span><span>--------------------------------------------------------------------------------<br /></span><span>PAPI Version : 5.3.2.0<br /></span><span>Vendor string and code : GenuineIntel (1)<br /></span><span>Model string and code : Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz (45)<br /></span><span>CPU Revision : 7.000000<br /></span><span>CPUID Info : Family: 6 Model: 45 Stepping: 7<br /></span><span>CPU Max Megahertz : 2601<br /></span><span>CPU Min Megahertz : 1200<br /></span><span>Hdw Threads per core : 1<br /></span><span>Cores per Socket : 8<br /></span><span>Sockets : 2<br /></span><span>NUMA Nodes : 2<br /></span><span>CPUs per Node : 8<br /></span><span>Total CPUs : 16<br /></span><span>Running in a VM : no<br /></span><span>Number Hardware Counters : 11<br /></span><span>Max Multiplex Counters : 32<br /></span><span>--------------------------------------------------------------------------------<br /></span><span>Name Code Avail Deriv Description (Note)<br /></span><span>PAPI_L1_DCM 0x80000000 Yes No Level 1 data cache misses<br /></span><span>PAPI_L1_ICM 0x80000001 Yes No Level 1 instruction cache misses<br /></span><span>PAPI_L2_DCM 0x80000002 Yes Yes Level 2 data cache misses<br /></span><span>PAPI_L2_ICM 0x80000003 Yes No Level 2 instruction cache misses<br /></span><span>PAPI_L3_DCM 0x80000004 No No Level 3 data cache misses<br /></span><span>PAPI_L3_ICM 0x80000005 No No Level 3 instruction cache misses<br /></span><span>PAPI_L1_TCM 0x80000006 Yes Yes Level 1 cache misses<br /></span><span>PAPI_L2_TCM 0x80000007 Yes No Level 2 cache misses<br /></span><span>PAPI_L3_TCM 0x80000008 Yes No Level 3 cache misses<br />.... </span></pre>
+<h3 class=" ">papi_native_avail</h3>
+<p><span>Prints which native events are available on the current CPU.</span></p>
+<h3 class=" "><span class="s1">papi_cost</span></h3>
+<p><span>Measures the cost (in cycles) of basic PAPI operations.</span></p>
+<h3 class=" "><span>papi_mem_info</span></h3>
+<p><span>Prints information about the memory architecture of the current CPU.</span></p>
+<h2 class=" ">PAPI API</h2>
+<p>PAPI provides two kinds of events:Â </p>
+<ul>
+<li><strong>Preset events </strong>is a set of predefined common CPU events, <span>standardized</span>Â across platforms.</li>
+<li><strong>Native events </strong>is a set of all events supported by the current hardware. This is a larger set of features than preset. For other components than CPU, only native events are usually available.</li>
+</ul>
+<div></div>
+<p>To use PAPI in your application, you need to link the appropriate include file.</p>
+<ul>
+<li><span class="monospace">papi.h</span> for C</li>
+<li><span class="monospace">f77papi.h</span> for Fortran 77</li>
+<li><span class="monospace">f90papi.h</span> for Fortran 90</li>
+<li><span class="monospace">fpapi.h</span> for Fortran with preprocessor</li>
+</ul>
+<div></div>
+<div>The include path is automatically added by papi module to <span class="monospace">$INCLUDE</span>.</div>
+<h3 class=" ">High level API</h3>
+<p>Please refer to <a class="external-link" href="http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:High_Level" target="_self" title="">http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:High_Level</a> for a description of the High level API.</p>
+<h3 class=" ">Low level API</h3>
+<p>Please refer to <a class="external-link" href="http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:Low_Level" target="_self" title="">http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:Low_Level</a> for a description of the Low level API.</p>
+<h3 class=" ">Timers</h3>
+<p>PAPI provides the most accurate timers the platform can support. See <a class="external-link" href="http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:Timers" target="_self" title="">http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:Timers</a></p>
+<h3 class=" ">System information</h3>
+<p>PAPI can be used to query some system infromation, such as CPU name and MHz. See <a class="external-link" href="http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:System_Information" target="_self" title="">http://icl.cs.utk.edu/projects/papi/wiki/PAPIC:System_Information</a></p>
+<h2 class=" ">Example</h2>
+<p>The following example prints MFLOPS rate of a naive matrix-matrix multiplication :</p>
+<pre class=" ">#include <stdlib.h><br />#include <stdio.h><br />#include "papi.h"<br /><span>#define SIZE 1000<br /><br /></span><span>int main(int argc, char **argv) {<br /></span><span> float matrixa[SIZE][SIZE], matrixb[SIZE][SIZE], mresult[SIZE][SIZE];<br /></span><span> float real_time, proc_time, mflops;<br /></span><span> long long flpins;<br /></span><span> int retval;<br /></span><span> int i,j,k;<br /><br /></span><span> /* Initialize the Matrix arrays */<br /></span><span> for ( i=0; i<SIZE*SIZE; i++ ){<br /></span><span> mresult[0][i] = 0.0;<br /></span><span> matrixa[0][i] = matrixb[0][i] = rand()*(float)1.1;Â <br /></span><span> }<br /></span><span> Â <br /></span><span> /* Setup PAPI library and begin collecting data from the counters */<br /></span><span> if((retval=PAPI_flops( &real_time, &proc_time, &flpins, &mflops))<PAPI_OK)<br /></span><span> printf("Error!");<br /><br /></span><span> /* A naive Matrix-Matrix multiplication */<br /></span><span> for (i=0;i<SIZE;i++)<br /></span><span> for(j=0;j<SIZE;j++)<br /></span><span> for(k=0;k<SIZE;k++)<br /></span><span> mresult[i][j]=mresult[i][j] + matrixa[i][k]*matrixb[k][j];<br /><br /></span><span> /* Collect the data into the variables passed in */<br /></span><span> if((retval=PAPI_flops( &real_time, &proc_time, &flpins, &mflops))<PAPI_OK)<br /></span><span> printf("Error!");<br /></span><span> <br /> printf("Real_time:\t%f\nProc_time:\t%f\nTotal flpins:\t%lld\nMFLOPS:\t\t%f\n", real_time, proc_time, flpins, mflops);<br /></span><span> PAPI_shutdown();<br /></span><span> return 0;<br /></span><span>}</span></pre>
+<p>Â Now compile and run the example :</p>
+<pre class=" ">$ gcc matrix.c -o matrix -lpapi<br />$ ./matrix<br /><span>Real_time: 8.852785<br /></span><span>Proc_time: 8.850000<br /></span><span>Total flpins: 6012390908<br /></span><span>MFLOPS: 679.366211</span><span>Â </span></pre>
+<p class=" ">Let's try with optimizations enabled :</p>
+<pre class=" ">$ gcc -O3 matrix.c -o matrix -lpapi<br />$ ./matrix<br /><span>Real_time: 0.000020<br /></span><span>Proc_time: 0.000000<br /></span><span>Total flpins: 6<br /></span><span>MFLOPS: inf</span></pre>
+<p class=" ">Now we see a seemingly strange result - the multiplication took no time and only 6 floating point instructions were issued. This is because the compiler optimizations have completely removed the multiplication loop, as the result is actually not used anywhere in the program. We can fix this by adding some "dummy" code at the end of the Matrix-Matrix multiplication routine :</p>
+<pre class=" ">for (i=0; i<SIZE;i++)<br /> for (j=0; j<SIZE; j++)<br /> if (mresult[i][j] == -1.0) printf("x");</pre>
+<p class=" ">Now the compiler won't remove the multiplication loop. (However it is still not that smart to see that the result won't ever be negative). Now run the code again:</p>
+<pre class=" ">$ gcc -O3 matrix.c -o matrix -lpapi<br />$ ./matrix<br /><span>Real_time: 8.795956<br /></span><span>Proc_time: 8.790000<br /></span><span>Total flpins: 18700983160<br /></span><span>MFLOPS: 2127.529297</span><span>Â </span></pre>
+<h3 class=" ">Intel Xeon Phi</h3>
+<p class="exclamation">PAPI currently supports only a subset of counters on the Intel Xeon Phi processor compared to Intel Xeon, for example the floating point operations counter is missing.</p>
+<p>To use PAPI in <a href="../intel-xeon-phi.html" title="" target="_self" class="internal-link">Intel Xeon Phi</a> native applications, you need to load module with "<span class="monospace">-mic</span>" suffix, for example "<span class="monospace">papi/5.3.2-mic</span>" :</p>
+<pre class=" ">$ module load papi/5.3.2-mic</pre>
+<p class=" ">Then, compile your application in the following way:</p>
+<pre class=" "><span class="s1">$ module load intel<br />$ icc -mmic -Wl,-rpath,/apps/intel/composer_xe_2013.5.192/compiler/lib/mic matrix-mic.c -o matrix-mic -lpapi -lpfm</span></pre>
+<p class=" ">To execute the application on MIC, you need to manually set <span class="monospace">LD_LIBRARY_PATH :</span></p>
+<pre class=" "><span class="monospace">$ qsub -q qmic -A NONE-0-0 -I<br />$ ssh mic0<br />$ export LD_LIBRARY_PATH=/apps/tools/papi/5.4.0-mic/lib/ <br />$ ./matrix-mic </span></pre>
+<p class=" ">Alternatively, you can link PAPI statically (<span class="monospace">-static</span> flag), then <span class="monospace">LD_LIBRARY_PATH</span> does not need to be set.</p>
+<p class=" ">You can also execute the PAPI tools on MIC :</p>
+<pre class=" "><span class="s1">$ /apps/tools/papi/5.4.0-mic/bin/papi_native_avail</span></pre>
+<p class=" ">To use PAPI in offload mode, you need to provide both host and MIC versions of PAPI:</p>
+<pre class=" "><span class="s1">$ module load papi/5.4.0<br />$ icc matrix-offload.c -o matrix-offload -offload-option,mic,compiler,"-L$PAPI_HOME-mic/lib -lpapi" -lpapi</span></pre>
+<h2 class=" ">References</h2>
+<ol>
+<li><a class="external-link" href="http://icl.cs.utk.edu/papi/" target="_self" title="">http://icl.cs.utk.edu/papi/</a>Â Main project page</li>
+<li><a class="external-link" href="http://icl.cs.utk.edu/projects/papi/wiki/Main_Page" target="_self" title="">http://icl.cs.utk.edu/projects/papi/wiki/Main_Page</a>Â Wiki</li>
+<li><a class="external-link" href="http://icl.cs.utk.edu/papi/docs/" target="_self" title="">http://icl.cs.utk.edu/papi/docs/</a> API Documentation</li>
+</ol>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
index a63c21f3b..06e249181 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
@@ -49,22 +49,22 @@ CPU.
$ papi_avail
Available events and hardware information.
--------------------------------------------------------------------------------
- PAPI Version 5.3.2.0
- Vendor string and code GenuineIntel (1)
- Model string and code Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz (45)
- CPU Revision 7.000000
- CPUID Info Family6 Model45 Stepping7
- CPU Max Megahertz 2601
- CPU Min Megahertz 1200
- Hdw Threads per core 1
- Cores per Socket 8
- Sockets 2
- NUMA Nodes 2
- CPUs per Node 8
- Total CPUs 16
- Running in a VM no
- Number Hardware Counters 11
- Max Multiplex Counters 32
+ PAPI Version : 5.3.2.0
+ Vendor string and code : GenuineIntel (1)
+ Model string and code : Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz (45)
+ CPU Revision : 7.000000
+ CPUID Info : Family: 6 Model: 45 Stepping: 7
+ CPU Max Megahertz : 2601
+ CPU Min Megahertz : 1200
+ Hdw Threads per core : 1
+ Cores per Socket : 8
+ Sockets : 2
+ NUMA Nodes : 2
+ CPUs per Node : 8
+ Total CPUs : 16
+ Running in a VM : no
+ Number Hardware Counters : 11
+ Max Multiplex Counters : 32
--------------------------------------------------------------------------------
Name Code Avail Deriv Description (Note)
PAPI_L1_DCM 0x80000000 Yes No Level 1 data cache misses
@@ -185,19 +185,19 @@ multiplication :
$ gcc matrix.c -o matrix -lpapi
$ ./matrix
- Real_time8.852785
- Proc_time8.850000
- Total flpins6012390908
- MFLOPS679.366211Â
+ Real_time: 8.852785
+ Proc_time: 8.850000
+ Total flpins: 6012390908
+ MFLOPS: 679.366211Â
Let's try with optimizations enabled :
$ gcc -O3 matrix.c -o matrix -lpapi
$ ./matrix
- Real_time0.000020
- Proc_time0.000000
- Total flpins6
- MFLOPSinf
+ Real_time: 0.000020
+ Proc_time: 0.000000
+ Total flpins: 6
+ MFLOPS: inf
Now we see a seemingly strange result - the multiplication took no time
and only 6 floating point instructions were issued. This is because the
@@ -216,10 +216,10 @@ run the code again:
$ gcc -O3 matrix.c -o matrix -lpapi
$ ./matrix
- Real_time8.795956
- Proc_time8.790000
- Total flpins18700983160
- MFLOPS2127.529297Â
+ Real_time: 8.795956
+ Proc_time: 8.790000
+ Total flpins: 18700983160
+ MFLOPS: 2127.529297Â
### Intel Xeon Phi
@@ -269,4 +269,3 @@ References
3. <http://icl.cs.utk.edu/papi/docs/> API Documentation
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.html
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index 000000000..45bb17418
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+ <h2 class=" "><span>Introduction</span></h2>
+<p><a class="external-link" href="http://www.scalasca.org/" target="_self" title="">Scalasca</a> is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks – in particular those concerning communication and synchronization – and offers guidance in exploring their causes.</p>
+<p>Scalasca supports profiling of MPI, OpenMP and hybrid MPI+OpenMP applications.</p>
+<h2 class=" ">Installed versions</h2>
+<p>There are currently two versions of Scalasca 2.0 <a href="../../environment-and-modules.html" title="" target="_self" class="internal-link">modules</a> installed on Anselm:</p>
+<ul>
+<li>
+<p class="p1"><span class="s1"><span class="monospace">scalasca2/2.0-gcc-openmpi</span>, for usage with <a href="../compilers.html" title="" target="_self" class="internal-link">GNU Compiler</a> and <a href="../mpi-1/Running_OpenMPI.html" title="" target="_self" class="internal-link">OpenMPI</a>,</span></p>
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+<li>
+<p class="p1"><span class="s1"><span class="monospace">scalasca2/2.0-icc-impi</span>, for usage with <a href="../compilers.html" title="" target="_self" class="internal-link">Intel Compiler</a> and <a href="../mpi-1/running-mpich2.html" title="" target="_self" class="internal-link">Intel MPI</a>.</span></p>
+</li>
+</ul>
+<h2 class=" ">Usage</h2>
+<p>Profiling a parallel application with Scalasca consists of three steps:</p>
+<ol>
+<li>Instrumentation, compiling the application such way, that the profiling data can be generated.</li>
+<li>Runtime measurement, running the application with the Scalasca profiler to collect performance data.</li>
+<li>Analysis of reports</li>
+</ol>
+<h3 class=" ">Instrumentation</h3>
+<p>Instrumentation via "<span class="monospace">scalasca -instrument</span>" is discouraged. Use <a href="score-p.html" title="" target="_self" class="internal-link">Score-P instrumentation</a>.</p>
+<h3 class=" ">Runtime measurement</h3>
+<p>After the application is instrumented, runtime measurement can be performed with the "<span class="monospace">scalasca -analyze</span>" command. The syntax is :</p>
+<p><span class="monospace">scalasca -analyze [scalasca options] [launcher] [launcher options] [program] [program options]</span></p>
+<p>An example :</p>
+<pre class=" ">$ <span class="monospace">scalasca -analyze mpirun -np 4 ./mympiprogram</span></pre>
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+<dl><dt>-t Enable trace data collection. By default, only summary data are collected.</dt><dt>-e <directory> Specify a directory to save the collected data to. By default, Scalasca saves the data to a directory with prefix <span>scorep_, followed by name of the executable and launch configuration.</span></dt><dt><span><br /></span></dt></dl>
+<p class="exclamation">Scalasca can generate a huge amount of data, especially if tracing is enabled. Please consider saving the data to a <a href="../../storage.html" title="" target="_self" class="internal-link">scratch directory</a>.</p>
+<h3 class=" ">Analysis of reports</h3>
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+<p>To launch the analysis, run :</p>
+<pre class="fragment">scalasca -examine [options] <experiment_directory></pre>
+<p class=" ">If you do not wish to launch the GUI tool, use the "-s" option :</p>
+<pre class="fragment">scalasca -examine -s <experiment_directory></pre>
+<p class=" ">Alternatively you can open CUBE and load the data directly from here. Keep in mind that in that case the preprocessing is not done and not all metrics will be shown in the viewer.</p>
+<p class=" ">Refer to <a href="cube.html" title="" target="_self" class="internal-link">CUBE documentation</a>Â on usage of the GUI viewer.</p>
+<h2 class=" ">References</h2>
+<ol>
+<li><a class="external-link" href="http://www.scalasca.org/" target="_self" title="">http://www.scalasca.org/</a></li>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
index 7e306c7c3..19c86697b 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
@@ -107,4 +107,3 @@ References
1. <http://www.scalasca.org/>
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.html
new file mode 100644
index 000000000..88138b2eb
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+ <h2 class=" ">Introduction</h2>
+<p>The <a class="external-link" href="http://www.vi-hps.org/projects/score-p/" target="_self" title="">Score-P measurement infrastructure</a> is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications. </p>
+<p>Score-P can be used as an instrumentation tool for <a href="scalasca.html" title="" target="_self" class="internal-link">Scalasca</a>.</p>
+<h2 class=" ">Installed versions</h2>
+<p>There are currently two versions of Score-P version 1.2.6 <a href="../../environment-and-modules.html" title="" target="_self" class="internal-link">modules</a>Â installed on Anselm :</p>
+<ul>
+<li>
+<p class="p1"><span class="s1">scorep/1.2.3-gcc-openmpi<span>, for usage with </span><a href="../compilers.html" title="" target="_self" class="internal-link">GNU Compiler</a><span> and </span><a href="../mpi-1/Running_OpenMPI.html" title="" target="_self" class="internal-link">OpenMPI</a><span>,</span></span></p>
+</li>
+<li>
+<p class="p1"><span class="s1">scorep/1.2.3-icc-impi<span>, for usage with </span><a href="../compilers.html" title="" target="_self" class="internal-link">Intel Compiler</a><span> and </span><a href="../mpi-1/running-mpich2.html" title="" target="_self" class="internal-link">Intel MPI</a><span>.</span></span></p>
+</li>
+</ul>
+<h2 class=" ">Instrumentation</h2>
+<p><span>There are three ways to instrument your parallel applications in order to enable performance data collection :</span></p>
+<ol>
+<li><span>Automated instrumentation using compiler</span></li>
+<li><span>Manual instrumentation using API calls</span></li>
+<li><span>Manual instrumentation using directives</span></li>
+</ol>
+<h3 class=" ">Automated instrumentation</h3>
+<p>is the easiest method. Score-P will automatically add instrumentation to every routine entry and exit using compiler hooks, and will intercept MPI calls and OpenMP regions. This method might, however, produce a large number of data. If you want to focus on profiler a specific regions of your code, consider using the manual instrumentation methods. To use automated instrumentation, simply prepend <span class="monospace">scorep</span> to your compilation command. For example, replace :Â </p>
+<pre class="fragment">$ mpif90 -c foo.f90
+$ mpif90 -c bar.f90
+$ mpif90 -o myapp foo.o bar.o</pre>
+<p class=" ">with :</p>
+<pre class="fragment">$ scorep mpif90 -c foo.f90
+$ scorep mpif90 -c bar.f90
+$ scorep mpif90 -o myapp foo.o bar.o</pre>
+<p class=" ">Usually your program is compiled using a Makefile or similar script, so it advisable to add the <span class="monospace">scorep</span> command to your definition of variables <span class="monospace">CC</span>, <span class="monospace">CXX</span>, <span class="monospace">FCC</span> etc.</p>
+<p class=" ">It is important that <span class="monospace">scorep</span> is prepended also to the linking command, in order to link with Score-P instrumentation libraries.</p>
+<h3 class=" "><span>Manual instrumentation using API calls</span></h3>
+<p class=" ">To use this kind of instrumentation, use <span class="monospace">scorep</span> with switch <span class="monospace">--user</span>. You will then mark regions to be instrumented by inserting API calls.</p>
+<p class=" ">An example in C/C++ :</p>
+<pre class=" ">#include <scorep/SCOREP_User.h><br />void foo()<br />{<br /> SCOREP_USER_REGION_DEFINE( my_region_handle )<br /> // more declarations<br /> SCOREP_USER_REGION_BEGIN( my_region_handle, "foo", SCOREP_USER_REGION_TYPE_COMMON )<br /> // do something<br /> SCOREP_USER_REGION_END( my_region_handle )<br />}</pre>
+<p class=" ">Â and Fortran :</p>
+<pre class=" ">#include "scorep/SCOREP_User.inc"<br />subroutine foo<br /> SCOREP_USER_REGION_DEFINE( my_region_handle )<br /> ! more declarations<br /> SCOREP_USER_REGION_BEGIN( my_region_handle, "foo", SCOREP_USER_REGION_TYPE_COMMON )<br /> ! do something<br /> SCOREP_USER_REGION_END( my_region_handle )<br />end subroutine foo</pre>
+<p>Please refer to the <a class="external-link" href="https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf" target="_self" title="">documentation for description of the API</a>.</p>
+<h3 class=" "><span>Manual instrumentation using directives</span></h3>
+<p>This method uses POMP2 directives to mark regions to be instrumented. To use this method, use command <span class="monospace">scorep --pomp.</span></p>
+<p>Example directives in C/C++ :</p>
+<pre class=" ">void foo(...)<br />{<br /> /* declarations */<br /> #pragma pomp inst begin(foo)<br /> ...<br /> if (<condition>)<br /> {<br /> #pragma pomp inst altend(foo)<br /> return;<br /> }<br /> ...<br /> #pragma pomp inst end(foo)<br />}</pre>
+<p><span>and in Fortran :</span></p>
+<pre class=" ">subroutine foo(...)<br /> !declarations<br /> !POMP$ INST BEGIN(foo)<br /> ...<br /> if (<condition>) then<br /><span> !POMP$ INST ALTEND(foo)<br /></span><span> return<br /></span><span> end if<br /></span><span> ...<br /></span><span> !POMP$ INST END(foo)<br /></span><span>end subroutine foo</span></pre>
+<p>The directives are ignored if the program is compiled without Score-P. Again, please refer to the <a class="external-link" href="https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf" target="_self" title="">documentation</a> for a more elaborate description.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
index 48772480e..b4cd5497a 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
@@ -146,4 +146,3 @@ Again, please refer to the
[documentation](https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf)
for a more elaborate description.
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+ <h2 class=" ">Introduction</h2>
+<p>We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations.<br />On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.</p>
+<h2 class=" ">Intel debugger</h2>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">X display</a> for running the GUI.</p>
+<pre class=" ">$ module load intel<br />$ idb</pre>
+<p>Read more at the <a href="../intel-suite/intel-debugger.html" title="" target="_self" class="internal-link">Intel Debugger</a> page.</p>
+<h2 class=" ">Allinea Forge (DDT/MAP)</h2>
+<p>Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
+<pre class=" ">$ module load Forge<br />$ forge</pre>
+<p>Read more at the <a href="allinea-ddt.html" title="" target="_self" class="internal-link">Allinea DDT</a> page.</p>
+<h2 class=" ">Allinea Performance Reports</h2>
+<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.</p>
+<pre class=" ">$ module load PerformanceReports/6.0 <br />$ perf-report mpirun -n 64 ./my_application argument01 argument02</pre>
+<p class=" ">Read more at the <a href="allinea-performance-reports.html" title="" target="_self" class="internal-link">Allinea Performance Reports</a> page.</p>
+<h2 class=" ">RougeWave Totalview</h2>
+<p>TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.</p>
+<pre class=" ">$ module load totalview<br />$ totalview</pre>
+<p>Read more at the <a href="total-view.html" title="" target="_self" class="internal-link">Totalview</a> page.</p>
+<h2 class=" ">Vampir trace analyzer</h2>
+<p>Vampir is a GUI trace analyzer for traces in OTF format.</p>
+<pre>$ module load Vampir/8.5.0<br />$ vampir</pre>
+<p>Read more at the <a href="../../../salomon/software/debuggers/vampir.html" title="" target="_self" class="internal-link">Vampir</a> page.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md
index 847f19a51..fc017fcdd 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md
@@ -85,4 +85,3 @@ Vampir is a GUI trace analyzer for traces in OTF format.
Read more at
the [Vampir](../../../salomon/software/debuggers/vampir.html) page.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.html
new file mode 100644
index 000000000..8a033686f
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.html
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+ <dt>Info</dt>
+ <dd></dd>
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+
+ <div id="viewlet-above-content-title"></div>
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+ Total View
+ </h1>
+
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+ TotalView is a GUI-based source code multi-process, multi-thread debugger.
+ </div>
+
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+
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+ <h2 class=" ">License and Limitations for Anselm Users</h2>
+<p>On Anselm users can debug OpenMP or MPI code that runs up to 64 parallel processes. These limitation means that:<br /><br />Â Â Â 1 user can debug up 64 processes, or<br />Â Â Â 32 users can debug 2 processes, etc.<br /><br />Debugging of GPU accelerated codes is also supported.</p>
+<p>You can check the status of the licenses here:</p>
+<pre class=" ">cat /apps/user/licenses/totalview_features_state.txt</pre>
+<pre class=" "># totalview<br /># -------------------------------------------------<br /># FEATURE                      TOTAL  USED AVAIL<br /># -------------------------------------------------<br />TotalView_Team                    64     0    64<br />Replay                            64     0    64<br />CUDA                              64     0    64</pre>
+<h2 class=" ">Compiling Code to run with TotalView</h2>
+<h3 class=" ">Modules</h3>
+<p>Load all necessary modules to compile the code. For example:</p>
+<pre class=" ">module load intel<br /><br />module load impi  ... or ... module load openmpi/X.X.X-icc</pre>
+<p>Load the TotalView module:</p>
+<pre class=" ">module load totalview/8.12</pre>
+<p>Compile the code:</p>
+<pre class=" ">mpicc -g -O0 -o test_debug test.c<br /><br />mpif90 -g -O0 -o test_debug test.f</pre>
+<h3 class=" ">Compiler flags</h3>
+<p>Before debugging, you need to compile your code with theses flags:</p>
+<p class="exclamation"><strong>-g</strong> : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.<br /><br /><strong>-O0</strong> : Suppress all optimizations.</p>
+<h2 class=" ">Starting a Job with TotalView</h2>
+<p>Be sure to log in with an X window forwarding enabled. This could mean using the -X in the ssh:Â </p>
+<pre class=" ">ssh -X username@anselm.it4i.cz </pre>
+<p>Other options is to access login node using VNC. Please see the detailed information on how to use graphic user interface on Anselm <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33#VNC" title="" target="_self" class="internal-link">here</a>.</p>
+<p>From the login node an interactive session with X windows forwarding (-X option) can be started by following command:</p>
+<pre class=" ">qsub -I -X -A NONE-0-0 -q qexp -lselect=1:ncpus=16:mpiprocs=16,walltime=01:00:00 </pre>
+<p>Then launch the debugger with the totalview command followed by the name of the executable to debug.</p>
+<h3 class=" ">Debugging a serial code</h3>
+<p>To debug a serial code use:</p>
+<pre class=" ">totalview test_debug</pre>
+<h3 class=" ">Debugging a parallel code - option 1</h3>
+<p>To debug a parallel code compiled with <span><strong>OpenMPI</strong></span> you need to setup your TotalView environment:Â </p>
+<p class="callout"><strong>Please note:</strong> To be able to run parallel debugging procedure from the command line without stopping the debugger in the mpiexec source code you have to add the following function to your <strong>~/.tvdrc</strong> file:</p>
+<pre class=" ">proc mpi_auto_run_starter {loaded_id} {<br />Â Â Â set starter_programs {mpirun mpiexec orterun}<br />Â Â Â set executable_name [TV::symbol get $loaded_id full_pathname]<br />Â Â Â set file_component [file tail $executable_name]<br /><br />Â Â Â if {[lsearch -exact $starter_programs $file_component] != -1} {<br />Â Â Â Â Â Â Â puts "**************************************"<br />Â Â Â Â Â Â Â puts "Automatically starting $file_component"<br />Â Â Â Â Â Â Â puts "**************************************"<br />Â Â Â Â Â Â Â dgo<br />Â Â Â }<br />}<br /><br /># Append this function to TotalView's image load callbacks so that<br /># TotalView run this program automatically.<br /><br />dlappend TV::image_load_callbacks mpi_auto_run_starter</pre>
+<p>The source code of this function can be also found in</p>
+<pre class=" ">/apps/mpi/openmpi/intel/1.6.5/etc/openmpi-totalview.tcl</pre>
+<p class="callout">You can also add only following line to you ~/.tvdrc file instead of the entire function: <br /><br /><strong>source /apps/mpi/openmpi/intel/1.6.5/etc/openmpi-totalview.tcl</strong></p>
+<p>You need to do this step only once.</p>
+<p>Now you can run the parallel debugger using:</p>
+<pre class=" ">mpirun -tv -n 5 ./test_debug</pre>
+<p>When following dialog appears click on "Yes"</p>
+<p><img alt="" src="totalview1.png" title="" class="image-inline" /></p>
+<p>At this point the main TotalView GUI window will appear and you can insert the breakpoints and start debugging:</p>
+<p><img alt="" src="totalview2.png" title="" class="image-inline" /></p>
+<h3 class=" ">Debugging a parallel code - option 2</h3>
+<p>Other option to start new parallel debugging session from a command line is to let TotalView to execute mpirun by itself. In this case user has to specify a MPI implementation used to compile the source code. </p>
+<p>The following example shows how to start debugging session with Intel MPI:</p>
+<pre class=" ">module load intel/13.5.192 impi/4.1.1.036 totalview/8/13<br /><br />totalview -mpi "Intel MPI-Hydra" -np 8 ./hello_debug_impi</pre>
+<p>After running previous command you will see the same window as shown in the screenshot above.</p>
+<p>More information regarding the command line parameters of the TotalView can be found TotalView Reference Guide, Chapter 7: TotalView Command Syntax.  </p>
+<h2 class=" ">Documentation</h2>
+<p>[1] The <a class="external-link" href="http://www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview" target="_self" title="">TotalView documentation</a> web page is a good resource for learning more about some of the advanced TotalView features.</p>
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
index 3e8b2f087..8361a39a1 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
@@ -51,11 +51,11 @@ Compile the code:
Before debugging, you need to compile your code with theses flags:
-**-g** Generates extra debugging information usable by GDB. -g3
+**-g** : Generates extra debugging information usable by GDB. -g3
includes even more debugging information. This option is available for
GNU and INTEL C/C++ and Fortran compilers.
-**-O0** Suppress all optimizations.
+**-O0** : Suppress all optimizations.
Starting a Job with TotalView
-----------------------------
@@ -151,7 +151,7 @@ After running previous command you will see the same window as shown in
the screenshot above.
More information regarding the command line parameters of the TotalView
-can be found TotalView Reference Guide, Chapter 7TotalView Command
+can be found TotalView Reference Guide, Chapter 7: TotalView Command
Syntax. Â
Documentation
@@ -161,4 +161,3 @@ Documentation
documentation](http://www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview)
web page is a good resource for learning more about some of the advanced
TotalView features.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.html
new file mode 100644
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+ <h2 class=" ">About Valgrind</h2>
+<p class=" ">Valgrind is an open-source tool, used mainly for debuggig memory-related problems, such as memory leaks, use of uninitalized memory etc. in C/C++ applications. The toolchain was however extended over time with more functionality, such as debugging of threaded applications, cache profiling, not limited only to C/C++.</p>
+<p class=" ">Valgind is an extremely useful tool for debugging memory errors such as <a class="external-link" href="http://en.wikipedia.org/wiki/Off-by-one_error" target="_self" title="">off-by-one</a>. Valgrind uses a virtual machine and dynamic recompilation of binary code, because of that, you can expect that programs being debugged by Valgrind run 5-100 times slower.</p>
+<p class=" ">The main tools available in Valgrind are :</p>
+<ul>
+<li><strong>Memcheck</strong>, the original, must used and default tool. Verifies memory access in you program and can detect use of unitialized memory, out of bounds memory access, memory leaks, double free, etc.</li>
+<li><strong>Massif</strong>, a heap profiler.</li>
+<li><strong>Hellgrind</strong> and <strong>DRD</strong> can detect race conditions in multi-threaded applications.</li>
+<li><strong>Cachegrind</strong>, a cache profiler.</li>
+<li><strong>Callgrind</strong>, a callgraph analyzer.</li>
+<li>For a full list and detailed documentation, please refer to the <a class="external-link" href="http://valgrind.org/docs/" target="_self" title="">official Valgrind documentation</a>.</li>
+</ul>
+<h2 class=" ">Installed versions</h2>
+<p>There are two versions of Valgrind available on Anselm.</p>
+<ul>
+<li><span>Version 3.6.0, installed by operating system vendor in </span><span class="monospace">/usr/bin/valgrind. </span><span>This version is available by default, without the need to load any module. This version however does not provide additional MPI support.</span></li>
+<li><span><span>Version 3.9.0 with support for Intel MPI, available in <a href="../../environment-and-modules.html" title="" target="_self" class="internal-link">module</a>Â </span></span><span class="monospace">valgrind/3.9.0-impi. </span>After loading the module, this version replaces the default valgrind.</li>
+</ul>
+<h2 class=" ">Usage</h2>
+<p>Compile the application which you want to debug as usual. It is advisable to add compilation flags <span class="monospace">-g </span>(to add debugging information to the binary so that you will see original source code lines in the output) and <span class="monospace">-O0</span> (to disable compiler optimizations). </p>
+<p>For example, lets look at this C code, which has two problems :</p>
+<pre class=" ">#include <stdlib.h><br /><br />void f(void) <br />{<br /> int* x = malloc(10 * sizeof(int));<br /> x[10] = 0; // problem 1: heap block overrun<br />} // problem 2: memory leak -- x not freed<br /><br />int main(void)<br />{<br /> f();<br /> return 0;<br />}</pre>
+<p>Now, compile it with Intel compiler :</p>
+<pre class=" ">$ module add intel<br />$ icc -g valgrind-example.c -o valgrind-example </pre>
+<p>Now, lets run it with Valgrind. The syntax is :</p>
+<p><span class="monospace">valgrind [valgrind options] <your program binary> [your program options]</span></p>
+<p>If no Valgrind options are specified, Valgrind defaults to running Memcheck tool. Please refer to the Valgrind documentation for a full description of command line options.</p>
+<pre class=" ">$ valgrind ./valgrind-example<br />==12652== Memcheck, a memory error detector<br />==12652== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.<br />==12652== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info<br />==12652== Command: ./valgrind-example<br />==12652== <br /><span>==12652== Invalid write of size 4</span><br />==12652== at 0x40053E: f (valgrind-example.c:6)<br />==12652== by 0x40054E: main (valgrind-example.c:11)<br /><span>==12652== Address 0x5861068 is 0 bytes after a block of size 40 alloc'd</span><br />==12652== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)<br />==12652== by 0x400528: f (valgrind-example.c:5)<br />==12652== by 0x40054E: main (valgrind-example.c:11)<br />==12652== <br />==12652== <br />==12652== HEAP SUMMARY:<br />==12652== in use at exit: 40 bytes in 1 blocks<br />==12652== total heap usage: 1 allocs, 0 frees, 40 bytes allocated<br />==12652== <br />==12652== LEAK SUMMARY:<br /><span>==12652== definitely lost: 40 bytes in 1 blocks</span><br />==12652== indirectly lost: 0 bytes in 0 blocks<br />==12652== possibly lost: 0 bytes in 0 blocks<br />==12652== still reachable: 0 bytes in 0 blocks<br />==12652== suppressed: 0 bytes in 0 blocks<br />==12652== Rerun with --leak-check=full to see details of leaked memory<br />==12652== <br />==12652== For counts of detected and suppressed errors, rerun with: -v<br />==12652== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 6 from 6)</pre>
+<p>In the output we can see that Valgrind has detected both errors - the off-by-one memory access at line 5 and a memory leak of 40 bytes. If we want a detailed analysis of the memory leak, we need to run Valgrind with <span class="monospace">--leak-check=full</span> option :</p>
+<pre class=" ">$ valgrind --leak-check=full ./valgrind-example<br />==23856== Memcheck, a memory error detector<br />==23856== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.<br />==23856== Using Valgrind-3.6.0 and LibVEX; rerun with -h for copyright info<br />==23856== Command: ./valgrind-example<br />==23856== <br />==23856== Invalid write of size 4<br />==23856== at 0x40067E: f (valgrind-example.c:6)<br />==23856== by 0x40068E: main (valgrind-example.c:11)<br />==23856== Address 0x66e7068 is 0 bytes after a block of size 40 alloc'd<br />==23856== at 0x4C26FDE: malloc (vg_replace_malloc.c:236)<br />==23856== by 0x400668: f (valgrind-example.c:5)<br />==23856== by 0x40068E: main (valgrind-example.c:11)<br />==23856== <br />==23856== <br />==23856== HEAP SUMMARY:<br />==23856== in use at exit: 40 bytes in 1 blocks<br />==23856== total heap usage: 1 allocs, 0 frees, 40 bytes allocated<br />==23856== <br />==23856== 40 bytes in 1 blocks are definitely lost in loss record 1 of 1<br />==23856== at 0x4C26FDE: malloc (vg_replace_malloc.c:236)<br />==23856== by 0x400668: f (valgrind-example.c:5)<br />==23856== by 0x40068E: main (valgrind-example.c:11)<br />==23856== <br />==23856== LEAK SUMMARY:<br />==23856== definitely lost: 40 bytes in 1 blocks<br />==23856== indirectly lost: 0 bytes in 0 blocks<br />==23856== possibly lost: 0 bytes in 0 blocks<br />==23856== still reachable: 0 bytes in 0 blocks<br />==23856== suppressed: 0 bytes in 0 blocks<br />==23856== <br />==23856== For counts of detected and suppressed errors, rerun with: -v<br />==23856== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 6 from 6)</pre>
+<p>Now we can see that the memory leak is due to the <span class="monospace">malloc()</span> at line 6.</p>
+<h2 class=" "><span>Usage with MPI</span></h2>
+<p>Although Valgrind is not primarily a parallel debugger, it can be used to debug parallel applications as well. When launching your parallel applications, prepend the valgrind command. For example :</p>
+<pre class=" ">$ mpirun -np 4 valgrind myapplication</pre>
+<p class=" ">The default version without MPI support will however report a large number of false errors in the MPI library, such as :</p>
+<pre class=" ">==30166== Conditional jump or move depends on uninitialised value(s)<br />==30166== at 0x4C287E8: strlen (mc_replace_strmem.c:282)<br />==30166== by 0x55443BD: I_MPI_Processor_model_number (init_interface.c:427)<br />==30166== by 0x55439E0: I_MPI_Processor_arch_code (init_interface.c:171)<br />==30166== by 0x558D5AE: MPID_nem_impi_init_shm_configuration (mpid_nem_impi_extensions.c:1091)<br />==30166== by 0x5598F4C: MPID_nem_init_ckpt (mpid_nem_init.c:566)<br />==30166== by 0x5598B65: MPID_nem_init (mpid_nem_init.c:489)<br />==30166== by 0x539BD75: MPIDI_CH3_Init (ch3_init.c:64)<br />==30166== by 0x5578743: MPID_Init (mpid_init.c:193)<br />==30166== by 0x554650A: MPIR_Init_thread (initthread.c:539)<br />==30166== by 0x553369F: PMPI_Init (init.c:195)<br />==30166== by 0x4008BD: main (valgrind-example-mpi.c:18)</pre>
+<p class=" ">so it is better to use the MPI-enabled valgrind from module. The MPI version requires library <span class="monospace">/apps/tools/valgrind/3.9.0/impi/lib/valgrind/libmpiwrap-amd64-linux.so</span>, which must be included in the<span class="monospace"> LD_PRELOAD </span>environment variable.</p>
+<p class=" ">Lets look at this MPI example :</p>
+<pre class=" "><span>#include <</span><span>stdlib.h</span><span>><br /></span><span>#include <</span><span>mpi.h</span><span>></span><span>Â <br /><br /></span><span>int</span><span> main(</span><span>int</span><span> </span><span>argc</span><span>, char *</span><span>argv</span><span>[])<br /></span><span>{<br /></span><span>Â Â Â Â Â </span><span>int</span><span> *data = </span><span>malloc</span><span>(</span><span>sizeof</span><span>(</span><span>int</span><span>)*99);<br /></span><span><br />Â </span><span>Â Â Â Â </span><span>MPI_Init</span><span>(&</span><span>argc</span><span>, &</span><span>argv</span><span>);<br /></span><span>Â Â Â Â MPI_Bcast</span><span>(data, 100, MPI_INT, 0, MPI_COMM_WORLD);<br /></span><span>Â Â Â Â Â </span><span>MPI_Finalize</span><span>();</span><span>Â <br /></span><span><br />Â Â Â Â Â Â Â return 0;<br /></span><span>}</span></pre>
+<p class=" ">There are two errors - use of uninitialized memory and invalid length of the buffer. Lets debug it with valgrind :</p>
+<pre class=" ">$ module add intel impi<br />$ mpicc -g valgrind-example-mpi.c -o valgrind-example-mpi<br />$ module add valgrind/3.9.0-impi<br />$ <span>mpirun -np 2 -env LD_PRELOAD /apps/tools/valgrind/3.9.0/impi/lib/valgrind/libmpiwrap-amd64-linux.so valgrind ./valgrind-example-mpi</span></pre>
+<p class=" ">Prints this output : (note that there is output printed for every launched MPI process)</p>
+<pre class=" ">==31318== Memcheck, a memory error detector<br />==31318== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.<br />==31318== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info<br />==31318== Command: ./valgrind-example-mpi<br />==31318== <br />==31319== Memcheck, a memory error detector<br />==31319== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.<br />==31319== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info<br />==31319== Command: ./valgrind-example-mpi<br />==31319== <br />valgrind MPI wrappers 31319: Active for pid 31319<br />valgrind MPI wrappers 31319: Try MPIWRAP_DEBUG=help for possible options<br />valgrind MPI wrappers 31318: Active for pid 31318<br />valgrind MPI wrappers 31318: Try MPIWRAP_DEBUG=help for possible options<br />==31319== Unaddressable byte(s) found during client check request<br />==31319== at 0x4E35974: check_mem_is_addressable_untyped (libmpiwrap.c:960)<br />==31319== by 0x4E5D0FE: PMPI_Bcast (libmpiwrap.c:908)<br />==31319== by 0x400911: main (valgrind-example-mpi.c:20)<br />==31319== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd<br />==31319== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)<br />==31319== by 0x4007BC: main (valgrind-example-mpi.c:8)<br />==31319== <br />==31318== Uninitialised byte(s) found during client check request<br />==31318== at 0x4E3591D: check_mem_is_defined_untyped (libmpiwrap.c:952)<br />==31318== by 0x4E5D06D: PMPI_Bcast (libmpiwrap.c:908)<br />==31318== by 0x400911: main (valgrind-example-mpi.c:20)<br />==31318== Address 0x6929040 is 0 bytes inside a block of size 396 alloc'd<br />==31318== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)<br />==31318== by 0x4007BC: main (valgrind-example-mpi.c:8)<br />==31318== <br />==31318== Unaddressable byte(s) found during client check request<br />==31318== at 0x4E3591D: check_mem_is_defined_untyped (libmpiwrap.c:952)<br />==31318== by 0x4E5D06D: PMPI_Bcast (libmpiwrap.c:908)<br />==31318== by 0x400911: main (valgrind-example-mpi.c:20)<br />==31318== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd<br />==31318== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)<br />==31318== by 0x4007BC: main (valgrind-example-mpi.c:8)<br />==31318== <br />==31318== <br />==31318== HEAP SUMMARY:<br />==31318== in use at exit: 3,172 bytes in 67 blocks<br />==31318== total heap usage: 191 allocs, 124 frees, 81,203 bytes allocated<br />==31318== <br />==31319== <br />==31319== HEAP SUMMARY:<br />==31319== in use at exit: 3,172 bytes in 67 blocks<br />==31319== total heap usage: 175 allocs, 108 frees, 48,435 bytes allocated<br />==31319== <br />==31318== LEAK SUMMARY:<br />==31318== definitely lost: 408 bytes in 3 blocks<br />==31318== indirectly lost: 256 bytes in 1 blocks<br />==31318== possibly lost: 0 bytes in 0 blocks<br />==31318== still reachable: 2,508 bytes in 63 blocks<br />==31318== suppressed: 0 bytes in 0 blocks<br />==31318== Rerun with --leak-check=full to see details of leaked memory<br />==31318== <br />==31318== For counts of detected and suppressed errors, rerun with: -v<br />==31318== Use --track-origins=yes to see where uninitialised values come from<br />==31318== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 4 from 4)<br />==31319== LEAK SUMMARY:<br />==31319== definitely lost: 408 bytes in 3 blocks<br />==31319== indirectly lost: 256 bytes in 1 blocks<br />==31319== possibly lost: 0 bytes in 0 blocks<br />==31319== still reachable: 2,508 bytes in 63 blocks<br />==31319== suppressed: 0 bytes in 0 blocks<br />==31319== Rerun with --leak-check=full to see details of leaked memory<br />==31319== <br />==31319== For counts of detected and suppressed errors, rerun with: -v<br />==31319== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 4 from 4)</pre>
+<p class=" ">We can see that Valgrind has reported use of unitialised memory on the master process (which reads the array to be broadcasted) and use of unaddresable memory on both processes.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
index f8f5df73b..b1aa57fc5 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
@@ -62,8 +62,8 @@ For example, lets look at this C code, which has two problems :
void f(void)
{
int* x = malloc(10 * sizeof(int));
- x[10] = 0; // problem 1heap block overrun
- } // problem 2memory leak -- x not freed
+ x[10] = 0; // problem 1: heap block overrun
+ } // problem 2: memory leak -- x not freed
int main(void)
{
@@ -89,31 +89,31 @@ description of command line options.
==12652== Memcheck, a memory error detector
==12652== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
==12652== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
- ==12652== Command./valgrind-example
+ ==12652== Command: ./valgrind-example
==12652==
==12652== Invalid write of size 4
- ==12652== at 0x40053Ef (valgrind-example.c:6)
- ==12652== by 0x40054Emain (valgrind-example.c:11)
+ ==12652== at 0x40053E: f (valgrind-example.c:6)
+ ==12652== by 0x40054E: main (valgrind-example.c:11)
==12652== Address 0x5861068 is 0 bytes after a block of size 40 alloc'd
- ==12652== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
- ==12652== by 0x400528f (valgrind-example.c:5)
- ==12652== by 0x40054Emain (valgrind-example.c:11)
+ ==12652== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)
+ ==12652== by 0x400528: f (valgrind-example.c:5)
+ ==12652== by 0x40054E: main (valgrind-example.c:11)
==12652==
==12652==
==12652== HEAP SUMMARY:
- ==12652== in use at exit40 bytes in 1 blocks
- ==12652== total heap usage1 allocs, 0 frees, 40 bytes allocated
+ ==12652== in use at exit: 40 bytes in 1 blocks
+ ==12652== total heap usage: 1 allocs, 0 frees, 40 bytes allocated
==12652==
==12652== LEAK SUMMARY:
- ==12652== definitely lost40 bytes in 1 blocks
- ==12652== indirectly lost0 bytes in 0 blocks
- ==12652== possibly lost0 bytes in 0 blocks
- ==12652== still reachable0 bytes in 0 blocks
- ==12652== suppressed0 bytes in 0 blocks
+ ==12652== definitely lost: 40 bytes in 1 blocks
+ ==12652== indirectly lost: 0 bytes in 0 blocks
+ ==12652== possibly lost: 0 bytes in 0 blocks
+ ==12652== still reachable: 0 bytes in 0 blocks
+ ==12652== suppressed: 0 bytes in 0 blocks
==12652== Rerun with --leak-check=full to see details of leaked memory
==12652==
- ==12652== For counts of detected and suppressed errors, rerun with-v
- ==12652== ERROR SUMMARY1 errors from 1 contexts (suppressed6 from 6)
+ ==12652== For counts of detected and suppressed errors, rerun with: -v
+ ==12652== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 6 from 6)
In the output we can see that Valgrind has detected both errors - the
off-by-one memory access at line 5 and a memory leak of 40 bytes. If we
@@ -124,35 +124,35 @@ with <span class="monospace">--leak-check=full</span> option :
==23856== Memcheck, a memory error detector
==23856== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
==23856== Using Valgrind-3.6.0 and LibVEX; rerun with -h for copyright info
- ==23856== Command./valgrind-example
+ ==23856== Command: ./valgrind-example
==23856==
==23856== Invalid write of size 4
- ==23856== at 0x40067Ef (valgrind-example.c:6)
- ==23856== by 0x40068Emain (valgrind-example.c:11)
+ ==23856== at 0x40067E: f (valgrind-example.c:6)
+ ==23856== by 0x40068E: main (valgrind-example.c:11)
==23856== Address 0x66e7068 is 0 bytes after a block of size 40 alloc'd
- ==23856== at 0x4C26FDEmalloc (vg_replace_malloc.c:236)
- ==23856== by 0x400668f (valgrind-example.c:5)
- ==23856== by 0x40068Emain (valgrind-example.c:11)
+ ==23856== at 0x4C26FDE: malloc (vg_replace_malloc.c:236)
+ ==23856== by 0x400668: f (valgrind-example.c:5)
+ ==23856== by 0x40068E: main (valgrind-example.c:11)
==23856==
==23856==
==23856== HEAP SUMMARY:
- ==23856== in use at exit40 bytes in 1 blocks
- ==23856== total heap usage1 allocs, 0 frees, 40 bytes allocated
+ ==23856== in use at exit: 40 bytes in 1 blocks
+ ==23856== total heap usage: 1 allocs, 0 frees, 40 bytes allocated
==23856==
==23856== 40 bytes in 1 blocks are definitely lost in loss record 1 of 1
- ==23856== at 0x4C26FDEmalloc (vg_replace_malloc.c:236)
- ==23856== by 0x400668f (valgrind-example.c:5)
- ==23856== by 0x40068Emain (valgrind-example.c:11)
+ ==23856== at 0x4C26FDE: malloc (vg_replace_malloc.c:236)
+ ==23856== by 0x400668: f (valgrind-example.c:5)
+ ==23856== by 0x40068E: main (valgrind-example.c:11)
==23856==
==23856== LEAK SUMMARY:
- ==23856== definitely lost40 bytes in 1 blocks
- ==23856== indirectly lost0 bytes in 0 blocks
- ==23856== possibly lost0 bytes in 0 blocks
- ==23856== still reachable0 bytes in 0 blocks
- ==23856== suppressed0 bytes in 0 blocks
+ ==23856== definitely lost: 40 bytes in 1 blocks
+ ==23856== indirectly lost: 0 bytes in 0 blocks
+ ==23856== possibly lost: 0 bytes in 0 blocks
+ ==23856== still reachable: 0 bytes in 0 blocks
+ ==23856== suppressed: 0 bytes in 0 blocks
==23856==
- ==23856== For counts of detected and suppressed errors, rerun with-v
- ==23856== ERROR SUMMARY2 errors from 2 contexts (suppressed6 from 6)
+ ==23856== For counts of detected and suppressed errors, rerun with: -v
+ ==23856== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 6 from 6)
Now we can see that the memory leak is due to the <span
class="monospace">malloc()</span> at line 6.
@@ -170,17 +170,17 @@ The default version without MPI support will however report a large
number of false errors in the MPI library, such as :
==30166== Conditional jump or move depends on uninitialised value(s)
- ==30166== at 0x4C287E8strlen (mc_replace_strmem.c:282)
- ==30166== by 0x55443BDI_MPI_Processor_model_number (init_interface.c:427)
- ==30166== by 0x55439E0I_MPI_Processor_arch_code (init_interface.c:171)
- ==30166== by 0x558D5AEMPID_nem_impi_init_shm_configuration (mpid_nem_impi_extensions.c:1091)
- ==30166== by 0x5598F4CMPID_nem_init_ckpt (mpid_nem_init.c:566)
- ==30166== by 0x5598B65MPID_nem_init (mpid_nem_init.c:489)
- ==30166== by 0x539BD75MPIDI_CH3_Init (ch3_init.c:64)
- ==30166== by 0x5578743MPID_Init (mpid_init.c:193)
- ==30166== by 0x554650AMPIR_Init_thread (initthread.c:539)
- ==30166== by 0x553369FPMPI_Init (init.c:195)
- ==30166== by 0x4008BDmain (valgrind-example-mpi.c:18)
+ ==30166== at 0x4C287E8: strlen (mc_replace_strmem.c:282)
+ ==30166== by 0x55443BD: I_MPI_Processor_model_number (init_interface.c:427)
+ ==30166== by 0x55439E0: I_MPI_Processor_arch_code (init_interface.c:171)
+ ==30166== by 0x558D5AE: MPID_nem_impi_init_shm_configuration (mpid_nem_impi_extensions.c:1091)
+ ==30166== by 0x5598F4C: MPID_nem_init_ckpt (mpid_nem_init.c:566)
+ ==30166== by 0x5598B65: MPID_nem_init (mpid_nem_init.c:489)
+ ==30166== by 0x539BD75: MPIDI_CH3_Init (ch3_init.c:64)
+ ==30166== by 0x5578743: MPID_Init (mpid_init.c:193)
+ ==30166== by 0x554650A: MPIR_Init_thread (initthread.c:539)
+ ==30166== by 0x553369F: PMPI_Init (init.c:195)
+ ==30166== by 0x4008BD: main (valgrind-example-mpi.c:18)
so it is better to use the MPI-enabled valgrind from module. The MPI
version requires library <span
@@ -212,80 +212,79 @@ the buffer. Lets debug it with valgrind :
$ module add valgrind/3.9.0-impi
$ mpirun -np 2 -env LD_PRELOAD /apps/tools/valgrind/3.9.0/impi/lib/valgrind/libmpiwrap-amd64-linux.so valgrind ./valgrind-example-mpi
-Prints this output (note that there is output printed for every
+Prints this output : (note that there is output printed for every
launched MPI process)
==31318== Memcheck, a memory error detector
==31318== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
==31318== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
- ==31318== Command./valgrind-example-mpi
+ ==31318== Command: ./valgrind-example-mpi
==31318==
==31319== Memcheck, a memory error detector
==31319== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
==31319== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
- ==31319== Command./valgrind-example-mpi
+ ==31319== Command: ./valgrind-example-mpi
==31319==
- valgrind MPI wrappers 31319Active for pid 31319
- valgrind MPI wrappers 31319Try MPIWRAP_DEBUG=help for possible options
- valgrind MPI wrappers 31318Active for pid 31318
- valgrind MPI wrappers 31318Try MPIWRAP_DEBUG=help for possible options
+ valgrind MPI wrappers 31319: Active for pid 31319
+ valgrind MPI wrappers 31319: Try MPIWRAP_DEBUG=help for possible options
+ valgrind MPI wrappers 31318: Active for pid 31318
+ valgrind MPI wrappers 31318: Try MPIWRAP_DEBUG=help for possible options
==31319== Unaddressable byte(s) found during client check request
- ==31319== at 0x4E35974check_mem_is_addressable_untyped (libmpiwrap.c:960)
- ==31319== by 0x4E5D0FEPMPI_Bcast (libmpiwrap.c:908)
- ==31319== by 0x400911main (valgrind-example-mpi.c:20)
+ ==31319== at 0x4E35974: check_mem_is_addressable_untyped (libmpiwrap.c:960)
+ ==31319== by 0x4E5D0FE: PMPI_Bcast (libmpiwrap.c:908)
+ ==31319== by 0x400911: main (valgrind-example-mpi.c:20)
==31319== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd
- ==31319== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
- ==31319== by 0x4007BCmain (valgrind-example-mpi.c:8)
+ ==31319== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)
+ ==31319== by 0x4007BC: main (valgrind-example-mpi.c:8)
==31319==
==31318== Uninitialised byte(s) found during client check request
- ==31318== at 0x4E3591Dcheck_mem_is_defined_untyped (libmpiwrap.c:952)
- ==31318== by 0x4E5D06DPMPI_Bcast (libmpiwrap.c:908)
- ==31318== by 0x400911main (valgrind-example-mpi.c:20)
+ ==31318== at 0x4E3591D: check_mem_is_defined_untyped (libmpiwrap.c:952)
+ ==31318== by 0x4E5D06D: PMPI_Bcast (libmpiwrap.c:908)
+ ==31318== by 0x400911: main (valgrind-example-mpi.c:20)
==31318== Address 0x6929040 is 0 bytes inside a block of size 396 alloc'd
- ==31318== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
- ==31318== by 0x4007BCmain (valgrind-example-mpi.c:8)
+ ==31318== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)
+ ==31318== by 0x4007BC: main (valgrind-example-mpi.c:8)
==31318==
==31318== Unaddressable byte(s) found during client check request
- ==31318== at 0x4E3591Dcheck_mem_is_defined_untyped (libmpiwrap.c:952)
- ==31318== by 0x4E5D06DPMPI_Bcast (libmpiwrap.c:908)
- ==31318== by 0x400911main (valgrind-example-mpi.c:20)
+ ==31318== at 0x4E3591D: check_mem_is_defined_untyped (libmpiwrap.c:952)
+ ==31318== by 0x4E5D06D: PMPI_Bcast (libmpiwrap.c:908)
+ ==31318== by 0x400911: main (valgrind-example-mpi.c:20)
==31318== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd
- ==31318== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
- ==31318== by 0x4007BCmain (valgrind-example-mpi.c:8)
+ ==31318== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)
+ ==31318== by 0x4007BC: main (valgrind-example-mpi.c:8)
==31318==
==31318==
==31318== HEAP SUMMARY:
- ==31318== in use at exit3,172 bytes in 67 blocks
- ==31318== total heap usage191 allocs, 124 frees, 81,203 bytes allocated
+ ==31318== in use at exit: 3,172 bytes in 67 blocks
+ ==31318== total heap usage: 191 allocs, 124 frees, 81,203 bytes allocated
==31318==
==31319==
==31319== HEAP SUMMARY:
- ==31319== in use at exit3,172 bytes in 67 blocks
- ==31319== total heap usage175 allocs, 108 frees, 48,435 bytes allocated
+ ==31319== in use at exit: 3,172 bytes in 67 blocks
+ ==31319== total heap usage: 175 allocs, 108 frees, 48,435 bytes allocated
==31319==
==31318== LEAK SUMMARY:
- ==31318== definitely lost408 bytes in 3 blocks
- ==31318== indirectly lost256 bytes in 1 blocks
- ==31318== possibly lost0 bytes in 0 blocks
- ==31318== still reachable2,508 bytes in 63 blocks
- ==31318== suppressed0 bytes in 0 blocks
+ ==31318== definitely lost: 408 bytes in 3 blocks
+ ==31318== indirectly lost: 256 bytes in 1 blocks
+ ==31318== possibly lost: 0 bytes in 0 blocks
+ ==31318== still reachable: 2,508 bytes in 63 blocks
+ ==31318== suppressed: 0 bytes in 0 blocks
==31318== Rerun with --leak-check=full to see details of leaked memory
==31318==
- ==31318== For counts of detected and suppressed errors, rerun with-v
+ ==31318== For counts of detected and suppressed errors, rerun with: -v
==31318== Use --track-origins=yes to see where uninitialised values come from
- ==31318== ERROR SUMMARY2 errors from 2 contexts (suppressed4 from 4)
+ ==31318== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 4 from 4)
==31319== LEAK SUMMARY:
- ==31319== definitely lost408 bytes in 3 blocks
- ==31319== indirectly lost256 bytes in 1 blocks
- ==31319== possibly lost0 bytes in 0 blocks
- ==31319== still reachable2,508 bytes in 63 blocks
- ==31319== suppressed0 bytes in 0 blocks
+ ==31319== definitely lost: 408 bytes in 3 blocks
+ ==31319== indirectly lost: 256 bytes in 1 blocks
+ ==31319== possibly lost: 0 bytes in 0 blocks
+ ==31319== still reachable: 2,508 bytes in 63 blocks
+ ==31319== suppressed: 0 bytes in 0 blocks
==31319== Rerun with --leak-check=full to see details of leaked memory
==31319==
- ==31319== For counts of detected and suppressed errors, rerun with-v
- ==31319== ERROR SUMMARY1 errors from 1 contexts (suppressed4 from 4)
+ ==31319== For counts of detected and suppressed errors, rerun with: -v
+ ==31319== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 4 from 4)
We can see that Valgrind has reported use of unitialised memory on the
master process (which reads the array to be broadcasted) and use of
unaddresable memory on both processes.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.html b/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.html
new file mode 100644
index 000000000..60c7e7834
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+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a href="../../../salomon/software/debuggers/score-p.html" title="" target="_self" class="internal-link">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" src="../../../salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" title="Vampir screenshot" class="image-inline" /></h2>
+<h2 class=" ">Installed versions</h2>
+<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
+<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
+<h2>User manual</h2>
+<p>You can find the detailed user manual in PDF format in <span class="monospace">$EBROOTVAMPIR/doc/vampir-manual.pdf</span></p>
+<h2>References</h2>
+<ol>
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1. <https://www.vampir.eu>
-
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+ A library that implements the GASPI specification
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+ <h2 class=" ">Introduction</h2>
+<p>Programming Next Generation Supercomputers: GPI-2 is an API library for asynchronous interprocess, cross-node communication. It provides a flexible, scalable and fault tolerant interface for parallel applications.</p>
+<p>The GPI-2 library (<a class="external-link" href="http://www.gpi-site.com/gpi2/" target="_self" title="">www.gpi-site.com/gpi2/</a>) implements the GASPI specification (Global Address Space Programming Interface, <a class="external-link" href="http://www.gaspi.de/en/project.html" target="_self" title="">www.gaspi.de</a>). <span>GASPI is a Partitioned Global Address Space (PGAS) API. It aims at scalable, flexible and failure tolerant computing in massively parallel environments.</span></p>
+<h2 class=" ">Modules</h2>
+<p>The GPI-2, version 1.0.2 is available on Anselm via module gpi2:</p>
+<pre class=" ">$ module load gpi2</pre>
+<p>The module sets up environment variables, required for linking and running GPI-2 enabled applications. This particular command loads the default module, which is gpi2/1.0.2</p>
+<h2 class=" ">Linking</h2>
+<p class="callout">Link with -lGPI2 -libverbs</p>
+<p>Load the gpi2 module. Link using <strong>-lGPI2</strong> and <strong></strong> <strong>-libverbs </strong>switches to link your code against GPI-2. The GPI-2 requires the OFED infinband communication library ibverbs.</p>
+<h3 class=" ">Compiling and linking with Intel compilers</h3>
+<pre class=" ">$ module load intel<br />$ module load gpi2<br />$ icc myprog.c -o myprog.x -Wl,-rpath=$LIBRARY_PATH -lGPI2 -libverbs</pre>
+<h3 class=" ">Compiling and linking with GNU compilers</h3>
+<pre class=" ">$ module load gcc<br />$ module load gpi2<br />$ gcc myprog.c -o myprog.x -Wl,-rpath=$LIBRARY_PATH -lGPI2 -libverbs</pre>
+<h2 class=" ">Running the GPI-2 codes</h2>
+<p><span>gaspi_run</span></p>
+<p class="callout">gaspi_run starts the GPI-2 application</p>
+<p>The gaspi_run utility is used to start and run GPI-2 applications:</p>
+<pre class=" ">$ gaspi_run -m machinefile ./myprog.x</pre>
+<p>A machine file (<strong>machinefile</strong>) with the hostnames of nodes where the application will run, must be provided. The<strong></strong> machinefile lists all nodes on which to run, one entry per node per process. This file may be hand created or obtained from standard $PBS_NODEFILE:</p>
+<pre class=" ">$ cut -f1 -d"." $PBS_NODEFILE > machinefile</pre>
+<p>machinefile:</p>
+<pre class=" ">cn79<br />cn80</pre>
+<p>This machinefile will run 2 GPI-2 processes, one on node cn79 other on node cn80.</p>
+<p>machinefle:</p>
+<pre class=" ">cn79<br />cn79<br />cn80<br />cn80</pre>
+<p>This machinefile will run 4 GPI-2 processes, 2 on node cn79 o 2 on node cn80.</p>
+<p class="callout">Use the <strong>mpiprocs</strong> to control how many GPI-2 processes will run per node</p>
+<p>Example:</p>
+<pre class=" ">$ qsub -A OPEN-0-0 -q qexp -l select=2:ncpus=16:mpiprocs=16 -I </pre>
+<p class=" ">This example will produce $PBS_NODEFILE with 16 entries per node.</p>
+<h3 class=" ">gaspi_logger</h3>
+<p class="callout">gaspi_logger views the output form GPI-2 application ranks</p>
+<p>The gaspi_logger utility is used to view the output from all nodes except the master node (rank 0). The gaspi_logger is started, on another session, on the master node - the node where the gaspi_run is executed. The output of the application, when called with gaspi_printf(), will be redirected to the gaspi_logger. Other I/O routines (e.g. printf) will not.</p>
+<h2 class=" ">Example</h2>
+<p>Following is an example GPI-2 enabled code:</p>
+<pre class=" ">#include <GASPI.h><br />#include <stdlib.h><br /> <br />void success_or_exit ( const char* file, const int line, const int ec)<br />{<br /> if (ec != GASPI_SUCCESS)<br /> {<br /> gaspi_printf ("Assertion failed in %s[%i]:%d\n", file, line, ec);<br /> exit (1);<br /> }<br />}<br /> <br />#define ASSERT(ec) success_or_exit (__FILE__, __LINE__, ec);<br /> <br />int main(int argc, char *argv[])<br />{<br /> gaspi_rank_t rank, num;<br /> gaspi_return_t ret;<br /> <br /> /* Initialize GPI-2 */<br /> ASSERT( gaspi_proc_init(GASPI_BLOCK) );<br /> <br /> /* Get ranks information */<br /> ASSERT( gaspi_proc_rank(&rank) );<br /> ASSERT( gaspi_proc_num(&num) );<br /> <br /> gaspi_printf("Hello from rank %d of %d\n",<br /> rank, num);<br /> <br /> /* Terminate */<br /> ASSERT( gaspi_proc_term(GASPI_BLOCK) );<br /> <br /> return 0;<br />}</pre>
+<p class=" ">Load modules and compile:</p>
+<pre class=" ">$ module load gcc gpi2<br />$ gcc helloworld_gpi.c -o helloworld_gpi.x -Wl,-rpath=$LIBRARY_PATH -lGPI2 -libverbs</pre>
+<p class=" ">Submit the job and run the GPI-2 application</p>
+<pre class=" ">$ qsub -q qexp -l select=2:ncpus=1:mpiprocs=1,place=scatter,walltime=00:05:00 -I<span class="pln"><br />qsub: waiting for job 171247.dm2 to start<br />qsub: job 171247.dm2 ready<br /><br />cn79 $ module load gpi2<br />cn79 $ </span><span class="pln">cut -f1 -d"." $PBS_NODEFILE > machinefile<br />cn79 $ gaspi_run -m machinefile ./helloworld_gpi.x</span><br />Hello from rank 0 of 2</pre>
+<p class=" ">At the same time, in another session, you may start the gaspi logger:</p>
+<pre class=" ">$ ssh cn79<br />cn79 $ gaspi_logger<br />GASPI Logger (v1.1)<br />[cn80:0] Hello from rank 1 of 2</pre>
+<p class=" ">In this example, we compile the helloworld_gpi.c code using the<strong> gnu compiler</strong>Â (gcc) and link it to the GPI-2 and ibverbs library. The library search path is compiled in. For execution, we use the qexp queue, 2 nodes 1 core each. The GPI module must be loaded on the master compute node (in this example the cn79), gaspi_logger is used from different session to view the output of the second process.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md b/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
index 863ac31a8..8d25e7ec3 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
@@ -9,7 +9,7 @@ A library that implements the GASPI specification
Introduction
------------
-Programming Next Generation SupercomputersGPI-2 is an API library for
+Programming Next Generation Supercomputers: GPI-2 is an API library for
asynchronous interprocess, cross-node communication. It provides a
flexible, scalable and fault tolerant interface for parallel
applications.
@@ -159,8 +159,8 @@ Load modules and compile:
Submit the job and run the GPI-2 application
$ qsub -q qexp -l select=2:ncpus=1:mpiprocs=1,place=scatter,walltime=00:05:00 -I
- qsubwaiting for job 171247.dm2 to start
- qsubjob 171247.dm2 ready
+ qsub: waiting for job 171247.dm2 to start
+ qsub: job 171247.dm2 ready
cn79 $ module load gpi2
cn79 $ cut -f1 -d"." $PBS_NODEFILE > machinefile
@@ -180,3 +180,7 @@ library search path is compiled in. For execution, we use the qexp
queue, 2 nodes 1 core each. The GPI module must be loaded on the master
compute node (in this example the cn79), gaspi_logger is used from
different session to view the output of the second process.
+
+
+
+
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+ <div id="parent-fieldname-text-4bb3365f99d1429db46cb63af17f0375" class="">
+ <p>The Anselm cluster provides following elements of the Intel Parallel Studio XE</p>
+<table class="listing">
+<tbody>
+<tr><th>Intel Parallel Studio XE</th></tr>
+<tr class="even">
+<td>Intel Compilers</td>
+</tr>
+<tr class="odd">
+<td>Intel Debugger</td>
+</tr>
+<tr class="even">
+<td>Intel MKL Library</td>
+</tr>
+<tr class="odd">
+<td>Intel Integrated Performance Primitives Library</td>
+</tr>
+<tr class="even">
+<td>Intel Threading Building Blocks Library</td>
+</tr>
+</tbody>
+</table>
+<h2 class=" ">Intel compilers</h2>
+<p>The Intel compilers version 13.1.3 are available, via module intel. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.</p>
+<pre class=" ">$ module load intel<br />$ icc -v<br />$ ifort -v</pre>
+<p>Read more at the <a href="intel-suite/intel-compilers.html" title="" target="_self" class="internal-link">Intel Compilers</a> page.</p>
+<h2 class=" ">Intel debugger</h2>
+<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">X display</a> for running the GUI.</p>
+<pre class=" ">$ module load intel<br />$ idb</pre>
+<p>Read more at the <a href="intel-suite/intel-debugger.html" title="" target="_self" class="internal-link">Intel Debugger</a> page.</p>
+<h2 class=" ">Intel Math Kernel Library</h2>
+<p>Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.</p>
+<pre class=" ">$ module load mkl</pre>
+<p>Read more at the <a href="intel-suite/intel-mkl.html" title="" target="_self" class="internal-link">Intel MKL</a> page.</p>
+<h2 class=" ">Intel Integrated Performance Primitives</h2>
+<p>Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.</p>
+<pre class=" ">$ module load ipp</pre>
+<p>Read more at the <a href="intel-suite/intel-integrated-performance-primitives.html" title="" target="_self" class="internal-link">Intel IPP</a> page.</p>
+<h2 class=" ">Intel Threading Building Blocks</h2>
+<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.</p>
+<pre class=" ">$ module load tbb</pre>
+<p>Read more at the <a href="intel-suite/intel-tbb.html" title="" target="_self" class="internal-link">Intel TBB</a> page.</p>
+
+ </div>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md
index 02e5a0c39..20f127eb3 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md
@@ -51,7 +51,7 @@ Intel Math Kernel Library
Intel Math Kernel Library (Intel MKL) is a library of math kernel
subroutines, extensively threaded and optimized for maximum performance.
-Intel MKL unites and provides these basic componentsBLAS, LAPACK,
+Intel MKL unites and provides these basic components: BLAS, LAPACK,
ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
many more.
@@ -94,4 +94,3 @@ Read more at the [Intel TBB](intel-suite/intel-tbb.html)
page.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.html
new file mode 100644
index 000000000..f6ae8f378
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.html
@@ -0,0 +1,1116 @@
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+ <p>The Intel compilers version 13.1.1 are available, via module intel. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.</p>
+<pre class=" ">$ module load intel<br />$ icc -v<br />$ ifort -v</pre>
+<p class=" ">The intel compilers provide for vectorization of the code, via the AVX instructions and support threading parallelization via OpenMP</p>
+<p class=" ">For maximum performance on the Anselm cluster, compile your programs using the AVX instructions, with reporting where the vectorization was used. We recommend following compilation options for high performance</p>
+<pre class=" ">$ icc -ipo -O3 -vec -xAVX -vec-report1 myprog.c mysubroutines.c -o myprog.x<br />$ ifort -ipo -O3 -vec -xAVX -vec-report1 myprog.f mysubroutines.f -o myprog.x</pre>
+<p class=" ">In this example, we compile the program enabling interprocedural optimizations between source files (-ipo), aggresive loop optimizations (-O3) and vectorization (-vec -xAVX)</p>
+<p class=" ">The compiler recognizes the omp, simd, vector and ivdep pragmas for OpenMP parallelization and AVX vectorization. Enable the OpenMP parallelization by the <strong>-openmp</strong> compiler switch.</p>
+<pre class=" "><span>$Â icc -ipo -O3 -vec -xAVX -vec-report1Â </span>-openmp<span>Â myprog.c mysubroutines.c -o myprog.x</span><br /><span>$ ifort -ipo -O3 -vec -xAVX -vec-report1Â </span>-openmp<span>Â myprog.f mysubroutines.f -o myprog.x</span></pre>
+<p>Read more at <a class="external-link" href="http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/compiler/cpp-lin/index.htm" target="_self" title="">http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/compiler/cpp-lin/index.htm</a></p>
+<h2 class=" ">Sandy Bridge/Haswell binary compatibility</h2>
+<p>Anselm nodes are currently equipped with Sandy Bridge CPUs, while Salomon will use Haswell architecture. <span>The new processors are backward compatible with the Sandy Bridge nodes, so all programs that ran on the Sandy Bridge processors, should also run on the new Haswell nodes. </span><span>To get optimal performance out of the Haswell processors a program should make use of the special </span><span>AVX2 instructions for this processor. One can do this by recompiling codes with the compiler flags </span><span>designated to invoke these instructions. For the Intel compiler suite, there are two ways of doing </span><span>this:</span></p>
+<ul>
+<li><span>Using compiler flag (both for Fortran and C): <span class="monospace">-xCORE-AVX2</span>. This will create a binary </span><span class="s1">with AVX2 instructions, specifically for the Haswell processors. Note that the executable </span><span>will not run on Sandy Bridge nodes.</span></li>
+<li><span>Using compiler flags (both for Fortran and C): <span class="monospace">-xAVX -axCORE-AVX2</span>. This will </span><span>generate multiple, feature specific auto-dispatch code paths for Intel® processors, if there is </span><span>a performance benefit. So this binary will run both on Sandy Bridge and Haswell </span><span>processors. During runtime it will be decided which path to follow, dependent on which </span><span>processor you are running on. In general this will result in larger binaries.</span></li>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
index a85c6925a..5c6ac2b93 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
@@ -51,12 +51,12 @@ with the compiler flags </span><span>designated to invoke these
instructions. For the Intel compiler suite, there are two ways of
doing </span><span>this:</span>
-- <span>Using compiler flag (both for Fortran and C)<span
+- <span>Using compiler flag (both for Fortran and C): <span
class="monospace">-xCORE-AVX2</span>. This will create a
binary </span><span class="s1">with AVX2 instructions, specifically
for the Haswell processors. Note that the
executable </span><span>will not run on Sandy Bridge nodes.</span>
-- <span>Using compiler flags (both for Fortran and C)<span
+- <span>Using compiler flags (both for Fortran and C): <span
class="monospace">-xAVX -axCORE-AVX2</span>. This
will </span><span>generate multiple, feature specific auto-dispatch
code paths for Intel® processors, if there is </span><span>a
@@ -67,4 +67,3 @@ doing </span><span>this:</span>
will result in larger binaries.</span>
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.html
new file mode 100644
index 000000000..68d1c4d90
--- /dev/null
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+ <h2 class=" ">Debugging serial applications</h2>
+<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">X display</a> for running the GUI.</p>
+<pre class=" ">$ module load intel<br />$ idb</pre>
+<p>The debugger may run in text mode. To debug in text mode, use</p>
+<pre class=" ">$ idbc</pre>
+<p>To debug on the compute nodes, module intel must be loaded. <br />The GUI on compute nodes may be accessed using the same way as in <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">the GUI section </a></p>
+<p>Example:</p>
+<pre class=" ">$ qsub -q qexp -l select=1:ncpus=16 -X -I<br />qsub: waiting for job 19654.srv11 to start<br />qsub: job 19654.srv11 ready<br /><br />$ module load intel<br />$ module load java<br />$ icc -O0 -g myprog.c -o myprog.x<br />$ idb ./myprog.x</pre>
+<p>In this example, we allocate 1 full compute node, compile program myprog.c with debugging options -O0 -g and run the idb debugger interactively on the myprog.x executable. The GUI access is via X11 port forwarding provided by the PBS workload manager.</p>
+<h2 class=" ">Debugging parallel applications</h2>
+<p>Intel debugger is capable of debugging multithreaded and MPI parallel programs as well.</p>
+<h3 class=" ">Small number of MPI ranks</h3>
+<p>For debugging small number of MPI ranks, you may execute and debug each rank in separate xterm terminal (do not forget the <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">X display</a>). Using Intel MPI, this may be done in following way:</p>
+<pre class=" ">$ qsub -q qexp -l select=2:ncpus=16 -X -I<br />qsub: waiting for job 19654.srv11 to start<br />qsub: job 19655.srv11 ready<br /><br />$ module load intel impi<br />$ mpirun -ppn 1 -hostfile $PBS_NODEFILE --enable-x xterm -e idbc ./mympiprog.x</pre>
+<p>In this example, we allocate 2 full compute node, run xterm on each node and start idb debugger in command line mode, debugging two ranks of mympiprog.x application. The xterm will pop up for each rank, with idb prompt ready. The example is not limited to use of Intel MPI</p>
+<h3 class=" ">Large number of MPI ranks</h3>
+<p>Run the idb debugger from within the MPI debug option. This will cause the debugger to bind to all ranks and provide aggregated outputs across the ranks, pausing execution automatically just after startup. You may then set break points and step the execution manually. Using Intel MPI:</p>
+<pre class=" ">$ qsub -q qexp -l select=2:ncpus=16 -X -I<br />qsub: waiting for job 19654.srv11 to start<br />qsub: job 19655.srv11 ready<br /><br />$ module load intel impi<br />$ mpirun -n 32 -idb ./mympiprog.x</pre>
+<h3 class=" ">Debugging multithreaded application</h3>
+<p>Run the idb debugger in GUI mode. The menu Parallel contains number of tools for debugging multiple threads. One of the most useful tools is the <strong>Serialize Execution</strong> tool, which serializes execution of concurrent threads for easy orientation and identification of concurrency related bugs.</p>
+<h2 class=" ">Further information</h2>
+<p>Exhaustive manual on idb features and usage is published at Intel website, <a class="external-link" href="http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/debugger/user_guide/index.htm" target="_self" title="">http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/debugger/user_guide/index.htm</a></p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
index d495ec314..e5fa269a5 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
@@ -30,8 +30,8 @@ section](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/
Example:
$ qsub -q qexp -l select=1:ncpus=16 -X -I
- qsubwaiting for job 19654.srv11 to start
- qsubjob 19654.srv11 ready
+ qsub: waiting for job 19654.srv11 to start
+ qsub: job 19654.srv11 ready
$ module load intel
$ module load java
@@ -57,8 +57,8 @@ display](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/
Using Intel MPI, this may be done in following way:
$ qsub -q qexp -l select=2:ncpus=16 -X -I
- qsubwaiting for job 19654.srv11 to start
- qsubjob 19655.srv11 ready
+ qsub: waiting for job 19654.srv11 to start
+ qsub: job 19655.srv11 ready
$ module load intel impi
$ mpirun -ppn 1 -hostfile $PBS_NODEFILE --enable-x xterm -e idbc ./mympiprog.x
@@ -76,8 +76,8 @@ the ranks, pausing execution automatically just after startup. You may
then set break points and step the execution manually. Using Intel MPI:
$ qsub -q qexp -l select=2:ncpus=16 -X -I
- qsubwaiting for job 19654.srv11 to start
- qsubjob 19655.srv11 ready
+ qsub: waiting for job 19654.srv11 to start
+ qsub: job 19655.srv11 ready
$ module load intel impi
$ mpirun -n 32 -idb ./mympiprog.x
@@ -98,4 +98,3 @@ website,
<http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/debugger/user_guide/index.htm>
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.html
new file mode 100644
index 000000000..76216c3f1
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.html
@@ -0,0 +1,1115 @@
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+ <h2 class=" ">Intel Integrated Performance Primitives</h2>
+<p>Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX vector instructions is available, via module ipp. The IPP is a very rich library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax, as well as cryptographic functions, linear algebra functions and many more.</p>
+<p class="callout">Check out IPP before implementing own math functions for data processing, it is likely already there.</p>
+<pre class=" ">$ module load ipp</pre>
+<p>The module sets up environment variables, required for linking and running ipp enabled applications.</p>
+<h2 class=" ">IPP example</h2>
+<pre class=" ">#include "ipp.h"<br />#include <stdio.h><br />int main(int argc, char* argv[])<br />{<br /> const IppLibraryVersion *lib;<br /> Ipp64u fm;<br /> IppStatus status;<br /><br /> status= ippInit(); //IPP initialization with the best optimization layer<br /> if( status != ippStsNoErr ) {<br /> printf("IppInit() Error:\n");<br /> printf("%s\n", ippGetStatusString(status) );<br /> return -1;<br /> }<br /><br /> //Get version info<br /> lib = ippiGetLibVersion();<br /> printf("%s %s\n", lib->Name, lib->Version);<br /><br /> //Get CPU features enabled with selected library level<br /> fm=ippGetEnabledCpuFeatures();<br /> printf("SSE :%c\n",(fm>>1)&1?'Y':'N');<br /> printf("SSE2 :%c\n",(fm>>2)&1?'Y':'N');<br /> printf("SSE3 :%c\n",(fm>>3)&1?'Y':'N');<br /> printf("SSSE3 :%c\n",(fm>>4)&1?'Y':'N');<br /> printf("SSE41 :%c\n",(fm>>6)&1?'Y':'N');<br /> printf("SSE42 :%c\n",(fm>>7)&1?'Y':'N');<br /> printf("AVX :%c\n",(fm>>8)&1 ?'Y':'N');<br /> printf("AVX2 :%c\n", (fm>>15)&1 ?'Y':'N' );<br /> printf("----------\n");<br /> printf("OS Enabled AVX :%c\n", (fm>>9)&1 ?'Y':'N');<br /> printf("AES :%c\n", (fm>>10)&1?'Y':'N');<br /> printf("CLMUL :%c\n", (fm>>11)&1?'Y':'N');<br /> printf("RDRAND :%c\n", (fm>>13)&1?'Y':'N');<br /> printf("F16C :%c\n", (fm>>14)&1?'Y':'N');<br /><br /> return 0;<br />}</pre>
+<p>Â Compile above example, using any compiler and the ipp module.</p>
+<pre class=" ">$ module load intel<br />$ module load ipp<br /><br />$ icc testipp.c -o testipp.x -lippi -lipps -lippcore</pre>
+<p>You will need the ipp module loaded to run the ipp enabled executable. This may be avoided, by compiling library search paths into the executable</p>
+<pre class=" ">$ module load intel<br />$ module load ipp<br /><br />$ icc testipp.c -o testipp.x -Wl,-rpath=$LIBRARY_PATH -lippi -lipps -lippcore</pre>
+<h2 class=" ">Code samples and documentation</h2>
+<p>Intel provides number of <a class="external-link" href="https://software.intel.com/en-us/articles/code-samples-for-intel-integrated-performance-primitives-library" target="_self" title="">Code Samples for IPP</a>, illustrating use of IPP.</p>
+<p>Read full documentation on IPP <a class="external-link" href="http://software.intel.com/sites/products/search/search.php?q=&x=15&y=6&product=ipp&version=7.1&docos=lin" target="_self" title="">on Intel website,</a> in particular the <a class="external-link" href="http://software.intel.com/sites/products/documentation/doclib/ipp_sa/71/ipp_manual/index.htm" target="_self" title="">IPP Reference manual.</a></p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
index 7fc4dfc63..743c5ec1b 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
@@ -95,4 +95,3 @@ in particular the [IPP Reference
manual.](http://software.intel.com/sites/products/documentation/doclib/ipp_sa/71/ipp_manual/index.htm)
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.html
new file mode 100644
index 000000000..e1086f265
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.html
@@ -0,0 +1,1162 @@
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+ Intel MKL
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+ <div class="section" id="GUID-316F80A0-5B6B-4776-A343-D780A4F97798">
+<h2 class=" ">Intel Math Kernel Library</h2>
+<p>Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL provides these basic math kernels:</p>
+<a name="d4841e16"></a>
+<ul id="d4841e16">
+<li id="d4841e18"><a name="d4841e18"></a>BLAS (level 1, 2, and 3) and LAPACK linear algebra routines, offering vector, vector-matrix, and matrix-matrix operations.</li>
+<li id="d4841e21"><a name="d4841e21"></a>The PARDISO direct sparse solver, an iterative sparse solver, and supporting sparse BLAS (level 1, 2, and 3) routines for solving sparse systems of equations.</li>
+<li id="d4841e24"><a name="d4841e24"></a>ScaLAPACK distributed processing linear algebra routines for Linux* and Windows* operating systems, as well as the Basic Linear Algebra Communications Subprograms (BLACS) and the Parallel Basic Linear Algebra Subprograms (PBLAS).</li>
+<li id="d4841e27"><a name="d4841e27"></a>Fast Fourier transform (FFT) functions in one, two, or three dimensions with support for mixed radices (not limited to sizes that are powers of 2), as well as distributed versions of these functions.</li>
+<li id="d4841e30"><a name="d4841e30"></a>Vector Math Library (VML) routines for optimized mathematical operations on vectors.</li>
+<li id="d4841e34"><a name="d4841e34"></a>Vector Statistical Library (VSL) routines, which offer high-performance vectorized random number generators (RNG) for several probability distributions, convolution and correlation routines, and summary statistics functions.</li>
+<li id="d4841e37"><a name="d4841e37"></a>Data Fitting Library, which provides capabilities for spline-based approximation of functions, derivatives and integrals of functions, and search.</li>
+<li>Extended Eigensolver, a shared memory version of an eigensolver based on the Feast Eigenvalue Solver.</li>
+</ul>
+</div>
+<p id="GUID-9AE2AC5E-EE1B-4ADA-9686-88AC98114A99">For details see the <a class="external-link" href="http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mklman/index.htm" target="_self" title="">Intel MKL Reference Manual</a>.</p>
+<p>Intel MKL version 13.5.192 is available on Anselm</p>
+<pre class=" ">$ module load mkl</pre>
+<p>The module sets up environment variables, required for linking and running mkl enabled applications. The most important variables are the $MKLROOT, $MKL_INC_DIR, $MKL_LIB_DIR and $MKL_EXAMPLES</p>
+<p class="callout">The MKL library may be linked using any compiler. <br />With intel compiler use -mkl option to link default threaded MKL.</p>
+<h3 class=" ">Interfaces</h3>
+<p class=" ">The MKL library provides number of interfaces. The fundamental once are the LP64 and ILP64. The Intel MKL ILP64 libraries use the 64-bit integer type (necessary for indexing large arrays, with more than 2<sup id="GUID-009D71C5-A667-418A-B71B-0A4588D03BD2">31</sup>-1 elements), whereas the LP64 libraries index arrays with the 32-bit integer type.</p>
+<table class="listing">
+<tbody>
+<tr><th>Interface</th><th>Integer type</th></tr>
+<tr>
+<td>LP64</td>
+<td>32-bit, int, integer(kind=4), MPI_INT</td>
+</tr>
+<tr>
+<td>ILP64</td>
+<td>64-bit, long int, integer(kind=8), MPI_INT64</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" ">Linking</h3>
+<p>Linking MKL libraries may be complex. Intel <a class="external-link" href="http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor" target="_self" title="">mkl link line advisor</a> helps. See also <a class="anchor-link" href="intel-mkl.html#examples" target="_self" title="">examples</a> below.</p>
+<p>You will need the mkl module loaded to run the mkl enabled executable. This may be avoided, by compiling library search paths into the executable. Include rpath on the compile line:</p>
+<pre class=" ">$ icc .... -Wl,-rpath=$LIBRARY_PATH ...</pre>
+<h3 class=" ">Threading</h3>
+<p class="callout">Advantage in using the MKL library is that it brings threaded parallelization to applications that are otherwise not parallel.</p>
+<p>For this to work, the application must link the threaded MKL library (default). Number and behaviour of MKL threads may be controlled via the OpenMP environment variables, such as OMP_NUM_THREADS and KMP_AFFINITY. MKL_NUM_THREADS takes precedence over OMP_NUM_THREADS</p>
+<pre class=" ">$ export OMP_NUM_THREADS=16<br />$ export KMP_AFFINITY=granularity=fine,compact,1,0</pre>
+<p>The application will run with 16 threads with affinity optimized for fine grain parallelization.</p>
+<h2 class=" "><a name="examples"></a>Examples</h2>
+<p>Number of examples, demonstrating use of the MKL library and its linking is available on Anselm, in the $MKL_EXAMPLES directory. In the examples below, we demonstrate linking MKL to Intel and GNU compiled program for multi-threaded matrix multiplication.</p>
+<h3 class=" ">Working with examples</h3>
+<pre class=" ">$ module load intel<br />$ module load mkl<br />$ cp -a $MKL_EXAMPLES/cblas /tmp/<br />$ cd /tmp/cblas<br /><br />$ make sointel64 function=cblas_dgemm</pre>
+<p>In this example, we compile, link and run the cblas_dgemm example, demonstrating use of MKL example suite installed on Anselm.</p>
+<h3 class=" ">Example: MKL and Intel compiler</h3>
+<pre class=" ">$ module load intel<br />$ module load mkl<br />$ cp -a $MKL_EXAMPLES/cblas /tmp/<br />$ cd /tmp/cblas<br />$ <br />$ icc -w source/cblas_dgemmx.c source/common_func.c -mkl -o cblas_dgemmx.x<br />$ ./cblas_dgemmx.x data/cblas_dgemmx.d<br /><br /></pre>
+<p>In this example, we compile, link and run the cblas_dgemm example, demonstrating use of MKL with icc -mkl option. Using the -mkl option is equivalent to:</p>
+<pre class=" ">$ icc -w source/cblas_dgemmx.c source/common_func.c -o cblas_dgemmx.x \<br />-I$MKL_INC_DIR -L$MKL_LIB_DIR -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5</pre>
+<p>In this example, we compile and link the cblas_dgemm example, using LP64 interface to threaded MKL and Intel OMP threads implementation.</p>
+<h3 class=" ">Example: MKL and GNU compiler</h3>
+<pre class=" ">$ module load gcc<br />$ module load mkl<br />$ cp -a $MKL_EXAMPLES/cblas /tmp/<br />$ cd /tmp/cblas<br /> <br />$ gcc -w source/cblas_dgemmx.c source/common_func.c -o cblas_dgemmx.x \<br />-lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lm<br /><br />$ ./cblas_dgemmx.x data/cblas_dgemmx.d</pre>
+<p>In this example, we compile, link and run the cblas_dgemm example, using LP64 interface to threaded MKL and gnu OMP threads implementation.</p>
+<h2 class=" ">MKL and MIC accelerators</h2>
+<p>The MKL is capable to automatically offload the computations o the MIC accelerator. See section <a href="../intel-xeon-phi.html" title="" target="_self" class="internal-link">Intel Xeon Phi</a> for details.</p>
+<h2 class=" ">Further reading</h2>
+<p>Read more on <a class="external-link" href="http://software.intel.com/en-us/intel-mkl" target="_self" title="">Intel website</a>, in particular the <a class="external-link" href="https://software.intel.com/en-us/intel-mkl/documentation/linux" target="_self" title="">MKL users guide</a>.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
index a23db3acd..e731e0871 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
@@ -144,7 +144,7 @@ program for multi-threaded matrix multiplication.
In this example, we compile, link and run the cblas_dgemm example,
demonstrating use of MKL example suite installed on Anselm.
-### ExampleMKL and Intel compiler
+### Example: MKL and Intel compiler
$ module load intel
$ module load mkl
@@ -164,7 +164,7 @@ equivalent to:
In this example, we compile and link the cblas_dgemm example, using
LP64 interface to threaded MKL and Intel OMP threads implementation.
-### ExampleMKL and GNU compiler
+### Example: MKL and GNU compiler
$ module load gcc
$ module load mkl
@@ -195,4 +195,3 @@ particular the [MKL users
guide](https://software.intel.com/en-us/intel-mkl/documentation/linux).
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.html
new file mode 100644
index 000000000..ac7435b56
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.html
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+ <div id="parent-fieldname-text-4bb3365f99d1429db46cb63af17f0375" class="">
+ <p>The Anselm cluster provides following elements of the Intel Parallel Studio XE</p>
+<table class="listing">
+<tbody>
+<tr><th>Intel Parallel Studio XE</th></tr>
+<tr class="even">
+<td>Intel Compilers</td>
+</tr>
+<tr class="odd">
+<td>Intel Debugger</td>
+</tr>
+<tr class="even">
+<td>Intel MKL Library</td>
+</tr>
+<tr class="odd">
+<td>Intel Integrated Performance Primitives Library</td>
+</tr>
+<tr class="even">
+<td>Intel Threading Building Blocks Library</td>
+</tr>
+</tbody>
+</table>
+<h2 class=" ">Intel compilers</h2>
+<p>The Intel compilers version 13.1.3 are available, via module intel. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.</p>
+<pre class=" ">$ module load intel<br />$ icc -v<br />$ ifort -v</pre>
+<p>Read more at the <a href="intel-compilers.html" title="" target="_self" class="internal-link">Intel Compilers</a> page.</p>
+<h2 class=" ">Intel debugger</h2>
+<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">X display</a> for running the GUI.</p>
+<pre class=" ">$ module load intel<br />$ idb</pre>
+<p>Read more at the <a href="intel-debugger.html" title="" target="_self" class="internal-link">Intel Debugger</a> page.</p>
+<h2 class=" ">Intel Math Kernel Library</h2>
+<p>Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.</p>
+<pre class=" ">$ module load mkl</pre>
+<p>Read more at the <a href="intel-mkl.html" title="" target="_self" class="internal-link">Intel MKL</a> page.</p>
+<h2 class=" ">Intel Integrated Performance Primitives</h2>
+<p>Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.</p>
+<pre class=" ">$ module load ipp</pre>
+<p>Read more at the <a href="intel-integrated-performance-primitives.html" title="" target="_self" class="internal-link">Intel IPP</a> page.</p>
+<h2 class=" ">Intel Threading Building Blocks</h2>
+<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.</p>
+<pre class=" ">$ module load tbb</pre>
+<p>Read more at the <a href="intel-tbb.html" title="" target="_self" class="internal-link">Intel TBB</a> page.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md
index 7461a92ab..1d4309ba0 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md
@@ -51,7 +51,7 @@ Intel Math Kernel Library
Intel Math Kernel Library (Intel MKL) is a library of math kernel
subroutines, extensively threaded and optimized for maximum performance.
-Intel MKL unites and provides these basic componentsBLAS, LAPACK,
+Intel MKL unites and provides these basic components: BLAS, LAPACK,
ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
many more.
@@ -91,4 +91,3 @@ manner.
Read more at the [Intel TBB](intel-tbb.html) page.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.html b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.html
new file mode 100644
index 000000000..414fd9d5c
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.html
@@ -0,0 +1,1115 @@
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+ <h2 class=" ">Intel Threading Building Blocks</h2>
+<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner. The tasks are executed by a runtime scheduler and may be offloaded to <a href="../intel-xeon-phi.html" title="" target="_self" class="internal-link">MIC accelerator</a>.</p>
+<p>Intel TBB version 4.1 is available on Anselm</p>
+<pre class=" ">$ module load tbb</pre>
+<p>The module sets up environment variables, required for linking and running tbb enabled applications.</p>
+<p class="callout">Link the tbb library, using -ltbb</p>
+<h2 class=" ">Examples</h2>
+<p>Number of examples, demonstrating use of TBB and its built-in scheduler is available on Anselm, in the $TBB_EXAMPLES directory.</p>
+<pre class=" ">$ module load intel<br />$ module load tbb<br />$ cp -a $TBB_EXAMPLES/common $TBB_EXAMPLES/parallel_reduce /tmp/<br />$ cd /tmp/parallel_reduce/primes<br />$ icc -O2 -DNDEBUG -o primes.x main.cpp primes.cpp -ltbb<br />$ ./primes.x</pre>
+<p>In this example, we compile, link and run the primes example, demonstrating use of parallel task-based reduce in computation of prime numbers.</p>
+<p>You will need the tbb module loaded to run the tbb enabled executable. This may be avoided, by compiling library search paths into the executable.</p>
+<pre class=" ">$ icc -O2 -o primes.x main.cpp primes.cpp -Wl,-rpath=$LIBRARY_PATH -ltbb</pre>
+<h2 class=" ">Further reading</h2>
+<p>Read more on Intel website, <a class="external-link" href="http://software.intel.com/sites/products/documentation/doclib/tbb_sa/help/index.htm" target="_self" title="">http://software.intel.com/sites/products/documentation/doclib/tbb_sa/help/index.htm</a></p>
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+ <p>Intel Xeon Phi can be programmed in several modes. The default mode on Anselm is offload mode, but all modes described in this document are supported.</p>
+<h2 class=" ">Intel Utilities for Xeon Phi</h2>
+<p class=" ">To get access to a compute node with Intel Xeon Phi accelerator, use the PBS interactive session</p>
+<pre class=" ">$ <b><span>qsub -I -q qmic -A </span><span>NONE-0-0<br /></span></b></pre>
+<p class=" ">To set up the environment module "Intel" has to be loaded</p>
+<pre class=" ">$ <b id="docs-internal-guid-682b5230-f75a-61fe-6896-fa351a3da434"><span>module load intel/13.5.192</span></b></pre>
+<p>Information about the hardware can be obtained by running the micinfo program on the host.</p>
+<pre class=" "><strong>$ /usr/bin/micinfo</strong></pre>
+<p>The output of the "micinfo" utility executed on one of the Anselm node is as follows. (note: to get PCIe related details the command has to be run with root privileges)</p>
+<pre class=" ">MicInfo Utility Log<br /><br />Created Mon Jul 22 00:23:50 2013<br /><br /><br />       System Info<br />               HOST OS                : Linux<br />               OS Version             : 2.6.32-279.5.2.bl6.Bull.33.x86_64<br />               Driver Version         : 6720-15<br />               MPSS Version           : 2.1.6720-15<br />               Host Physical Memory   : 98843 MB<br /><br />Device No: 0, Device Name: mic0<br /><br />       Version<br />               Flash Version           : 2.1.03.0386<br />               SMC Firmware Version    : 1.15.4830<br />               SMC Boot Loader Version : 1.8.4326<br />               uOS Version             : 2.6.38.8-g2593b11<br />               Device Serial Number    : ADKC30102482<br /><br />       Board<br />               Vendor ID               : 0x8086<br />               Device ID               : 0x2250<br />               Subsystem ID            : 0x2500<br />               Coprocessor Stepping ID : 3<br />               PCIe Width              : x16<br />               PCIe Speed              : 5 GT/s<br />               PCIe Max payload size   : 256 bytes<br />               PCIe Max read req size  : 512 bytes<br />               Coprocessor Model       : 0x01<br />               Coprocessor Model Ext   : 0x00<br />               Coprocessor Type        : 0x00<br />               Coprocessor Family      : 0x0b<br />               Coprocessor Family Ext  : 0x00<br />               Coprocessor Stepping    : B1<br />               Board SKU               : B1PRQ-5110P/5120D<br />               ECC Mode                : Enabled<br />               SMC HW Revision         : Product 225W Passive CS<br /><br />       Cores<br />               Total No of Active Cores : 60<br />               Voltage                 : 1032000 uV<br />               Frequency               : 1052631 kHz<br /><br />       Thermal<br />               Fan Speed Control       : N/A<br />               Fan RPM                 : N/A<br />               Fan PWM                 : N/A<br />               Die Temp                : 49 C<br /><br />       GDDR<br />               GDDR Vendor             : Elpida<br />               GDDR Version            : 0x1<br />               GDDR Density            : 2048 Mb<br />               GDDR Size               : 7936 MB<br />               GDDR Technology         : GDDR5<br />               GDDR Speed              : 5.000000 GT/s<br />               GDDR Frequency          : 2500000 kHz<br />               GDDR Voltage            : 1501000 uV<br /><br /></pre>
+<h2 class=" ">Offload Mode</h2>
+<p>To compile a code for Intel Xeon Phi a MPSS stack has to be installed on the machine where compilation is executed. Currently the MPSS stack is only installed on compute nodes equipped with accelerators.</p>
+<pre class=" ">$ <b><span>qsub -I -q qmic -A </span><span>NONE-0-0</span></b><br />$ <b id="docs-internal-guid-682b5230-f75a-61fe-6896-fa351a3da434"><span>module load intel/13.5.192</span></b></pre>
+<p class=" ">For debugging purposes it is also recommended to set environment variable "OFFLOAD_REPORT". Value can be set from 0 to 3, where higher number means more debugging information.</p>
+<pre class=" "><strong>export OFFLOAD_REPORT=3</strong></pre>
+<p>A very basic example of code that employs offload programming technique is shown in the next listing. Please note that this code is sequential and utilizes only single core of the accelerator.</p>
+<pre class=" "><strong>$ vim source-offload.cpp</strong></pre>
+<pre class=" ">#include <iostream><br /><br />int main(int argc, char* argv[])<br />{<br />Â Â Â const int niter = 100000;<br />Â Â Â double result = 0;<br /><br />Â #pragma offload target(mic)<br />Â Â Â for (int i = 0; i < niter; ++i) {<br />Â Â Â Â Â Â Â const double t = (i + 0.5) / niter;<br />Â Â Â Â Â Â Â result += 4.0 / (t * t + 1.0);<br />Â Â Â }<br />Â Â Â result /= niter;<br />Â Â Â std::cout << "Pi ~ " << result << '\n';<br />}</pre>
+<p class=" ">To compile a code using Intel compiler run</p>
+<pre class=" ">$ <b id="docs-internal-guid-682b5230-f75c-afdc-a14d-16c9bb7c4b0b"><span>icc source-offload.cpp -o bin-offload</span></b></pre>
+<p class=" ">To execute the code, run the following command on the host</p>
+<pre class=" "><b><span>./bin-offload</span></b></pre>
+<h3 class=" ">Parallelization in Offload Mode Using OpenMP</h3>
+<p class=" ">One way of paralelization a code for Xeon Phi is using OpenMP directives. The following example shows code for parallel vector addition. </p>
+<pre class=" ">$ vim ./vect-add<strong> </strong></pre>
+<pre class=" ">#include <stdio.h><br /><br />typedef int T;<br /><br />#define SIZE 1000<br /><br />#pragma offload_attribute(push, target(mic))<br />T in1[SIZE];<br />T in2[SIZE];<br />T res[SIZE];<br />#pragma offload_attribute(pop)<br /><br />// MIC function to add two vectors<br />__attribute__((target(mic))) add_mic(T *a, T *b, T *c, int size) {<br />Â int i = 0;<br />Â #pragma omp parallel for<br />Â Â Â for (i = 0; i < size; i++)<br />Â Â Â Â Â c[i] = a[i] + b[i];<br />}<br /><br />// CPU function to add two vectors<br />void add_cpu (T *a, T *b, T *c, int size) {<br />Â int i;<br />Â for (i = 0; i < size; i++)<br />Â Â Â c[i] = a[i] + b[i];<br />}<br /><br />// CPU function to generate a vector of random numbers<br />void random_T (T *a, int size) {<br />Â int i;<br />Â for (i = 0; i < size; i++)<br />Â Â Â a[i] = rand() % 10000; // random number between 0 and 9999<br />}<br /><br />// CPU function to compare two vectors<br />int compare(T *a, T *b, T size ){<br />Â int pass = 0;<br />Â int i;<br />Â for (i = 0; i < size; i++){<br />Â Â Â if (a[i] != b[i]) {<br />Â Â Â Â Â printf("Value mismatch at location %d, values %d and %d\n",i, a[i], b[i]);<br />Â Â Â Â Â pass = 1;<br />Â Â Â }<br />Â }<br />Â if (pass == 0) printf ("Test passed\n"); else printf ("Test Failed\n");<br />Â return pass;<br />}<br /><br /><br />int main()<br />{<br />Â int i;<br />Â random_T(in1, SIZE);<br />Â random_T(in2, SIZE);<br /><br />Â #pragma offload target(mic) in(in1,in2)Â inout(res)<br />Â {<br /><br />Â Â Â // Parallel loop from main function<br />Â Â Â #pragma omp parallel for<br />Â Â Â for (i=0; i<SIZE; i++)<br />Â Â Â Â Â res[i] = in1[i] + in2[i];<br /><br />Â Â Â // or parallel loop is called inside the function<br />Â Â Â add_mic(in1, in2, res, SIZE);<br /><br />Â }<br /><br /><br />Â //Check the results with CPU implementation<br />Â T res_cpu[SIZE];<br />Â add_cpu(in1, in2, res_cpu, SIZE);<br />Â compare(res, res_cpu, SIZE);<br /><br />}</pre>
+<p>During the compilation Intel compiler shows which loops have been vectorized in both host and accelerator. This can be enabled with compiler option "-vec-report2". To compile and execute the code run</p>
+<pre class=" "><strong>$ icc vect-add.c -openmp_report2 -vec-report2 -o vect-add</strong><br /><br /><strong>$ ./vect-add </strong></pre>
+<p>Some interesting compiler flags useful not only for code debugging are:</p>
+<p class="callout">Debugging <br />Â openmp_report[0|1|2] - controls the compiler based vectorization diagnostic level <br />Â vec-report[0|1|2] - controls the OpenMP parallelizer diagnostic level<br /><br />Performance ooptimization<br />Â xhost - FOR HOST ONLY - to generate AVX (Advanced Vector Extensions) instructions.</p>
+<h2 class=" ">Automatic Offload using Intel MKL Library</h2>
+<p>Intel MKL includes an Automatic Offload (AO) feature that enables computationally intensive MKL functions called in user code to benefit from attached Intel Xeon Phi coprocessors automatically and transparently.</p>
+<p class="callout">Behavioral of automatic offload mode is controlled by functions called within the program or by environmental variables. Complete list of controls is listed <a class="external-link" href="http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm" target="_self" title=""><span class="external-link">here</span></a>.</p>
+<p>The Automatic Offload may be enabled by either an MKL function call within the code:</p>
+<pre class=" ">mkl_mic_enable();</pre>
+<p>or by setting environment variable</p>
+<pre class=" ">$ export MKL_MIC_ENABLE=1</pre>
+<p>To get more information about automatic offload please refer to "<a class="external-link" href="http://software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf" target="_self" title="">Using Intel® MKL Automatic Offload on Intel ® Xeon Phi™ Coprocessors</a>" white paper or <a class="external-link" href="https://software.intel.com/en-us/articles/intel-math-kernel-library-documentation" target="_self" title=""><span class="external-link">Intel MKL documentation</span></a>.</p>
+<h3 class=" ">Automatic offload example</h3>
+<p>At first get an interactive PBS session on a node with MIC accelerator and load "intel" module that automatically loads "mkl" module as well.</p>
+<pre class=" ">$ qsub -I -q qmic -A OPEN-0-0 -l select=1:ncpus=16<br />$ module load intel</pre>
+<p>Following example show how to automatically offload an SGEMM (single precision - g<span dir="auto">eneral matrix multiply</span>) function to MIC coprocessor. The code can be copied to a file and compiled without any necessary modification. </p>
+<pre class=" ">$ vim sgemm-ao-short.c</pre>
+<pre class=" ">#include <stdio.h><br />#include <stdlib.h><br />#include <malloc.h><br />#include <stdint.h><br /><br />#include "mkl.h"<br /><br />int main(int argc, char **argv)<br />{<br />       float *A, *B, *C; /* Matrices */<br /><br />       MKL_INT N = 2560; /* Matrix dimensions */<br />       MKL_INT LD = N; /* Leading dimension */<br />       int matrix_bytes; /* Matrix size in bytes */<br />       int matrix_elements; /* Matrix size in elements */<br /><br />       float alpha = 1.0, beta = 1.0; /* Scaling factors */<br />       char transa = 'N', transb = 'N'; /* Transposition options */<br /><br />       int i, j; /* Counters */<br /><br />       matrix_elements = N * N;<br />       matrix_bytes = sizeof(float) * matrix_elements;<br /><br />       /* Allocate the matrices */<br />       A = malloc(matrix_bytes); B = malloc(matrix_bytes); C = malloc(matrix_bytes);<br /><br />       /* Initialize the matrices */<br />       for (i = 0; i < matrix_elements; i++) {<br />               A[i] = 1.0; B[i] = 2.0; C[i] = 0.0;<br />       }<br /><br />       printf("Computing SGEMM on the host\n");<br />       sgemm(&transa, &transb, &N, &N, &N, &alpha, A, &N, B, &N, &beta, C, &N);<br /><br />       printf("Enabling Automatic Offload\n");<br />       /* Alternatively, set environment variable MKL_MIC_ENABLE=1 */<br />       mkl_mic_enable();<br />       <br />       int ndevices = mkl_mic_get_device_count(); /* Number of MIC devices */<br />       printf("Automatic Offload enabled: %d MIC devices present\n",  ndevices);<br /><br />       printf("Computing SGEMM with automatic workdivision\n");<br />       sgemm(&transa, &transb, &N, &N, &N, &alpha, A, &N, B, &N, &beta, C, &N);<br /><br />       /* Free the matrix memory */<br />       free(A); free(B); free(C);<br /><br />       printf("Done\n");<br /><br />   return 0;<br />}</pre>
+<p class="callout">Please note: This example is simplified version of an example from MKL. The expanded version can be found here: <strong>$MKL_EXAMPLES/mic_ao/blasc/source/sgemm.c</strong></p>
+<p>To compile a code using Intel compiler use:</p>
+<pre class=" ">$ icc -mkl sgemm-ao-short.c -o sgemm</pre>
+<p>For debugging purposes enable the offload report to see more information about automatic offloading.</p>
+<pre class=" ">$ export OFFLOAD_REPORT=2</pre>
+<p>The output of a code should look similar to following listing, where lines starting with [MKL] are generated by offload reporting:</p>
+<pre class=" ">Computing SGEMM on the host<br />Enabling Automatic Offload<br />Automatic Offload enabled: 1 MIC devices present<br />Computing SGEMM with automatic workdivision<br />[MKL] [MIC --] [AO Function]Â Â Â SGEMM<br />[MKL] [MIC --] [AO SGEMM Workdivision]Â 0.00 1.00<br />[MKL] [MIC 00] [AO SGEMM CPU Time]Â Â Â Â Â 0.463351 seconds<br />[MKL] [MIC 00] [AO SGEMM MIC Time]Â Â Â Â Â 0.179608 seconds<br />[MKL] [MIC 00] [AO SGEMM CPU->MIC Data] 52428800 bytes<br />[MKL] [MIC 00] [AO SGEMM MIC->CPU Data] 26214400 bytes<br />Done</pre>
+<p>Â </p>
+<h2 class=" ">Native Mode</h2>
+<p>In the native mode a program is executed directly on Intel Xeon Phi without involvement of the host machine. Similarly to offload mode, the code is compiled on the host computer with Intel compilers.</p>
+<p>To compile a code user has to be connected to a compute with MIC and load Intel compilers module. To get an interactive session on a compute node with an Intel Xeon Phi and load the module use following commands:Â </p>
+<pre class=" ">$ <b><span>qsub -I -q qmic -A </span><span>NONE-0-0<br /><br />$ module load intel/13.5.192<br /></span></b></pre>
+<p class="callout">Please note that particular version of the Intel module is specified. This information is used later to specify the correct library paths.</p>
+<p>To produce a binary compatible with Intel Xeon Phi architecture user has to specify "-mmic" compiler flag. Two compilation examples are shown below. The first example shows how to compile OpenMP parallel code "vect-add.c" for host only:</p>
+<pre class=" "><strong>$ icc -xhost -no-offload -fopenmp vect-add.c -o vect-add-host</strong></pre>
+<p>To run this code on host, use:</p>
+<pre class=" "><strong>$ ./vect-add-host</strong></pre>
+<p>The second example shows how to compile the same code for Intel Xeon Phi:</p>
+<pre class=" "><strong>$ icc -mmic -fopenmp vect-add.c -o vect-add-mic</strong></pre>
+<h3 class=" ">Execution of the Program in Native Mode on Intel Xeon Phi</h3>
+<p>The user access to the Intel Xeon Phi is through the SSH. Since user home directories are mounted using NFS on the accelerator, users do not have to copy binary files or libraries between the host and accelerator. Â </p>
+<p class=" ">To connect to the accelerator run:</p>
+<pre class=" "><strong>$ ssh mic0</strong></pre>
+<p>If the code is sequential, it can be executed directly:</p>
+<pre class=" "><strong>mic0 $ ~/path_to_binary/vect-add-seq-mic</strong></pre>
+<p>If the code is parallelized using OpenMP a set of additional libraries is required for execution. To locate these libraries new path has to be added to the LD_LIBRARY_PATH environment variable prior to the execution:</p>
+<pre class=" "><strong>mic0 $ export LD_LIBRARY_PATH=/apps/intel/composer_xe_2013.5.192/compiler/lib/mic:$LD_LIBRARY_PATH</strong></pre>
+<p class="callout">Please note that the path exported in the previous example contains path to a specific compiler (here the version is 5.192). This version number has to match with the version number of the Intel compiler module that was used to compile the code on the host computer.</p>
+<p class=" ">For your information the list of libraries and their location required for execution of an OpenMP parallel code on Intel Xeon Phi is:<span class="discreet visualHighlight"></span></p>
+<p class="callout"><span>/apps/intel/composer_xe_2013.5.192/compiler/lib/mic<br /><br />libiomp5.so <br />libimf.so <br />libsvml.so <br />libirng.so <br />libintlc.so.5 <br /></span></p>
+<p class=" "><span>Finally, to run the compiled code use: </span></p>
+<pre class=" "><strong>$ ~/path_to_binary/vect-add-mic</strong></pre>
+<h2 class=" "><span>OpenCL</span></h2>
+<p><span>OpenCL (Open Computing Language) is an open standard for general-purpose parallel programming for diverse mix of multi-core CPUs, GPU coprocessors, and other parallel processors. OpenCL provides a flexible execution model and uniform programming environment for software developers to write portable code for systems running on both the CPU and graphics processors or accelerators like the Intel® Xeon Phi.</span></p>
+<p><span>On Anselm OpenCL is installed only on compute nodes with MIC accelerator, therefore OpenCL code can be compiled only on these nodes. </span></p>
+<pre class=" "><span>module load opencl-sdk opencl-rt<br /></span></pre>
+<p><span>Always load "opencl-sdk" (providing devel files like headers) and "opencl-rt" (providing dynamic library libOpenCL.so) modules to compile and link OpenCL code. Load "opencl-rt" for running your compiled code.<br /></span></p>
+<p><span>There are two basic examples of OpenCL code in the following directory: </span></p>
+<pre class=" "><span><strong>/apps/intel/opencl-examples/</strong><br /></span></pre>
+<p><span>First example "CapsBasic" detects OpenCL compatible hardware, here CPU and MIC, and prints basic information about the capabilities of it. <br /></span></p>
+<pre class=" "><strong>/apps/intel/opencl-examples/CapsBasic/capsbasic</strong></pre>
+<p><span>To compile and run the example copy it to your home directory, get a PBS interactive session on of the nodes with MIC and run make for compilation. Make files are very basic and shows how the OpenCL code can be compiled on Anselm. </span></p>
+<pre class=" "><strong>$ cp /apps/intel/opencl-examples/CapsBasic/* .</strong><br /><strong>$ qsub -I -q qmic -A NONE-0-0</strong><br /><strong>$ make</strong></pre>
+<p><span>The compilation command for this example is: </span></p>
+<pre class=" "><strong>$ g++ capsbasic.cpp -lOpenCL -o capsbasic -I/apps/intel/opencl/include/</strong></pre>
+<p><span>After executing the complied binary file, following output should be displayed. <br /></span></p>
+<pre class=" "><span><strong>./capsbasic</strong><br /><br /><strong>Number of available platforms: 1</strong><br /><strong>Platform names:</strong><br /><strong>Â Â Â [0] Intel(R) OpenCL [Selected]</strong><br /><strong>Number of devices available for each type:</strong><br /><strong>Â Â Â CL_DEVICE_TYPE_CPU: 1</strong><br /><strong>Â Â Â CL_DEVICE_TYPE_GPU: 0</strong><br /><strong>Â Â Â CL_DEVICE_TYPE_ACCELERATOR: 1</strong><br /><br /><strong>*** Detailed information for each device ***</strong><br /><br /><strong>CL_DEVICE_TYPE_CPU[0]</strong><br /><strong>Â Â Â CL_DEVICE_NAME:Â Â Â Â Â Â Â Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz</strong><br /><strong>Â Â Â CL_DEVICE_AVAILABLE: 1</strong><br /><br /><strong>...</strong><br /><br /><strong>CL_DEVICE_TYPE_ACCELERATOR[0]</strong><br /><strong>Â Â Â CL_DEVICE_NAME: Intel(R) Many Integrated Core Acceleration Card</strong><br /><strong>Â Â Â CL_DEVICE_AVAILABLE: 1</strong><br /><br /><strong>...</strong><br /></span></pre>
+<p class="callout"><span>More information about this example can be found on Intel website: <a href="http://software.intel.com/en-us/vcsource/samples/caps-basic/">http://software.intel.com/en-us/vcsource/samples/caps-basic/</a><br /></span></p>
+<p class=" "><span>The second example that can be found in "/apps/intel/opencl-examples" </span><span>directory is General Matrix Multiply. You can follow the the same procedure to download the example to your directory and compile it. <br /></span></p>
+<pre class=" "><strong>$ cp -r /apps/intel/opencl-examples/* .</strong><br /><strong>$ qsub -I -q qmic -A NONE-0-0</strong><br /><strong>$ cd GEMM <br />$ make</strong></pre>
+<p class=" "><span>The compilation command for this example is: </span></p>
+<pre class=" "><span><strong>$ g++ cmdoptions.cpp gemm.cpp ../common/basic.cpp ../common/cmdparser.cpp ../common/oclobject.cpp -I../common -lOpenCL -o gemm -I/apps/intel/opencl/include/</strong><br /></span></pre>
+<p class=" "><span>To see the performance of Intel Xeon Phi performing the DGEMM run the example as follows: </span></p>
+<pre class=" "><span><strong>./gemm -d 1</strong><br /><strong>Platforms (1):</strong><br /><strong> [0] Intel(R) OpenCL [Selected]</strong><br /><strong>Devices (2):</strong><br /><strong> [0] Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz</strong><br /><strong> [1] Intel(R) Many Integrated Core Acceleration Card [Selected]</strong><br /><strong>Build program options: "-DT=float -DTILE_SIZE_M=1 -DTILE_GROUP_M=16 -DTILE_SIZE_N=128 -DTILE_GROUP_N=1 -DTILE_SIZE_K=8"</strong><br /><strong>Running gemm_nn kernel with matrix size: 3968x3968</strong><br /><strong>Memory row stride to ensure necessary alignment: 15872 bytes</strong><br /><strong>Size of memory region for one matrix: 62980096 bytes</strong><br /><strong>Using alpha = 0.57599 and beta = 0.872412</strong><br /><strong>...<br />Host time: 0.292953 sec.</strong><br /><strong>Host perf: 426.635 GFLOPS</strong><br /><strong>Host time: 0.293334 sec.</strong><br /><strong>Host perf: 426.081 GFLOPS</strong><br /><strong>...</strong><br /></span></pre>
+<p class="callout"><span>Please note: GNU compiler is used to compile the OpenCL codes for Intel MIC. You do not need to load Intel compiler module. <br /></span></p>
+<h2 class=" "><span>MPIÂ </span></h2>
+<h3 class=" ">Environment setup and compilation</h3>
+<p class=" ">Again an MPI code for Intel Xeon Phi has to be compiled on a compute node with accelerator and MPSS software stack installed. To get to a compute node with accelerator use:</p>
+<pre class=" ">$ <b><span>qsub -I -q qmic -A </span><span>NONE-0-0</span></b></pre>
+<p class=" ">The only supported implementation of MPI standard for Intel Xeon Phi is Intel MPI. To setup a fully functional development environment a combination of Intel compiler and Intel MPI has to be used. On a host load following modules before compilation:</p>
+<pre class=" "><strong>$ module load intel/13.5.192 impi/4.1.1.036</strong> </pre>
+<p class=" ">To compile an MPI code for host use:</p>
+<pre class=" "><strong>$ mpiicc -xhost -o mpi-test mpi-test.c</strong></pre>
+<p class=" ">To compile the same code for Intel Xeon Phi architecture use:</p>
+<pre class=" "><strong>$ mpiicc -mmic -o mpi-test-mic mpi-test.c</strong></pre>
+<p>An example of basic MPI version of "hello-world" example in C language, that can be executed on both host and Xeon Phi is (can be directly copy and pasted to a .c file)</p>
+<pre class=" ">#include <stdio.h><br />#include <mpi.h><br /><br /><br />int main (argc, argv)<br />Â Â Â Â int argc;<br />Â Â Â Â char *argv[];<br />{<br />Â int rank, size;<br /><br />Â int len;<br />Â char node[MPI_MAX_PROCESSOR_NAME];<br /><br />Â MPI_Init (&argc, &argv);Â Â Â Â Â /* starts MPI */<br />Â MPI_Comm_rank (MPI_COMM_WORLD, &rank);Â Â Â Â Â Â Â /* get current process id */<br />Â MPI_Comm_size (MPI_COMM_WORLD, &size);Â Â Â Â Â Â Â /* get number of processes */<br /><br />Â MPI_Get_processor_name(node,&len);<br /><br />Â printf( "Hello world from process %d of %d on host %s \n", rank, size, node );<br />Â MPI_Finalize();<br />Â return 0; <br />}</pre>
+<h3 class=" ">MPI programming models</h3>
+<p><span>Intel MPI for the Xeon Phi coprocessors offers different MPI programming models:</span></p>
+<p class="callout"><strong>Host-only model</strong> - all MPI ranks reside on the host. The coprocessors can be used by using offload pragmas. (Using MPI calls inside offloaded code is not supported.)<strong><br /><br />Coprocessor-only model</strong> - all MPI ranks reside only on the coprocessors.<br /><br /><strong>Symmetric model</strong> - the MPI ranks reside on both the host and the coprocessor. Most general MPI case.</p>
+<h3 class=" "><span>Host-only model</span></h3>
+<p class=" "><span></span>In this case all environment variables are set by modules, so to execute the compiled MPI program on a single node, use:</p>
+<pre class=" "><strong>$ mpirun -np 4 ./mpi-test</strong></pre>
+<p>The output should be similar to:</p>
+<pre class=" ">Hello world from process 1 of 4 on host cn207<br />Hello world from process 3 of 4 on host cn207<br />Hello world from process 2 of 4 on host cn207<br />Hello world from process 0 of 4 on host cn207</pre>
+<h3 class=" ">Coprocessor-only model</h3>
+<p class=" "><span>There are two ways how to execute an MPI code on a single coprocessor: 1.) lunch the program using "<strong>mpirun</strong>" from the coprocessor; or 2.) lunch the task using "<strong>mpiexec.hydra</strong>" from a host. <br /></span></p>
+<p><strong>Execution on coprocessor</strong>Â </p>
+<p>Similarly to execution of OpenMP programs in native mode, since the environmental module are not supported on MIC, user has to setup paths to Intel MPI libraries and binaries manually. One time setup can be done by creating a "<strong>.profile</strong>" file in user's home directory. This file sets up the environment on the MIC automatically once user access to the accelerator through the SSH.</p>
+<pre class=" ">$ <b id="docs-internal-guid-739185ef-4ba1-96b6-ed2f-45da8a2b73f9"><span>vim ~/.profile </span></b></pre>
+<pre class=" ">PS1='[\u@\h \W]\$ '<br />export PATH=/usr/bin:/usr/sbin:/bin:/sbin<br /><br />#OpenMP<br />export LD_LIBRARY_PATH=/apps/intel/composer_xe_2013.5.192/compiler/lib/mic:$LD_LIBRARY_PATH<br /><br />#Intel MPI <br />export LD_LIBRARY_PATH=/apps/intel/impi/4.1.1.036/mic/lib/:$LD_LIBRARY_PATH<br />export PATH=/apps/intel/impi/4.1.1.036/mic/bin/:$PATH</pre>
+<p class="callout">Please note: <br />Â - this file sets up both environmental variable for both MPI and OpenMP libraries.<br />Â - this file sets up the paths to a particular version of Intel MPI library and particular version of an Intel compiler. These versions have to match with loaded modules.</p>
+<p class=" ">To access a MIC accelerator located on a node that user is currently connected to, use:</p>
+<pre class=" ">$ ssh mic0</pre>
+<p class=" ">or in case you need specify a MIC accelerator on a particular node, use:</p>
+<pre class=" ">$ ssh cn207-mic0</pre>
+<p class=" ">To run the MPI code in parallel on multiple core of the accelerator, use:</p>
+<pre class=" ">$ mpirun -np 4 ./mpi-test-mic</pre>
+<p class=" ">The output should be similar to:</p>
+<pre class=" ">Hello world from process 1 of 4 on host cn207-mic0<br />Hello world from process 2 of 4 on host cn207-mic0<br />Hello world from process 3 of 4 on host cn207-mic0<br />Hello world from process 0 of 4 on host cn207-mic0</pre>
+<p><strong><br /></strong></p>
+<p><strong>Execution on host</strong></p>
+<p>If the MPI program is launched from host instead of the coprocessor, the environmental variables are not set using the ".profile" file. Therefore user has to specify library paths from the command line when calling "mpiexec".</p>
+<p>First step is to tell mpiexec that the MPI should be executed on a local accelerator by setting up the environmental variable "I_MPI_MIC"</p>
+<pre class=" "><strong>$ export I_MPI_MIC=1</strong></pre>
+<p>Now the MPI program can be executed as:</p>
+<pre class=" ">$ <b id="docs-internal-guid-739185ef-4bb6-852f-9000-e3083ee1e76c"><span>mpiexec.hydra -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/ -host mic0 -n 4 ~/mpi-test-mic<br /></span></b></pre>
+<p class=" ">or using mpirun</p>
+<pre class=" ">$ <b id="docs-internal-guid-739185ef-4bb6-852f-9000-e3083ee1e76c"><span>mpirun -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/ -host mic0 -n 4 ~/mpi-test-mic<br /></span></b></pre>
+<p class="callout">Please note:<br />Â - the full path to the binary has to specified (here: "<b id="docs-internal-guid-739185ef-4bb6-852f-9000-e3083ee1e76c"><span>~/mpi-test-mic</span></b>") <br />Â - the LD_LIBRARY_PATH has to match with Intel MPI module used to compile the MPI code</p>
+<p class=" ">The output should be again similar to:</p>
+<pre class=" ">Hello world from process 1 of 4 on host cn207-mic0<br />Hello world from process 2 of 4 on host cn207-mic0<br />Hello world from process 3 of 4 on host cn207-mic0<br />Hello world from process 0 of 4 on host cn207-mic0</pre>
+<p class="callout">Please note that the "mpiexec.hydra" requires a file "<b id="docs-internal-guid-739185ef-4bc0-04bf-f978-e263bb4527e2"><span>pmi_proxy</span></b>" from Intel MPI library to be copied to the MIC filesystem. If the file is missing please contact the system administrators. A simple test to see if the file is present is to execute:</p>
+<pre class=" ">Â Â <span class="monospace">$ ssh mic0 ls /bin/pmi_proxy</span><br />Â <span class="monospace">/bin/pmi_proxy</span></pre>
+<p><strong><br /></strong></p>
+<p><strong>Execution on host - MPI processes distributed over multiple accelerators on multiple nodes</strong></p>
+<p class=" "><span>To get access to multiple nodes with MIC accelerator, user has to use PBS to allocate the resources. To start interactive session, that allocates 2 compute nodes = 2 MIC accelerators run qsub command with following parameters: </span></p>
+<pre class=" "><strong>$ qsub -I -q qmic -A NONE-0-0 -l select=2:ncpus=16<br /><br />$ module load intel/13.5.192 impi/4.1.1.036<br /></strong></pre>
+<p class=" "><span>This command connects user through ssh to one of the nodes immediately. To see the other nodes that have been allocated use: </span></p>
+<pre class=" "><span>$ cat $PBS_NODEFILE</span></pre>
+<p class=" "><span>For example: </span></p>
+<pre class=" "><span>cn204.bullx<br />cn205.bullx<br /></span></pre>
+<p class=" "><span>This output means that the PBS allocated nodes cn204 and cn205, which means that user has direct access to "<strong>cn204-mic0</strong>" and "<strong>cn-205-mic0</strong>" accelerators.</span></p>
+<p class="callout"><span>Please note: At this point user can connect to any of the allocated nodes or any of the allocated MIC accelerators using ssh: <br />- to connect to the second node : <strong><span class="monospace">$ ssh cn205</span></strong> <br /><span>- to connect to the accelerator on the first node from the first node: <span class="monospace"><strong>$ ssh cn204-mic0</strong></span></span> or <strong><span class="monospace">$ ssh mic0</span> </strong><br /><strong>-</strong> to connect to the accelerator on the second node from the first node: <span class="monospace"><strong>$ ssh cn205-mic0</strong></span><br /></span></p>
+<p><span>At this point we expect that correct modules are loaded and binary is compiled. For parallel execution the mpiexec.hydra is used.</span> Again the first step is to tell mpiexec that the MPI can be executed on MIC accelerators by setting up the environmental variable "I_MPI_MIC"</p>
+<pre class=" "><strong>$ export I_MPI_MIC=1</strong></pre>
+<p class=" "><span>The launch the MPI program use:</span></p>
+<pre class=" "><strong>$ mpiexec.hydra -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/ \<br /> -genv I_MPI_FABRICS_LIST tcp \<br />Â -genv I_MPI_FABRICS shm:tcp \<br />Â -genv I_MPI_TCP_NETMASK=10.1.0.0/16 \<br /> -host cn204-mic0 -n 4 ~/mpi-test-mic \<br />: -host cn205-mic0 -n 6 ~/mpi-test-mic</strong></pre>
+<p class=" ">or using mpirun:</p>
+<pre class=" "><strong>$ mpirun -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/ \<br /> -genv I_MPI_FABRICS_LIST tcp \<br />Â -genv I_MPI_FABRICS shm:tcp \<br />Â -genv I_MPI_TCP_NETMASK=10.1.0.0/16 \<br /> -host cn204-mic0 -n 4 ~/mpi-test-mic \<br />: -host cn205-mic0 -n 6 ~/mpi-test-mic</strong></pre>
+<p class=" ">In this case four MPI processes are executed on accelerator cn204-mic and six processes are executed on accelerator cn205-mic0. The sample output (sorted after execution) is:</p>
+<pre class=" ">Hello world from process 0 of 10 on host cn204-mic0<br />Hello world from process 1 of 10 on host cn204-mic0<br />Hello world from process 2 of 10 on host cn204-mic0<br />Hello world from process 3 of 10 on host cn204-mic0<br />Hello world from process 4 of 10 on host cn205-mic0<br />Hello world from process 5 of 10 on host cn205-mic0<br />Hello world from process 6 of 10 on host cn205-mic0<br />Hello world from process 7 of 10 on host cn205-mic0<br />Hello world from process 8 of 10 on host cn205-mic0<br />Hello world from process 9 of 10 on host cn205-mic0</pre>
+<p class=" ">The same way MPI program can be executed on multiple hosts:Â </p>
+<pre class=" "><strong>$ mpiexec.hydra -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/ </strong>\<br /><strong> -genv I_MPI_FABRICS_LIST tcp <br />Â -genv I_MPI_FABRICS shm:tcp <br />Â -genv I_MPI_TCP_NETMASK=10.1.0.0/16<br /> -host cn204 -n 4 ~/mpi-test \</strong><br /><strong>: -host cn205 -n 6 ~/mpi-test</strong></pre>
+<h3 class=" "><span>Symmetric model </span></h3>
+<p><span>In a symmetric mode MPI programs are executed on both host computer(s) and MIC accelerator(s). Since MIC has a different architecture and requires different binary file produced by the Intel compiler two different files has to be compiled before MPI program is executed. </span></p>
+<p><span>In the previous section we have compiled two binary files, one for hosts "<strong>mpi-test</strong>" and one for MIC accelerators "<strong>mpi-test-mic</strong>". These two binaries can be executed at once using mpiexec.hydra:<br /></span></p>
+<pre class=" "><span>$ <strong>mpiexec.hydra</strong> \<br /><span> -genv I_MPI_FABRICS_LIST tcp \<br /> -genv I_MPI_FABRICS shm:tcp \<br />Â -genv I_MPI_TCP_NETMASK=10.1.0.0/16 \<br /> -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/ \<br /> -host cn205 -n 2 ~/mpi-test \<br />: -host cn205-mic0 -n 2 ~/mpi-test-mic<br /></span></span></pre>
+<p>In this example the first two parameters (line 2 and 3) sets up required environment variables for execution. The third line specifies binary that is executed on host (here cn205) and the last line specifies the binary that is execute on the accelerator (here cn205-mic0).</p>
+<p class=" "><span>The output of the program is: </span></p>
+<pre class=" "><span>Hello world from process 0 of 4 on host cn205<br />Hello world from process 1 of 4 on host cn205<br />Hello world from process 2 of 4 on host cn205-mic0<br />Hello world from process 3 of 4 on host cn205-mic0<br /></span></pre>
+<p class=" "><span>The execution procedure can be simplified by using the mpirun command with the machine file a a parameter. Machine file contains list of all nodes and accelerators that should used to execute MPI processes. </span></p>
+<p class=" "><span>An example of a machine file that uses 2 <span>hosts (<strong>cn205</strong> and <strong>cn206</strong>) and 2 accelerators <strong>(cn205-mic0</strong> and <strong>cn206-mic0</strong>) to run 2 MPI processes on each</span> of them:<br /></span></p>
+<pre class=" "><span>$ cat hosts_file_mix<br />cn205:2<br />cn205-mic0:2<br />cn206:2<br />cn206-mic0:2<br /></span></pre>
+<p class=" "><span>In addition if a naming convention is set in a way that the name of the binary for host is <strong>"bin_name"</strong> and the name of the binary for the accelerator is <strong>"bin_name-mic"</strong> then by setting up the environment variable <strong>I_MPI_MIC_POSTFIX</strong> to <strong>"-mic"</strong> user do not have to specify the names of booth binaries. In this case mpirun needs just the name of the host binary file (i.e. "mpi-test") and uses the suffix to get a name of the binary for accelerator (i..e. "mpi-test-mic"). <br /></span></p>
+<pre class=" "><span>$ export I_MPI_MIC_POSTFIX=-mic</span></pre>
+<p>Â <span>To run the MPI code using mpirun and the machine file "hosts_file_mix" use: <br /></span></p>
+<pre class=" "><span>$ mpirun \<br /> -genv I_MPI_FABRICS shm:tcp \<br /> -genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/ \<br /> -genv I_MPI_FABRICS_LIST tcp \<br />Â -genv I_MPI_FABRICS shm:tcp \<br />Â -genv I_MPI_TCP_NETMASK=10.1.0.0/16 \<br /> -machinefile hosts_file_mix \<br /> ~/mpi-test<br /></span></pre>
+<p class=" "><span>A possible output of the MPI "hello-world" example executed on two hosts and two accelerators is:<br /></span></p>
+<pre class=" "><span>Hello world from process 0 of 8 on host cn204<br />Hello world from process 1 of 8 on host cn204<br />Hello world from process 2 of 8 on host cn204-mic0<br />Hello world from process 3 of 8 on host cn204-mic0<br />Hello world from process 4 of 8 on host cn205<br />Hello world from process 5 of 8 on host cn205<br />Hello world from process 6 of 8 on host cn205-mic0<br />Hello world from process 7 of 8 on host cn205-mic0<br /></span></pre>
+<p class="callout">Please note: At this point the MPI communication between MIC accelerators on different nodes uses 1Gb Ethernet only.</p>
+<p><strong>Using the PBS automatically generated node-files <br /></strong></p>
+<p>PBS also generates a set of node-files that can be used instead of manually creating a new one every time. Three node-files are genereated:</p>
+<p class="callout"><strong>Host only node-file:</strong> <br />Â - /lscratch/${PBS_JOBID}/nodefile-cn<br /><strong>MIC only node-file</strong>: <br />Â - /lscratch/${PBS_JOBID}/nodefile-mic<br /><strong>Host and MIC node-file</strong>: <br />Â - /lscratch/${PBS_JOBID}/nodefile-mix</p>
+<p>Please note each host or accelerator is listed only per files. User has to specify how many jobs should be executed per node using "-n" parameter of the mpirun command.</p>
+<h2 class=" ">Optimization</h2>
+<p class=" ">For more details about optimization techniques please read Intel document <a class="external text" href="http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization" rel="nofollow" title="http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization">Optimization and Performance Tuning for Intel® Xeon Phi™ Coprocessors</a>.</p>
+<p>Â </p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md b/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
index 4acd24133..485f6a98a 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
@@ -28,7 +28,7 @@ the micinfo program on the host.
$ /usr/bin/micinfo
The output of the "micinfo" utility executed on one of the Anselm node
-is as follows. (noteto get PCIe related details the command has to be
+is as follows. (note: to get PCIe related details the command has to be
run with root privileges)
MicInfo Utility Log
@@ -37,60 +37,60 @@ run with root privileges)
       System Info
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â HOST OSÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Linux
-                OS Version             2.6.32-279.5.2.bl6.Bull.33.x86_64
-                Driver Version         6720-15
-                MPSS Version           2.1.6720-15
-                Host Physical Memory   98843 MB
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â HOST OSÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â : Linux
+                OS Version             : 2.6.32-279.5.2.bl6.Bull.33.x86_64
+                Driver Version         : 6720-15
+                MPSS Version           : 2.1.6720-15
+                Host Physical Memory   : 98843 MB
- Device No0, Device Namemic0
+ Device No: 0, Device Name: mic0
       Version
-                Flash Version           2.1.03.0386
-                SMC Firmware Version    1.15.4830
-                SMC Boot Loader Version 1.8.4326
-                uOS Version             2.6.38.8-g2593b11
-                Device Serial Number    ADKC30102482
+                Flash Version           : 2.1.03.0386
+                SMC Firmware Version    : 1.15.4830
+                SMC Boot Loader Version : 1.8.4326
+                uOS Version             : 2.6.38.8-g2593b11
+                Device Serial Number    : ADKC30102482
       Board
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Vendor IDÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â 0x8086
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Device IDÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â 0x2250
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Subsystem IDÂ Â Â Â Â Â Â Â Â Â Â Â 0x2500
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Coprocessor Stepping IDÂ 3
-                PCIe Width              x16
-                PCIe Speed              5 GT/s
-                PCIe Max payload size   256 bytes
-                PCIe Max read req size  512 bytes
-                Coprocessor Model       0x01
-                Coprocessor Model Ext   0x00
-                Coprocessor Type        0x00
-                Coprocessor Family      0x0b
-                Coprocessor Family Ext  0x00
-                Coprocessor Stepping    B1
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Board SKUÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â B1PRQ-5110P/5120D
-                ECC Mode                Enabled
-                SMC HW Revision         Product 225W Passive CS
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Vendor IDÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â : 0x8086
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Device IDÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â : 0x2250
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Subsystem IDÂ Â Â Â Â Â Â Â Â Â Â Â : 0x2500
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Coprocessor Stepping IDÂ : 3
+                PCIe Width              : x16
+                PCIe Speed              : 5 GT/s
+                PCIe Max payload size   : 256 bytes
+                PCIe Max read req size  : 512 bytes
+                Coprocessor Model       : 0x01
+                Coprocessor Model Ext   : 0x00
+                Coprocessor Type        : 0x00
+                Coprocessor Family      : 0x0b
+                Coprocessor Family Ext  : 0x00
+                Coprocessor Stepping    : B1
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Board SKUÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â : B1PRQ-5110P/5120D
+                ECC Mode                : Enabled
+                SMC HW Revision         : Product 225W Passive CS
       Cores
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Total No of Active Cores 60
-                Voltage                 1032000 uV
-                Frequency               1052631 kHz
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Total No of Active Cores : 60
+                Voltage                 : 1032000 uV
+                Frequency               : 1052631 kHz
       Thermal
-                Fan Speed Control       N/A
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Fan RPMÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â N/A
- Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Fan PWMÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â N/A
-                Die Temp                49 C
+                Fan Speed Control       : N/A
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Fan RPMÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â : N/A
+ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Fan PWMÂ Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â : N/A
+                Die Temp                : 49 C
       GDDR
-                GDDR Vendor             Elpida
-                GDDR Version            0x1
-                GDDR Density            2048 Mb
-                GDDR Size               7936 MB
-                GDDR Technology         GDDR5
-                GDDR Speed              5.000000 GT/s
-                GDDR Frequency          2500000 kHz
-                GDDR Voltage            1501000 uV
+                GDDR Vendor             : Elpida
+                GDDR Version            : 0x1
+                GDDR Density            : 2048 Mb
+                GDDR Size               : 7936 MB
+                GDDR Technology         : GDDR5
+                GDDR Speed              : 5.000000 GT/s
+                GDDR Frequency          : 2500000 kHz
+                GDDR Voltage            : 1501000 uV
Offload Mode
------------
@@ -325,7 +325,7 @@ any necessary modification.Â
       mkl_mic_enable();
      Â
       int ndevices = mkl_mic_get_device_count(); /* Number of MIC devices */
-        printf("Automatic Offload enabled%d MIC devices presentn",  ndevices);
+        printf("Automatic Offload enabled: %d MIC devices presentn",  ndevices);
       printf("Computing SGEMM with automatic workdivisionn");
       sgemm(&transa, &transb, &N, &N, &N, &alpha, A, &N, B, &N, &beta, C, &N);
@@ -338,7 +338,7 @@ any necessary modification.Â
   return 0;
}
-Please noteThis example is simplified version of an example from MKL.
+Please note: This example is simplified version of an example from MKL.
The expanded version can be found here:
**$MKL_EXAMPLES/mic_ao/blasc/source/sgemm.c**
@@ -356,7 +356,7 @@ lines starting with [MKL] are generated by offload reporting:
Computing SGEMM on the host
Enabling Automatic Offload
- Automatic Offload enabled1 MIC devices present
+ Automatic Offload enabled: 1 MIC devices present
Computing SGEMM with automatic workdivision
[MKL] [MIC --] [AO Function]Â Â Â SGEMM
[MKL] [MIC --] [AO SGEMM Workdivision]Â 0.00 1.00
@@ -442,7 +442,7 @@ libirng.so
libintlc.so.5
</span>
-<span>Finally, to run the compiled code use</span>
+<span>Finally, to run the compiled code use: </span>
$ ~/path_to_binary/vect-add-mic
@@ -469,7 +469,7 @@ and link OpenCL code. Load "opencl-rt" for running your compiled code.
</span>
<span>There are two basic examples of OpenCL code in the following
-directory</span>
+directory: </span>
/apps/intel/opencl-examples/
@@ -489,7 +489,7 @@ be compiled on Anselm. </span>
$ qsub -I -q qmic -A NONE-0-0
$ make
-<span>The compilation command for this example is</span>
+<span>The compilation command for this example is: </span>
$ g++ capsbasic.cpp -lOpenCL -o capsbasic -I/apps/intel/opencl/include/
@@ -499,25 +499,25 @@ be displayed.
./capsbasic
- Number of available platforms1
+ Number of available platforms: 1
Platform names:
   [0] Intel(R) OpenCL [Selected]
Number of devices available for each type:
- Â Â Â CL_DEVICE_TYPE_CPU1
- Â Â Â CL_DEVICE_TYPE_GPU0
- Â Â Â CL_DEVICE_TYPE_ACCELERATOR1
+ Â Â Â CL_DEVICE_TYPE_CPU: 1
+ Â Â Â CL_DEVICE_TYPE_GPU: 0
+ Â Â Â CL_DEVICE_TYPE_ACCELERATOR: 1
*** Detailed information for each device ***
CL_DEVICE_TYPE_CPU[0]
   CL_DEVICE_NAME:       Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
- Â Â Â CL_DEVICE_AVAILABLE1
+ Â Â Â CL_DEVICE_AVAILABLE: 1
...
CL_DEVICE_TYPE_ACCELERATOR[0]
- Â Â Â CL_DEVICE_NAMEIntel(R) Many Integrated Core Acceleration Card
- Â Â Â CL_DEVICE_AVAILABLE1
+ Â Â Â CL_DEVICE_NAME: Intel(R) Many Integrated Core Acceleration Card
+ Â Â Â CL_DEVICE_AVAILABLE: 1
...
@@ -536,12 +536,12 @@ to your directory and compile it.Â
$ cd GEMM
$ make
-<span>The compilation command for this example is</span>
+<span>The compilation command for this example is: </span>
$ g++ cmdoptions.cpp gemm.cpp ../common/basic.cpp ../common/cmdparser.cpp ../common/oclobject.cpp -I../common -lOpenCL -o gemm -I/apps/intel/opencl/include/
<span>To see the performance of Intel Xeon Phi performing the DGEMM run
-the example as follows</span>
+the example as follows: </span>
./gemm -d 1
Platforms (1):
@@ -549,19 +549,19 @@ the example as follows</span>
Devices (2):
[0] Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
[1] Intel(R) Many Integrated Core Acceleration Card [Selected]
- Build program options"-DT=float -DTILE_SIZE_M=1 -DTILE_GROUP_M=16 -DTILE_SIZE_N=128 -DTILE_GROUP_N=1 -DTILE_SIZE_K=8"
- Running gemm_nn kernel with matrix size3968x3968
- Memory row stride to ensure necessary alignment15872 bytes
- Size of memory region for one matrix62980096 bytes
+ Build program options: "-DT=float -DTILE_SIZE_M=1 -DTILE_GROUP_M=16 -DTILE_SIZE_N=128 -DTILE_GROUP_N=1 -DTILE_SIZE_K=8"
+ Running gemm_nn kernel with matrix size: 3968x3968
+ Memory row stride to ensure necessary alignment: 15872 bytes
+ Size of memory region for one matrix: 62980096 bytes
Using alpha = 0.57599 and beta = 0.872412
...
- Host time0.292953 sec.
- Host perf426.635 GFLOPS
- Host time0.293334 sec.
- Host perf426.081 GFLOPS
+ Host time: 0.292953 sec.
+ Host perf: 426.635 GFLOPS
+ Host time: 0.293334 sec.
+ Host perf: 426.081 GFLOPS
...
-<span>Please noteGNU compiler is used to compile the OpenCL codes for
+<span>Please note: GNU compiler is used to compile the OpenCL codes for
Intel MIC. You do not need to load Intel compiler module.
</span>
@@ -651,7 +651,7 @@ The output should be similar to:
### Coprocessor-only model
<span>There are two ways how to execute an MPI code on a single
-coprocessor1.) lunch the program using "**mpirun**" from the
+coprocessor: 1.) lunch the program using "**mpirun**" from the
coprocessor; or 2.) lunch the task using "**mpiexec.hydra**" from a
host.
</span>
@@ -759,7 +759,7 @@ accelerators on multiple nodes**
<span>To get access to multiple nodes with MIC accelerator, user has to
use PBS to allocate the resources. To start interactive session, that
allocates 2 compute nodes = 2 MIC accelerators run qsub command with
-following parameters</span>
+following parameters: </span>
$ qsub -I -q qmic -A NONE-0-0 -l select=2:ncpus=16
@@ -771,7 +771,7 @@ immediately. To see the other nodes that have been allocated use:
$ cat $PBS_NODEFILE
-<span>For example</span>
+<span>For example: </span>
cn204.bullx
cn205.bullx
@@ -780,15 +780,15 @@ immediately. To see the other nodes that have been allocated use:
which means that user has direct access to "**cn204-mic0**" and
"**cn-205-mic0**" accelerators.</span>
-<span>Please noteAt this point user can connect to any of the
+<span>Please note: At this point user can connect to any of the
allocated nodes or any of the allocated MIC accelerators using ssh:
-- to connect to the second node **<span class="monospace">$ ssh
+- to connect to the second node : **<span class="monospace">$ ssh
cn205</span>**
<span>- to connect to the accelerator on the first node from the first
-node<span class="monospace">**$ ssh cn204-mic0**</span></span> or
+node: <span class="monospace">**$ ssh cn204-mic0**</span></span> or
**<span class="monospace">$ ssh mic0</span>**
**-** to connect to the accelerator on the second node from the first
-node<span class="monospace">**$ ssh cn205-mic0**</span>
+node: <span class="monospace">**$ ssh cn205-mic0**</span>
</span>
<span>At this point we expect that correct modules are loaded and binary
@@ -805,7 +805,7 @@ MIC accelerators by setting up the environmental variable "I_MPI_MIC"
 -genv I_MPI_FABRICS shm:tcp
 -genv I_MPI_TCP_NETMASK=10.1.0.0/16
-host cn204-mic0 -n 4 ~/mpi-test-mic
- -host cn205-mic0 -n 6 ~/mpi-test-mic
+ : -host cn205-mic0 -n 6 ~/mpi-test-mic
or using mpirun:
@@ -814,7 +814,7 @@ or using mpirun:
 -genv I_MPI_FABRICS shm:tcp
 -genv I_MPI_TCP_NETMASK=10.1.0.0/16
-host cn204-mic0 -n 4 ~/mpi-test-mic
- -host cn205-mic0 -n 6 ~/mpi-test-mic
+ : -host cn205-mic0 -n 6 ~/mpi-test-mic
In this case four MPI processes are executed on accelerator cn204-mic
and six processes are executed on accelerator cn205-mic0. The sample
@@ -838,7 +838,7 @@ The same way MPI program can be executed on multiple hosts:Â
 -genv I_MPI_FABRICS shm:tcp
 -genv I_MPI_TCP_NETMASK=10.1.0.0/16
-host cn204 -n 4 ~/mpi-test
- -host cn205 -n 6 ~/mpi-test
+ : -host cn205 -n 6 ~/mpi-test
### <span>Symmetric model </span>
@@ -859,14 +859,14 @@ These two binaries can be executed at once using mpiexec.hydra:
 -genv I_MPI_TCP_NETMASK=10.1.0.0/16
-genv LD_LIBRARY_PATH /apps/intel/impi/4.1.1.036/mic/lib/
-host cn205 -n 2 ~/mpi-test
- -host cn205-mic0 -n 2 ~/mpi-test-mic
+ : -host cn205-mic0 -n 2 ~/mpi-test-mic
In this example the first two parameters (line 2 and 3) sets up required
environment variables for execution. The third line specifies binary
that is executed on host (here cn205) and the last line specifies the
binary that is execute on the accelerator (here cn205-mic0).
-<span>The output of the program is</span>
+<span>The output of the program is: </span>
Hello world from process 0 of 4 on host cn205
Hello world from process 1 of 4 on host cn205
@@ -927,7 +927,7 @@ hosts and two accelerators is:
Hello world from process 6 of 8 on host cn205-mic0
Hello world from process 7 of 8 on host cn205-mic0
-Please noteAt this point the MPI communication between MIC
+Please note: At this point the MPI communication between MIC
accelerators on different nodes uses 1Gb Ethernet only.
**Using the PBS automatically generated node-files
@@ -956,3 +956,7 @@ Coprocessors](http://software.intel.com/en-us/articles/optimization-and-performa
.text}.
Â
+
+
+
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.html b/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.html
new file mode 100644
index 000000000..4ef71f0f0
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.html
@@ -0,0 +1,1161 @@
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+ <div id="parent-fieldname-text-2d8d49e87ab042dab1fba609153dd57f" class="">
+ <p>On Anselm cluster there are also installed commercial software applications, also known as ISV (Independent Software Vendor), which are subjects to licensing. The licenses are limited and their usage may be restricted only to some users or user groups.</p>
+<p>Currently Flex License Manager based licensing is supported on the cluster for products Ansys, Comsol and Matlab. More information about the applications can be found in the general <a href="../software.1.html" title="" target="_self" class="internal-link">Software</a> section.</p>
+<p>If an ISV application was purchased for educational (research) purposes and also for commercial purposes, then there are always two separate versions maintained and suffix "edu" is used in the name of the non-commercial version.</p>
+<h2 class=" ">Overview of the licenses usage</h2>
+<p class="callout">The overview is generated every minute and is accessible from web or command line interface.</p>
+<h3 class=" ">Web interface</h3>
+<p>For each license there is a table, which provides the information about the name, number of available (purchased/licensed), number of used and number of free license features</p>
+<p><a class="external-link" href="https://extranet.it4i.cz/anselm/licenses" target="_self" title="">https://extranet.it4i.cz/anselm/licenses</a></p>
+<h3 class=" ">Text interface</h3>
+<p>For each license there is a unique text file, which provides the information about the name, number of available (purchased/licensed), number of used and number of free license features. The text files are accessible from the Anselm command prompt.<a name="Licence"></a></p>
+<table class="listing">
+<tbody>
+<tr><th>Product</th><th>File with license state</th><th>Note</th></tr>
+<tr>
+<td>ansys</td>
+<td>/apps/user/licenses/ansys_features_state.txt</td>
+<td>Commercial</td>
+</tr>
+<tr>
+<td>comsol</td>
+<td>/apps/user/licenses/comsol_features_state.txt</td>
+<td>Commercial</td>
+</tr>
+<tr>
+<td>comsol-edu</td>
+<td>/apps/user/licenses/comsol-edu_features_state.txt</td>
+<td>Non-commercial only</td>
+</tr>
+<tr>
+<td>matlab</td>
+<td>/apps/user/licenses/matlab_features_state.txt</td>
+<td>Commercial</td>
+</tr>
+<tr>
+<td>matlab-edu</td>
+<td>/apps/user/licenses/matlab-edu_features_state.txt</td>
+<td>Non-commercial only</td>
+</tr>
+</tbody>
+</table>
+<p>The file has a header which serves as a legend. All the info in the legend starts with a hash (#) so it can be easily filtered when parsing the file via a script.</p>
+<p>Example of the Commercial Matlab license state:</p>
+<pre class=" ">$ cat /apps/user/licenses/matlab_features_state.txt<br /># matlab<br /># -------------------------------------------------<br /># FEATURE TOTAL USED AVAIL<br /># -------------------------------------------------<br />MATLAB 1 1 0<br />SIMULINK 1 0 1<br />Curve_Fitting_Toolbox 1 0 1<br />Signal_Blocks 1 0 1<br />GADS_Toolbox 1 0 1<br />Image_Toolbox 1 0 1<br />Compiler 1 0 1<br />Neural_Network_Toolbox 1 0 1<br />Optimization_Toolbox 1 0 1<br />Signal_Toolbox 1 0 1<br />Statistics_Toolbox 1 0 1</pre>
+<h2 class=" ">License tracking in PBS Pro scheduler and users usage</h2>
+<p>Each feature of each license is accounted and checked by the scheduler of PBS Pro. If you ask for certain licences, the scheduler won't start the job until the asked licenses are free (available). This prevents to crash batch jobs, just because of <span class="short_text" id="result_box"><span class="hps">unavailability</span></span> of the needed licenses.</p>
+<p>The general format of the name is:</p>
+<p><strong>feature__APP__FEATURE</strong></p>
+<p>Names of applications (APP):</p>
+<ul>
+<li>ansys</li>
+<li>comsol</li>
+<li>comsol-edu</li>
+<li>matlab</li>
+<li>matlab-edu</li>
+</ul>
+<p>Â </p>
+<p>To get the FEATUREs of a license take a look into the corresponding state file (<a class="anchor-link" href="isv_licenses.html#Licence" target="_self" title="">see above</a>), or use:</p>
+<table class="listing">
+<tbody>
+<tr><th>Application</th><th>List of provided features</th></tr>
+<tr>
+<td>ansys</td>
+<td>
+<pre>$ grep -v "#" /apps/user/licenses/ansys_features_state.txt | cut -f1 -d' '</pre>
+</td>
+</tr>
+<tr>
+<td>comsol</td>
+<td>
+<pre>$ grep -v "#" /apps/user/licenses/comsol_features_state.txt | cut -f1 -d' '</pre>
+</td>
+</tr>
+<tr>
+<td>comsol-edu</td>
+<td>
+<pre>$ grep -v "#" /apps/user/licenses/comsol-edu_features_state.txt | cut -f1 -d' '</pre>
+</td>
+</tr>
+<tr>
+<td>matlab</td>
+<td>
+<pre>$ grep -v "#" /apps/user/licenses/matlab_features_state.txt | cut -f1 -d' '</pre>
+</td>
+</tr>
+<tr>
+<td>matlab-edu</td>
+<td>
+<pre>$ grep -v "#" /apps/user/licenses/matlab-edu_features_state.txt | cut -f1 -d' '</pre>
+</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<p>Example of PBS Pro resource name, based on APP and FEATURE name:</p>
+<table class="listing">
+<tbody>
+<tr><th>Application</th><th>Feature</th><th>PBS Pro resource name</th></tr>
+<tr>
+<td>ansys</td>
+<td>acfd</td>
+<td>feature__ansys__acfd</td>
+</tr>
+<tr>
+<td>ansys</td>
+<td>aa_r</td>
+<td>feature__ansys__aa_r</td>
+</tr>
+<tr>
+<td>comsol</td>
+<td>COMSOL</td>
+<td>feature__comsol__COMSOL</td>
+</tr>
+<tr>
+<td>comsol</td>
+<td>HEATTRANSFER</td>
+<td>feature__comsol__HEATTRANSFER</td>
+</tr>
+<tr>
+<td>comsol-edu</td>
+<td>COMSOLBATCH</td>
+<td>feature__comsol-edu__COMSOLBATCH</td>
+</tr>
+<tr>
+<td>comsol-edu</td>
+<td>STRUCTURALMECHANICS</td>
+<td>feature__comsol-edu__STRUCTURALMECHANICS</td>
+</tr>
+<tr>
+<td>matlab</td>
+<td>MATLAB</td>
+<td>feature__matlab__MATLAB</td>
+</tr>
+<tr>
+<td>matlab</td>
+<td>Image_Toolbox</td>
+<td>feature__matlab__Image_Toolbox</td>
+</tr>
+<tr>
+<td>matlab-edu</td>
+<td>MATLAB_Distrib_Comp_Engine</td>
+<td>feature__matlab-edu__MATLAB_Distrib_Comp_Engine</td>
+</tr>
+<tr>
+<td>matlab-edu</td>
+<td>Image_Acquisition_Toolbox</td>
+<td>
+<p>feature__matlab-edu__Image_Acquisition_Toolbox</p>
+</td>
+</tr>
+</tbody>
+</table>
+<p class=" "><strong>Be aware, that the resource names in PBS Pro are CASE SENSITIVE!</strong></p>
+<h3 class=" ">Example of qsub statement</h3>
+<p>Run an interactive PBS job with 1 Matlab EDU license, 1 Distributed Computing Toolbox and 32 Distributed Computing Engines (running on 32 cores):</p>
+<pre class=" ">$ qsub -I -q qprod -A PROJECT_ID -l select=2:ncpus=16 -l feature__matlab-edu__MATLAB=1 -l feature__matlab-edu__Distrib_Computing_Toolbox=1 -l feature__matlab-edu__MATLAB_Distrib_Comp_Engine=32</pre>
+<p>The license is used and accounted only with the real usage of the product. So in this example, the general Matlab is used after Matlab is run vy the user and not at the time, when the shell of the interactive job is started. Also the Distributed Computing licenses are used at the time, when the user uses the distributed parallel computation in Matlab (e. g. issues pmode start, matlabpool, etc.).</p>
+<p>Â </p>
+
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+ <a href="https://extranet.it4i.cz">Extranet</a>
+ <a href="http://prace.it4i.cz/">HPC & PRACE</a>
+ <a href="http://study.it4i.cz/">HPC Study</a>
+ <a href="../../salomon.html">Dokumentace pro Salomon</a>
+ <a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
+ <a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
+ </p>
+ <!-- nagios_check_http_expect_string -->
+</div>
+
+ </div>
+ </div>
+
+ <!-- TODO -->
+ <!-- nagios_check_http_expect_string -->
+ <!-- TODO -->
+
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+</body>
+</html>
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md b/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
index 93eb5a863..bc415273d 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
@@ -225,3 +225,7 @@ time, when the user uses the distributed parallel computation in Matlab
(e. g. issues pmode start, matlabpool, etc.).
Â
+
+
+
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/java.html b/docs.it4i.cz/anselm-cluster-documentation/software/java.html
new file mode 100644
index 000000000..a49f91650
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/java.html
@@ -0,0 +1,1012 @@
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+
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+ Java
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+ Java on ANSELM
+ </div>
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+<dl id="document-toc" class="portlet toc" style="display: none">
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+ <div id="content-core">
+
+
+
+ <div id="parent-fieldname-text-9d0cd0bfa29d41d888378945b3f141f4" class="">
+ <p>Java is available on Anselm cluster. Activate java by loading the java module</p>
+<pre class=" ">$ module load java</pre>
+<p>Note that the java module must be loaded on the compute nodes as well, in order to run java on compute nodes.</p>
+<p>Check for java version and path</p>
+<pre class=" ">$ java -version<br />$ which java</pre>
+<p class=" ">With the module loaded, not only the runtime environment (JRE), but also the development environment (JDK) with the compiler is available.</p>
+<pre class=" ">$ javac -version<br />$ which javac</pre>
+<p class=" ">Java applications may use MPI for interprocess communication, in conjunction with OpenMPI. Read more on <a class="external-link" href="http://www.open-mpi.org/faq/?category=java" target="_self" title="">http://www.open-mpi.org/faq/?category=java</a>.<br />This functionality is currently not supported on Anselm cluster. In case you require the java interface to MPI, please contact <a class="external-link" href="https://support.it4i.cz/rt/" target="_self" title="">Anselm support</a>.</p>
+
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+<li class="navTreeItem visualNoMarker section-environment-and-modules">
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+
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+
+ <span>ANSYS</span>
+ </a>
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+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-comsol">
+
+
+
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+ <a href="comsol.html" title=" A finite element analysis, solver and Simulation software" class="state-published navTreeFolderish contenttype-folder">
+
+ <span>COMSOL</span>
+ </a>
+
+
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+
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+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-debuggers">
+
+
+
+
+ <a href="debuggers.1.html" title="A collection of development tools" class="state-published navTreeFolderish contenttype-folder">
+
+ <span>Debuggers and profilers</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-chemistry">
+
+
+
+
+ <a href="chemistry.html" title="Tools for computational chemistry." class="state-published navTreeFolderish contenttype-folder">
+
+ <span>Chemistry and Materials science</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-intel-suite">
+
+
+
+
+ <a href="intel-suite.html" title="The Intel Parallel Studio XE" class="state-published navTreeFolderish contenttype-folder">
+
+ <span>Intel Parallel studio</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-mpi-1">
+
+
+
+
+ <a href="mpi-1.html" title="Message Passing Interface libraries on ANSELM" class="state-published navTreeFolderish contenttype-folder">
+
+ <span>MPI</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-numerical-libraries">
+
+
+
+
+ <a href="numerical-libraries.html" title="Libraries for numerical computations" class="state-published navTreeFolderish contenttype-folder">
+
+ <span>Numerical Libraries</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-numerical-languages">
+
+
+
+
+ <a href="numerical-languages.1.html" title="Interpreted languages for numerical computations" class="state-published navTreeFolderish contenttype-folder">
+
+ <span>Numerical languages</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-virtualization">
+
+
+
+
+ <a href="virtualization.html" title="" class="state-published navTreeFolderish contenttype-folder">
+
+ <span>Virtualization</span>
+ </a>
+
+
+
+
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+
+
+<li class="navTreeItem visualNoMarker section-compilers">
+
+
+
+
+ <a href="compilers.html" title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document">
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+ </a>
+
+
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+
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+
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+<li class="navTreeItem visualNoMarker section-intel-xeon-phi">
+
+
+
+
+ <a href="intel-xeon-phi.html" title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document">
+
+ <span>Intel Xeon Phi</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-isv_licenses">
+
+
+
+
+ <a href="isv_licenses.html" title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document">
+
+ <span>ISV Licenses</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeCurrentNode section-java">
+
+
+
+
+ <a href="java.html" title="Java on ANSELM" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document">
+
+ <span>Java</span>
+ </a>
+
+
+
+
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+
+
+<li class="navTreeItem visualNoMarker section-nvidia-cuda">
+
+
+
+
+ <a href="nvidia-cuda.html" title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document">
+
+ <span>nVidia CUDA</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeFolderish section-omics-master-1">
+
+
+
+
+ <a href="omics-master-1.html" title="" class="state-published navTreeFolderish contenttype-folder">
+
+ <span>OMICS Master</span>
+ </a>
+
+
+
+
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+
+
+<li class="navTreeItem visualNoMarker section-openfoam">
+
+
+
+
+ <a href="openfoam.html" title="A free, open source CFD software package" class="state-published contenttype-document">
+
+ <span>OpenFOAM</span>
+ </a>
+
+
+
+
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+
+
+<li class="navTreeItem visualNoMarker section-operating-system">
+
+
+
+
+ <a href="operating-system.html" title="The operating system, deployed on ANSELM" class="state-published contenttype-document">
+
+ <span>Operating System</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-paraview">
+
+
+
+
+ <a href="paraview.html" title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document">
+
+ <span>ParaView</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-gpi2">
+
+
+
+
+ <a href="gpi2.html" title="A library that implements the GASPI specification" class="state-published contenttype-document">
+
+ <span>GPI-2</span>
+ </a>
+
+
+
+
+</li>
+
+
+
+
+ </ul>
+
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+ <div id="parent-fieldname-text-4b4619955af540b9baf879db3e40193a" class="">
+ <h2 class=" ">Setting up MPI Environment</h2>
+<p>The Anselm cluster provides several implementations of the MPI library:</p>
+<table class="listing">
+<tbody>
+<tr><th>MPI Library</th><th>Thread support</th></tr>
+<tr class="even">
+<td>
+<p>The highly optimized and stable <strong>bullxmpi 1.2.4.1</strong></p>
+</td>
+<td><strong></strong>Partial thread support up to MPI_THREAD_SERIALIZED</td>
+</tr>
+<tr class="odd">
+<td>The<strong> Intel MPI 4.1</strong></td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE</td>
+</tr>
+<tr class="even">
+<td>The <a class="external-link" href="http://www.open-mpi.org/" target="_self" title=""><strong>OpenMPI 1.6.5</strong></a></td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE, BLCR c/r support</td>
+</tr>
+<tr class="even">
+<td>The OpenMPI 1.8.1</td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE, MPI-3.0 support</td>
+</tr>
+<tr class="odd">
+<td>The<strong> <strong>mpich2 1.9</strong></strong></td>
+<td>Full thread support up to<strong> </strong>MPI_THREAD_MULTIPLE, BLCR c/r support</td>
+</tr>
+</tbody>
+</table>
+<ul></ul>
+<p class="callout">MPI libraries are activated via the environment modules.</p>
+<p>Look up section modulefiles/mpi in module avail</p>
+<pre class=" ">$ module avail<br />------------------------- /opt/modules/modulefiles/mpi -------------------------<br />bullxmpi/bullxmpi-1.2.4.1 mvapich2/1.9-icc<br />impi/4.0.3.008 openmpi/1.6.5-gcc(default)<br />impi/4.1.0.024 openmpi/1.6.5-gcc46<br />impi/4.1.0.030 openmpi/1.6.5-icc<br />impi/4.1.1.036(default) openmpi/1.8.1-gcc<br />openmpi/1.8.1-gcc46<br />mvapich2/1.9-gcc(default) openmpi/1.8.1-gcc49<br />mvapich2/1.9-gcc46 openmpi/1.8.1-icc</pre>
+<p>There are default compilers associated with any particular MPI implementation. The defaults may be changed, the MPI libraries may be used in conjunction with any compiler.<br />The defaults are selected via the modules in following way</p>
+<table class="listing" summary="Modules selecting the MPI environment">
+<tbody>
+<tr><th>Module</th><th>MPI</th><th>Compiler suite</th></tr>
+<tr class="even">
+<td>PrgEnv-gnu</td>
+<td>bullxmpi-1.2.4.1</td>
+<td>bullx GNU 4.4.6</td>
+</tr>
+<tr class="odd">
+<td>PrgEnv-intel</td>
+<td>Intel MPI 4.1.1</td>
+<td>Intel 13.1.1</td>
+</tr>
+<tr class="even">
+<td>bullxmpi</td>
+<td>bullxmpi-1.2.4.1</td>
+<td>none, select via module</td>
+</tr>
+<tr class="odd">
+<td>impi</td>
+<td>Intel MPI 4.1.1</td>
+<td>none, select via module</td>
+</tr>
+<tr class="even">
+<td>openmpi</td>
+<td>OpenMPI 1.6.5</td>
+<td>GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers</td>
+</tr>
+<tr class="even">
+<td>openmpi</td>
+<td>OpenMPI 1.8.1</td>
+<td>GNU compilers 4.8.1, GNU compilers 4.4.6, GNU compilers 4.9.0, Intel Compilers</td>
+</tr>
+<tr class="odd">
+<td>mvapich2</td>
+<td>MPICH2 1.9</td>
+<td>GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers</td>
+</tr>
+</tbody>
+</table>
+<p>Examples:</p>
+<pre class=" ">$ module load openmpi</pre>
+<p>In this example, we activate the latest openmpi with latest GNU compilers</p>
+<p>To use openmpi with the intel compiler suite, use</p>
+<pre class=" ">$ module load intel<br />$ module load openmpi/1.6.5-icc</pre>
+<p>In this example, the openmpi 1.6.5 using intel compilers is activated</p>
+<h2 class=" ">Compiling MPI Programs</h2>
+<p class="callout">After setting up your MPI environment, compile your program using one of the mpi wrappers</p>
+<pre class=" ">$ mpicc -v<br />$ mpif77 -v<br />$ mpif90 -v</pre>
+<p>Example program:</p>
+<pre class=" ">// helloworld_mpi.c<br />#include <stdio.h><br /><br />#include<mpi.h><br /><br />int main(int argc, char **argv) {<br /><br />int len;<br />int rank, size;<br />char node[MPI_MAX_PROCESSOR_NAME];<br /><br />// Initiate MPI<br />MPI_Init(&argc, &argv);<br />MPI_Comm_rank(MPI_COMM_WORLD,&rank);<br />MPI_Comm_size(MPI_COMM_WORLD,&size);<br /><br />// Get hostame and print<br />MPI_Get_processor_name(node,&len);<br />printf("Hello world! from rank %d of %d on host %s\n",rank,size,node);<br /><br />// Finalize and exit<br />MPI_Finalize();<br /><br />return 0;<br />}</pre>
+<p>Compile the above example with</p>
+<pre class=" ">$ mpicc helloworld_mpi.c -o helloworld_mpi.x</pre>
+<h2 class=" ">Running MPI Programs</h2>
+<p class="callout">The MPI program executable must be compatible with the loaded MPI module. <br />Always compile and execute using the very same MPI module.</p>
+<p>It is strongly discouraged to mix mpi implementations. Linking an application with one MPI implementation and running mpirun/mpiexec form other implementation may result in unexpected errors.</p>
+<p>The MPI program executable must be available within the same path on all nodes. This is automatically fulfilled on the /home and /scratch filesystem. You need to preload the executable, if running on the local scratch /lscratch filesystem.</p>
+<h3 class=" ">Ways to run MPI programs</h3>
+<p>Optimal way to run an MPI program depends on its memory requirements, memory access pattern and communication pattern.</p>
+<p class="callout">Consider these ways to run an MPI program:<br />1. One MPI process per node, 16 threads per process<br />2. Two MPI processes per node, 8 threads per process<br />3. 16 MPI processes per node, 1 thread per process.</p>
+<p class=" "><strong>One MPI</strong> process per node, using 16 threads, is most useful for memory demanding applications, that make good use of processor cache memory and are not memory bound. This is also a preferred way for communication intensive applications as one process per node enjoys full bandwidth access to the network interface. </p>
+<p class=" "><strong>Two MPI</strong> processes per node, using 8 threads each, bound to processor socket is most useful for memory bandwidth bound applications such as BLAS1 or FFT, with scalable memory demand. However, note that the two processes will share access to the network interface. The 8 threads and socket binding should ensure maximum memory access bandwidth and minimize communication, migration and numa effect overheads.</p>
+<p class="callout">Important! Bind every OpenMP thread to a core!</p>
+<p>In the previous two cases with one or two MPI processes per node, the operating system might still migrate OpenMP threads between cores. You want to avoid this by setting the KMP_AFFINITY or GOMP_CPU_AFFINITY environment variables.</p>
+<p class=" "><strong class=" ">16 MPI</strong> processes per node, using 1 thread each bound to processor core is most suitable for highly scalable applications with low communication demand.</p>
+<h3 class=" ">Running OpenMPI</h3>
+<p>The <strong>bullxmpi-1.2.4.1</strong> and <a class="external-link" href="http://www.open-mpi.org/" target="_self" title=""><strong>OpenMPI 1.6.5</strong></a> are both based on OpenMPI. Read more on <a href="mpi-1/Running_OpenMPI.html" title="" target="_self" class="internal-link">how to run OpenMPI</a> based MPI.</p>
+<h3 class=" ">Running MPICH2</h3>
+<p>The <strong>Intel MPI</strong> and <strong>mpich2 1.9</strong> are MPICH2 based implementations. Read more on <a href="mpi-1/running-mpich2.html" title="" target="_self" class="internal-link">how to run MPICH2</a> based MPI.</p>
+<p>The Intel MPI may run on the Intel Xeon Phi accelerators as well. Read more on <a href="intel-xeon-phi.html" title="" target="_self" class="internal-link">how to run Intel MPI on accelerators</a>.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1.md b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1.md
index 733077849..a46564ad7 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1.md
@@ -199,4 +199,3 @@ more on [how to run Intel MPI on
accelerators](intel-xeon-phi.html).
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.html b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.html
new file mode 100644
index 000000000..2268906fb
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+ <h2 class=" ">OpenMPI program execution</h2>
+<p>The OpenMPI programs may be executed only via the PBS Workload manager, by entering an appropriate queue. On Anselm, the <strong>bullxmpi-1.2.4.1</strong> and <strong>OpenMPI 1.6.5</strong> are OpenMPI based MPI implementations.</p>
+<h3 class=" ">Basic usage</h3>
+<p class="callout">Use the mpiexec to run the OpenMPI code.</p>
+<p>Example:</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=16 -I<br />qsub: waiting for job 15210.srv11 to start<br />qsub: job 15210.srv11 ready<br /><br />$ pwd<br />/home/username<br /><br />$ module load openmpi<br />$ mpiexec -pernode ./helloworld_mpi.x<br />Hello world! from rank 0 of 4 on host cn17<br />Hello world! from rank 1 of 4 on host cn108<br />Hello world! from rank 2 of 4 on host cn109<br />Hello world! from rank 3 of 4 on host cn110</pre>
+<p class="callout">Please be aware, that in this example, the directive<strong> -pernode</strong> is used to run only <strong>one task per node</strong>, which is normally an unwanted behaviour (unless you want to run hybrid code with just one MPI and 16 OpenMP tasks per node). In normal MPI programs <strong>omit the -pernode directive</strong> to run up to 16 MPI tasks per each node.</p>
+<p class=" ">In this example, we allocate 4 nodes via the express queue interactively. We set up the openmpi environment and interactively run the helloworld_mpi.x program.<br />Note that the executable <span class="monospace">helloworld_mpi.x</span> must be available within the same path on all nodes. This is automatically fulfilled on the /home and /scratch filesystem.</p>
+<p class=" ">You need to preload the executable, if running on the local scratch /lscratch filesystem</p>
+<pre class=" ">$ pwd<br />/lscratch/15210.srv11<br /><br />$ mpiexec -pernode --preload-binary ./helloworld_mpi.x<br />Hello world! from rank 0 of 4 on host cn17<br />Hello world! from rank 1 of 4 on host cn108<br />Hello world! from rank 2 of 4 on host cn109<br />Hello world! from rank 3 of 4 on host cn110</pre>
+<p class=" ">In this example, we assume the executable <span class="monospace">helloworld_mpi.x</span> is present on compute node cn17 on local scratch. We call the mpiexec whith the <strong>--preload-binary</strong> argument (valid for openmpi). The mpiexec will copy the executable from cn17 to the <span class="monospace">/lscratch/15210.srv11</span> directory on cn108, cn109 and cn110 and execute the program.</p>
+<p class="callout">MPI process mapping may be controlled by PBS parameters.</p>
+<p class=" ">The mpiprocs and ompthreads parameters allow for selection of number of running MPI processes per node as well as number of OpenMP threads per MPI process.</p>
+<h3 class=" ">One MPI process per node</h3>
+<p class=" ">Follow this example to run one MPI process per node, 16 threads per process. </p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=16:mpiprocs=1:ompthreads=16 -I<br /><br />$ module load openmpi<br /><br />$ mpiexec --bind-to-none ./helloworld_mpi.x</pre>
+<p>In this example, we demonstrate recommended way to run an MPI application, using 1 MPI processes per node and 16 threads per socket, on 4 nodes.</p>
+<h3 class=" ">Two MPI processes per node</h3>
+<p class=" ">Follow this example to run two MPI processes per node, 8 threads per process. Note the options to mpiexec.</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=16:mpiprocs=2:ompthreads=8 -I<br /><br />$ module load openmpi<br /><br />$ mpiexec -bysocket -bind-to-socket ./helloworld_mpi.x</pre>
+<p>In this example, we demonstrate recommended way to run an MPI application, using 2 MPI processes per node and 8 threads per socket, each process and its threads bound to a separate processor socket of the node, on 4 nodes</p>
+<h3 class=" ">16 MPI processes per node</h3>
+<p class=" ">Follow this example to run 16 MPI processes per node, 1 thread per process. Note the options to mpiexec.</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=16:mpiprocs=16:ompthreads=1 -I<br /><br />$ module load openmpi<br /><br />$ mpiexec -bycore -bind-to-core ./helloworld_mpi.x</pre>
+<p>In this example, we demonstrate recommended way to run an MPI application, using 16 MPI processes per node, single threaded. Each process is bound to separate processor core, on 4 nodes.</p>
+<h3 class=" ">OpenMP thread affinity</h3>
+<p class="callout">Important! Bind every OpenMP thread to a core!</p>
+<p>In the previous two examples with one or two MPI processes per node, the operating system might still migrate OpenMP threads between cores. You might want to avoid this by setting these environment variable for GCC OpenMP:</p>
+<pre class=" "><span class="s1">$ export GOMP_CPU_AFFINITY="0-15"</span></pre>
+<p>or this one for Intel OpenMP:</p>
+<pre class=" ">$ export KMP_AFFINITY=granularity=fine,compact,1,0</pre>
+<p class=" ">As of OpenMP 4.0 (supported by GCC 4.9 and later and Intel 14.0 and later) the following variables may be used for Intel or GCC:</p>
+<pre class=" ">$ export OMP_PROC_BIND=true<br />$ export OMP_PLACES=cores </pre>
+<h2 class=" "><span>OpenMPI Process Mapping and Binding</span></h2>
+<p>The mpiexec allows for precise selection of how the MPI processes will be mapped to the computational nodes and how these processes will bind to particular processor sockets and cores.</p>
+<p>MPI process mapping may be specified by a hostfile or rankfile input to the mpiexec program. Altough all implementations of MPI provide means for process mapping and binding, following examples are valid for the openmpi only.</p>
+<h3 class=" ">Hostfile</h3>
+<p>Example hostfile</p>
+<pre class=" ">cn110.bullx<br />cn109.bullx<br />cn108.bullx<br />cn17.bullx</pre>
+<p class=" ">Use the hostfile to control process placement</p>
+<pre class=" ">$ mpiexec -hostfile hostfile ./helloworld_mpi.x<br />Hello world! from rank 0 of 4 on host cn110<br />Hello world! from rank 1 of 4 on host cn109<br />Hello world! from rank 2 of 4 on host cn108<br />Hello world! from rank 3 of 4 on host cn17</pre>
+<p>In this example, we see that ranks have been mapped on nodes according to the order in which nodes show in the hostfile</p>
+<h3 class=" ">Rankfile</h3>
+<p>Exact control of MPI process placement and resource binding is provided by specifying a rankfile</p>
+<p class="callout">Appropriate binding may boost performance of your application.</p>
+<p>Example rankfile</p>
+<pre class=" ">rank 0=cn110.bullx slot=1:0,1<br />rank 1=cn109.bullx slot=0:*<br />rank 2=cn108.bullx slot=1:1-2<br />rank 3=cn17.bullx slot=0:1,1:0-2<br />rank 4=cn109.bullx slot=0:*,1:*</pre>
+<p>This rankfile assumes 5 ranks will be running on 4 nodes and provides exact mapping and binding of the processes to the processor sockets and cores</p>
+<p>Explanation: <br /> rank 0 will be bounded to cn110, socket1 core0 and core1 <br /> rank 1 will be bounded to cn109, socket0, all cores <br /> rank 2 will be bounded to cn108, socket1, core1 and core2<br /> rank 3 will be bounded to cn17, socket0 core1, socket1 core0, core1, core2<br /> rank 4 will be bounded to cn109, all cores on both sockets</p>
+<pre class=" ">$ mpiexec -n 5 -rf rankfile --report-bindings ./helloworld_mpi.x<br />[cn17:11180] MCW rank 3 bound to socket 0[core 1] socket 1[core 0-2]: [. B . . . . . .][B B B . . . . .] (slot list 0:1,1:0-2)<br />[cn110:09928] MCW rank 0 bound to socket 1[core 0-1]: [. . . . . . . .][B B . . . . . .] (slot list 1:0,1)<br />[cn109:10395] MCW rank 1 bound to socket 0[core 0-7]: [B B B B B B B B][. . . . . . . .] (slot list 0:*)<br />[cn108:10406] MCW rank 2 bound to socket 1[core 1-2]: [. . . . . . . .][. B B . . . . .] (slot list 1:1-2)<br />[cn109:10406] MCW rank 4 bound to socket 0[core 0-7] socket 1[core 0-7]: [B B B B B B B B][B B B B B B B B] (slot list 0:*,1:*)<br />Hello world! from rank 3 of 5 on host cn17<br />Hello world! from rank 1 of 5 on host cn109<br />Hello world! from rank 0 of 5 on host cn110<br />Hello world! from rank 4 of 5 on host cn109<br />Hello world! from rank 2 of 5 on host cn108</pre>
+<p>In this example we run 5 MPI processes (5 ranks) on four nodes. The rankfile defines how the processes will be mapped on the nodes, sockets and cores. The <strong>--report-bindings</strong> option was used to print out the actual process location and bindings. Note that ranks 1 and 4 run on the same node and their core binding overlaps.</p>
+<p>It is users responsibility to provide correct number of ranks, sockets and cores.</p>
+<h3 class=" ">Bindings verification</h3>
+<p>In all cases, binding and threading may be verified by executing for example:</p>
+<pre class=" ">$ mpiexec -bysocket -bind-to-socket --report-bindings echo<br />$ mpiexec -bysocket -bind-to-socket numactl --show<br />$ mpiexec -bysocket -bind-to-socket echo $OMP_NUM_THREADS</pre>
+<h2 class=" ">Changes in OpenMPI 1.8</h2>
+<p>Some options have changed in OpenMPI version 1.8.</p>
+<table class="plain">
+<tbody>
+<tr><th>version 1.6.5</th><th>version 1.8.1</th></tr>
+<tr>
+<td>--bind-to-none</td>
+<td>--bind-to none</td>
+</tr>
+<tr>
+<td>--bind-to-core</td>
+<td>--bind-to core</td>
+</tr>
+<tr>
+<td>--bind-to-socket</td>
+<td>--bind-to socket</td>
+</tr>
+<tr>
+<td>-bysocket</td>
+<td>--map-by socket</td>
+</tr>
+<tr>
+<td>-bycore</td>
+<td>--map-by core</td>
+</tr>
+<tr>
+<td>-pernode</td>
+<td>
+<p class="p1"><span class="s1">--map-by ppr:1:node</span></p>
+</td>
+</tr>
+</tbody>
+</table>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
index 91af995dc..e6a572e9f 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
@@ -19,8 +19,8 @@ Use the mpiexec to run the OpenMPI code.
Example:
$ qsub -q qexp -l select=4:ncpus=16 -I
- qsubwaiting for job 15210.srv11 to start
- qsubjob 15210.srv11 ready
+ qsub: waiting for job 15210.srv11 to start
+ qsub: job 15210.srv11 ready
$ pwd
/home/username
@@ -199,11 +199,11 @@ core2
rank 4 will be bounded to cn109, all cores on both sockets
$ mpiexec -n 5 -rf rankfile --report-bindings ./helloworld_mpi.x
- [cn17:11180] MCW rank 3 bound to socket 0[core 1] socket 1[core 0-2][. B . . . . . .][B B B . . . . .] (slot list 0:1,1:0-2)
- [cn110:09928] MCW rank 0 bound to socket 1[core 0-1][. . . . . . . .][B B . . . . . .] (slot list 1:0,1)
- [cn109:10395] MCW rank 1 bound to socket 0[core 0-7][B B B B B B B B][. . . . . . . .] (slot list 0:*)
- [cn108:10406] MCW rank 2 bound to socket 1[core 1-2][. . . . . . . .][. B B . . . . .] (slot list 1:1-2)
- [cn109:10406] MCW rank 4 bound to socket 0[core 0-7] socket 1[core 0-7][B B B B B B B B][B B B B B B B B] (slot list 0:*,1:*)
+ [cn17:11180] MCW rank 3 bound to socket 0[core 1] socket 1[core 0-2]: [. B . . . . . .][B B B . . . . .] (slot list 0:1,1:0-2)
+ [cn110:09928] MCW rank 0 bound to socket 1[core 0-1]: [. . . . . . . .][B B . . . . . .] (slot list 1:0,1)
+ [cn109:10395] MCW rank 1 bound to socket 0[core 0-7]: [B B B B B B B B][. . . . . . . .] (slot list 0:*)
+ [cn108:10406] MCW rank 2 bound to socket 1[core 1-2]: [. . . . . . . .][. B B . . . . .] (slot list 1:1-2)
+ [cn109:10406] MCW rank 4 bound to socket 0[core 0-7] socket 1[core 0-7]: [B B B B B B B B][B B B B B B B B] (slot list 0:*,1:*)
Hello world! from rank 3 of 5 on host cn17
Hello world! from rank 1 of 5 on host cn109
Hello world! from rank 0 of 5 on host cn110
@@ -273,4 +273,3 @@ Some options have changed in OpenMPI version 1.8.
</table>
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.html b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.html
new file mode 100644
index 000000000..40087a3d5
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.html
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+ MPI
+ </h1>
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+ <div id="parent-fieldname-text-4b4619955af540b9baf879db3e40193a" class="">
+ <h2 class=" ">Setting up MPI Environment</h2>
+<p>The Anselm cluster provides several implementations of the MPI library:</p>
+<table class="listing">
+<tbody>
+<tr><th>MPI Library</th><th>Thread support</th></tr>
+<tr class="even">
+<td>
+<p>The highly optimized and stable <strong>bullxmpi 1.2.4.1</strong></p>
+</td>
+<td><strong></strong>Partial thread support up to MPI_THREAD_SERIALIZED</td>
+</tr>
+<tr class="odd">
+<td>The<strong> Intel MPI 4.1</strong></td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE</td>
+</tr>
+<tr class="even">
+<td>The <a class="external-link" href="http://www.open-mpi.org/" target="_self" title=""><strong>OpenMPI 1.6.5</strong></a></td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE, BLCR c/r support</td>
+</tr>
+<tr class="even">
+<td>The OpenMPI 1.8.1</td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE, MPI-3.0 support</td>
+</tr>
+<tr class="odd">
+<td>The<strong> <strong>mpich2 1.9</strong></strong></td>
+<td>Full thread support up to<strong> </strong>MPI_THREAD_MULTIPLE, BLCR c/r support</td>
+</tr>
+</tbody>
+</table>
+<ul></ul>
+<p class="callout">MPI libraries are activated via the environment modules.</p>
+<p>Look up section modulefiles/mpi in module avail</p>
+<pre class=" ">$ module avail<br />------------------------- /opt/modules/modulefiles/mpi -------------------------<br />bullxmpi/bullxmpi-1.2.4.1 mvapich2/1.9-icc<br />impi/4.0.3.008 openmpi/1.6.5-gcc(default)<br />impi/4.1.0.024 openmpi/1.6.5-gcc46<br />impi/4.1.0.030 openmpi/1.6.5-icc<br />impi/4.1.1.036(default) openmpi/1.8.1-gcc<br />openmpi/1.8.1-gcc46<br />mvapich2/1.9-gcc(default) openmpi/1.8.1-gcc49<br />mvapich2/1.9-gcc46 openmpi/1.8.1-icc</pre>
+<p>There are default compilers associated with any particular MPI implementation. The defaults may be changed, the MPI libraries may be used in conjunction with any compiler.<br />The defaults are selected via the modules in following way</p>
+<table class="listing" summary="Modules selecting the MPI environment">
+<tbody>
+<tr><th>Module</th><th>MPI</th><th>Compiler suite</th></tr>
+<tr class="even">
+<td>PrgEnv-gnu</td>
+<td>bullxmpi-1.2.4.1</td>
+<td>bullx GNU 4.4.6</td>
+</tr>
+<tr class="odd">
+<td>PrgEnv-intel</td>
+<td>Intel MPI 4.1.1</td>
+<td>Intel 13.1.1</td>
+</tr>
+<tr class="even">
+<td>bullxmpi</td>
+<td>bullxmpi-1.2.4.1</td>
+<td>none, select via module</td>
+</tr>
+<tr class="odd">
+<td>impi</td>
+<td>Intel MPI 4.1.1</td>
+<td>none, select via module</td>
+</tr>
+<tr class="even">
+<td>openmpi</td>
+<td>OpenMPI 1.6.5</td>
+<td>GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers</td>
+</tr>
+<tr class="even">
+<td>openmpi</td>
+<td>OpenMPI 1.8.1</td>
+<td>GNU compilers 4.8.1, GNU compilers 4.4.6, GNU compilers 4.9.0, Intel Compilers</td>
+</tr>
+<tr class="odd">
+<td>mvapich2</td>
+<td>MPICH2 1.9</td>
+<td>GNU compilers 4.8.1, GNU compilers 4.4.6, Intel Compilers</td>
+</tr>
+</tbody>
+</table>
+<p>Examples:</p>
+<pre class=" ">$ module load openmpi</pre>
+<p>In this example, we activate the latest openmpi with latest GNU compilers</p>
+<p>To use openmpi with the intel compiler suite, use</p>
+<pre class=" ">$ module load intel<br />$ module load openmpi/1.6.5-icc</pre>
+<p>In this example, the openmpi 1.6.5 using intel compilers is activated</p>
+<h2 class=" ">Compiling MPI Programs</h2>
+<p class="callout">After setting up your MPI environment, compile your program using one of the mpi wrappers</p>
+<pre class=" ">$ mpicc -v<br />$ mpif77 -v<br />$ mpif90 -v</pre>
+<p>Example program:</p>
+<pre class=" ">// helloworld_mpi.c<br />#include <stdio.h><br /><br />#include<mpi.h><br /><br />int main(int argc, char **argv) {<br /><br />int len;<br />int rank, size;<br />char node[MPI_MAX_PROCESSOR_NAME];<br /><br />// Initiate MPI<br />MPI_Init(&argc, &argv);<br />MPI_Comm_rank(MPI_COMM_WORLD,&rank);<br />MPI_Comm_size(MPI_COMM_WORLD,&size);<br /><br />// Get hostame and print<br />MPI_Get_processor_name(node,&len);<br />printf("Hello world! from rank %d of %d on host %s\n",rank,size,node);<br /><br />// Finalize and exit<br />MPI_Finalize();<br /><br />return 0;<br />}</pre>
+<p>Compile the above example with</p>
+<pre class=" ">$ mpicc helloworld_mpi.c -o helloworld_mpi.x</pre>
+<h2 class=" ">Running MPI Programs</h2>
+<p class="callout">The MPI program executable must be compatible with the loaded MPI module. <br />Always compile and execute using the very same MPI module.</p>
+<p>It is strongly discouraged to mix mpi implementations. Linking an application with one MPI implementation and running mpirun/mpiexec form other implementation may result in unexpected errors.</p>
+<p>The MPI program executable must be available within the same path on all nodes. This is automatically fulfilled on the /home and /scratch filesystem. You need to preload the executable, if running on the local scratch /lscratch filesystem.</p>
+<h3 class=" ">Ways to run MPI programs</h3>
+<p>Optimal way to run an MPI program depends on its memory requirements, memory access pattern and communication pattern.</p>
+<p class="callout">Consider these ways to run an MPI program:<br />1. One MPI process per node, 16 threads per process<br />2. Two MPI processes per node, 8 threads per process<br />3. 16 MPI processes per node, 1 thread per process.</p>
+<p class=" "><strong>One MPI</strong> process per node, using 16 threads, is most useful for memory demanding applications, that make good use of processor cache memory and are not memory bound. This is also a preferred way for communication intensive applications as one process per node enjoys full bandwidth access to the network interface. </p>
+<p class=" "><strong>Two MPI</strong> processes per node, using 8 threads each, bound to processor socket is most useful for memory bandwidth bound applications such as BLAS1 or FFT, with scalable memory demand. However, note that the two processes will share access to the network interface. The 8 threads and socket binding should ensure maximum memory access bandwidth and minimize communication, migration and numa effect overheads.</p>
+<p class="callout">Important! Bind every OpenMP thread to a core!</p>
+<p>In the previous two cases with one or two MPI processes per node, the operating system might still migrate OpenMP threads between cores. You want to avoid this by setting the KMP_AFFINITY or GOMP_CPU_AFFINITY environment variables.</p>
+<p class=" "><strong class=" ">16 MPI</strong> processes per node, using 1 thread each bound to processor core is most suitable for highly scalable applications with low communication demand.</p>
+<h3 class=" ">Running OpenMPI</h3>
+<p>The <strong>bullxmpi-1.2.4.1</strong> and <a class="external-link" href="http://www.open-mpi.org/" target="_self" title=""><strong>OpenMPI 1.6.5</strong></a> are both based on OpenMPI. Read more on <a href="Running_OpenMPI.html" title="" target="_self" class="internal-link">how to run OpenMPI</a> based MPI.</p>
+<h3 class=" ">Running MPICH2</h3>
+<p>The <strong>Intel MPI</strong> and <strong>mpich2 1.9</strong> are MPICH2 based implementations. Read more on <a href="running-mpich2.html" title="" target="_self" class="internal-link">how to run MPICH2</a> based MPI.</p>
+<p>The Intel MPI may run on the Intel Xeon Phi accelerators as well. Read more on <a href="../intel-xeon-phi.html" title="" target="_self" class="internal-link">how to run Intel MPI on accelerators</a>.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
index c9d34ad3b..83fdb81cf 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
@@ -199,4 +199,3 @@ more on [how to run Intel MPI on
accelerators](../intel-xeon-phi.html).
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.html b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.html
new file mode 100644
index 000000000..cffa05799
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.html
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+ MPI4Py (MPI for Python)
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+ <h2 class=" ">Introduction</h2>
+<p>MPI for Python provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.</p>
+<p>This package is constructed on top of the MPI-1/2 specifications and provides an object oriented interface which closely follows MPI-2 C++ bindings. It supports point-to-point (sends, receives) and collective (broadcasts, scatters, gathers) communications of any picklable Python object, as well as optimized communications of Python object exposing the single-segment buffer interface (NumPy arrays, builtin bytes/string/array objects).</p>
+<p>On Anselm MPI4Py is available in standard Python modules.</p>
+<h2 class=" ">Modules</h2>
+<p>MPI4Py is build for OpenMPI. Before you start with MPI4Py you need to load Python and OpenMPI modules.</p>
+<pre><span>$ module load python<br />$ module load </span><span>openmpi</span></pre>
+<h2 class=" ">Execution</h2>
+<p>You need to import MPI to your python program. Include the following line to the python script:</p>
+<pre class=" ">from mpi4py import MPI</pre>
+<p>The MPI4Py enabled python programs <a href="Running_OpenMPI.html" title="" target="_self" class="internal-link">execute as any other OpenMPI</a> code.The simpliest way is to run</p>
+<pre><span>$ mpiexec python <script>.py</span></pre>
+<p><span>For example</span></p>
+<pre>$ mpiexec python hello_world.py</pre>
+<h2 class=" ">Examples</h2>
+<h3 class=" ">Hello world!</h3>
+<pre><span class="kn">from</span> <span class="nn">mpi4py</span> <span class="kn">import</span> <span class="n">MPI<br /><br />comm = MPI.COMM_WORLD<br /><br />print "Hello! I'm rank %d from %d running in total..." % (comm.rank, comm.size)<br /><br />comm.Barrier() Â # wait for everybody to synchronize<br /></span></pre>
+<h3 class=" "><span>Collective Communication with NumPy arrays</span></h3>
+<pre class=" "><span class="kn">from</span> <span class="nn">mpi4py</span> <span class="kn">import</span> <span class="n">MPI</span>
+from __future__ import division<br />import numpy as np<br /><br />comm = MPI.COMM_WORLD<br /><br />print("-"*78)<br />print(" Running on %d cores" % comm.size)<br />print("-"*78)<br /><br />comm.Barrier()<br /><br /># Prepare a vector of N=5 elements to be broadcasted...<br />N = 5<br />if comm.rank == 0:<br />Â Â A = np.arange(N, dtype=np.float64) Â Â # rank 0 has proper data<br />else:<br />Â Â A = np.empty(N, dtype=np.float64) Â Â # all other just an empty array<br /><br /># Broadcast A from rank 0 to everybody<br />comm.Bcast( [A, MPI.DOUBLE] )<br /><br /># Everybody should now have the same...<br />print "[%02d] %s" % (comm.rank, A)</pre>
+<p class=" ">Execute the above code as:</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=16:mpiprocs=16:ompthreads=1 -I<br /><br />$ module load python openmpi<br /><br />$ mpiexec -bycore -bind-to-core python hello_world.py</pre>
+<p class=" ">In this example, we run MPI4Py enabled code on 4 nodes, 16 cores per node (total of 64 processes), each python process is bound to a different core.<br />More examples and documentation can be found on <a class="external-link" href="https://pythonhosted.org/mpi4py/usrman/index.html" target="_blank" title="">MPI for Python webpage</a>.</p>
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+ <h2 class=" ">MPICH2 program execution</h2>
+<p>The MPICH2 programs use mpd daemon or ssh connection to spawn processes, no PBS support is needed. However the PBS allocation is required to access compute nodes. On Anselm, the <strong>Intel MPI</strong> and <strong>mpich2 1.9</strong> are MPICH2 based MPI implementations.</p>
+<h3 class=" ">Basic usage</h3>
+<p class="callout">Use the mpirun to execute the MPICH2 code.</p>
+<p>Example:</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=16 -I<br />qsub: waiting for job 15210.srv11 to start<br />qsub: job 15210.srv11 ready<br /><br class=" " />$ module load impi<br /><br />$ mpirun -ppn 1 -hostfile $PBS_NODEFILE ./helloworld_mpi.x<br />Hello world! from rank 0 of 4 on host cn17<br />Hello world! from rank 1 of 4 on host cn108<br />Hello world! from rank 2 of 4 on host cn109<br />Hello world! from rank 3 of 4 on host cn110</pre>
+<p class=" ">In this example, we allocate 4 nodes via the express queue interactively. We set up the intel MPI environment and interactively run the helloworld_mpi.x program. We request MPI to spawn 1 process per node.<br />Note that the executable helloworld_mpi.x must be available within the same path on all nodes. This is automatically fulfilled on the /home and /scratch filesystem.</p>
+<p class=" ">You need to preload the executable, if running on the local scratch /lscratch filesystem</p>
+<pre class=" ">$ pwd<br />/lscratch/15210.srv11<br />$ mpirun -ppn 1 -hostfile $PBS_NODEFILE cp /home/username/helloworld_mpi.x .<br />$ mpirun -ppn 1 -hostfile $PBS_NODEFILE ./helloworld_mpi.x<br />Hello world! from rank 0 of 4 on host cn17<br />Hello world! from rank 1 of 4 on host cn108<br />Hello world! from rank 2 of 4 on host cn109<br />Hello world! from rank 3 of 4 on host cn110</pre>
+<p class=" ">In this example, we assume the executable helloworld_mpi.x is present on shared home directory. We run the cp command via mpirun, copying the executable from shared home to local scratch . Second mpirun will execute the binary in the /lscratch/15210.srv11 directory on nodes cn17, cn108, cn109 and cn110, one process per node.</p>
+<p class="callout">MPI process mapping may be controlled by PBS parameters.</p>
+<p class=" ">The mpiprocs and ompthreads parameters allow for selection of number of running MPI processes per node as well as number of OpenMP threads per MPI process.</p>
+<h3 class=" ">One MPI process per node</h3>
+<p class=" ">Follow this example to run one MPI process per node, 16 threads per process. Note that no options to mpirun are needed</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=16:mpiprocs=1:ompthreads=16 -I<br /><br />$ module load mvapich2<br /><br />$ mpirun ./helloworld_mpi.x</pre>
+<p class=" ">In this example, we demonstrate recommended way to run an MPI application, using 1 MPI processes per node and 16 threads per socket, on 4 nodes.</p>
+<h3 class=" ">Two MPI processes per node</h3>
+<p class=" ">Follow this example to run two MPI processes per node, 8 threads per process. Note the options to mpirun for mvapich2. No options are needed for impi.</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=16:mpiprocs=2:ompthreads=8 -I<br /><br />$ module load mvapich2<br /><br />$ mpirun -bind-to numa ./helloworld_mpi.x</pre>
+<p>In this example, we demonstrate recommended way to run an MPI application, using 2 MPI processes per node and 8 threads per socket, each process and its threads bound to a separate processor socket of the node, on 4 nodes</p>
+<h3 class=" ">16 MPI processes per node</h3>
+<p class=" ">Follow this example to run 16 MPI processes per node, 1 thread per process. Note the options to mpirun for mvapich2. No options are needed for impi.</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=16:mpiprocs=16:ompthreads=1 -I<br /><br />$ module load mvapich2<br /><br />$ mpirun -bind-to core ./helloworld_mpi.x</pre>
+<p>In this example, we demonstrate recommended way to run an MPI application, using 16 MPI processes per node, single threaded. Each process is bound to separate processor core, on 4 nodes.</p>
+<h3 class=" ">OpenMP thread affinity</h3>
+<p class="callout">Important! Bind every OpenMP thread to a core!</p>
+<p>In the previous two examples with one or two MPI processes per node, the operating system might still migrate OpenMP threads between cores. You might want to avoid this by setting these environment variable for GCC OpenMP:</p>
+<pre class=" "><span class="s1">$ export GOMP_CPU_AFFINITY="0-15"</span></pre>
+<p>or this one for Intel OpenMP:</p>
+<pre class=" ">$ export KMP_AFFINITY=granularity=fine,compact,1,0</pre>
+<p class=" ">As of OpenMP 4.0 (supported by GCC 4.9 and later and Intel 14.0 and later) the following variables may be used for Intel or GCC:</p>
+<pre class=" ">$ export OMP_PROC_BIND=true<br />$ export OMP_PLACES=cores </pre>
+<p>Â </p>
+<h2 class=" ">MPICH2 Process Mapping and Binding</h2>
+<p>The mpirun allows for precise selection of how the MPI processes will be mapped to the computational nodes and how these processes will bind to particular processor sockets and cores.</p>
+<h3 class=" ">Machinefile</h3>
+<p>Process mapping may be controlled by specifying a machinefile input to the mpirun program. Altough all implementations of MPI provide means for process mapping and binding, following examples are valid for the impi and mvapich2 only.</p>
+<p>Example machinefile</p>
+<pre class=" ">cn110.bullx<br />cn109.bullx<br />cn108.bullx<br />cn17.bullx<br />cn108.bullx</pre>
+<p class=" ">Use the machinefile to control process placement</p>
+<pre class=" ">$ mpirun -machinefile machinefile helloworld_mpi.x<br />Hello world! from rank 0 of 5 on host cn110<br />Hello world! from rank 1 of 5 on host cn109<br />Hello world! from rank 2 of 5 on host cn108<br />Hello world! from rank 3 of 5 on host cn17<br />Hello world! from rank 4 of 5 on host cn108</pre>
+<p>In this example, we see that ranks have been mapped on nodes according to the order in which nodes show in the machinefile</p>
+<h3 class=" ">Process Binding</h3>
+<p>The Intel MPI automatically binds each process and its threads to the corresponding portion of cores on the processor socket of the node, no options needed. The binding is primarily controlled by environment variables. Read more about mpi process binding on <a class="external-link" href="https://software.intel.com/sites/products/documentation/hpc/ics/impi/41/lin/Reference_Manual/Environment_Variables_Process_Pinning.htm" target="_self" title="">Intel website</a>. The MPICH2 uses the -bind-to option Use -bind-to numa or -bind-to core to bind the process on single core or entire socket.</p>
+<h3 class=" ">Bindings verification</h3>
+<p>In all cases, binding and threading may be verified by executing</p>
+<pre class=" ">$ mpirun -bindto numa numactl --show<br />$ mpirun -bindto numa echo $OMP_NUM_THREADS</pre>
+<h2 class=" ">Intel MPI on Xeon Phi</h2>
+<p>The<a href="../intel-xeon-phi.html" title="" target="_self" class="internal-link"> MPI section of Intel Xeon Phi chapter</a> provides details on how to run Intel MPI code on Xeon Phi architecture.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
index e5544d588..cc828bcf5 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
@@ -20,8 +20,8 @@ Use the mpirun to execute the MPICH2 code.
Example:
$ qsub -q qexp -l select=4:ncpus=16 -I
- qsubwaiting for job 15210.srv11 to start
- qsubjob 15210.srv11 ready
+ qsub: waiting for job 15210.srv11 to start
+ qsub: job 15210.srv11 ready
$ module load impi
@@ -193,4 +193,3 @@ chapter](../intel-xeon-phi.html) provides details on how
to run Intel MPI code on Xeon Phi architecture.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.html
new file mode 100644
index 000000000..c5b0f1d19
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.html
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+<p>This section contains a collection of high-level interpreted languages, primarily intended for numerical computations.</p>
+<h2 class=" ">Matlab</h2>
+<p>MATLAB<sup>®</sup> is a high-level language and interactive environment for numerical computation, visualization, and programming.</p>
+<pre class=" ">$ module load MATLAB/2015b-EDU<br />$ matlab</pre>
+<p>Read more at the <a href="numerical-languages/matlab.html" title="" target="_self" class="internal-link">Matlab<span class="internal-link"></span> page</a>.</p>
+<h2 class=" ">Octave</h2>
+<p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.</p>
+<pre class=" ">$ module load Octave<br />$ octave</pre>
+<p>Read more at the <a href="numerical-languages/octave.html" title="" target="_self" class="internal-link">Octave page</a>.</p>
+<h2 class=" ">R</h2>
+<p>The R is an interpreted language and environment for statistical computing and graphics.</p>
+<pre class=" ">$ module load R<br />$ R</pre>
+<p>Read more at the <a href="numerical-languages/r.html" title="" target="_self" class="internal-link">R page</a>.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.md
index 36d4b0079..ea7c7b006 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.md
@@ -49,4 +49,3 @@ computing and graphics.
Read more at the [R page](numerical-languages/r.html).
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.html
new file mode 100644
index 000000000..ddac86445
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.html
@@ -0,0 +1,1232 @@
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+ Matlab
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+ <h2 class=" ">Introduction</h2>
+<p>Matlab is available in versions R2015a and R2015b. There are always two variants of the release:</p>
+<ul>
+<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
+<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
+</ul>
+<p>Â </p>
+<p>To load the latest version of Matlab load the module</p>
+<pre class=" ">$ module load MATLAB</pre>
+<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
+<pre class=" ">$ module avail MATLAB</pre>
+<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
+<p>If you require the Matlab GUI, please follow the general informations about <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">running graphical applications</a>.</p>
+<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">here</a>) is recommended.</p>
+<p>To run Matlab with GUI, use</p>
+<pre class=" ">$ matlab</pre>
+<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
+<pre class=" ">$ matlab -nodesktop -nosplash</pre>
+<p>plots, images, etc... will be still available.</p>
+<h2 class=" "><a name="running-parallel-matlab-using-distributed-computing-toolbox---engine"></a>Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
+<p class="exclamation">Distributed toolbox is available only for the EDU variant</p>
+<p class=" ">The MPIEXEC mode available in previous versions is no longer available in MATLAB 2015. Also, the programming interface has changed. Refer to <a class="external-link" href="http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1" target="_self" title="">Release Notes</a>.</p>
+<p class=" ">Delete previously used file mpiLibConf.m, we have observed crashes when using Intel MPI.</p>
+<p class=" ">To use Distributed Computing, you first need to setup a parallel profile. We have provided the profile for you, you can either import it in MATLAB command line:</p>
+<pre class=" ">>> parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings')<br /><br />ans = <br /><br />SalomonPBSPro </pre>
+<p class=" ">Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to :</p>
+<p class=" ">/apps/all/MATLAB/2015a-EDU/SalomonPBSPro.settings</p>
+<p class=" ">With the new mode, MATLAB itself launches the workers via PBS, so you can either use interactive mode or a batch mode on one node, but the actual parallel processing will be done in a separate job started by MATLAB itself. Alternatively, you can use "local" mode to run parallel code on just a single node.</p>
+<p class="exclamation">The profile is confusingly named Salomon, but you can use it also on Anselm.</p>
+<h3 class=" ">Parallel Matlab interactive session</h3>
+<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">this page</a>.</p>
+<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
+<p>This qsub command example shows how to run Matlab on a single node.</p>
+<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing Engines licenses.</p>
+<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
+<pre class=" ">r1i0n17$ module load MATLAB/2015b-EDU<br />r1i0n17$ matlab &</pre>
+<h3 class=" "><a name="parallel-matlab-batch-job-in-local-mode"></a>Parallel Matlab batch job in Local mode</h3>
+<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
+<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/work/user/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load MATLAB/2015a-EDU<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
+<p>Submit the jobscript using qsub</p>
+<pre class=" ">$ qsub ./jobscript</pre>
+<h3 class=" ">Parallel Matlab Local mode program example</h3>
+<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
+<pre class=" ">cluster = parcluster('local')</pre>
+<p class=" ">This script creates scheduler object "cluster" of type "local" that starts workers locally. </p>
+<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling parpool(sched, ...) function. </p>
+<p class=" ">The last step is to start matlabpool with "cluster" object and correct number of workers. We have 24 cores per node, so we start 24 workers.</p>
+<pre class=" ">parpool(cluster,16);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />parpool close</pre>
+<p>The complete example showing how to use Distributed Computing Toolbox in local mode is shown here. </p>
+<pre class=" ">cluster = parcluster('local');<br />cluster<br /><br />parpool(cluster,24);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />parpool close<br />quit</pre>
+<p>You can copy and paste the example in a .m file and execute. Note that the parpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
+<h3 class=" ">Parallel Matlab Batch job using PBS mode (workers spawned in a separate job)</h3>
+<p>This mode uses PBS scheduler to launch the parallel pool. It uses the SalomonPBSPro profile that needs to be imported to Cluster Manager, as mentioned before. This methodod uses MATLAB's PBS Scheduler interface - it spawns the workers in a separate job submitted by MATLAB using qsub.</p>
+<p>This is an example of m-script using PBS mode:</p>
+<pre class=" ">cluster = parcluster('SalomonPBSPro');
+set(cluster, 'SubmitArguments', '-A OPEN-0-0');
+set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=16');
+set(cluster, 'NumWorkers', 160);
+
+pool = parpool(cluster, 160);
+
+n=2000;
+
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
+
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
+
+% shut down parallel pool
+delete(pool)
+</pre>
+<p class=" ">Note that we first construct a cluster object using the imported profile, then set some important options, namely : SubmitArguments, where you need to specify accounting id, and ResourceTemplate, where you need to specify number of nodes to run the job. </p>
+<p class=" ">You can start this script using batch mode the same way as in Local mode example.</p>
+<h3 class=" ">Parallel Matlab Batch with direct launch (workers spawned within the existing job)</h3>
+<p>This method is a "hack" invented by us to emulate the mpiexec functionality found in previous MATLAB versions. We leverage the MATLAB Generic Scheduler interface, but instead of submitting the workers to PBS, we launch the workers directly within the running job, thus we avoid the issues with master script and workers running in separate jobs (issues with license not available, waiting for the worker's job to spawn etc.)</p>
+<p>Please note that this method is experimental.</p>
+<p>For this method, you need to use SalomonDirect profile, import it using <a class="anchor-link" href="copy_of_matlab.html#running-parallel-matlab-using-distributed-computing-toolbox---engine" target="_self" title="">the same way as SalomonPBSPro</a> </p>
+<p>This is an example of m-script using direct mode:</p>
+<pre class=" "><br />parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonDirect.settings')<br />cluster = parcluster('SalomonDirect');
+set(cluster, 'NumWorkers', 48);
+
+pool = parpool(cluster, 48);
+
+n=2000;
+
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
+
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
+
+% shut down parallel pool
+delete(pool)</pre>
+<h3 class=" ">Non-interactive Session and Licenses</h3>
+<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a href="../isv_licenses.html" title="" target="_self" class="internal-link">look here</a>.</p>
+<p>In case of non-interactive session please read the <a href="../isv_licenses.html" title="" target="_self" class="internal-link">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
+<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
+<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
+<table class="plain">
+<tbody>
+<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
+<tr>
+<td>16</td>
+<td>384</td>
+<td>831</td>
+</tr>
+<tr>
+<td>8</td>
+<td>192</td>
+<td>807</td>
+</tr>
+<tr>
+<td>4</td>
+<td>96</td>
+<td>483</td>
+</tr>
+<tr>
+<td>2</td>
+<td>48</td>
+<td>16</td>
+</tr>
+</tbody>
+</table>
+<h2>MATLAB on UV2000Â </h2>
+<p>UV2000 machine available in queue "qfat" can be used for MATLAB computations. This is a SMP NUMA machine with large amount of RAM, which can be beneficial for certain types of MATLAB jobs. CPU cores are allocated in chunks of 8 for this machine.</p>
+<p>You can use MATLAB on UV2000 in two parallel modes :</p>
+<h3>Threaded mode</h3>
+<p class=" ">Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set <span class="monospace">maxNumCompThreads </span>accordingly and certain operations, such as <span class="monospace">fft, \, eig, svd</span>, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.<span class="monospace"><br /></span></p>
+<h3 class=" ">Local cluster mode</h3>
+<p>You can also use Parallel Toolbox on UV2000. Use l<a class="anchor-link" href="copy_of_matlab.html#parallel-matlab-batch-job-in-local-mode" target="_self" title="">ocal cluster mode</a>, "SalomonPBSPro" profile will not work.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
index 1670df220..f2db3e2e2 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
@@ -163,7 +163,7 @@ script before Distributed Computing Toolbox is started.
This script creates scheduler object "cluster" of type "local" that
starts workers locally.Â
-Please noteEvery Matlab script that needs to initialize/use matlabpool
+Please note: Every Matlab script that needs to initialize/use matlabpool
has to contain these three lines prior to calling parpool(sched, ...)
function.Â
@@ -242,7 +242,7 @@ This is an example of m-script using PBS mode:
delete(pool)
Note that we first construct a cluster object using the imported
-profile, then set some important options, namely SubmitArguments,
+profile, then set some important options, namely : SubmitArguments,
where you need to specify accounting id, and ResourceTemplate, where you
need to specify number of nodes to run the job.Â
@@ -349,4 +349,3 @@ mode](copy_of_matlab.html#parallel-matlab-batch-job-in-local-mode),
Â
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.html
new file mode 100644
index 000000000..edfe85f30
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.html
@@ -0,0 +1,1091 @@
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+ <h2 class=" ">Introduction</h2>
+<p>This section contains a collection of high-level interpreted languages, primarily intended for numerical computations.</p>
+<h2 class=" ">Matlab</h2>
+<p>MATLAB<sup>®</sup> is a high-level language and interactive environment for numerical computation, visualization, and programming.</p>
+<pre class=" ">$ module load MATLAB/2015b-EDU<br />$ matlab</pre>
+<p>Read more at the <a href="matlab.html" title="" target="_self" class="internal-link">Matlab<span class="internal-link"></span> page</a>.</p>
+<h2 class=" ">Octave</h2>
+<p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.</p>
+<pre class=" ">$ module load Octave<br />$ octave</pre>
+<p>Read more at the <a href="octave.html" title="" target="_self" class="internal-link">Octave page</a>.</p>
+<h2 class=" ">R</h2>
+<p>The R is an interpreted language and environment for statistical computing and graphics.</p>
+<pre class=" ">$ module load R<br />$ R</pre>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md
index bd810e85d..3c03b655c 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md
@@ -48,4 +48,3 @@ computing and graphics.
Read more at the [R page](r.html).
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.html
new file mode 100644
index 000000000..d31b054b8
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.html
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+ <h2 class=" ">Introduction</h2>
+<p class="exclamation">This document relates to the old versions R2013 and R2014. For MATLAB 2015, please use <a href="copy_of_matlab.html" title="" target="_self" class="internal-link">this documentation instead</a>.</p>
+<p>Matlab is available in the latest stable version. There are always two variants of the release:</p>
+<ul>
+<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
+<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
+</ul>
+<p>Â </p>
+<p>To load the latest version of Matlab load the module</p>
+<pre class=" ">$ module load matlab</pre>
+<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
+<pre class=" ">$ module avail matlab</pre>
+<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
+<p>If you require the Matlab GUI, please follow the general informations about <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">running graphical applications</a>.</p>
+<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">here</a>) is recommended.</p>
+<p>To run Matlab with GUI, use</p>
+<pre class=" ">$ matlab</pre>
+<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
+<pre class=" ">$ matlab -nodesktop -nosplash</pre>
+<p>plots, images, etc... will be still available.</p>
+<h2 class=" ">Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
+<p>Recommended parallel mode for running parallel Matlab on Anselm is MPIEXEC mode. In this mode user allocates resources through PBS prior to starting Matlab. Once resources are granted the main Matlab instance is started on the first compute node assigned to job by PBS and workers are started on all remaining nodes. User can use both interactive and non-interactive PBS sessions. This mode guarantees that the data processing is not performed on login nodes, but all processing is on compute nodes.</p>
+<p>Â <img alt="Parallel Matlab" src="Matlab.png" title="Parallel Matlab" class="image-inline" /></p>
+<p>For the performance reasons Matlab should use system MPI. On Anselm the supported MPI implementation for Matlab is Intel MPI. To switch to system MPI user has to override default Matlab setting by creating new configuration file in its home directory. The path and file name has to be exactly the same as in the following listing:</p>
+<pre class=" "><strong>$ vim ~/matlab/mpiLibConf.m </strong></pre>
+<pre class=" "><strong>function [lib, extras] = mpiLibConf</strong><br /><strong>%MATLAB MPI Library overloading for Infiniband Networks</strong><br /><br /><strong>mpich = '/opt/intel/impi/4.1.1.036/lib64/';</strong><br /><br /><strong>disp('Using Intel MPI 4.1.1.036 over Infiniband')</strong><br /><br /><strong>lib = strcat(mpich, 'libmpich.so');</strong><br /><strong>mpl = strcat(mpich, 'libmpl.so');</strong><br /><strong>opa = strcat(mpich, 'libopa.so');</strong><br /><br /><strong>extras = {};</strong></pre>
+<p>System MPI library allows Matlab to communicate through 40Gbps Infiniband QDR interconnect instead of slower 1Gb ethernet network.</p>
+<p class="callout">Please note: The path to MPI library in "mpiLibConf.m" has to match with version of loaded Intel MPI module. In this example the version 4.1.1.036 of Iintel MPI is used by Matlab and therefore module impi/4.1.1.036Â has to be loaded prior to starting Matlab.</p>
+<h3 class=" ">Parallel Matlab interactive session</h3>
+<p>Once this file is in place, user can request resources from PBS. Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a href="https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">this page</a>.</p>
+<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=4:ncpus=16:mpiprocs=16 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
+<p>This qsub command example shows how to run Matlab with 32 workers in following configuration: 2 nodes (use all 16 cores per node) and 16 workers = mpirocs per node (-l select=2:ncpus=16:mpiprocs=16). If user requires to run smaller number of workers per node then the "mpiprocs" parameter has to be changed.</p>
+<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 32 Distributed Computing Engines licenses.</p>
+<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
+<pre class=" ">cn79$ module load matlab/R2013a-EDU<br />cn79$ module load impi/4.1.1.036<br />cn79$ matlab &</pre>
+<h3 class=" ">Parallel Matlab batch job</h3>
+<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
+<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=2:ncpus=16:mpiprocs=16:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load matlab/R2013a-EDU<br />module load impi/4.1.1.036<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
+<p>Submit the jobscript using qsub</p>
+<pre class=" ">$ qsub ./jobscript</pre>
+<h3 class=" ">Parallel Matlab program example</h3>
+<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
+<pre class=" ">sched = findResource('scheduler', 'type', 'mpiexec');<br />set(sched, 'MpiexecFileName', '/apps/intel/impi/4.1.1/bin/mpirun');<br />set(sched, 'EnvironmentSetMethod', 'setenv');</pre>
+<p class=" ">This script creates scheduler object "sched" of type "mpiexec" that starts workers using mpirun tool. To use correct version of mpirun, the second line specifies the path to correct version of system Intel MPI library.</p>
+<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling matlabpool(sched, ...) function. </p>
+<p class=" ">The last step is to start matlabpool with "sched" object and correct number of workers. In this case qsub asked for total number of 32 cores, therefore the number of workers is also set to 32.</p>
+<pre class=" ">matlabpool(sched,32);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />matlabpool close</pre>
+<p>The complete example showing how to use Distributed Computing Toolbox is show here. </p>
+<pre class=" ">sched = findResource('scheduler', 'type', 'mpiexec');<br />set(sched, 'MpiexecFileName', '/apps/intel/impi/4.1.1/bin/mpirun')<br />set(sched, 'EnvironmentSetMethod', 'setenv')<br />set(sched, 'SubmitArguments', '') <br />sched<br /><br />matlabpool(sched,32);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />matlabpool close<br />quit</pre>
+<p>You can copy and paste the example in a .m file and execute. Note that the matlabpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
+<h3 class=" ">Non-interactive Session and Licenses</h3>
+<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a href="../isv_licenses.html" title="" target="_self" class="internal-link">look here</a>.</p>
+<p>In case of non-interactive session please read the <a href="../isv_licenses.html" title="" target="_self" class="internal-link">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
+<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
+<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
+<table class="plain">
+<tbody>
+<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
+<tr>
+<td>16</td>
+<td>256</td>
+<td>1008</td>
+</tr>
+<tr>
+<td>8</td>
+<td>128</td>
+<td>534</td>
+</tr>
+<tr>
+<td>4</td>
+<td>64</td>
+<td>333</td>
+</tr>
+<tr>
+<td>2</td>
+<td>32</td>
+<td>210</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<p>Â </p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md
index e25d87501..513fdcd2f 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md
@@ -97,7 +97,7 @@ be exactly the same as in the following listing:
System MPI library allows Matlab to communicate through 40Gbps
Infiniband QDR interconnect instead of slower 1Gb ethernet network.
-Please noteThe path to MPI library in "mpiLibConf.m" has to match with
+Please note: The path to MPI library in "mpiLibConf.m" has to match with
version of loaded Intel MPI module. In this example the version
4.1.1.036 of Iintel MPI is used by Matlab and therefore module
impi/4.1.1.036Â has to be loaded prior to starting Matlab.
@@ -115,7 +115,7 @@ page](https://docs.it4i.cz/anselm-cluster-documentation/software/numerical-langu
-l feature__matlab__MATLAB=1
This qsub command example shows how to run Matlab with 32 workers in
-following configuration2 nodes (use all 16 cores per node) and 16
+following configuration: 2 nodes (use all 16 cores per node) and 16
workers = mpirocs per node (-l select=2:ncpus=16:mpiprocs=16). If user
requires to run smaller number of workers per node then the "mpiprocs"
parameter has to be changed.
@@ -184,7 +184,7 @@ starts workers using mpirun tool. To use correct version of mpirun, the
second line specifies the path to correct version of system Intel MPI
library.
-Please noteEvery Matlab script that needs to initialize/use matlabpool
+Please note: Every Matlab script that needs to initialize/use matlabpool
has to contain these three lines prior to calling matlabpool(sched, ...)
function.Â
@@ -264,4 +264,3 @@ amount of time. For your information please see the following table:
Â
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.html
new file mode 100644
index 000000000..058ed73c5
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.html
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+ <div id="parent-fieldname-text-121a02f2c3d04e95b9a3dca29b1abf7f" class="">
+ <h2 class=" ">Introduction</h2>
+<p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable. Read more on <a class="external-link" href="http://www.gnu.org/software/octave/" target="_self" title="">http://www.gnu.org/software/octave/</a><strong></strong></p>
+<p><strong><br /></strong>Two versions of octave are available on Anselm, via module</p>
+<table class="listing">
+<tbody>
+<tr><th style="text-align: left; ">Version</th><th style="text-align: left; ">module</th></tr>
+<tr class="even">
+<td>Octave 3.8.2, compiled with GCC and Multithreaded MKL</td>
+<td>Octave/3.8.2-gimkl-2.11.5</td>
+</tr>
+<tr class="odd">
+<td>Octave 4.0.1, compiled with GCC and Multithreaded MKL</td>
+<td>Octave/4.0.1-gimkl-2.11.5</td>
+</tr>
+<tr class="odd">
+<td>Octave 4.0.0, compiled with <span>GCC and OpenBLAS</span></td>
+<td>Octave/4.0.0-foss-2015g</td>
+</tr>
+</tbody>
+</table>
+<h2 class=" ">Â Modules and execution</h2>
+<pre class=" ">$ module load Octave</pre>
+<p>The octave on Anselm is linked to highly optimized MKL mathematical library. This provides threaded parallelization to many octave kernels, notably the linear algebra subroutines. Octave runs these heavy calculation kernels without any penalty. By default, octave would parallelize to 16 threads. You may control the threads by setting the OMP_NUM_THREADS environment variable.</p>
+<p>To run octave interactively, log in with ssh -X parameter for X11 forwarding. Run octave:</p>
+<pre class=" ">$ octave</pre>
+<p>To run octave in batch mode, write an octave script, then write a bash jobscript and execute via the qsub command. By default, octave will use 16 threads when running MKL kernels.</p>
+<pre class=" ">#!/bin/bash<br /><br /># change to local scratch directory<br />cd /lscratch/$PBS_JOBID || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/octcode.m .<br /><br /># load octave module<br />module load octave<br /><br /># execute the calculation<br />octave -q --eval octcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in octcode.m file, outputs in output.out file. See the single node jobscript example in the <a class="internal-link" href="http://support.it4i.cz/docs/anselm-cluster-documentation/resource-allocation-and-job-execution" target="_self" title="">Job execution section</a>.</p>
+<p>The octave c compiler mkoctfile calls the GNU gcc 4.8.1 for compiling native c code. This is very useful for running native c subroutines in octave environment.</p>
+<pre class=" ">$ mkoctfile -v</pre>
+<p>Octave may use MPI for interprocess communication<br />This functionality is currently not supported on Anselm cluster. In case you require the octave interface to MPI, please contact <a class="external-link" href="https://support.it4i.cz/rt/" target="_self" title="">Anselm support</a>.</p>
+<h2 class=" ">Xeon Phi Support</h2>
+<p>Octave may take advantage of the Xeon Phi accelerators. This will only work on the <a href="../intel-xeon-phi.html" title="" target="_self" class="internal-link">Intel Xeon Phi</a> <a href="../../compute-nodes.html" title="" target="_self" class="internal-link">accelerated nodes</a>.</p>
+<h3 class=" ">Automatic offload support</h3>
+<p>Octave can accelerate BLAS type operations (in particular the Matrix Matrix multiplications] on the Xeon Phi accelerator, via <a href="../intel-xeon-phi.html#section-3" title="" target="_self" class="external-link">Automatic Offload using the MKL library</a></p>
+<p>Example</p>
+<pre class=" ">$ export OFFLOAD_REPORT=2<br />$ export MKL_MIC_ENABLE=1<br />$ module load octave<br />$ octave -q<br />octave:1> A=rand(10000); B=rand(10000);<br />octave:2> tic; C=A*B; toc<br />[MKL] [MIC --] [AO Function]Â Â Â DGEMM<br />[MKL] [MIC --] [AO DGEMM Workdivision]Â Â Â 0.32 0.68<br />[MKL] [MIC 00] [AO DGEMM CPU Time]Â Â Â 2.896003 seconds<br />[MKL] [MIC 00] [AO DGEMM MIC Time]Â Â Â 1.967384 seconds<br />[MKL] [MIC 00] [AO DGEMM CPU->MIC Data]Â Â Â 1347200000 bytes<br />[MKL] [MIC 00] [AO DGEMM MIC->CPU Data]Â Â Â 2188800000 bytes<br />Elapsed time is 2.93701 seconds.</pre>
+<p>In this example, the calculation was automatically divided among the CPU cores and the Xeon Phi MIC accelerator, reducing the total runtime from 6.3 secs down to 2.9 secs.</p>
+<h3 class=" ">Native support</h3>
+<p>A version of <a href="../intel-xeon-phi.html#section-4" title="" target="_self" class="external-link">native</a> Octave is compiled for Xeon Phi accelerators. Some limitations apply for this version:</p>
+<ul>
+<li>Only command line support. GUI, graph plotting etc. is not supported.</li>
+<li>Command history in interactive mode is not supported.</li>
+</ul>
+<p>Octave is linked with parallel Intel MKL, so it best suited for batch processing of tasks that utilize BLAS, LAPACK and FFT operations. By default, number of threads is set to 120, you can control this with <span><span class="monospace">OMP_NUM_THREADS</span> environment variable. </span></p>
+<p class="exclamation">Calculations that do not employ parallelism (either by using parallel MKL eg. via matrix operations, <span class="monospace">fork()</span> function, <a class="external-link" href="http://octave.sourceforge.net/parallel/" target="_self" title="">parallel package</a> or other mechanism) will actually run slower than on host CPU.</p>
+<p><span>To use Octave on a node with Xeon Phi:</span></p>
+<pre class=" ">$ ssh mic0 # login to the MIC card<br />$ source<span> /apps/tools/octave/3.8.2-mic/bin/octave-env.sh # set up environment variables<br />$ <span>octave -q /apps/tools/octave/3.8.2-mic/example/test0.m # run an example</span>Â </span></pre>
+<p><span>Â </span></p>
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+ <!-- nagios_check_http_expect_string -->
+ <!-- TODO -->
+
+</div>
+</body>
+</html>
+
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<span>Â </span>
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+ <h2 class=" " id="parent-fieldname-title">Introduction</h2>
+<p class=" ">The R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible.</p>
+<div id="content-core">
+<div id="parent-fieldname-text-4a9d341ec7e54eecbc6b9c0d8f470ebc">
+<p>One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.</p>
+<p>Another convenience is the ease with which the C code or third party libraries may be integrated within R.</p>
+<p>Extensive support for parallel computing is available within R.</p>
+<p>Read more on <a class="external-link" href="http://www.r-project.org/" target="_self" title="">http://www.r-project.org/</a>, <a class="external-link" href="http://cran.r-project.org/doc/manuals/r-release/R-lang.html" target="_self" title="">http://cran.r-project.org/doc/manuals/r-release/R-lang.html</a></p>
+<h2 class=" ">Modules</h2>
+<p><strong></strong>The R version 3.0.1 is available on Anselm, along with GUI interface Rstudio</p>
+<table class="listing">
+<tbody>
+<tr><th style="text-align: left; ">Application</th><th style="text-align: left; ">Version</th><th style="text-align: left; ">module</th></tr>
+<tr class="even">
+<td><strong>R</strong></td>
+<td>R 3.0.1</td>
+<td>R</td>
+</tr>
+<tr class="odd">
+<td><strong>Rstudio</strong></td>
+<td>Rstudio 0.97</td>
+<td>Rstudio</td>
+</tr>
+</tbody>
+</table>
+<pre class=" ">$ module load R</pre>
+<h2 class=" ">Execution</h2>
+<p><a name="interactive-execution"></a>The R on Anselm is linked to highly optimized MKL mathematical library. This provides threaded parallelization to many R kernels, notably the linear algebra subroutines. The R runs these heavy calculation kernels without any penalty. By default, the R would parallelize to 16 threads. You may control the threads by setting the OMP_NUM_THREADS environment variable.</p>
+<h3 class=" ">Interactive execution</h3>
+<p>To run R interactively, using Rstudio GUI, log in with ssh -X parameter for X11 forwarding. Run rstudio:</p>
+<pre class=" ">$ module load Rstudio<br />$ rstudio</pre>
+<h3 class=" ">Batch execution</h3>
+<p>To run R in batch mode, write an R script, then write a bash jobscript and execute via the qsub command. By default, R will use 16 threads when running MKL kernels.</p>
+<p>Example jobscript:</p>
+<pre class=" ">#!/bin/bash<br /><br /># change to local scratch directory<br />cd /lscratch/$PBS_JOBID || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/rscript.R .<br /><br /># load R module<br />module load R<br /><br /># execute the calculation<br />R CMD BATCH rscript.R routput.out<br /><br /># copy output file to home<br />cp routput.out $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_self" class="internal-link">Job execution section</a>.</p>
+<h2 class=" ">Parallel R</h2>
+<p>Parallel execution of R may be achieved in many ways. One approach is the implied parallelization due to linked libraries or specially enabled functions, as <a class="anchor-link" href="r.html#interactive-execution" target="_self" title="">described above</a>. In the following sections, we focus on explicit parallelization, where parallel constructs are directly stated within the R script.</p>
+<h2 class=" "><a name="package-parallel"></a>Package parallel</h2>
+<p class=" ">The package parallel provides support for parallel computation, including by forking (taken from package multicore), by sockets (taken from package snow) and random-number generation.</p>
+<p class=" ">The package is activated this way:</p>
+<pre class=" ">$ R<br />> library(parallel)</pre>
+<p class=" ">More information and examples may be obtained directly by reading the documentation available in R</p>
+<pre class=" ">> ?parallel<br />> library(help = "parallel")<br />> <span class="internal-link">vignette("parallel")</span></pre>
+<p class=" ">Download the package <a href="package-parallel-vignette" title="" target="_self" class="internal-link">parallell</a> vignette.</p>
+<p class=" ">The forking is the most simple to use. Forking family of functions provide parallelized, drop in replacement for the serial apply() family of functions.</p>
+<p class="callout">Forking via package parallel provides functionality similar to OpenMP construct<br />#omp parallel for <br /><br />Only cores of single node can be utilized this way!</p>
+<p class=" ">Forking example:</p>
+<pre class=" ">library(parallel)<br /><br />#integrand function<br />f <- function(i,h) {<br />x <- h*(i-0.5)<br />return (4/(1 + x*x))<br />}<br /><br />#initialize<br />size <- detectCores()<br /><br />while (TRUE)<br />{<br /> #read number of intervals<br /> cat("Enter the number of intervals: (0 quits) ")<br /> fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)<br /><br /> if(n<=0) break<br /><br /> #run the calculation<br /> n <- max(n,size)<br /> h <- 1.0/n<br /><br /> i <- seq(1,n);<br /> pi3 <- h*sum(simplify2array(mclapply(i,f,h,mc.cores=size)));<br /><br /> #print results<br /> cat(sprintf("Value of PI %16.14f, diff= %16.14f\n",pi3,pi3-pi))<br />}<br /><br /></pre>
+<p>The above example is the classic parallel example for calculating the number π. Note the <strong>detectCores()</strong> and <strong>mclapply()</strong> functions.<br />Execute the example as:</p>
+<pre class=" ">$ R --slave --no-save --no-restore -f pi3p.R</pre>
+<p>Every evaluation of the integrad function runs in parallel on different process.</p>
+<h2 class=" ">Package Rmpi</h2>
+<p class="callout">package Rmpi provides an interface (wrapper) to MPI APIs.</p>
+<p>It also provides interactive R slave environment. On Anselm, Rmpi provides interface to the <a href="../mpi-1/Running_OpenMPI.html" title="" target="_self" class="internal-link">OpenMPI</a>.</p>
+<p>Read more on Rmpi at <a class="external-link" href="http://cran.r-project.org/web/packages/Rmpi/" target="_self" title="">http://cran.r-project.org/web/packages/Rmpi/</a>, reference manual is available at <a class="external-link" href="http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf" target="_self" title="">http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf</a></p>
+<p>When using package Rmpi, both openmpi and R modules must be loaded</p>
+<pre class=" ">$ module load openmpi<br />$ module load R</pre>
+<p>Rmpi may be used in three basic ways. The static approach is identical to executing any other MPI programm. In addition, there is Rslaves dynamic MPI approach and the mpi.apply approach. In the following section, we will use the number π integration example, to illustrate all these concepts.</p>
+<h3 class=" "><a name="static-rmpi"></a>static Rmpi</h3>
+<p>Static Rmpi programs are executed via mpiexec, as any other MPI programs. Number of processes is static - given at the launch time.</p>
+<p>Static Rmpi example:</p>
+<pre class=" ">library(Rmpi)<br /><br />#integrand function<br />f <- function(i,h) {<br />x <- h*(i-0.5)<br />return (4/(1 + x*x))<br />}<br /><br />#initialize<br />invisible(mpi.comm.dup(0,1))<br />rank <- mpi.comm.rank()<br />size <- mpi.comm.size()<br />n<-0<br /><br />while (TRUE)<br />{<br /> #read number of intervals<br /> if (rank==0) {<br /> cat("Enter the number of intervals: (0 quits) ")<br /> fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)<br /> }<br /><br /> #broadcat the intervals<br /> n <- mpi.bcast(as.integer(n),type=1)<br /><br /> if(n<=0) break<br /><br /> #run the calculation<br /> n <- max(n,size)<br /> h <- 1.0/n<br /><br /> i <- seq(rank+1,n,size);<br /> mypi <- h*sum(sapply(i,f,h));<br /><br /> pi3 <- mpi.reduce(mypi)<br /><br /> #print results<br /> if (rank==0) cat(sprintf("Value of PI %16.14f, diff= %16.14f\n",pi3,pi3-pi))<br />}<br /><br />mpi.quit()</pre>
+<p>The above is the static MPI example for calculating the number π. Note the <strong>library(Rmpi) </strong>and<strong> mpi.comm.dup()</strong> function calls.<br />Execute the example as:</p>
+<pre class=" ">$ mpiexec R --slave --no-save --no-restore -f pi3.R</pre>
+<h3 class=" ">dynamic Rmpi</h3>
+<p>Dynamic Rmpi programs are executed by calling the R directly. openmpi module must be still loaded. The R slave processes will be spawned by a function call within the Rmpi program.</p>
+<p>Dynamic Rmpi example:</p>
+<pre class=" ">#integrand function<br />f <- function(i,h) {<br />x <- h*(i-0.5)<br />return (4/(1 + x*x))<br />}<br /><br />#the worker function<br />workerpi <- function()<br />{<br />#initialize<br />rank <- mpi.comm.rank()<br />size <- mpi.comm.size()<br />n<-0<br /><br />while (TRUE)<br />{<br /> #read number of intervals<br /> if (rank==0) {<br /> cat("Enter the number of intervals: (0 quits) ")<br /> fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)<br /> }<br /><br /> #broadcat the intervals<br /> n <- mpi.bcast(as.integer(n),type=1)<br /><br /> if(n<=0) break<br /><br /> #run the calculation<br /> n <- max(n,size)<br /> h <- 1.0/n<br /><br /> i <- seq(rank+1,n,size);<br /> mypi <- h*sum(sapply(i,f,h));<br /><br /> pi3 <- mpi.reduce(mypi)<br /><br /> #print results<br /> if (rank==0) cat(sprintf("Value of PI %16.14f, diff= %16.14f\n",pi3,pi3-pi))<br />}<br />}<br /><br />#main<br />library(Rmpi)<br /><br />cat("Enter the number of slaves: ")<br />fp<-file("stdin"); ns<-scan(fp,nmax=1); close(fp)<br /><br />mpi.spawn.Rslaves(nslaves=ns)<br />mpi.bcast.Robj2slave(f)<br />mpi.bcast.Robj2slave(workerpi)<br /><br />mpi.bcast.cmd(workerpi())<br />workerpi()<br /><br /><br />mpi.quit()</pre>
+<p>The above example is the dynamic MPI example for calculating the number π. Both master and slave processes carry out the calculation. Note the <strong>mpi.spawn.Rslaves(), mpi.bcast.Robj2slave() </strong>and the<strong> mpi.bcast.cmd()</strong> function calls.<br />Execute the example as:</p>
+<pre class=" ">$ R --slave --no-save --no-restore -f pi3Rslaves.R</pre>
+<h3 class=" ">mpi.apply Rmpi</h3>
+<p>mpi.apply is a specific way of executing Dynamic Rmpi programs.</p>
+<p class="callout">mpi.apply() family of functions provide MPI parallelized, drop in replacement for the serial apply() family of functions.</p>
+<p>Execution is identical to other dynamic Rmpi programs.</p>
+<p>mpi.apply Rmpi example:</p>
+<pre class=" ">#integrand function<br />f <- function(i,h) {<br />x <- h*(i-0.5)<br />return (4/(1 + x*x))<br />}<br /><br />#the worker function<br />workerpi <- function(rank,size,n)<br />{<br /> #run the calculation<br /> n <- max(n,size)<br /> h <- 1.0/n<br /><br /> i <- seq(rank,n,size);<br /> mypi <- h*sum(sapply(i,f,h));<br /><br /> return(mypi)<br />}<br /><br />#main<br />library(Rmpi)<br /><br />cat("Enter the number of slaves: ")<br />fp<-file("stdin"); ns<-scan(fp,nmax=1); close(fp)<br /><br />mpi.spawn.Rslaves(nslaves=ns)<br />mpi.bcast.Robj2slave(f)<br />mpi.bcast.Robj2slave(workerpi)<br /><br />while (TRUE)<br />{<br /> #read number of intervals<br /> cat("Enter the number of intervals: (0 quits) ")<br /> fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)<br /> if(n<=0) break<br /><br /> #run workerpi<br /> i=seq(1,2*ns)<br /> pi3=sum(mpi.parSapply(i,workerpi,2*ns,n))<br /><br /> #print results<br /> cat(sprintf("Value of PI %16.14f, diff= %16.14f\n",pi3,pi3-pi))<br />}<br /><br />mpi.quit()</pre>
+<p>The above is the mpi.apply MPI example for calculating the number π. Only the slave processes carry out the calculation. Note the <strong>mpi.parSapply(), </strong> function call. The package <span class="anchor-link">parallel <a class="anchor-link" href="r.html#package-parallel" target="_self" title="">example</a></span><a class="anchor-link" href="r.html#package-parallel" target="_self" title=""> above</a> may be trivially adapted (for much better performance) to this structure using the mclapply() in place of mpi.parSapply().</p>
+<p>Execute the example as:</p>
+<pre class=" ">$ R --slave --no-save --no-restore -f pi3parSapply.R</pre>
+<h2 class=" ">Combining parallel and Rmpi</h2>
+<p>Currently, the two packages can not be combined for hybrid calculations.</p>
+<h2 class=" ">Parallel execution</h2>
+<p>The R parallel jobs are executed via the PBS queue system exactly as any other parallel jobs. User must create an appropriate jobscript and submit via the <strong>qsub</strong></p>
+<p>Example jobscript for <a class="anchor-link" href="r.html#static-rmpi" target="_self" title="">static Rmpi</a> parallel R execution, running 1 process per core:</p>
+<pre class=" ">#!/bin/bash<br />#PBS -q qprod<br />#PBS -N Rjob<br />#PBS -l select=100:ncpus=16:mpiprocs=16:ompthreads=1<br /><br /># change to scratch directory<span class="pln"><br />SCRDIR</span><span class="pun">=/</span><span class="pln">scratch</span><span class="pun">/</span><span class="pln">$USER</span><span class="pun">/</span><span class="pln">myjob</span><br /><span class="pln">cd $SCRDIR </span><span class="pun">||</span><span class="pln"> exit</span><br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/rscript.R .<br /><br /># load R and openmpi module<br />module load R<br />module load openmpi<br /><br /># execute the calculation<br />mpiexec -bycore -bind-to-core R --slave --no-save --no-restore -f rscript.R<br /><br /># copy output file to home<br />cp routput.out $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
+For more information about jobscripts and MPI execution refer to the <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_self" class="internal-link">Job submission</a> and general <a href="../mpi-1.html" title="" target="_self" class="internal-link">MPI</a> sections.</div>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
index 599a75972..0b552a03a 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
@@ -153,7 +153,7 @@ Forking example:
while (TRUE)
{
#read number of intervals
- cat("Enter the number of intervals(0 quits) ")
+ cat("Enter the number of intervals: (0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
if(n<=0) break
@@ -227,7 +227,7 @@ Static Rmpi example:
{
#read number of intervals
if (rank==0) {
- cat("Enter the number of intervals(0 quits) ")
+ cat("Enter the number of intervals: (0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
}
@@ -283,7 +283,7 @@ Dynamic Rmpi example:
{
#read number of intervals
if (rank==0) {
- cat("Enter the number of intervals(0 quits) ")
+ cat("Enter the number of intervals: (0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
}
@@ -309,7 +309,7 @@ Dynamic Rmpi example:
#main
library(Rmpi)
- cat("Enter the number of slaves")
+ cat("Enter the number of slaves: ")
fp<-file("stdin"); ns<-scan(fp,nmax=1); close(fp)
mpi.spawn.Rslaves(nslaves=ns)
@@ -363,7 +363,7 @@ mpi.apply Rmpi example:
#main
library(Rmpi)
- cat("Enter the number of slaves")
+ cat("Enter the number of slaves: ")
fp<-file("stdin"); ns<-scan(fp,nmax=1); close(fp)
mpi.spawn.Rslaves(nslaves=ns)
@@ -373,7 +373,7 @@ mpi.apply Rmpi example:
while (TRUE)
{
#read number of intervals
- cat("Enter the number of intervals(0 quits) ")
+ cat("Enter the number of intervals: (0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
if(n<=0) break
@@ -446,4 +446,3 @@ and general [MPI](../mpi-1.html) sections.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries.html
new file mode 100644
index 000000000..73423db1a
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries.html
@@ -0,0 +1,1318 @@
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+ FFTW
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+ The discrete Fourier transform in one or more dimensions, MPI parallel
+ </div>
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+ <p>Â </p>
+<p><abbr title="Fastest Fourier Transform in the West">FFTW</abbr> is a C subroutine library for computing the discrete Fourier transform in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). The FFTW library allows for MPI parallel, in-place discrete Fourier transform, with data distributed over number of nodes.<strong></strong></p>
+<p><strong><br /></strong>Two versions, <strong>3.3.3</strong> and <strong>2.1.5</strong> of FFTW are available on Anselm, each compiled for <strong>Intel MPI</strong> and <strong>OpenMPI</strong> using <strong>intel</strong> and <strong>gnu</strong> compilers. These are available via modules:</p>
+<table class="listing">
+<tbody>
+<tr><th>Version</th><th>Parallelization</th><th>module</th><th>linker options</th></tr>
+<tr class="even">
+<td>FFTW3 gcc<br />3.3.3</td>
+<td>pthread, OpenMP</td>
+<td>fftw3/3.3.3-gcc</td>
+<td>-lfftw3, -lfftw3_threads<br />-lfftw3_omp</td>
+</tr>
+<tr class="odd">
+<td>
+<p>FFTW3 icc<br />3.3.3</p>
+</td>
+<td>pthread, OpenMP</td>
+<td>fftw3</td>
+<td>-lfftw3, -lfftw3_threads<br />-lfftw3_omp</td>
+</tr>
+<tr class="even">
+<td>
+<p>FFTW2 gcc<br />2.1.5</p>
+</td>
+<td>pthread</td>
+<td>fftw2/2.1.5-gcc</td>
+<td>-lfftw, -lfftw_threads</td>
+</tr>
+<tr class="odd">
+<td>FFTW2 icc<br />2.1.5</td>
+<td>pthread</td>
+<td>fftw2</td>
+<td>-lfftw, -lfftw_threads</td>
+</tr>
+<tr class="even">
+<td>FFTW3 gcc<br />3.3.3</td>
+<td>OpenMPI</td>
+<td>fftw-mpi3/3.3.3-gcc</td>
+<td>-lfftw3_mpi</td>
+</tr>
+<tr class="odd">
+<td>FFTW3 icc<br />3.3.3</td>
+<td>Intel MPI</td>
+<td>fftw3-mpi</td>
+<td>-lfftw3_mpi</td>
+</tr>
+<tr class="even">
+<td>FFTW2 gcc<br />2.1.5</td>
+<td>OpenMPI</td>
+<td>fftw2-mpi/2.1.5-gcc</td>
+<td>-lfftw_mpi</td>
+</tr>
+<tr class="odd">
+<td>FFTW2 gcc<br />2.1.5</td>
+<td>IntelMPI</td>
+<td>fftw2-mpi/2.1.5-gcc</td>
+<td>-lfftw_mpi</td>
+</tr>
+</tbody>
+</table>
+<pre class=" ">$ module load fftw3</pre>
+<p>The module sets up environment variables, required for linking and running fftw enabled applications. Make sure that the choice of fftw module is consistent with your choice of MPI library. Mixing MPI of different implementations may have unpredictable results.</p>
+<h2 class=" ">Example</h2>
+<pre class=" ">#include <fftw3-mpi.h><br />int main(int argc, char **argv)<br />{<br />Â Â Â const ptrdiff_t N0 = 100, N1 = 1000;<br />Â Â Â fftw_plan plan;<br />Â Â Â fftw_complex *data;<br />Â Â Â ptrdiff_t alloc_local, local_n0, local_0_start, i, j;<br /><br />Â Â Â MPI_Init(&argc, &argv);<br />Â Â Â fftw_mpi_init();<br /><br />Â Â Â /* get local data size and allocate */<br />Â Â Â alloc_local = fftw_mpi_local_size_2d(N0, N1, MPI_COMM_WORLD,<br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â &local_n0, &local_0_start);<br />Â Â Â data = fftw_alloc_complex(alloc_local);<br /><br />Â Â Â /* create plan for in-place forward DFT */<br />Â Â Â plan = fftw_mpi_plan_dft_2d(N0, N1, data, data, MPI_COMM_WORLD,<br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â FFTW_FORWARD, FFTW_ESTIMATE);<br /><br />Â Â Â /* initialize data */<br />Â Â Â for (i = 0; i < local_n0; ++i) for (j = 0; j < N1; ++j)<br />Â Â Â {Â Â data[i*N1 + j][0] = i;<br />Â Â Â Â Â Â Â data[i*N1 + j][1] = j; }<br /><br />Â Â Â /* compute transforms, in-place, as many times as desired */<br />Â Â Â fftw_execute(plan);<br /><br />Â Â Â fftw_destroy_plan(plan);<br /><br />Â Â Â MPI_Finalize();<br />}</pre>
+<p>Load modules and compile:</p>
+<pre class=" ">$ module load impi intel<br />$ module load fftw3-mpi<br /><br />$ mpicc testfftw3mpi.c -o testfftw3mpi.x -Wl,-rpath=$LIBRARY_PATH -lfftw3_mpi</pre>
+<p class=" "><span class="internal-link">Run the example as <a href="../mpi-1/running-mpich2.html" title="" target="_self" class="internal-link">Intel MPI program</a></span>.</p>
+<p class=" ">Read more on FFTW usage on the <a class="external-link" href="http://www.fftw.org/fftw3_doc/" target="_self" title="">FFTW website.</a><br /><br /></p>
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
index 9b9eb0720..ac19c671d 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
@@ -153,4 +153,3 @@ program](../mpi-1/running-mpich2.html)</span>.
Read more on FFTW usage on the [FFTW
website.](http://www.fftw.org/fftw3_doc/)
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.html
new file mode 100644
index 000000000..2198e163e
--- /dev/null
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+ GSL
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+ The GNU Scientific Library. Provides a wide range of mathematical routines.
+ </div>
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+ <h2 class=" ">Introduction</h2>
+<p>The GNU Scientific Library (GSL) provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total. The routines have been written from scratch in C, and present a modern Applications Programming Interface (API) for C programmers, allowing wrappers to be written for very high level languages.</p>
+<p>The library covers a wide range of topics in numerical computing. Routines are available for the following areas:</p>
+<table>
+<tbody>
+<tr>
+<td></td>
+<td>Complex Numbers</td>
+<td>Roots of Polynomials</td>
+</tr>
+<tr>
+<td></td>
+<td>Special Functions</td>
+<td>Vectors and Matrices</td>
+</tr>
+<tr>
+<td></td>
+<td>Permutations</td>
+<td>Combinations</td>
+</tr>
+<tr>
+<td></td>
+<td>Sorting</td>
+<td>BLAS Support</td>
+</tr>
+<tr>
+<td></td>
+<td>Linear Algebra</td>
+<td>CBLAS Library</td>
+</tr>
+<tr>
+<td></td>
+<td>Fast Fourier Transforms</td>
+<td>Eigensystems</td>
+</tr>
+<tr>
+<td></td>
+<td>Random Numbers</td>
+<td>Quadrature</td>
+</tr>
+<tr>
+<td></td>
+<td>Random Distributions</td>
+<td>Quasi-Random Sequences</td>
+</tr>
+<tr>
+<td></td>
+<td>Histograms</td>
+<td>Statistics</td>
+</tr>
+<tr>
+<td></td>
+<td>Monte Carlo Integration</td>
+<td>N-Tuples</td>
+</tr>
+<tr>
+<td></td>
+<td>Differential Equations</td>
+<td>Simulated Annealing</td>
+</tr>
+<tr>
+<td></td>
+<td>Numerical Differentiation</td>
+<td>Interpolation</td>
+</tr>
+<tr>
+<td></td>
+<td>Series Acceleration</td>
+<td>Chebyshev Approximations</td>
+</tr>
+<tr>
+<td></td>
+<td>Root-Finding</td>
+<td>Discrete Hankel Transforms</td>
+</tr>
+<tr>
+<td></td>
+<td>Least-Squares Fitting</td>
+<td>Minimization</td>
+</tr>
+<tr>
+<td></td>
+<td>IEEE Floating-Point</td>
+<td>Physical Constants</td>
+</tr>
+<tr>
+<td></td>
+<td>Basis Splines</td>
+<td>Wavelets</td>
+</tr>
+</tbody>
+</table>
+<h2 class=" ">Modules</h2>
+<p>The GSL 1.16 is available on Anselm, compiled for GNU and Intel compiler. These variants are available via modules:</p>
+<table class="listing">
+<tbody>
+<tr><th>Module</th><th>Compiler</th></tr>
+<tr class="odd">
+<td>gsl/1.16-gcc</td>
+<td>gcc 4.8.6</td>
+</tr>
+<tr class="even">
+<td>gsl/1.16-icc(default)</td>
+<td>icc</td>
+</tr>
+</tbody>
+</table>
+<pre class=" ">Â $ module load gsl</pre>
+<p>The module sets up environment variables, required for linking and running GSL enabled applications. This particular command loads the default module, which is gsl/1.16-icc</p>
+<h2 class=" ">Linking</h2>
+<p>Load an appropriate gsl module. Link using <strong>-lgsl</strong> switch to link your code against GSL. The GSL depends on cblas API to BLAS library, which must be supplied for linking. The BLAS may be provided, for example from the MKL library, as well as from the BLAS GSL library (-lgslcblas). Using the MKL is recommended.</p>
+<h3 class=" ">Compiling and linking with Intel compilers</h3>
+<pre class=" ">$ module load intel<br />$ module load gsl<br />$ icc myprog.c -o myprog.x -Wl,-rpath=$LIBRARY_PATH -mkl -lgsl</pre>
+<h3 class=" ">Compiling and linking with GNU compilers</h3>
+<pre class=" ">$ module load gcc<br />$ module load mkl<br />$ module load gsl/1.16-gcc<br />$ gcc myprog.c -o myprog.x -Wl,-rpath=$LIBRARY_PATH -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lgsl</pre>
+<h2 class=" ">Example</h2>
+<p class=" ">Following is an example of discrete wavelet transform implemented by GSL:</p>
+<pre class=" ">#include <stdio.h><br />#include <math.h><br />#include <gsl/gsl_sort.h><br />#include <gsl/gsl_wavelet.h><br /><br />int<br />main (int argc, char **argv)<br />{<br />Â int i, n = 256, nc = 20;<br />Â double *data = malloc (n * sizeof (double));<br />Â double *abscoeff = malloc (n * sizeof (double));<br />Â size_t *p = malloc (n * sizeof (size_t));<br /><br />Â gsl_wavelet *w;<br />Â gsl_wavelet_workspace *work;<br /><br />Â w = gsl_wavelet_alloc (gsl_wavelet_daubechies, 4);<br />Â work = gsl_wavelet_workspace_alloc (n);<br /><br />Â for (i=0; i<n; i++)<br />Â data[i] = sin (3.141592654*(double)i/256.0);<br /><br />Â gsl_wavelet_transform_forward (w, data, 1, n, work);<br /><br />Â for (i = 0; i < n; i++)<br />Â Â Â {<br />Â Â Â Â Â abscoeff[i] = fabs (data[i]);<br />Â Â Â }<br />Â <br />Â gsl_sort_index (p, abscoeff, 1, n);<br />Â <br />Â for (i = 0; (i + nc) < n; i++)<br />Â Â Â data[p[i]] = 0;<br />Â <br />Â gsl_wavelet_transform_inverse (w, data, 1, n, work);<br />Â <br />Â for (i = 0; i < n; i++)<br />Â Â Â {<br />Â Â Â Â Â printf ("%g\n", data[i]);<br />Â Â Â }<br />Â <br />Â gsl_wavelet_free (w);<br />Â gsl_wavelet_workspace_free (work);<br /><br />Â free (data);<br />Â free (abscoeff);<br />Â free (p);<br />Â return 0;<br />}</pre>
+<p class=" ">Load modules and compile:</p>
+<pre class=" ">$ module load intel gsl<br />icc dwt.c -o dwt.x -Wl,-rpath=$LIBRARY_PATH -mkl -lgsl</pre>
+<p class=" ">In this example, we compile the dwt.c code using the Intel compiler and link it to the MKL and GSL library, note the -mkl and -lgsl options. The library search path is compiled in, so that no modules are necessary to run the code.<br /><br /></p>
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+</div>
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+ Hierarchical Data Format library. Serial and MPI parallel version.
+ </div>
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+ <p>Â </p>
+<p><a href="http://www.hdfgroup.org/HDF5/">HDF5 (Hierarchical Data Format)</a> is a general purpose library and file format for storing scientific data. HDF5 can store two primary objects: datasets and groups. A dataset is essentially a multidimensional array of data elements, and a group is a structure for organizing objects in an HDF5 file. Using these two basic objects, one can create and store almost any kind of scientific data structure, such as images, arrays of vectors, and structured and unstructured grids. You can also mix and match them in HDF5 files according to your needs.</p>
+<p>Versions <strong>1.8.11</strong> and <strong>1.8.13</strong> of HDF5 library are available on Anselm, compiled for <strong>Intel MPI</strong> and <strong>OpenMPI</strong> using <strong>intel</strong> and <strong>gnu</strong> compilers. These are available via modules:</p>
+<table class="listing">
+<tbody>
+<tr><th>Version</th><th>Parallelization</th><th>module</th><th>C linker options</th><th>C++ linker options</th><th>Fortran linker options</th></tr>
+<tr class="even">
+<td>HDF5 icc serial</td>
+<td>pthread</td>
+<td>hdf5/1.8.11</td>
+<td>$HDF5_INC $HDF5_SHLIB</td>
+<td>$HDF5_INC $HDF5_CPP_LIB</td>
+<td>$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+<tr class="odd">
+<td>
+<p>HDF5 icc parallel MPI</p>
+</td>
+<td>pthread, IntelMPI</td>
+<td>hdf5-parallel/1.8.11</td>
+<td>$HDF5_INC $HDF5_SHLIB</td>
+<td>Not supported</td>
+<td>$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+<tr class="even">
+<td>HDF5 icc serial</td>
+<td>pthread</td>
+<td>hdf5/1.8.13</td>
+<td>$HDF5_INC $HDF5_SHLIB</td>
+<td>$HDF5_INC $HDF5_CPP_LIB</td>
+<td>$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+<tr class="odd">
+<td>
+<p>HDF5 icc parallel MPI</p>
+</td>
+<td>pthread, IntelMPI</td>
+<td>hdf5-parallel/1.8.13</td>
+<td>$HDF5_INC $HDF5_SHLIB</td>
+<td>Not supported</td>
+<td>$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+<tr class="even">
+<td>
+<p>HDF5 gcc parallel MPI</p>
+</td>
+<td>pthread, OpenMPI 1.6.5, gcc 4.8.1</td>
+<td>hdf5-parallel/1.8.11-gcc</td>
+<td>$HDF5_INC $HDF5_SHLIB</td>
+<td>Not supported</td>
+<td>$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+<tr class="even">
+<td>
+<p>HDF5 gcc parallel MPI</p>
+</td>
+<td>pthread, OpenMPI 1.6.5, gcc 4.8.1</td>
+<td>hdf5-parallel/1.8.13-gcc</td>
+<td>$HDF5_INC $HDF5_SHLIB</td>
+<td>Not supported</td>
+<td>$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+<tr class="even">
+<td>
+<p>HDF5 gcc parallel MPI</p>
+</td>
+<td>pthread, OpenMPI 1.8.1, gcc 4.9.0</td>
+<td>hdf5-parallel/1.8.13-gcc49</td>
+<td>$HDF5_INC $HDF5_SHLIB</td>
+<td>Not supported</td>
+<td>$HDF5_INC $HDF5_F90_LIB</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<pre class=" ">$ module load hdf5-parallel</pre>
+<p>The module sets up environment variables, required for linking and running HDF5 enabled applications. Make sure that the choice of HDF5 module is consistent with your choice of MPI library. Mixing MPI of different implementations may have unpredictable results.</p>
+<p class="callout">Be aware, that GCC version of <strong>HDF5 1.8.11</strong> has serious performance issues, since it's compiled with -O0 optimization flag. This version is provided only for testing of code compiled only by GCC and IS NOT recommended for production computations. For more informations, please see: <a class="external-link" href="http://www.hdfgroup.org/ftp/HDF5/prev-releases/ReleaseFiles/release5-1811" target="_self" title="">http://www.hdfgroup.org/ftp/HDF5/prev-releases/ReleaseFiles/release5-1811</a><br />All GCC versions of <strong>HDF5 1.8.13</strong> are not affected by the bug, are compiled with -O3 optimizations and are recommended for production computations.</p>
+<h2 class=" ">Example</h2>
+<pre class=" ">#include "hdf5.h"<br />#define FILE "dset.h5"<br /><br />int main() {<br /><br /> hid_t file_id, dataset_id, dataspace_id; /* identifiers */<br /> hsize_t dims[2];<br /> herr_t status;<br /> int i, j, dset_data[4][6];<br /><br /> /* Create a new file using default properties. */<br /> file_id = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);<br /><br /> /* Create the data space for the dataset. */<br /> dims[0] = 4;<br /> dims[1] = 6;<br /> dataspace_id = H5Screate_simple(2, dims, NULL);<br /><br /> /* Initialize the dataset. */<br /> for (i = 0; i < 4; i++)<br /> for (j = 0; j < 6; j++)<br /> dset_data[i][j] = i * 6 + j + 1;<br /><br /><br /> /* Create the dataset. */<br /> dataset_id = H5Dcreate2(file_id, "/dset", H5T_STD_I32BE, dataspace_id,<br /> H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);<br /><br /> /* Write the dataset. */<br /> status = H5Dwrite(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,<br /> dset_data);<br /><br /> status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,<br /> dset_data);<br /><br /> /* End access to the dataset and release resources used by it. */<br /> status = H5Dclose(dataset_id);<br /><br /> /* Terminate access to the data space. */<br /> status = H5Sclose(dataspace_id);<br /><br /> /* Close the file. */<br /> status = H5Fclose(file_id);<br />}</pre>
+<p>Load modules and compile:</p>
+<pre class=" ">$ module load intel impi<br />$ module load hdf5-parallel<br /><br />$ mpicc hdf5test.c -o hdf5test.x -Wl,-rpath=$LIBRARY_PATH $HDF5_INC $HDF5_SHLIB</pre>
+<p><span class="internal-link">Run the example as <a href="../anselm-cluster-documentation/software/mpi-1/running-mpich2.html" title="" target="_self" class="internal-link">Intel MPI program</a></span>.</p>
+<p>For further informations, please see the website: <a class="external-link" href="http://www.hdfgroup.org/HDF5/" target="_self" title="">http://www.hdfgroup.org/HDF5/</a></p>
+<p>Â </p>
+<p>Â </p>
+<p>Â </p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
index 5b7a00770..54bf5a49f 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
@@ -6,7 +6,7 @@ Hierarchical Data Format library. Serial and MPI parallel version.
[HDF5 (Hierarchical Data Format)](http://www.hdfgroup.org/HDF5/) is a
general purpose library and file format for storing scientific data.
-HDF5 can store two primary objectsdatasets and groups. A dataset is
+HDF5 can store two primary objects: datasets and groups. A dataset is
essentially a multidimensional array of data elements, and a group is a
structure for organizing objects in an HDF5 file. Using these two basic
objects, one can create and store almost any kind of scientific data
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+<pre class=" ">$ module load mkl</pre>
+<p>Read more at the <a href="../intel-suite/intel-mkl.html" title="" target="_self" class="internal-link">Intel MKL</a> page.</p>
+<h2 class=" ">Intel Integrated Performance Primitives</h2>
+<p>Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.</p>
+<pre class=" ">$ module load ipp</pre>
+<p>Read more at the <a href="../intel-suite/intel-integrated-performance-primitives.html" title="" target="_self" class="internal-link">Intel IPP</a> page.</p>
+<h2 class=" ">Intel Threading Building Blocks</h2>
+<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
index d16537c36..946850e12 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
@@ -11,7 +11,7 @@ Intel Math Kernel Library
Intel Math Kernel Library (Intel MKL) is a library of math kernel
subroutines, extensively threaded and optimized for maximum performance.
-Intel MKL unites and provides these basic componentsBLAS, LAPACK,
+Intel MKL unites and provides these basic components: BLAS, LAPACK,
ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
many more.
@@ -52,3 +52,7 @@ manner.
Read more at the [Intel
TBB](../intel-suite/intel-tbb.html) page.
+
+
+
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.html
new file mode 100644
index 000000000..eaaf3be43
--- /dev/null
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+ <h3 class=" ">Compiling and linking with MAGMA</h3>
+<p>To be able to compile and link code with MAGMA library user has to load following module:</p>
+<pre class=" ">$ module load magma/1.3.0-mic</pre>
+<p>To make compilation more user friendly module also sets these two environment variables:</p>
+<p class="callout">MAGMA_INC - contains paths to the MAGMA header files (to be used for compilation step) <br /><br />MAGMA_LIBS - contains paths to MAGMA libraries (to be used for linking step).  </p>
+<p>Compilation example:</p>
+<pre class=" ">$ icc -mkl -O3 -DHAVE_MIC -DADD_ -Wall <strong><span>$MAGMA_INC</span></strong> -c testing_dgetrf_mic.cpp -o testing_dgetrf_mic.o<br /><br />$ icc -mkl -O3 -DHAVE_MIC -DADD_ -Wall -fPIC -Xlinker -zmuldefs -Wall -DNOCHANGE -DHOST testing_dgetrf_mic.o -o testing_dgetrf_mic <strong><span>$MAGMA_LIBS</span></strong></pre>
+<p>Â </p>
+<h3 class=" ">Running MAGMA code</h3>
+<p>MAGMA implementation for Intel MIC requires a MAGMA server running on accelerator prior to executing the user application. The server can be started and stopped using following scripts:</p>
+<p class="callout">To start MAGMA server use: <br /><strong>$MAGMAROOT/start_magma_server</strong><br /><br />To stop the server use: <br /><strong>$MAGMAROOT/stop_magma_server</strong><br /><br />For deeper understanding how the MAGMA server is started, see the following script: <br /><strong>$MAGMAROOT/launch_anselm_from_mic.sh</strong></p>
+<p>To test if the MAGMA server runs properly we can run one of examples that are part of the MAGMA installation:</p>
+<pre class=" ">[user@cn204 ~]$ <strong>$MAGMAROOT/testing/testing_dgetrf_mic</strong><br /><br />[user@cn204 ~]$ <strong>export OMP_NUM_THREADS=16</strong><br /><br />[lriha@cn204 ~]$ <strong>$MAGMAROOT/testing/testing_dgetrf_mic</strong><br />Usage: /apps/libs/magma-mic/magmamic-1.3.0/testing/testing_dgetrf_mic [options] [-h|--help]<br /><br />Â MÂ Â Â Â NÂ Â Â Â CPU GFlop/s (sec)Â Â MAGMA GFlop/s (sec)Â Â ||PA-LU||/(||A||*N)<br />=========================================================================<br />Â 1088Â 1088Â Â Â Â ---Â Â (Â ---Â )Â Â Â Â 13.93 (Â Â 0.06)Â Â Â Â ---<br />Â 2112Â 2112Â Â Â Â ---Â Â (Â ---Â )Â Â Â Â 77.85 (Â Â 0.08)Â Â Â Â ---<br />Â 3136Â 3136Â Â Â Â ---Â Â (Â ---Â )Â Â Â 183.21 (Â Â 0.11)Â Â Â Â ---<br />Â 4160Â 4160Â Â Â Â ---Â Â (Â ---Â )Â Â Â 227.52 (Â Â 0.21)Â Â Â Â ---<br />Â 5184Â 5184Â Â Â Â ---Â Â (Â ---Â )Â Â Â 258.61 (Â Â 0.36)Â Â Â Â ---<br />Â 6208Â 6208Â Â Â Â ---Â Â (Â ---Â )Â Â Â 333.12 (Â Â 0.48)Â Â Â Â ---<br />Â 7232Â 7232Â Â Â Â ---Â Â (Â ---Â )Â Â Â 416.52 (Â Â 0.61)Â Â Â Â ---<br />Â 8256Â 8256Â Â Â Â ---Â Â (Â ---Â )Â Â Â 446.97 (Â Â 0.84)Â Â Â Â ---<br />Â 9280Â 9280Â Â Â Â ---Â Â (Â ---Â )Â Â Â 461.15 (Â Â 1.16)Â Â Â Â ---<br />10304 10304Â Â Â Â ---Â Â (Â ---Â )Â Â Â 500.70 (Â Â 1.46)Â Â Â Â ---</pre>
+<p>Â </p>
+<p class="callout">Please note: MAGMA contains several benchmarks and examples that can be found in:<br /><strong>$MAGMAROOT/testing/</strong></p>
+<p class="callout">MAGMA relies on the performance of all CPU cores as well as on the performance of the accelerator. Therefore on Anselm number of CPU OpenMP threads has to be set to 16: Â <strong> <br />export OMP_NUM_THREADS=16</strong></p>
+<p>Â </p>
+<p>See more details at <a class="external-link" href="http://icl.cs.utk.edu/magma/" target="_self" title="">MAGMA home page</a>.</p>
+<h2 class=" ">References</h2>
+<p>[1] MAGMA MIC: Linear Algebra Library for Intel Xeon Phi Coprocessors, Jack Dongarra et. al, <a class="external-link" href="http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf" target="_self" title="">http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf<br /></a><br /><br /></p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
index d8f63e440..77bac5a4e 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
@@ -51,7 +51,7 @@ that are part of the MAGMA installation:
[user@cn204 ~]$ export OMP_NUM_THREADS=16
[lriha@cn204 ~]$ $MAGMAROOT/testing/testing_dgetrf_mic
- Usage/apps/libs/magma-mic/magmamic-1.3.0/testing/testing_dgetrf_mic [options] [-h|--help]
+ Usage: /apps/libs/magma-mic/magmamic-1.3.0/testing/testing_dgetrf_mic [options] [-h|--help]
 M    N    CPU GFlop/s (sec)  MAGMA GFlop/s (sec)  ||PA-LU||/(||A||*N)
=========================================================================
@@ -68,13 +68,13 @@ that are part of the MAGMA installation:
Â
-Please noteMAGMA contains several benchmarks and examples that can be
+Please note: MAGMA contains several benchmarks and examples that can be
found in:
**$MAGMAROOT/testing/**
MAGMA relies on the performance of all CPU cores as well as on the
performance of the accelerator. Therefore on Anselm number of CPU OpenMP
-threads has to be set to 16Â **
+threads has to be set to 16: Â **
export OMP_NUM_THREADS=16**
Â
@@ -85,9 +85,8 @@ page](http://icl.cs.utk.edu/magma/).
References
----------
-[1] MAGMA MICLinear Algebra Library for Intel Xeon Phi Coprocessors,
+[1] MAGMA MIC: Linear Algebra Library for Intel Xeon Phi Coprocessors,
Jack Dongarra et. al,Â
[http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf
](http://icl.utk.edu/projectsfiles/magma/pubs/24-MAGMA_MIC_03.pdf)
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.html
new file mode 100644
index 000000000..68cbf3794
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.html
@@ -0,0 +1,1199 @@
+
+<!DOCTYPE html>
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+ PETSc
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+ PETSc is a suite of building blocks for the scalable solution of scientific and engineering applications modelled by partial differential equations. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.
+ </div>
+
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+ <h2>Introduction</h2>
+<p>PETSc (Portable, Extensible Toolkit for Scientific Computation) is a suite of building blocks (data structures and routines) for the scalable solution of scientific and engineering applications modelled by partial differential equations. It allows thinking in terms of high-level objects (matrices) instead of low-level objects (raw arrays). Written in C language but can also be called from FORTRAN, C++, Python and Java codes. It supports MPI, shared memory, and GPUs through CUDA or OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.</p>
+<h2>Resources</h2>
+<ul>
+<li><a href="http://www.mcs.anl.gov/petsc/">project webpage</a></li>
+<li><a href="http://www.mcs.anl.gov/petsc/documentation/">documentation</a><ul>
+<li><a href="http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf">PETSc Users Manual (PDF)</a></li>
+<li><a href="http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/singleindex.html">index of all manual pages</a></li>
+</ul>
+</li>
+<li>PRACE Video Tutorial <a href="http://www.youtube.com/watch?v=asVaFg1NDqY">part 1</a>,
+<a href="http://www.youtube.com/watch?v=ubp_cSibb9I">part 2</a>,
+<a href="http://www.youtube.com/watch?v=vJAAAQv-aaw">part 3</a>,
+<a href="http://www.youtube.com/watch?v=BKVlqWNh8jY">part 4</a>,
+<a href="http://www.youtube.com/watch?v=iXkbLEBFjlM">part 5</a></li>
+</ul>
+<h2>Modules</h2>
+<p>You can start using PETSc on Anselm by loading the PETSc module.
+Module names obey this pattern:</p>
+<pre><code># module load petsc/version-compiler-mpi-blas-variant, e.g.
+ module load petsc/3.4.4-icc-impi-mkl-opt
+</code></pre>
+<p>where <code>variant</code> is replaced by one of <code>{dbg, opt, threads-dbg, threads-opt}</code>. The <code>opt</code> variant is compiled without debugging information (no <code>-g</code> option) and with aggressive compiler optimizations (<code>-O3 -xAVX</code>). This variant is suitable for performance measurements and production runs. In all other cases use the debug (<code>dbg</code>) variant, because it contains debugging information, performs validations and self-checks, and provides a clear stack trace and message in case of an error. The other two variants <code>threads-dbg</code> and <code>threads-opt</code> are <code>dbg</code> and <code>opt</code>, respectively, built with <a href="http://www.mcs.anl.gov/petsc/features/threads.html">OpenMP and pthreads threading support</a>.</p>
+<h2>External libraries</h2>
+<p>PETSc needs at least MPI, BLAS and LAPACK. These dependencies are currently satisfied with Intel MPI and Intel MKL in Anselm <code>petsc</code> modules.</p>
+<p>PETSc can be linked with a plethora of <a href="http://www.mcs.anl.gov/petsc/miscellaneous/external.html">external numerical libraries</a>, extending PETSc functionality, e.g. direct linear system solvers, preconditioners or partitioners. See below a list of libraries currently included in Anselm <code>petsc</code> modules.</p>
+<p>All these libraries can be used also alone, without PETSc.
+Their static or shared program libraries are available in <code>$PETSC_DIR/$PETSC_ARCH/lib</code> and header files in <code>$PETSC_DIR/$PETSC_ARCH/include</code>. <code>PETSC_DIR</code> and <code>PETSC_ARCH</code> are environment variables pointing to a specific PETSc instance based on the petsc module loaded.</p>
+<h3>Libraries linked to PETSc on Anselm (as of 11 April 2015)</h3>
+<ul>
+<li>dense linear algebra<ul>
+<li><a href="http://libelemental.org/">Elemental</a></li>
+</ul>
+</li>
+<li>sparse linear system solvers<ul>
+<li><a href="https://software.intel.com/en-us/node/470282">Intel MKL Pardiso</a></li>
+<li><a href="http://mumps.enseeiht.fr/">MUMPS</a></li>
+<li><a href="http://pastix.gforge.inria.fr/">PaStiX</a></li>
+<li><a href="http://faculty.cse.tamu.edu/davis/suitesparse.html">SuiteSparse</a></li>
+<li><a href="http://crd.lbl.gov/~xiaoye/SuperLU/#superlu">SuperLU</a></li>
+<li><a href="http://crd.lbl.gov/~xiaoye/SuperLU/#superlu_dist">SuperLU_Dist</a></li>
+</ul>
+</li>
+<li>input/output<ul>
+<li><a href="http://sourceforge.net/projects/exodusii/">ExodusII</a></li>
+<li><a href="http://www.hdfgroup.org/HDF5/">HDF5</a></li>
+<li><a href="http://www.unidata.ucar.edu/software/netcdf/">NetCDF</a></li>
+</ul>
+</li>
+<li>partitioning<ul>
+<li><a href="http://www.cs.sandia.gov/CRF/chac.html">Chaco</a></li>
+<li><a href="http://glaros.dtc.umn.edu/gkhome/metis/metis/overview">METIS</a></li>
+<li><a href="http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview">ParMETIS</a></li>
+<li><a href="http://www.labri.fr/perso/pelegrin/scotch/">PT-Scotch</a></li>
+</ul>
+</li>
+<li>preconditioners & multigrid<ul>
+<li><a href="http://acts.nersc.gov/hypre/">Hypre</a></li>
+<li><a href="http://trilinos.sandia.gov/packages/ml/">Trilinos ML</a></li>
+<li><a href="https://bitbucket.org/petsc/pkg-spai">SPAI - Sparse Approximate Inverse</a></li>
+</ul>
+</li>
+</ul>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md
index 4ac0c50db..2441fd2bb 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md
@@ -104,4 +104,3 @@ petsc module loaded.
- [Trilinos ML](http://trilinos.sandia.gov/packages/ml/)
- [SPAI - Sparse Approximate
Inverse](https://bitbucket.org/petsc/pkg-spai)
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.html b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.html
new file mode 100644
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+ Trilinos
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+ Packages for large scale scientific and engineering problems. Provides MPI and hybrid parallelization.
+ </div>
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+ <div id="content-core">
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+ <div id="parent-fieldname-text-0c47f15849c64fa68fa58445c34bcefc" class="">
+ <h3 class=" ">Introduction</h3>
+<p>Trilinos is a collection of software packages for the numerical solution of large scale scientific and engineering problems. It is based on C++ and feautures modern object-oriented design. Both serial as well as parallel computations based on MPI and hybrid parallelization are supported within Trilinos packages.</p>
+<h3 class=" ">Installed packages</h3>
+<p>Current Trilinos installation on ANSELM contains (among others) the following main packages</p>
+<ul>
+<li><strong>Epetra</strong> - core linear algebra package containing classes for manipulation with serial and distributed vectors, matrices, and graphs. Dense linear solvers are supported via interface to BLAS and LAPACK (Intel MKL on ANSELM). Its extension <strong>EpetraExt</strong> contains e.g. methods for matrix-matrix multiplication.</li>
+<li><strong>Tpetra</strong> - next-generation linear algebra package. Supports 64bit indexing and arbitrary data type using C++ templates.</li>
+<li><strong>Belos</strong> - library of various iterative solvers (CG, block CG, GMRES, block GMRES etc.).</li>
+<li><strong>Amesos</strong> - interface to direct sparse solvers.</li>
+<li><strong>Anasazi</strong> - framework for large-scale eigenvalue algorithms.</li>
+<li><strong>IFPACK</strong> - distributed algebraic preconditioner (includes e.g. incomplete LU factorization)</li>
+<li><strong>Teuchos</strong> - common tools packages. This package contains classes for memory management, output, performance monitoring, BLAS and LAPACK wrappers etc.</li>
+</ul>
+<p>For the full list of Trilinos packages, descriptions of their capabilities, and user manuals see <a class="external-link" href="http://trilinos.sandia.gov" target="_self" title="">http://trilinos.sandia.gov.</a></p>
+<h3 class=" ">Installed version</h3>
+<p>Currently, Trilinos in version 11.2.3 compiled with Intel Compiler is installed on ANSELM.</p>
+<h3 class=" ">Compilling against Trilinos</h3>
+<p>First, load the appropriate module:</p>
+<pre class=" ">$ module load trilinos</pre>
+<p class=" ">For the compilation of CMake-aware project, Trilinos provides the FIND_PACKAGE( Trilinos ) capability, which makes it easy to build against Trilinos, including linking against the correct list of libraries. For details, see <a class="external-link" href="http://trilinos.sandia.gov/Finding_Trilinos.txt" target="_self" title="">http://trilinos.sandia.gov/Finding_Trilinos.txt</a></p>
+<p class=" ">For compiling using simple makefiles, Trilinos provides Makefile.export system, which allows users to include important Trilinos variables directly into their makefiles. This can be done simply by inserting the following line into the makefile:</p>
+<pre class=" ">include Makefile.export.Trilinos</pre>
+<p class=" ">or</p>
+<pre class=" ">include Makefile.export.<package></pre>
+<p class=" ">if you are interested only in a specific Trilinos package. This will give you access to the variables such as Trilinos_CXX_COMPILER, Trilinos_INCLUDE_DIRS, Trilinos_LIBRARY_DIRS etc. For the detailed description and example makefile see <a class="external-link" href="http://trilinos.sandia.gov/Export_Makefile.txt" target="_self" title="">http://trilinos.sandia.gov/Export_Makefile.txt</a>.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
index 784ae3d64..ce966e34b 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
@@ -70,3 +70,7 @@ give you access to the variables such as Trilinos_CXX_COMPILER,
Trilinos_INCLUDE_DIRS, Trilinos_LIBRARY_DIRS etc. For the detailed
description and example makefile see
<http://trilinos.sandia.gov/Export_Makefile.txt>.
+
+
+
+
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.html b/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.html
new file mode 100644
index 000000000..a18b4508a
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.html
@@ -0,0 +1,1040 @@
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+ <h2 class=" ">CUDA Programming on Anselm</h2>
+<p class=" ">The default programming model for GPU accelerators on Anselm is Nvidia CUDA. To set up the environment for CUDA use</p>
+<pre class=" "><span>$ module load cuda</span></pre>
+<p class=" ">If the user code is hybrid and uses both CUDA and MPI, the MPI environment has to be set up as well. One way to do this is to use the PrgEnv-gnu module, which sets up correct combination of GNU compiler and MPI library.</p>
+<pre class=" ">$ module load PrgEnv-gnu</pre>
+<p class=" ">CUDA code can be compiled directly on login1 or login2 nodes. User does not have to use compute nodes with GPU accelerator for compilation. To compile a CUDA source code, use nvcc compiler.</p>
+<pre class=" ">$ nvcc --version</pre>
+<p class=" "><span>CUDA Toolkit comes with large number of examples, that can be helpful to start with. To compile and test these examples user should copy them to its home directory </span></p>
+<pre class=" ">$ cd ~<br />$ mkdir cuda-samples<br />$ cp -R /apps/nvidia/cuda/6.5.14/samples/* ~/cuda-samples/</pre>
+<p class=" ">To compile an examples, change directory to the particular example (here the example used is deviceQuery) and run "make" to start the compilation</p>
+<pre class=" ">$ cd ~/cuda-samples/1_Utilities/deviceQuery<br />$ make </pre>
+<p class=" ">To run the code user can use PBS interactive session to get access to a node from qnvidia queue (note: use your project name with parameter -A in the qsub command) and execute the binary file</p>
+<pre class=" ">$ qsub -I -q qnvidia -A OPEN-0-0<br />$ module load cuda<br />$Â ~/cuda-samples/1_Utilities/deviceQuery/deviceQuery</pre>
+<p class=" ">Expected output of the deviceQuery example executed on a node with Tesla K20m is</p>
+<pre class=" ">CUDA Device Query (Runtime API) version (CUDART static linking)<br /><br />Detected 1 CUDA Capable device(s)<br /><br />Device 0: "Tesla K20m"<br />CUDA Driver Version / Runtime Version 5.0 / 5.0<br />CUDA Capability Major/Minor version number: 3.5<br />Total amount of global memory: 4800 MBytes (5032706048 bytes)<br />(13) Multiprocessors x (192) CUDA Cores/MP: 2496 CUDA Cores<br />GPU Clock rate: 706 MHz (0.71 GHz)<br />Memory Clock rate: 2600 Mhz <br />Memory Bus Width: 320-bit<br />L2 Cache Size: 1310720 bytes<br />Max Texture Dimension Size (x,y,z) 1D=(65536), 2D=(65536,65536), 3D=(4096,4096,4096)<br />Max Layered Texture Size (dim) x layers 1D=(16384) x 2048, 2D=(16384,16384) x 2048<br />Total amount of constant memory: 65536 bytes <br />Total amount of shared memory per block: 49152 bytes<br />Total number of registers available per block: 65536<br />Warp size: 32<br />Maximum number of threads per multiprocessor: 2048<br />Maximum number of threads per block: 1024 <br />Maximum sizes of each dimension of a block: 1024 x 1024 x 64<br />Maximum sizes of each dimension of a grid: 2147483647 x 65535 x 65535<br />Maximum memory pitch: 2147483647 bytes<br />Texture alignment: 512 bytes<br />Concurrent copy and kernel execution: Yes with 2 copy engine(s)<br />Run time limit on kernels: No<br />Integrated GPU sharing Host Memory: No<br />Support host page-locked memory mapping: Yes<br />Alignment requirement for Surfaces: Yes <br />Device has ECC support: Enabled <br />Device supports Unified Addressing (UVA): Yes<br />Device PCI Bus ID / PCI location ID: 2 / 0<br />Compute Mode: <br />< Default (multiple host threads can use ::cudaSetDevice() with device simultaneously) > <br />deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 5.0, CUDA Runtime Version = 5.0, NumDevs = 1, Device0 = Tesla K20m </pre>
+<h3 class=" ">Code example</h3>
+<p class=" ">In this section we provide a basic CUDA based vector addition code example. You can directly copy and paste the code to test it. </p>
+<pre class=" ">$ vim test.cu</pre>
+<pre class=" ">#define N (2048*2048)<br />#define THREADS_PER_BLOCK 512<br /><br />#include <stdio.h><br />#include <stdlib.h><br /><br />// GPU kernel function to add two vectors <br />__global__ void add_gpu( int *a, int *b, int *c, int n){<br /> Â int index = threadIdx.x + blockIdx.x * blockDim.x;<br />Â if (index < n)<br />Â c[index] = a[index] + b[index];<br />}<br /><br />// CPU function to add two vectors <br />void add_cpu (int *a, int *b, int *c, int n) {<br /> Â for (int i=0; i < n; i++)<br /> c[i] = a[i] + b[i];<br />}<br /><br />// CPU function to generate a vector of random integers<br />void random_ints (int *a, int n) {<br /> Â for (int i = 0; i < n; i++)<br />Â a[i] = rand() % 10000; // random number between 0 and 9999<br />}<br /><br />// CPU function to compare two vectors <br />int compare_ints( int *a, int *b, int n ){<br /> Â int pass = 0;<br />Â for (int i = 0; i < N; i++){<br />Â if (a[i] != b[i]) {<br />Â printf("Value mismatch at location %d, values %d and %d\n",i, a[i], b[i]);<br />Â pass = 1;<br />Â }<br />Â }<br />Â if (pass == 0) printf ("Test passed\n"); else printf ("Test Failed\n");<br />Â return pass;<br />}<br /><br /><br />int main( void ) {<br />Â <br /> Â int *a, *b, *c; // host copies of a, b, c<br /> Â int *dev_a, *dev_b, *dev_c; // device copies of a, b, c<br /> Â int size = N * sizeof( int ); // we need space for N integers<br /><br />Â // Allocate GPU/device copies of dev_a, dev_b, dev_c<br />Â cudaMalloc( (void**)&dev_a, size );<br />Â cudaMalloc( (void**)&dev_b, size );<br />Â cudaMalloc( (void**)&dev_c, size );<br /><br />Â // Allocate CPU/host copies of a, b, c<br />Â a = (int*)malloc( size );<br />Â b = (int*)malloc( size );<br />Â c = (int*)malloc( size );<br />Â <br />Â // Fill input vectors with random integer numbers<br />Â random_ints( a, N );<br />Â random_ints( b, N );<br /><br />Â // copy inputs to device<br />Â cudaMemcpy( dev_a, a, size, cudaMemcpyHostToDevice );<br />Â cudaMemcpy( dev_b, b, size, cudaMemcpyHostToDevice );<br /><br />Â // launch add_gpu() kernel with blocks and threads<br />Â add_gpu<<< N/THREADS_PER_BLOCK, THREADS_PER_BLOCK >>>( dev_a, dev_b, dev_c, N );<br /><br />Â // copy device result back to host copy of c<br />Â cudaMemcpy( c, dev_c, size, cudaMemcpyDeviceToHost );<br /><br />Â //Check the results with CPU implementation <br />Â int *c_h; c_h = (int*)malloc( size );<br />Â add_cpu (a, b, c_h, N);<br />Â compare_ints(c, c_h, N);<br /><br />Â // Clean CPU memory allocations<br />Â free( a ); free( b ); free( c ); free (c_h);<br /><br />Â // Clean GPU memory allocations<br />Â cudaFree( dev_a );<br />Â cudaFree( dev_b );<br />Â cudaFree( dev_c );<br /><br />Â return 0;<br />}</pre>
+<p class=" ">This code can be compiled using following command</p>
+<pre class=" ">$ nvcc test.cu -o test_cuda</pre>
+<p class=" ">To run the code use interactive PBS session to get access to one of the GPU accelerated nodes</p>
+<pre class=" ">$ qsub -I -q qnvidia -A OPEN-0-0<br />$ module load cuda<br />$Â ./test.cuda</pre>
+<h2 class=" ">CUDA Libraries</h2>
+<h3 class=" ">CuBLAS</h3>
+<p class=" ">The NVIDIA CUDA Basic Linear Algebra Subroutines (cuBLAS) library is a GPU-accelerated version of the complete standard BLAS library with 152 standard BLAS routines. Basic description of the library together with basic performance comparison with MKL can be found <a class="external-link" href="https://developer.nvidia.com/cublas" target="_self" title="Nvidia cuBLAS">here</a>.</p>
+<p class=" "><strong>CuBLAS example: SAXPY</strong></p>
+<p class=" ">SAXPY function multiplies the vector x by the scalar alpha and adds it to the vector y overwriting the latest vector with the result. The description of the cuBLAS function can be found in <a class="external-link" href="http://docs.nvidia.com/cuda/cublas/index.html#cublas-lt-t-gt-axpy" target="_self" title="Nvidia CUDA documentation ">NVIDIA CUDA documentation</a>. Code can be pasted in the file and compiled without any modification.</p>
+<pre class=" ">/* Includes, system */<br />#include <stdio.h><br />#include <stdlib.h><br /><br />/* Includes, cuda */<br />#include <cuda_runtime.h><br />#include <cublas_v2.h><br /><br />/* Vector size */<br />#define NÂ (32)<br /><br />/* Host implementation of a simple version of saxpi */<br />void saxpy(int n, float alpha, const float *x, float *y)<br />{<br />Â Â Â for (int i = 0; i < n; ++i)<br />Â Â Â y[i] = alpha*x[i] + y[i];<br />}<br /><br />/* Main */<br />int main(int argc, char **argv)<br />{<br />Â Â Â float *h_X, *h_Y, *h_Y_ref;<br />Â Â Â float *d_X = 0;<br />Â Â Â float *d_Y = 0;<br /><br />Â Â Â const float alpha = 1.0f;<br />Â Â Â int i;<br /><br />Â Â Â cublasHandle_t handle;<br /><br />Â Â Â /* Initialize CUBLAS */<br />Â Â Â printf("simpleCUBLAS test running..\n");<br />Â Â Â cublasCreate(&handle);<br /><br />Â Â Â /* Allocate host memory for the matrices */<br />Â Â Â h_X = (float *)malloc(N * sizeof(h_X[0]));<br />Â Â Â h_Y = (float *)malloc(N * sizeof(h_Y[0]));<br />Â Â Â h_Y_ref = (float *)malloc(N * sizeof(h_Y_ref[0]));<br /><br />Â Â Â /* Fill the matrices with test data */<br />Â Â Â for (i = 0; i < N; i++)<br />Â Â Â {<br />Â Â Â Â Â Â Â h_X[i] = rand() / (float)RAND_MAX;<br />Â Â Â Â Â Â Â h_Y[i] = rand() / (float)RAND_MAX;<br />Â Â Â Â Â Â Â h_Y_ref[i] = h_Y[i];<br />Â Â Â }<br /><br />Â Â Â /* Allocate device memory for the matrices */<br />Â Â Â cudaMalloc((void **)&d_X, N * sizeof(d_X[0]));<br />Â Â Â cudaMalloc((void **)&d_Y, N * sizeof(d_Y[0]));<br /><br />Â Â Â /* Initialize the device matrices with the host matrices */<br />Â Â Â cublasSetVector(N, sizeof(h_X[0]), h_X, 1, d_X, 1);<br />Â Â Â cublasSetVector(N, sizeof(h_Y[0]), h_Y, 1, d_Y, 1);<br /><br />Â Â Â /* Performs operation using plain C code */<br />Â Â Â saxpy(N, alpha, h_X, h_Y_ref);<br /><br />Â Â Â /* Performs operation using cublas */<br />Â Â Â cublasSaxpy(handle, N, &alpha, d_X, 1, d_Y, 1);<br /><br />Â Â Â /* Read the result back */<br />Â Â Â cublasGetVector(N, sizeof(h_Y[0]), d_Y, 1, h_Y, 1);<br /><br />Â Â Â /* Check result against reference */<br />Â Â Â for (i = 0; i < N; ++i)<br />Â Â Â Â Â Â Â printf("CPU res = %f \t GPU res = %f \t diff = %f \n", h_Y_ref[i], h_Y[i], h_Y_ref[i] - h_Y[i]);<br /><br />Â Â Â /* Memory clean up */<br />Â Â Â free(h_X); free(h_Y); free(h_Y_ref);<br />Â Â Â cudaFree(d_X); cudaFree(d_Y);<br /><br />Â Â Â /* Shutdown */<br />Â Â Â cublasDestroy(handle);<br />}</pre>
+<p class="callout">Â Please note: cuBLAS has its own function for data transfers between CPU and GPU memory:<br />Â - <a class="external-link" href="http://docs.nvidia.com/cuda/cublas/index.html#cublassetvector" target="_self" title="">cublasSetVector</a> - transfers data from CPU to GPU memory<br />Â - <a class="external-link" href="http://docs.nvidia.com/cuda/cublas/index.html#cublasgetvector" target="_self" title="">cublasGetVector</a> - transfers data from GPU to CPU memory</p>
+<p class=" ">Â To compile the code using NVCC compiler a "-lcublas" compiler flag has to be specified:</p>
+<pre class=" ">$ module load cuda<br />$ nvcc -lcublas test_cublas.cu -o test_cublas_nvcc</pre>
+<p class=" ">To compile the same code with GCC:</p>
+<pre class=" ">$ module load cuda<br />$ gcc -std=c99 test_cublas.c -o test_cublas_icc -lcublas -lcudart</pre>
+<p class=" ">To compile the same code with Intel compiler:</p>
+<pre class=" ">$ module load cuda intel<br />$ icc -std=c99 test_cublas.c -o test_cublas_icc -lcublas -lcudart</pre>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md b/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
index 2219ce798..11c93502f 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
@@ -42,7 +42,7 @@ the example used is deviceQuery) and run "make" to start the compilation
$ makeÂ
To run the code user can use PBS interactive session to get access to a
-node from qnvidia queue (noteuse your project name with parameter -A
+node from qnvidia queue (note: use your project name with parameter -A
in the qsub command) and execute the binary file
$ qsub -I -q qnvidia -A OPEN-0-0
@@ -56,35 +56,35 @@ K20m is
Detected 1 CUDA Capable device(s)
- Device 0"Tesla K20m"
+ Device 0: "Tesla K20m"
CUDA Driver Version / Runtime Version 5.0 / 5.0
- CUDA Capability Major/Minor version number3.5
- Total amount of global memory4800 MBytes (5032706048 bytes)
- (13) Multiprocessors x (192) CUDA Cores/MP2496 CUDA Cores
- GPU Clock rate706 MHz (0.71 GHz)
- Memory Clock rate2600 MhzÂ
- Memory Bus Width320-bit
- L2 Cache Size1310720 bytes
+ CUDA Capability Major/Minor version number: 3.5
+ Total amount of global memory: 4800 MBytes (5032706048 bytes)
+ (13) Multiprocessors x (192) CUDA Cores/MP: 2496 CUDA Cores
+ GPU Clock rate: 706 MHz (0.71 GHz)
+ Memory Clock rate: 2600 MhzÂ
+ Memory Bus Width: 320-bit
+ L2 Cache Size: 1310720 bytes
Max Texture Dimension Size (x,y,z) 1D=(65536), 2D=(65536,65536), 3D=(4096,4096,4096)
Max Layered Texture Size (dim) x layers 1D=(16384) x 2048, 2D=(16384,16384) x 2048
- Total amount of constant memory65536 bytesÂ
- Total amount of shared memory per block49152 bytes
- Total number of registers available per block65536
- Warp size32
- Maximum number of threads per multiprocessor2048
- Maximum number of threads per block1024Â
- Maximum sizes of each dimension of a block1024 x 1024 x 64
- Maximum sizes of each dimension of a grid2147483647 x 65535 x 65535
- Maximum memory pitch2147483647 bytes
- Texture alignment512 bytes
- Concurrent copy and kernel executionYes with 2 copy engine(s)
- Run time limit on kernelsNo
- Integrated GPU sharing Host MemoryNo
- Support host page-locked memory mappingYes
- Alignment requirement for SurfacesYesÂ
- Device has ECC supportEnabledÂ
- Device supports Unified Addressing (UVA)Yes
- Device PCI Bus ID / PCI location ID2 / 0
+ Total amount of constant memory: 65536 bytesÂ
+ Total amount of shared memory per block: 49152 bytes
+ Total number of registers available per block: 65536
+ Warp size: 32
+ Maximum number of threads per multiprocessor: 2048
+ Maximum number of threads per block: 1024Â
+ Maximum sizes of each dimension of a block: 1024 x 1024 x 64
+ Maximum sizes of each dimension of a grid: 2147483647 x 65535 x 65535
+ Maximum memory pitch: 2147483647 bytes
+ Texture alignment: 512 bytes
+ Concurrent copy and kernel execution: Yes with 2 copy engine(s)
+ Run time limit on kernels: No
+ Integrated GPU sharing Host Memory: No
+ Support host page-locked memory mapping: Yes
+ Alignment requirement for Surfaces: YesÂ
+ Device has ECC support: EnabledÂ
+ Device supports Unified Addressing (UVA): Yes
+ Device PCI Bus ID / PCI location ID: 2 / 0
Compute Mode:Â
< Default (multiple host threads can use ::cudaSetDevice() with device simultaneously) >Â
deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 5.0, CUDA Runtime Version = 5.0, NumDevs = 1, Device0 = Tesla K20mÂ
@@ -203,7 +203,7 @@ standard BLAS routines. Basic description of the library together with
basic performance comparison with MKL can be found
[here](https://developer.nvidia.com/cublas "Nvidia cuBLAS").
-**CuBLAS exampleSAXPY**
+**CuBLAS example: SAXPY**
SAXPY function multiplies the vector x by the scalar alpha and adds it
to the vector y overwriting the latest vector with the result. The
@@ -287,7 +287,7 @@ Code can be pasted in the file and compiled without any modification.
   cublasDestroy(handle);
}
-Â Please notecuBLAS has its own function for data transfers between CPU
+Â Please note: cuBLAS has its own function for data transfers between CPU
and GPU memory:
 -
[cublasSetVector](http://docs.nvidia.com/cuda/cublas/index.html#cublassetvector)
@@ -311,3 +311,7 @@ To compile the same code with Intel compiler:
$ module load cuda intel
$ icc -std=c99 test_cublas.c -o test_cublas_icc -lcublas -lcudart
+
+
+
+
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index 000000000..403806a90
--- /dev/null
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+<h3 class=" ">Access</h3>
+<p>TEAM is available at the following address :Â <a class="external-link" href="http://omics.it4i.cz/team/" target="_self" title="">http://omics.it4i.cz/team/</a></p>
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+<h3 class=" ">Diagnostic component (TEAM)</h3>
+<p class="6Tekstletter">VCF files are scanned by this diagnostic tool for known diagnostic disease-associated variants. When no diagnostic mutation is found, the file can be sent to the disease-causing gene discovery tool to see wheter new disease associated variants can be found.</p>
+<p class="6Tekstletter">TEAM <span>(27)</span> is an intuitive and easy-to-use web tool that fills the gap between the predicted mutations and the final diagnostic in targeted enrichment sequencing analysis. The tool searches for known diagnostic mutations, corresponding to a disease panel, among the predicted patient’s variants. Diagnostic variants for the disease are taken from four databases of disease-related variants (HGMD-public, HUMSAVAR , ClinVar and COSMIC) If no primary diagnostic variant is found, then a list of secondary findings that can help to establish a diagnostic is produced. TEAM also provides with an interface for the definition of and customization of panels, by means of which, genes and mutations can be added or discarded to adjust panel definitions. </p>
+<p class="6Tekstletter"><img alt="Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases." src="images/fig5.png.1" title="fig5.png" class="image-inline" /></p>
+</div>
+<p>Â </p>
+<p align="center" class="6Tekstletter"><b><i>Figure 5. </i></b><i>Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases.</i></p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
index 33d4b8a6c..227075b00 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
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+ <dt>Info</dt>
+ <dd></dd>
+ </dl>
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+ <img width="16" height="16" src="https://docs.it4i.cz/png.png" alt="Obrázek PNG image" />
+ <a href="images/fig1.png/view.html" class="contenttype-image state-missing-value url">Fig 1</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">OMICS MASTER solution overview. Data is produced in the external labs and comes to IT4I (represented by the blue dashed line). The data pre-processor converts raw data into a list of variants and annotations for each sequenced patient. These lists files together with primary and secondary (alignment) data files are stored in IT4I sequence DB and uploaded to the discovery (candidate priorization) or diagnostic component where they can be analysed directly by the user that produced them, depending of the experimental design carried out.</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+ <img width="16" height="16" src="https://docs.it4i.cz/png.png" alt="Obrázek PNG image" />
+ <a href="images/fig2.png/view.html" class="contenttype-image state-missing-value url">fig2.png</a>
+ </span>
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+
+
+
+
+
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+
+ </dt>
+
+ <dd>
+ <span class="description">FASTQ file.</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+ <img width="16" height="16" src="https://docs.it4i.cz/png.png" alt="Obrázek PNG image" />
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+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">Mandatory fields in the SAM format.</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+ <img width="16" height="16" src="https://docs.it4i.cz/png.png" alt="Obrázek PNG image" />
+ <a href="images/fig3.png/view.html" class="contenttype-image state-missing-value url">fig3.png</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">SAM format file. The â€@SQ’ line in the header section gives the order of reference sequences. Notably, r001 is the name of a read pair. According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is the second read in the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to 37 on the reverse strand (32). Read r002 has three soft-clipped (unaligned) bases. The coordinate shown in SAM is the position of the first aligned base. The CIGAR string for this alignment contains a P (padding) operation which correctly aligns the inserted sequences. Padding operations can be absent when an aligner does not support multiple sequence alignment. The last six bases of read r003 map to position 9, and the first five to position 29 on the reverse strand. The hard clipping operation H indicates that the clipped sequence is not present in the sequence field. The NM tag gives the number of mismatches. Read r004 is aligned across an intron, indicated by the N operation.</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+ <img width="16" height="16" src="https://docs.it4i.cz/png.png" alt="Obrázek PNG image" />
+ <a href="images/fig4.png/view.html" class="contenttype-image state-missing-value url">fig4.png</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">a) Example of valid VCF. The header lines ##fileformat and #CHROM are mandatory, the rest is optional but strongly recommended. Each line of the body describes variants present in the sampled population at one genomic position or region. All alternate alleles are listed in the ALT column and referenced from the genotype fields as 1-based indexes to this list; the reference haplotype is designated as 0. For multiploid data, the separator indicates whether the data are phased (|) or unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in this figure occur on the same chromosome in SAMPLE1. The first data line shows an example of a deletion (present in SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the second line shows a SNP and an insertion; the third a SNP; the fourth a large structural variant described by the annotation in the INFO column, the coordinate is that of the base before the variant. (b–f ) Alignments and VCF representations of different sequence variants: SNP, insertion, deletion, replacement, and a large deletion. The REF columns shows the reference bases replaced by the haplotype in the ALT column. The coordinate refers to the first reference base. (g) Users are advised to use simplest representation possible and lowest coordinate in cases where the position is ambiguous.</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+ <img width="16" height="16" src="https://docs.it4i.cz/png.png" alt="Obrázek PNG image" />
+ <a href="images/fig5.png/view.html" class="contenttype-image state-missing-value url">fig5.png</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">Interface of the application. Panels for defining targeted regions of interest can be set up by just drag and drop known disease genes or disease definitions from the lists. Thus, virtual panels can be interactively improved as the knowledge of the disease increases.</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+ <img width="16" height="16" src="https://docs.it4i.cz/png.png" alt="Obrázek PNG image" />
+ <a href="images/fig6.png/view.html" class="contenttype-image state-missing-value url">fig6.png</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">Web interface to the prioritization tool. This figure shows the interface of the web tool for candidate gene prioritization with the filters available. The tool includes a genomic viewer (Genome Maps 30) that enables the representation of the variants in the corresponding genomic coordinates.</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+ <img width="16" height="16" src="https://docs.it4i.cz/png.png" alt="Obrázek PNG image" />
+ <a href="images/fig7.png/view.html" class="contenttype-image state-missing-value url">fig7.png</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">TEAM upload panel. Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts.</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+ <img width="16" height="16" src="https://docs.it4i.cz/png.png" alt="Obrázek PNG image" />
+ <a href="images/fig7x.png/view.html" class="contenttype-image state-missing-value url">fig7x.png</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">The panel manager. The elements used to define a panel are (A) disease terms, (B) diagnostic mutations and (C) genes. Arrows represent actions that can be taken in the panel manager. Panels can be defined by using the known mutations and genes of a particular disease. This can be done by dragging them to the Primary Diagnostic box (action D). This action, in addition to defining the diseases in the Primary Diagnostic box, automatically adds the corresponding genes to the Genes box. The panels can be customized by adding new genes (action F) or removing undesired genes (action G). New disease mutations can be added independently or associated to an already existing disease term (action E). Disease terms can be removed by simply dragging themback (action H).</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+ <img width="16" height="16" src="https://docs.it4i.cz/png.png" alt="Obrázek PNG image" />
+ <a href="images/fig8.png/view.html" class="contenttype-image state-missing-value url">fig8.png</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description. </span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+ <img width="16" height="16" src="https://docs.it4i.cz/png.png" alt="Obrázek PNG image" />
+ <a href="images/fig9.png/view.html" class="contenttype-image state-missing-value url">fig9.png</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">This picture shows all the information associated to the variants. If a variant has an associated phenotype we could see it in the last column. In this case, the variant 7:132481242 C>T is associated to the phenotype: large intestine tumor.</span>
+ </dd>
+
+
+
+ </dl>
+
+
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig1.png/image_view_fullscreen.html b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig1.png/image_view_fullscreen.html
new file mode 100644
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig1.png/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig1.png/view.html
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig2.png/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig2.png/view.html
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+ SAM format file. The â€@SQ’ line in the header section gives the order of reference sequences. Notably, r001 is the name of a read pair. According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is the second read in the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to 37 on the reverse strand (32). Read r002 has three soft-clipped (unaligned) bases. The coordinate shown in SAM is the position of the first aligned base. The CIGAR string for this alignment contains a P (padding) operation which correctly aligns the inserted sequences. Padding operations can be absent when an aligner does not support multiple sequence alignment. The last six bases of read r003 map to position 9, and the first five to position 29 on the reverse strand. The hard clipping operation H indicates that the clipped sequence is not present in the sequence field. The NM tag gives the number of mismatches. Read r004 is aligned across an intron, indicated by the N operation.
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig4.png/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig4.png/view.html
new file mode 100644
index 000000000..44913678e
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig4.png/view.html
@@ -0,0 +1,1119 @@
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig5.png/image_view_fullscreen.html b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig5.png/image_view_fullscreen.html
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig5.png/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig5.png/view.html
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig7x.png/view.html b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig7x.png/view.html
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+ The human NGS data processing solution
+
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+ <h2 class=" ">Introduction</h2>
+<p>The scope of this OMICS MASTER solution is restricted to human genomics research (disease causing gene discovery in whole human genome or exome) or diagnosis (panel sequencing), although it could be extended in the future to other usages.</p>
+<p>The pipeline inputs the raw data produced by the sequencing machines and undergoes a processing procedure that consists on a quality control, the mapping and variant calling steps that result in a file containing the set of variants in the sample. From this point, the prioritization component or the diagnostic component can be launched. </p>
+<p><img alt="OMICS MASTER solution overview. Data is produced in the external labs and comes to IT4I (represented by the blue dashed line). The data pre-processor converts raw data into a list of variants and annotations for each sequenced patient. These lists files together with primary and secondary (alignment) data files are stored in IT4I sequence DB and uploaded to the discovery (candidate priorization) or diagnostic component where they can be analysed directly by the user that produced them, depending of the experimental design carried out." src="images/fig1.png" title="Fig 1" class="image-inline" /></p>
+<p align="center" style="text-align: left; "><b><i>Figure 1.</i></b><i> OMICS MASTER solution overview. D</i><i>ata is produced in the external labs and comes to IT4I (represented by the blue dashed line). The data pre-processor converts raw data into a list of variants and annotations for each sequenced patient. These lists files together with primary and secondary (alignment) data files are stored in IT4I sequence DB and uploaded to the discovery (candidate prioritization) or diagnostic component where they can be analyzed directly by the user that produced them, depending of the experimental design carried out</i>.<span style="text-align: left; ">Â </span></p>
+<p>Typical genomics pipelines are composed by several components that need to be launched manually. The advantage of OMICS MASTER pipeline is that all these components are invoked sequentially in an automated way.</p>
+<p>OMICS MASTER pipeline inputs a FASTQ file and outputs an enriched VCF file. This pipeline is able to queue all the jobs to PBS by only launching a process taking all the necessary input files and creates the intermediate and final folders</p>
+<p>Let’s see each of the OMICS MASTER solution components:</p>
+<h2 class=" ">Components</h2>
+<div>
+<h3 class=" ">Processing</h3>
+<p class="Default">This component is composed by a set of programs that carry out quality controls, alignment, realignment, variant calling and variant annotation. It turns raw data from the sequencing machine into files containing lists of variants (VCF) that once annotated, can be used by the following components (discovery and diagnosis).</p>
+<p class="Default">We distinguish three types of sequencing instruments: bench sequencers (MySeq, IonTorrent, and Roche Junior, although this last one is about being discontinued), which produce relatively Genomes in the clinic</p>
+<p class="Default">low throughput (tens of million reads), and high end sequencers, which produce high throughput (hundreds of million reads) among which we have Illumina HiSeq 2000 (and new models) and SOLiD. All of them but SOLiD produce data in sequence format. SOLiD produces data in a special format called colour space that require of specific software for the mapping process. Once the mapping has been done, the rest of the pipeline is identical. Anyway, SOLiD is a technology which is also about being discontinued by the manufacturer so, this type of data will be scarce in the future.</p>
+<h4 class=" ">Quality control, preprocessing and statistics for FASTQ</h4>
+<p class="6Tekstletter"><b>Component:</b><span> Hpg-Fastq & FastQC.</span></p>
+<p class="6Tekstletter">These steps are carried out over the original FASTQ file with optimized scripts and includes the following steps: sequence cleansing, estimation of base quality scores, elimination of duplicates and statistics.</p>
+<p class="6Tekstletter"><b>Input: </b>FASTQ file.</p>
+<p class="6Tekstletter"><b>Output: </b>FASTQ file plus an HTML file containing statistics on the data. </p>
+<p class="exclamation"><strong>FASTQ format <br /></strong><span>It represents the nucleotide sequence and its corresponding quality scores.<br /><br /></span><strong><img alt="FASTQ file." src="images/fig2.png" title="fig2.png" class="image-inline" /><br /><b><i>Figure 2.</i></b></strong><i> FASTQ file.</i><strong><br /></strong></p>
+<h4>Mapping</h4>
+<p class="6Tekstletter"><b>Component: </b>Hpg-aligner.<b></b></p>
+<p class="6Tekstletter">Sequence reads are mapped over the human reference genome. SOLiD reads are not covered by this solution; they should be mapped with specific software (among the few available options, SHRiMP seems to be the best one). For the rest of NGS machine outputs we use HPG Aligner. HPG-Aligner is an innovative solution, based on a combination of mapping with BWT and local alignment with Smith-Waterman (SW), that drastically increases mapping accuracy (97% versus 62-70% by current mappers, in the most common scenarios). This proposal provides a simple and fast solution that maps almost all the reads, even those containing a high number of mismatches or indels.</p>
+<p class="6Tekstletter"><b>Input:</b> FASTQ file.</p>
+<p class="6Tekstletter"><b>Output: </b>Aligned file in BAM format.<b></b></p>
+<p class=" "><strong>Sequence Alignment/Map (SAM)</strong><br /><br /><span>It is a human readable tab-delimited format in which each read and its alignment is represented on a single line. The format can represent unmapped reads, reads that are mapped to unique locations, and reads that are mapped to multiple locations.<br /><br /></span><span>The SAM format </span><sup>(1)</sup><span> consists of one header section and one alignment section. The lines in the header section start with character â€@’, and lines in the alignment section do not. All lines are TAB delimited.<br /><br /><span>In SAM, each alignment line has 11 mandatory fields and a variable number of optional fields. The mandatory fields are briefly described in Table 1. They must be present but their value can be a </span></span>â€*’<span><span> or a zero (depending on the field) if the corresponding information is unavailable.</span>  </span></p>
+<div align="center">
+<table class="plain">
+<tbody>
+<tr>
+<td>
+<p><b>No.</b></p>
+</td>
+<td>
+<p><b>Name</b></p>
+</td>
+<td>
+<p><b>Description</b></p>
+</td>
+</tr>
+<tr>
+<td>
+<p>1</p>
+</td>
+<td>
+<p>QNAME</p>
+</td>
+<td>
+<p>Query NAME of the read or the read pair</p>
+</td>
+</tr>
+<tr>
+<td>
+<p>2</p>
+</td>
+<td>
+<p>FLAG</p>
+</td>
+<td>
+<p>Bitwise FLAG (pairing,strand,mate strand,etc.)</p>
+</td>
+</tr>
+<tr>
+<td>
+<p>3</p>
+</td>
+<td>
+<p>RNAMEÂ </p>
+</td>
+<td>
+<p>Reference sequence NAME</p>
+</td>
+</tr>
+<tr>
+<td>
+<p>4</p>
+</td>
+<td>
+<p>POSÂ </p>
+</td>
+<td>
+<p>1-Based  leftmost POSition of clipped alignment</p>
+</td>
+</tr>
+<tr>
+<td>
+<p>5</p>
+</td>
+<td>
+<p>MAPQÂ </p>
+</td>
+<td>
+<p>MAPping Quality (Phred-scaled)</p>
+</td>
+</tr>
+<tr>
+<td>
+<p>6</p>
+</td>
+<td>
+<p>CIGARÂ </p>
+</td>
+<td>
+<p>Extended CIGAR string (operations:MIDNSHP)</p>
+</td>
+</tr>
+<tr>
+<td>
+<p>7</p>
+</td>
+<td>
+<p>MRNMÂ </p>
+</td>
+<td>
+<p>Mate REference NaMe ('=^' if same RNAME)</p>
+</td>
+</tr>
+<tr>
+<td>
+<p>8</p>
+</td>
+<td>
+<p>MPOSÂ </p>
+</td>
+<td>
+<p>1-Based leftmost Mate POSition</p>
+</td>
+</tr>
+<tr>
+<td>
+<p>9</p>
+</td>
+<td>
+<p>ISIZEÂ </p>
+</td>
+<td>
+<p>Inferred Insert SIZEÂ </p>
+</td>
+</tr>
+<tr>
+<td>
+<p>10</p>
+</td>
+<td>
+<p>SEQÂ </p>
+</td>
+<td>
+<p>Query SEQuence on the same strand as the reference</p>
+</td>
+</tr>
+<tr>
+<td>
+<p>11</p>
+</td>
+<td>
+<p>QUALÂ </p>
+</td>
+<td>
+<p>Query QUALity (ASCII-33=Phred base quality)</p>
+</td>
+</tr>
+</tbody>
+</table>
+</div>
+<p class=" "><span><br /><br /></span><b><i>Table 1.</i></b><i> Mandatory fields in the SAM format.<br /><span><br />The standard CIGAR description of pairwise alignment defines three operations: â€M’ for match/mismatch, â€I’ for insertion compared with the reference and â€D’ for deletion. The extended CIGAR proposed in SAM added four more operations: â€N’ for skipped bases on the reference, â€S’ for soft clipping, â€H’ for hard clipping and â€P’ for padding. These support splicing, clipping, multi-part and padded alignments. Figure 3 shows examples of CIGAR strings for different types of alignments. <br /><br /><img alt="SAM format file. The â€@SQ’ line in the header section gives the order of reference sequences. Notably, r001 is the name of a read pair. According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is the second read in the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to 37 on the reverse strand (32). Read r002 has three soft-clipped (unaligned) bases. The coordinate shown in SAM is the position of the first aligned base. The CIGAR string for this alignment contains a P (padding) operation which correctly aligns the inserted sequences. Padding operations can be absent when an aligner does not support multiple sequence alignment. The last six bases of read r003 map to position 9, and the first five to position 29 on the reverse strand. The hard clipping operation H indicates that the clipped sequence is not present in the sequence field. The NM tag gives the number of mismatches. Read r004 is aligned across an intron, indicated by the N operation." src="images/fig3.png" title="fig3.png" class="image-inline" /><br /><b><i><br />Figure 3.</i></b><i> SAM format file. The â€@SQ’ line in the header section gives the order of reference sequences. Notably, r001 is the name of a read pair. According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is the second read in the pair (128) and regarded as properly paired (1 + 2); its mate is mapped to 37 on the reverse strand (32). Read r002 has three soft-clipped (unaligned) bases. The coordinate shown in SAM is the position of the first aligned base. The CIGAR string for this alignment contains a P (padding) operation which correctly aligns the inserted sequences. Padding operations can be absent when an aligner does not support multiple sequence alignment. The last six bases of read r003 map to position 9, and the first five to position 29 on the reverse strand. The hard clipping operation H indicates that the clipped sequence is not present in the sequence field. The NM tag gives the number of mismatches. Read r004 is aligned across an intron, indicated by the N operation.</i></span></i></p>
+<p class=" "><strong>Binary Alignment/Map (BAM)</strong><br /><br /><span>BAM is the binary representation of SAM and keeps exactly the same information as SAM. BAM uses lossless compression to reduce the size of the data by about 75% and provides an indexing system that allows reads that overlap a region of the genome to be retrieved and rapidly traversed. </span></p>
+<h4>Quality control, preprocessing and statistics for BAM</h4>
+<p class="6Tekstletter"><b>Component: </b>Hpg-Fastq & FastQC. Some features:</p>
+<ul>
+<li>Quality control: % reads with N errors, % reads with multiple mappings, strand bias, paired-end insert, ...</li>
+<li>Filtering: by number of errors, number of hits, …
+<ul>
+<li>Comparator: stats, intersection, ...</li>
+</ul>
+</li>
+</ul>
+<p class="6Tekstletter"><b>Input: </b>BAM file.</p>
+<p class="6Tekstletter"><b>Output: </b>BAM file plus an HTML file containing statistics. </p>
+<h4>Variant Calling</h4>
+<p><b>Component:</b> GATK.</p>
+<p>Identification of single nucleotide variants and indels on the alignments is performed using the Genome Analysis Toolkit (GATK). GATK <sup>(2)</sup> is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.</p>
+<p><b>Input:</b> BAM</p>
+<p><b>Output:</b> VCF</p>
+<p class=" "><strong>Variant Call Format (VCF)</strong><br /><br /><span>VCF </span><sup>(3)</sup><span> is a standardized format for storing the most prevalent types of sequence variation, including SNPs, indels and larger structural variants, together with rich annotations. The format was developed with the primary intention to represent human genetic variation, but its use is not restricted </span><span>to diploid genomes and can be used in different contexts as well. Its flexibility and user extensibility allows representation of a wide variety of genomic variation with respect to a single reference sequence.<br /><br /></span>A VCF file consists of a header section and a data section. The header contains an arbitrary number of metainformation lines, each starting with characters â€##’, and a TAB delimited field definition line, starting with a single â€#’ character. The meta-information header lines provide a standardized description of tags and annotations used in the data section. The use of meta-information allows the information stored within a VCF file to be tailored to the dataset in question. It can be also used to provide information about the means of file creation, date of creation, version of the reference sequence, software used and any other information relevant to the history of the file. The field definition line names eight mandatory columns, corresponding to data columns representing the chromosome (CHROM), a 1-based position of the start of the variant (POS), unique identifiers of the variant (ID), the reference allele (REF), a comma separated list of alternate non-reference alleles (ALT), a phred-scaled quality score (QUAL), site filtering information (FILTER) and a semicolon separated list of additional, user extensible annotation (INFO). In addition, if samples are present in the file, the mandatory header columns are followed by a FORMAT column and an arbitrary number of sample IDs that define the samples included in the VCF file. The FORMAT column is used to define the information contained within each subsequent genotype column, which consists of a colon separated list of fields. For example, the FORMAT field GT:GQ:DP in the fourth data entry of Figure 1a indicates that the subsequent entries contain information regarding the genotype, genotype quality and read depth for each sample. All data lines are TAB delimited and the number of fields in each data line must match the number of fields in the header line. It is strongly recommended that all annotation tags used are declared in the VCF header section.<br /><br /><img alt="a) Example of valid VCF. The header lines ##fileformat and #CHROM are mandatory, the rest is optional but strongly recommended. Each line of the body describes variants present in the sampled population at one genomic position or region. All alternate alleles are listed in the ALT column and referenced from the genotype fields as 1-based indexes to this list; the reference haplotype is designated as 0. For multiploid data, the separator indicates whether the data are phased (|) or unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in this figure occur on the same chromosome in SAMPLE1. The first data line shows an example of a deletion (present in SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the second line shows a SNP and an insertion; the third a SNP; the fourth a large structural variant described by the annotation in the INFO column, the coordinate is that of the base before the variant. (b–f ) Alignments and VCF representations of different sequence variants: SNP, insertion, deletion, replacement, and a large deletion. The REF columns shows the reference bases replaced by the haplotype in the ALT column. The coordinate refers to the first reference base. (g) Users are advised to use simplest representation possible and lowest coordinate in cases where the position is ambiguous." src="images/fig4.png" title="" class="image-inline" /><br /><b><br />Figure 4.</b><span> (a) Example of valid VCF. The header lines ##fileformat and #CHROM are mandatory, the rest is optional but strongly recommended. Each line of the body describes variants present in the sampled population at one genomic position or region. All alternate alleles are listed in the ALT column and referenced from the genotype fields as 1-based indexes to this list; the reference haplotype is designated as 0. For multiploid data, the separator indicates whether the data are phased (|) or unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in this figure occur on the same chromosome in SAMPLE1. The first data line shows an example of a deletion (present in SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the second line shows a SNP and an insertion; the third a SNP; the fourth a large structural variant described by the annotation in the INFO column, the coordinate is that of the base before the variant. (b–f ) Alignments and VCF representations of different sequence variants: SNP, insertion, deletion, replacement, and a large deletion. The REF columns shows the reference bases replaced by the haplotype in the ALT column. The coordinate refers to the first reference base. (g) Users are advised to use simplest representation possible and lowest coordinate in cases where the position is ambiguous.</span></p>
+<h3 class=" "><span>Annotating</span></h3>
+<p><b>Component:</b> HPG-Variant</p>
+<p>The functional consequences of every variant found are then annotated using the HPG-Variant software, which extracts from CellBase<b>, </b>the Knowledge database, all the information relevant on the predicted pathologic effect of the variants.</p>
+<p>VARIANT (VARIant Analysis Tool) <sup>(4)</sup> reports information on the variants found that include consequence type and annotations taken from different databases and repositories (SNPs and variants from dbSNP and 1000 genomes, and disease-related variants from the Genome-Wide Association Study (GWAS) catalog, Online Mendelian Inheritance in Man (OMIM), Catalog of Somatic Mutations in Cancer (COSMIC) mutations, etc. VARIANT also produces a rich variety of annotations that include information on the regulatory (transcription factor or miRNAbinding sites, etc.) or structural roles, or on the selective pressures on the sites affected by the variation. This information allows extending the conventional reports beyond the coding regions and expands the knowledge on the contribution of non-coding or synonymous variants to the phenotype studied.</p>
+<p><b>Input:</b> VCF</p>
+<p><b>Output:</b> The output of this step is the Variant Calling Format (VCF) file, which contains changes with respect to the reference genome with the corresponding QC and functional annotations.</p>
+<h4>CellBase</h4>
+<p>CellBase<sup>(5)</sup>Â is a relational database integrates biological information from different sources and includes:</p>
+<p><b>Core features: </b></p>
+<p>We took genome sequences, genes, transcripts, exons, cytobands or cross references (xrefs) identifiers (IDs)Â <span>from Ensembl </span><sup>(6)</sup><span>. Protein information including sequences, xrefs or protein features (natural variants, mutagenesis sites, post-translational modifications, etc.) were imported from UniProt </span><sup>(7)</sup><span>.</span></p>
+<p><b>Regulatory: </b></p>
+<p>CellBase imports miRNA from miRBase <sup>(8)</sup>; curated and non-curated miRNA targets from miRecords <sup>(9)</sup>, <span>miRTarBase </span><sup>(10)</sup><span>, TargetScan</span><sup>(11)</sup><span> and microRNA.org </span><sup>(12)</sup><span> and CpG islands and conserved regions from the UCSC database </span><sup>(13)</sup><span>.</span><span> </span></p>
+<p><b>Functional annotation</b></p>
+<p>OBO Foundry <sup>(14)</sup> develops many biomedical ontologies that are implemented in OBO format. We designed a SQL schema to store these OBO ontologies and >30 ontologies were imported. OBO ontology term annotations were taken from Ensembl <sup>(6)</sup>. InterPro <sup>(15)</sup> annotations were also imported.</p>
+<p><b>Variation</b></p>
+<p>CellBase includes SNPs from dbSNP <sup>(16)</sup>; SNP population frequencies from HapMap <sup>(17)</sup>, 1000 genomes project <sup>(18)</sup> and Ensembl <sup>(6)</sup>; phenotypically annotated SNPs were imported from NHRI GWAS Catalog <sup>(19)</sup>,<sup>Â </sup><span>HGMD </span><sup>(20)</sup><span>, Open Access GWAS Database </span><sup>(21)</sup><span>, UniProt </span><sup>(7)</sup><span> and OMIM </span><sup>(22)</sup><span>; mutations from COSMICÂ </span><sup>(23)</sup><span> and structural variations from Ensembl </span><sup>(6)</sup><span>.</span><span>Â </span></p>
+<p><b>Systems biology</b></p>
+<p>We also import systems biology information like interactome information from IntAct <sup>(24)</sup>. Reactome <sup>(25)</sup><span> stores pathway and interaction information in BioPAX </span><sup>(26)</sup><span> format. BioPAX data exchange format </span><span>enables the integration of diverse pathway resources. We successfully solved the problem of storing data released in BioPAX format into a SQL relational schema, which allowed us importing Reactome in CellBase.</span></p>
+<div>
+<h3 class=" "><a href="diagnostic-component-team.html" title="" target="_self" class="internal-link">Diagnostic component (TEAM)</a></h3>
+<h3 class=" "><a href="priorization-component-bierapp.html" title="" target="_self" class="internal-link"> Priorization component (BiERApp)</a></h3>
+</div>
+<h2 class=" ">Usage</h2>
+<p>First of all, we should load <span class="monospace">ngsPipeline</span> module:</p>
+<pre class=" ">$ module load ngsPipeline</pre>
+<p>This command will load <span class="monospace">python/2.7.5</span> module and all the required modules (<span class="monospace">hpg-aligner</span>, <span class="monospace">gatk</span>, etc)</p>
+<p><span> If we launch ngsPipeline with â€-h’, we will get the usage help: </span></p>
+<pre class=" "><span>$ ngsPipeline -h<br />Usage: ngsPipeline.py [-h] -i INPUT -o OUTPUT -p PED --project PROJECT --queue <br />           QUEUE [--stages-path STAGES_PATH] [--email EMAIL]<br /> [--prefix PREFIX] [-s START] [-e END] --log<br /><br />Python pipeline<br /><br />optional arguments:<br /> -h, --help       show this help message and exit<br /> -i INPUT, --input INPUT<br /> -o OUTPUT, --output OUTPUT<br />            Output Data directory<br /> -p PED, --ped PED   Ped file with all individuals<br /> --project PROJECT   Project Id<br /> --queue QUEUE     Queue Id<br /> --stages-path STAGES_PATH<br />            Custom Stages path<br /> --email EMAIL     Email<br /> --prefix PREFIX    Prefix name for Queue Jobs name<br /> -s START, --start START<br />            Initial stage<br /> -e END, --end END   Final stage<br /> --log         Log to file<br /></span></pre>
+<p>Â </p>
+<p>Let us see a brief description of the arguments:</p>
+<p>Â Â Â Â Â <i>-h --help</i>. Show the help.</p>
+<p>     <i>-i, --input. </i>The input data directory. This directory must to have a special structure. We have to create one folder per sample (with the same name). These folders will host the fastq files. These fastq files must have the following pattern “sampleName” + “_” + “1 or 2” + “.fq”. 1 for the first pair (in paired-end sequences), and 2 for the second one.</p>
+<p>Â Â Â Â Â <i>-o , --output. </i>The output folder. This folder will contain all the intermediate and final folders. When the pipeline will be executed completely, we could remove the intermediate folders and keep only the final one (with the VCF file containing all the variants)</p>
+<p>Â Â Â Â Â <i>-p , --ped</i>. The ped file with the pedigree. This file contains all the sample names. These names must coincide with the names of the input folders. If our input folder contains more samples than the .ped file, the pipeline will use only the samples from the .ped file.</p>
+<p>Â Â Â Â Â <i>--email.</i> Email for PBS notifications.</p>
+<p>Â Â Â Â Â <i>--prefix. </i>Prefix for PBS Job names.</p>
+<p>Â Â Â Â <i>-s, --start & -e, --end. </i>Â Initial and final stage. If we want to launch the pipeline in a specific stage we must use -s. If we want to end the pipeline in a specific stage we must use -e.</p>
+<p>Â Â Â Â Â <i>--log</i>. Using log argument NGSpipeline will prompt all the logs to this file.</p>
+<p><span>    </span><i>--project</i><span>. Project ID of your supercomputer allocation. </span></p>
+<p><span>Â Â Â Â <i>--queue</i>. <a href="../../resource-allocation-and-job-execution/introduction.html" title="" target="_self" class="internal-link">Queue</a> to run the jobs in.</span></p>
+<p>Â <span>Input, output and ped arguments are mandatory. If the output folder does not exist, the pipeline will create it.</span></p>
+<h2 class=" "><span>Examples</span></h2>
+<p>This is an example usage of NGSpipeline:</p>
+<p>We have a folder with the following structure in <span><span class="monospace">/apps/bio/omics/1.0/sample_data/</span>Â </span><span>:</span></p>
+<pre class=" ">/apps/bio/omics/1.0/sample_data<br />└── data<br /> ├── file.ped<br /> ├── sample1<br /> │  ├── sample1_1.fq<br /> │  └── sample1_2.fq<br /> └── sample2<br /> ├── sample2_1.fq<br /> └── sample2_2.fq</pre>
+<p>The ped file (<span class="monospace">file.ped</span>) contains the following info:<span>Â </span></p>
+<pre class=" ">#family_ID sample_ID parental_ID maternal_ID sex phenotype <br />FAM sample_A 0 0 1 1 <br />FAM sample_B 0 0 2 2 </pre>
+<p>Now, lets load the NGSPipeline module and copy the sample data to a <a href="../../storage.html" title="" target="_self" class="internal-link">scratch directory</a> :</p>
+<pre class=" ">$ module load ngsPipeline<br />$ mkdir -p /scratch/$USER/omics/results<br />$ cp -r /apps/bio/omics/1.0/sample_data /scratch/$USER/omics/</pre>
+<p class=" ">Now, we can launch the pipeline (replace OPEN-0-0 with your Project ID) :</p>
+<pre class=" ">$ ngsPipeline -i /scratch/$USER/omics/sample_data/data -o /scratch/$USER/omics/results -p /scratch/$USER/omics/sample_data/data/file.ped --project OPEN-0-0 --queue qprod</pre>
+<p>This command submits the processing <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_self" class="internal-link">jobs to the queue</a>. </p>
+<p>If we want to re-launch the pipeline from stage 4 until stage 20 we should use the next command:</p>
+<pre class=" ">$ ngsPipeline -i /scratch/$USER/omics/sample_data/data -o /scratch/$USER/omics/results -p /scratch/$USER/omics/sample_data/data/file.ped -s 4 -e 20 --project OPEN-0-0 --queue qprod </pre>
+<h2 class=" "><span>Details on the pipeline</span></h2>
+<p><span>The pipeline calls the following tools:</span></p>
+<ul>
+<li><span><a class="external-link" href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" target="_self" title="">fastqc</a>, a<span>Â quality control tool for high throughput sequence data.</span></span></li>
+<li><span><a class="external-link" href="https://www.broadinstitute.org/gatk/" target="_self" title="">gatk</a>, <span>The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.</span></span></li>
+<li><span><a class="external-link" href="http://wiki.opencb.org/projects/hpg/doku.php?id=aligner:downloads" target="_self" title="">hpg-aligner</a>, <span>HPG Aligner has been designed to align short and long reads with high sensitivity, therefore any number of mismatches or indels are allowed. HPG Aligner implements and combines two well known algorithms: </span><em>Burrows-Wheeler Transform</em><span> (BWT) to speed-up mapping high-quality reads, and </span><em>Smith-Waterman</em><span> (SW) to increase sensitivity when reads cannot be mapped using BWT.</span></span></li>
+<li><span><span><span><a class="external-link" href="http://docs.bioinfo.cipf.es/projects/fastqhpc/wiki" target="_self" title="">hpg-fastq</a>, <span> a quality control tool for high throughput sequence data.</span></span></span></span></li>
+<li><span><span><span><span><a class="external-link" href="http://wiki.opencb.org/projects/hpg/doku.php?id=variant:downloads" target="_self" title="">hpg-variant</a>, <span>The HPG Variant suite is an ambitious project aimed to provide a complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics. It is being implemented using High Performance Computing technologies to provide the best performance possible.</span></span></span></span></span></li>
+<li><span><span><span><span><a class="external-link" href="http://picard.sourceforge.net/" target="_self" title="">picard</a>, <span>Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (HTSJDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.</span></span></span></span></span></li>
+<li><span><span><span><span><a class="external-link" href="http://samtools.sourceforge.net/samtools-c.shtml" target="_self" title="">samtools</a>, <span>SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.</span></span></span></span></span></li>
+<li><span><span><span><span><span><a class="external-link" href="http://snpeff.sourceforge.net/" target="_self" title="">snpEff</a>, <span>Genetic variant annotation and effect prediction toolbox.</span></span></span></span></span></span></li>
+</ul>
+<div></div>
+<div>This listing show which tools are used in each step of the pipeline :</div>
+<ul></ul>
+<ul>
+<li><span>stage-00: fastqc</span></li>
+<li><span>stage-01: hpg_fastq</span></li>
+<li><span>stage-02: fastqc</span></li>
+<li><span>stage-03: hpg_aligner and samtools</span></li>
+<li><span>stage-04: samtools</span></li>
+<li><span>stage-05: samtools</span></li>
+<li><span>stage-06: fastqc</span></li>
+<li><span>stage-07: picard</span></li>
+<li><span>stage-08: fastqc</span></li>
+<li><span>stage-09: picard</span></li>
+<li><span>stage-10: gatk</span></li>
+<li><span>stage-11: gatk</span></li>
+<li><span>stage-12: gatk</span></li>
+<li><span>stage-13: gatk</span></li>
+<li><span>stage-14: gatk</span></li>
+<li><span>stage-15: gatk</span></li>
+<li><span>stage-16: samtools</span></li>
+<li><span>stage-17: samtools</span></li>
+<li><span>stage-18: fastqc</span></li>
+<li><span>stage-19: gatk</span></li>
+<li><span>stage-20: gatk</span></li>
+<li><span>stage-21: gatk</span></li>
+<li><span>stage-22: gatk</span></li>
+<li><span>stage-23: gatk</span></li>
+<li><span>stage-24: hpg-variant</span></li>
+<li><span>stage-25: hpg-variant</span></li>
+<li><span>stage-26: snpEff</span></li>
+<li><span>stage-27: snpEff</span></li>
+<li><span>stage-28: hpg-variant</span></li>
+</ul>
+<h2 class=" "><span>Interpretation</span></h2>
+<p>The output folder contains all the subfolders with the intermediate data. This folder contains the final VCF with all the variants. This file can be uploaded into <a href="diagnostic-component-team.html" title="" target="_self" class="internal-link">TEAM</a> by using the VCF file button. It is important to note here that the entire management of the VCF file is local: no patient’s sequence data is sent over the Internet thus avoiding any problem of data privacy or confidentiality.</p>
+<p><span><img alt="TEAM upload panel. Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts." src="images/fig7.png" title="fig7.png" class="image-inline" /></span></p>
+<p align="center" style="text-align: left; "><b><i>Figure 7</i></b>. <i>TEAM upload panel.</i> <i>Once the file has been uploaded, a panel must be chosen from the Panel<b> </b>list. Then, pressing the Run button the diagnostic process starts.</i></p>
+<p>Once the file has been uploaded, a panel must be chosen from the Panel list. Then, pressing the Run button the diagnostic process starts. TEAM searches first for known diagnostic mutation(s) taken from four databases: HGMD-public <sup>(20)</sup>, <a class="external-link" href="http://www.uniprot.org/docs/humsavar" target="_self" title="">HUMSAVAR</a>, ClinVar <sup>(29)</sup> and COSMIC <sup>(23)</sup>.</p>
+<p><img alt="The panel manager. The elements used to define a panel are (A) disease terms, (B) diagnostic mutations and (C) genes. Arrows represent actions that can be taken in the panel manager. Panels can be defined by using the known mutations and genes of a particular disease. This can be done by dragging them to the Primary Diagnostic box (action D). This action, in addition to defining the diseases in the Primary Diagnostic box, automatically adds the corresponding genes to the Genes box. The panels can be customized by adding new genes (action F) or removing undesired genes (action G). New disease mutations can be added independently or associated to an already existing disease term (action E). Disease terms can be removed by simply dragging themback (action H)." src="images/fig7x.png" title="fig7x.png" class="image-inline" /></p>
+<p align="center" style="text-align: left; "><b><i>Figure 7.</i></b><i> The panel manager. The elements used to define a panel are (<b>A</b>) disease terms, (<b>B</b>) diagnostic mutations and (<b>C</b>) genes. Arrows represent actions that can be taken in the panel manager. Panels can be defined by using the known mutations and genes of a particular disease. This can be done by dragging them to the <b>Primary Diagnostic </b>box (action <b>D</b>). This action, in addition to defining the diseases in the <b>Primary Diagnostic </b>box, automatically adds the corresponding genes to the <b>Genes </b>box. The panels can be customized by adding new genes (action <b>F</b>) or removing undesired genes (action <b>G</b>). New disease mutations can be added independently or associated to an already existing disease term (action <b>E</b>). Disease terms can be removed by simply dragging them </i><i>back (action <b>H</b>).</i></p>
+<p>For variant discovering/filtering we should upload the VCF file into BierApp by using the following form:</p>
+<p align="center" style="text-align: left; "><i><img alt="BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description. " src="images/fig8.png" title="fig8.png" class="image-inline" /></i></p>
+<p align="center" style="text-align: left; "><i> <b><i>Figure 8.</i></b><i> BierApp VCF upload panel. It is recommended to choose a name for the job as well as a description.</i></i></p>
+<p>Each prioritization (â€job’) has three associated screens that facilitate the filtering steps. The first one, the â€Summary’ tab, displays a statistic of the data set analyzed, containing the samples analyzed, the number and types of variants found and its distribution according to consequence types. The second screen, in the â€Variants and effect’ tab, is the actual filtering tool, and the third one, the â€Genome view’ tab, offers a representation of the selected variants within the genomic context provided by an embedded version of <span>the Genome Maps Tool </span><sup>(30)</sup><span>.</span></p>
+<p align="center" style="text-align: left; "><i><i><img alt="This picture shows all the information associated to the variants. If a variant has an associated phenotype we could see it in the last column. In this case, the variant 7:132481242 C>T is associated to the phenotype: large intestine tumor." src="images/fig9.png" title="fig9.png" class="image-inline" /></i></i></p>
+<p align="center" style="text-align: left; "><i><i> <b><i>Figure 9.</i></b><i> This picture shows all the information associated to the variants. If a variant has an associated phenotype we could see it in the last column. In this case, the variant 7:132481242 C>T is associated to the phenotype: large intestine tumor.</i></i></i></p>
+<p align="center" style="text-align: left; "><i><br /></i></p>
+<p><span><br /></span></p>
+<h2 class=" "><span>References</span></h2>
+<ol>
+<li><span class="discreet">Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth5, Goncalo Abecasis6, Richard Durbin and 1000 Genome Project Data Processing Subgroup: The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25: 2078-2079.</span></li>
+<li><span class="discreet"><span>McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. </span><i>Genome Res </i><span>2010, 20:1297-1303.</span></span></li>
+<li><span class="discreet">Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert E. Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin, and 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics 2011, 27: 2156-2158.</span></li>
+<li><span class="discreet">Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J: VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing. Nucleic Acids Res 2012, 40:W54-58.</span></li>
+<li><span class="discreet">Bleda M, Tarraga J, de Maria A, Salavert F, Garcia-Alonso L, Celma M, Martin A, Dopazo J, Medina I: CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. Nucleic Acids Res 2012, 40:W609-614.</span></li>
+<li><span class="discreet">Flicek,P., Amode,M.R., Barrell,D., Beal,K., Brent,S., Carvalho-Silva,D., Clapham,P., Coates,G., Fairley,S., Fitzgerald,S. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84–D90.</span></li>
+<li><span class="discreet">UniProt Consortium. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res., 40, D71–D75.</span></li>
+<li><span class="discreet">Kozomara,A. and Griffiths-Jones,S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152–D157.</span></li>
+<li><span class="discreet">Xiao,F., Zuo,Z., Cai,G., Kang,S., Gao,X. and Li,T. (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res., 37, D105–D110.</span></li>
+<li><span class="discreet">Hsu,S.D., Lin,F.M., Wu,W.Y., Liang,C., Huang,W.C., Chan,W.L., Tsai,W.T., Chen,G.Z., Lee,C.J., Chiu,C.M. et al. (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res., 39, D163–D169.</span></li>
+<li><span class="discreet">Friedman,R.C., Farh,K.K., Burge,C.B. and Bartel,D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92–105.</span></li>
+<li><span class="discreet">Betel,D., Wilson,M., Gabow,A., Marks,D.S. and Sander,C. (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res., 36, D149–D153.</span></li>
+<li><span class="discreet">Dreszer,T.R., Karolchik,D., Zweig,A.S., Hinrichs,A.S., Raney,B.J., Kuhn,R.M., Meyer,L.R., Wong,M., Sloan,C.A., Rosenbloom,K.R. et al. (2012) The UCSC genome browser database: extensions and updates 2011. Nucleic Acids Res., 40, D918–D923.</span></li>
+<li><span class="discreet">Smith,B., Ashburner,M., Rosse,C., Bard,J., Bug,W., Ceusters,W., Goldberg,L.J., Eilbeck,K., Ireland,A., Mungall,C.J. et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol., 25, 1251–1255.</span></li>
+<li><span class="discreet">Hunter,S., Jones,P., Mitchell,A., Apweiler,R., Attwood,T.K.,Bateman,A., Bernard,T., Binns,D., Bork,P., Burge,S. et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res., 40, D306–D312.</span></li>
+<li><span class="discreet">Sherry,S.T., Ward,M.H., Kholodov,M., Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308–311.</span></li>
+<li><span class="discreet">Altshuler,D.M., Gibbs,R.A., Peltonen,L., Dermitzakis,E., Schaffner,S.F., Yu,F., Bonnen,P.E., de Bakker,P.I., Deloukas,P., Gabriel,S.B. et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature, 467, 52–58.</span></li>
+<li><span class="discreet">1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061–1073.</span></li>
+<li><span class="discreet">Hindorff,L.A., Sethupathy,P., Junkins,H.A., Ramos,E.M., Mehta,J.P., Collins,F.S. and Manolio,T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362–9367.</span></li>
+<li><span class="discreet">Stenson,P.D., Ball,E.V., Mort,M., Phillips,A.D., Shiel,J.A., Thomas,N.S., Abeysinghe,S., Krawczak,M. and Cooper,D.N. (2003) Human gene mutation database (HGMD): 2003 update. Hum. Mutat., 21, 577–581.</span></li>
+<li><span class="discreet">Johnson,A.D. and O’Donnell,C.J. (2009) An open access database of genome-wide association results. BMC Med. Genet, 10, 6.</span></li>
+<li><span class="discreet">McKusick,V. (1998) A Catalog of Human Genes and Genetic Disorders, 12th edn. John Hopkins University Press,Baltimore, MD.</span></li>
+<li><span class="discreet">Forbes,S.A., Bindal,N., Bamford,S., Cole,C., Kok,C.Y., Beare,D., Jia,M., Shepherd,R., Leung,K., Menzies,A. et al. (2011) COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Res., 39, D945–D950.</span></li>
+<li><span class="discreet">Kerrien,S., Aranda,B., Breuza,L., Bridge,A., Broackes-Carter,F., Chen,C., Duesbury,M., Dumousseau,M., Feuermann,M., Hinz,U. et al. (2012) The Intact molecular interaction database in 2012. Nucleic Acids Res., 40, D841–D846.</span></li>
+<li><span class="discreet">Croft,D., O’Kelly,G., Wu,G., Haw,R., Gillespie,M., Matthews,L., Caudy,M., Garapati,P., Gopinath,G., Jassal,B. et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res., 39, D691–D697.</span></li>
+<li><span class="discreet">Demir,E., Cary,M.P., Paley,S., Fukuda,K., Lemer,C., Vastrik,I.,Wu,G., D’Eustachio,P., Schaefer,C., Luciano,J. et al. (2010) The BioPAX community standard for pathway data sharing. Nature Biotechnol., 28, 935–942.</span></li>
+<li><span class="discreet">Alemán Z, GarcĂa-GarcĂa F, Medina I, Dopazo J (2014): A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications. Nucleic Acids Res 42: W83-7.</span></li>
+<li><span class="discreet"><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Alem%C3%A1n%20A%5BAuthor%5D&cauthor=true&cauthor_uid=24803668">Alemán A</a><span>, </span><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Garcia-Garcia%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668">Garcia-Garcia F</a><span>, </span><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Salavert%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668">Salavert F</a><span>, </span><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Medina%20I%5BAuthor%5D&cauthor=true&cauthor_uid=24803668">Medina I</a><span>, </span><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Dopazo%20J%5BAuthor%5D&cauthor=true&cauthor_uid=24803668">Dopazo J</a><span> (2014). A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. </span><a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=BiERapp" title="Nucleic acids research.">Nucleic Acids Res.</a><span>42 :W88-93.</span></span></li>
+<li><span class="discreet">Landrum,M.J., Lee,J.M., Riley,G.R., Jang,W., Rubinstein,W.S., Church,D.M. and Maglott,D.R. (2014) ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res., 42, D980–D985.</span></li>
+<li><span class="discreet">Medina I, Salavert F, Sanchez R, de Maria A, Alonso R, Escobar P, Bleda M, Dopazo J: Genome Maps, a new generation genome browser. Nucleic Acids Res 2013, 41:W41-46.</span></li>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
index a21c737a8..d55a09eeb 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
@@ -38,7 +38,7 @@ primary and secondary (alignment) data files are stored in IT4I sequence
DB and uploaded to the discovery (candidate prioritization) or
diagnostic component where they can be analyzed directly by the user
that produced them, depending of the experimental design carried
-out*.<span style="text-alignleft; ">Â </span>
+out*.<span style="text-align: left; ">Â </span>
Typical genomics pipelines are composed by several components that need
to be launched manually. The advantage of OMICS MASTER pipeline is that
@@ -63,7 +63,7 @@ annotation. It turns raw data from the sequencing machine into files
containing lists of variants (VCF) that once annotated, can be used by
the following components (discovery and diagnosis).
-We distinguish three types of sequencing instrumentsbench sequencers
+We distinguish three types of sequencing instruments: bench sequencers
(MySeq, IonTorrent, and Roche Junior, although this last one is about
being discontinued), which produce relatively Genomes in the clinic
@@ -82,7 +82,7 @@ the future.
**Component:**<span> Hpg-Fastq & FastQC.</span>
These steps are carried out over the original FASTQ file with optimized
-scripts and includes the following stepssequence cleansing, estimation
+scripts and includes the following steps: sequence cleansing, estimation
of base quality scores, elimination of duplicates and statistics.
**Input:** FASTQ file.
@@ -213,9 +213,9 @@ corresponding information is unavailable.</span>Â Â </span>
</span>***Table 1.*** *Mandatory fields in the SAM format.
<span>
The standard CIGAR description of pairwise alignment defines three
-operationsâ€M’ for match/mismatch, â€I’ for insertion compared with the
+operations: â€M’ for match/mismatch, â€I’ for insertion compared with the
reference and â€D’ for deletion. The extended CIGAR proposed in SAM added
-four more operationsâ€N’ for skipped bases on the reference, â€S’ for
+four more operations: â€N’ for skipped bases on the reference, â€S’ for
soft clipping, â€H’ for hard clipping and â€P’ for padding. These support
splicing, clipping, multi-part and padded alignments. Figure 3 shows
examples of CIGAR strings for different types of alignments.Â
@@ -264,10 +264,10 @@ traversed. </span>
**Component:** Hpg-Fastq & FastQC. Some features:
-- Quality control% reads with N errors, % reads with multiple
+- Quality control: % reads with N errors, % reads with multiple
mappings, strand bias, paired-end insert, ...
-- Filteringby number of errors, number of hits, …
- - Comparatorstats, intersection, ...
+- Filtering: by number of errors, number of hits, …
+ - Comparator: stats, intersection, ...
**Input:** BAM file.
@@ -342,7 +342,7 @@ two bases by another base (SAMPLE2); the second line shows a SNP and an
insertion; the third a SNP; the fourth a large structural variant
described by the annotation in the INFO column, the coordinate is that
of the base before the variant. (b–f ) Alignments and VCF
-representations of different sequence variantsSNP, insertion,
+representations of different sequence variants: SNP, insertion,
deletion, replacement, and a large deletion. The REF columns shows the
reference bases replaced by the haplotype in the ALT column. The
coordinate refers to the first reference base. (g) Users are advised to
@@ -363,7 +363,7 @@ SAMPLE1) and a replacement of two bases by another base (SAMPLE2); the
second line shows a SNP and an insertion; the third a SNP; the fourth a
large structural variant described by the annotation in the INFO column,
the coordinate is that of the base before the variant. (b–f ) Alignments
-and VCF representations of different sequence variantsSNP, insertion,
+and VCF representations of different sequence variants: SNP, insertion,
deletion, replacement, and a large deletion. The REF columns shows the
reference bases replaced by the haplotype in the ALT column. The
coordinate refers to the first reference base. (g) Users are advised to
@@ -474,7 +474,7 @@ class="monospace">gatk</span>, etc)
help:Â </span>
$ ngsPipeline -h
- UsagengsPipeline.py [-h] -i INPUT -o OUTPUT -p PED --project PROJECT --queue
+ Usage: ngsPipeline.py [-h] -i INPUT -o OUTPUT -p PED --project PROJECT --queue
           QUEUE [--stages-path STAGES_PATH] [--email EMAIL]
[--prefix PREFIX] [-s START] [-e END] --log
@@ -639,35 +639,35 @@ This listing show which tools are used in each step of the pipeline :
<!-- -->
-- <span>stage-00fastqc</span>
-- <span>stage-01hpg_fastq</span>
-- <span>stage-02fastqc</span>
-- <span>stage-03hpg_aligner and samtools</span>
-- <span>stage-04samtools</span>
-- <span>stage-05samtools</span>
-- <span>stage-06fastqc</span>
-- <span>stage-07picard</span>
-- <span>stage-08fastqc</span>
-- <span>stage-09picard</span>
-- <span>stage-10gatk</span>
-- <span>stage-11gatk</span>
-- <span>stage-12gatk</span>
-- <span>stage-13gatk</span>
-- <span>stage-14gatk</span>
-- <span>stage-15gatk</span>
-- <span>stage-16samtools</span>
-- <span>stage-17samtools</span>
-- <span>stage-18fastqc</span>
-- <span>stage-19gatk</span>
-- <span>stage-20gatk</span>
-- <span>stage-21gatk</span>
-- <span>stage-22gatk</span>
-- <span>stage-23gatk</span>
-- <span>stage-24hpg-variant</span>
-- <span>stage-25hpg-variant</span>
-- <span>stage-26snpEff</span>
-- <span>stage-27snpEff</span>
-- <span>stage-28hpg-variant</span>
+- <span>stage-00: fastqc</span>
+- <span>stage-01: hpg_fastq</span>
+- <span>stage-02: fastqc</span>
+- <span>stage-03: hpg_aligner and samtools</span>
+- <span>stage-04: samtools</span>
+- <span>stage-05: samtools</span>
+- <span>stage-06: fastqc</span>
+- <span>stage-07: picard</span>
+- <span>stage-08: fastqc</span>
+- <span>stage-09: picard</span>
+- <span>stage-10: gatk</span>
+- <span>stage-11: gatk</span>
+- <span>stage-12: gatk</span>
+- <span>stage-13: gatk</span>
+- <span>stage-14: gatk</span>
+- <span>stage-15: gatk</span>
+- <span>stage-16: samtools</span>
+- <span>stage-17: samtools</span>
+- <span>stage-18: fastqc</span>
+- <span>stage-19: gatk</span>
+- <span>stage-20: gatk</span>
+- <span>stage-21: gatk</span>
+- <span>stage-22: gatk</span>
+- <span>stage-23: gatk</span>
+- <span>stage-24: hpg-variant</span>
+- <span>stage-25: hpg-variant</span>
+- <span>stage-26: snpEff</span>
+- <span>stage-27: snpEff</span>
+- <span>stage-28: hpg-variant</span>
<span>Interpretation</span>
---------------------------
@@ -677,7 +677,7 @@ data. This folder contains the final VCF with all the variants. This
file can be uploaded into
[TEAM](diagnostic-component-team.html) by using the VCF
file button. It is important to note here that the entire management of
-the VCF file is localno patient’s sequence data is sent over the
+the VCF file is local: no patient’s sequence data is sent over the
Internet thus avoiding any problem of data privacy or confidentiality.
<span>,
ClinVar ^(29)^ and COSMIC ^(23)^.
@@ -745,13 +745,13 @@ context provided by an embedded version of <span>the Genome Maps Tool
****
*****Figure 9.*** *This picture shows all the information associated to
the variants. If a variant has an associated phenotype we could see it
in the last column. In this case, the variant 7:132481242 C>T is
-associated to the phenotypelarge intestine tumor.***
+associated to the phenotype: large intestine tumor.***
*
*
@@ -764,12 +764,12 @@ associated to the phenotypelarge intestine tumor.***
1. <span class="discreet">Heng Li, Bob Handsaker, Alec Wysoker, Tim
Fennell, Jue Ruan, Nils Homer, Gabor Marth5, Goncalo Abecasis6,
- Richard Durbin and 1000 Genome Project Data Processing SubgroupThe
+ Richard Durbin and 1000 Genome Project Data Processing Subgroup: The
Sequence Alignment/Map format and SAMtools. Bioinformatics 2009,
- 252078-2079.</span>
+ 25: 2078-2079.</span>
2. <span class="discreet"><span>McKenna A, Hanna M, Banks E, Sivachenko
A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S,
- Daly M, DePristo MAThe Genome Analysis Toolkita MapReduce
+ Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce
framework for analyzing next-generation DNA sequencing data.
</span>*Genome Res* <span>2010, 20:1297-1303.</span></span>
3. <span class="discreet">Petr Danecek, Adam Auton, Goncalo Abecasis,
@@ -777,14 +777,14 @@ associated to the phenotypelarge intestine tumor.***
Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean
McVean, Richard Durbin, and 1000 Genomes Project Analysis Group. The
variant call format and VCFtools. Bioinformatics 2011,
- 272156-2158.</span>
+ 27: 2156-2158.</span>
4. <span class="discreet">Medina I, De Maria A, Bleda M, Salavert F,
- Alonso R, Gonzalez CY, Dopazo JVARIANTCommand Line, Web service
+ Alonso R, Gonzalez CY, Dopazo J: VARIANT: Command Line, Web service
and Web interface for fast and accurate functional characterization
of variants found by Next-Generation Sequencing. Nucleic Acids Res
2012, 40:W54-58.</span>
5. <span class="discreet">Bleda M, Tarraga J, de Maria A, Salavert F,
- Garcia-Alonso L, Celma M, Martin A, Dopazo J, Medina ICellBase, a
+ Garcia-Alonso L, Celma M, Martin A, Dopazo J, Medina I: CellBase, a
comprehensive collection of RESTful web services for retrieving
relevant biological information from heterogeneous sources. Nucleic
Acids Res 2012, 40:W609-614.</span>
@@ -796,40 +796,40 @@ associated to the phenotypelarge intestine tumor.***
protein space at the Universal Protein Resource (UniProt). Nucleic
Acids Res., 40, D71–D75.</span>
8. <span class="discreet">Kozomara,A. and Griffiths-Jones,S. (2011)
- miRBaseintegrating microRNA annotation and deep-sequencing data.
+ miRBase: integrating microRNA annotation and deep-sequencing data.
Nucleic Acids Res., 39, D152–D157.</span>
9. <span class="discreet">Xiao,F., Zuo,Z., Cai,G., Kang,S., Gao,X.
- and Li,T. (2009) miRecordsan integrated resource for
+ and Li,T. (2009) miRecords: an integrated resource for
microRNA-target interactions. Nucleic Acids Res.,
37, D105–D110.</span>
10. <span class="discreet">Hsu,S.D., Lin,F.M., Wu,W.Y., Liang,C.,
Huang,W.C., Chan,W.L., Tsai,W.T., Chen,G.Z., Lee,C.J., Chiu,C.M.
- et al. (2011) miRTarBasea database curates experimentally
+ et al. (2011) miRTarBase: a database curates experimentally
validated microRNA-target interactions. Nucleic Acids Res.,
39, D163–D169.</span>
11. <span class="discreet">Friedman,R.C., Farh,K.K., Burge,C.B.
and Bartel,D.P. (2009) Most mammalian mRNAs are conserved targets
of microRNAs. Genome Res., 19, 92–105.</span>
12. <span class="discreet">Betel,D., Wilson,M., Gabow,A., Marks,D.S.
- and Sander,C. (2008) The microRNA.org resourcetargets
+ and Sander,C. (2008) The microRNA.org resource: targets
and expression. Nucleic Acids Res., 36, D149–D153.</span>
13. <span class="discreet">Dreszer,T.R., Karolchik,D., Zweig,A.S.,
Hinrichs,A.S., Raney,B.J., Kuhn,R.M., Meyer,L.R., Wong,M.,
Sloan,C.A., Rosenbloom,K.R. et al. (2012) The UCSC genome browser
- databaseextensions and updates 2011. Nucleic Acids Res.,
+ database: extensions and updates 2011. Nucleic Acids Res.,
40, D918–D923.</span>
14. <span class="discreet">Smith,B., Ashburner,M., Rosse,C., Bard,J.,
Bug,W., Ceusters,W., Goldberg,L.J., Eilbeck,K.,
- Ireland,A., Mungall,C.J. et al. (2007) The OBO Foundrycoordinated
+ Ireland,A., Mungall,C.J. et al. (2007) The OBO Foundry: coordinated
evolution of ontologies to support biomedical data integration. Nat.
Biotechnol., 25, 1251–1255.</span>
15. <span class="discreet">Hunter,S., Jones,P., Mitchell,A.,
Apweiler,R., Attwood,T.K.,Bateman,A., Bernard,T., Binns,D.,
- Bork,P., Burge,S. et al. (2012) InterPro in 2011new developments
+ Bork,P., Burge,S. et al. (2012) InterPro in 2011: new developments
in the family and domain prediction database. Nucleic Acids Res.,
40, D306–D312.</span>
16. <span class="discreet">Sherry,S.T., Ward,M.H., Kholodov,M.,
- Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K. (2001) dbSNPthe
+ Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K. (2001) dbSNP: the
NCBI database of genetic variation. Nucleic Acids Res.,
29, 308–311.</span>
17. <span class="discreet">Altshuler,D.M., Gibbs,R.A., Peltonen,L.,
@@ -857,7 +857,7 @@ associated to the phenotypelarge intestine tumor.***
Press,Baltimore, MD.</span>
23. <span class="discreet">Forbes,S.A., Bindal,N., Bamford,S., Cole,C.,
Kok,C.Y., Beare,D., Jia,M., Shepherd,R., Leung,K., Menzies,A. et al.
- (2011) COSMICmining complete cancer genomes in the catalogue of
+ (2011) COSMIC: mining complete cancer genomes in the catalogue of
somatic mutations in cancer. Nucleic Acids Res.,
39, D945–D950.</span>
24. <span class="discreet">Kerrien,S., Aranda,B., Breuza,L., Bridge,A.,
@@ -866,7 +866,7 @@ associated to the phenotypelarge intestine tumor.***
database in 2012. Nucleic Acids Res., 40, D841–D846.</span>
25. <span class="discreet">Croft,D., O’Kelly,G., Wu,G., Haw,R.,
Gillespie,M., Matthews,L., Caudy,M., Garapati,P.,
- Gopinath,G., Jassal,B. et al. (2011) Reactomea database of
+ Gopinath,G., Jassal,B. et al. (2011) Reactome: a database of
reactions, pathways and biological processes. Nucleic Acids Res.,
39, D691–D697.</span>
26. <span class="discreet">Demir,E., Cary,M.P., Paley,S., Fukuda,K.,
@@ -874,9 +874,9 @@ associated to the phenotypelarge intestine tumor.***
et al. (2010) The BioPAX community standard for pathway
data sharing. Nature Biotechnol., 28, 935–942.</span>
27. <span class="discreet">Alemán Z, GarcĂa-GarcĂa F, Medina I, Dopazo J
- (2014)A web tool for the design and management of panels of genes
+ (2014): A web tool for the design and management of panels of genes
for targeted enrichment and massive sequencing for
- clinical applications. Nucleic Acids Res 42W83-7.</span>
+ clinical applications. Nucleic Acids Res 42: W83-7.</span>
28. <span class="discreet">[Alemán
A](http://www.ncbi.nlm.nih.gov/pubmed?term=Alem%C3%A1n%20A%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)<span>, </span>[Garcia-Garcia
F](http://www.ncbi.nlm.nih.gov/pubmed?term=Garcia-Garcia%20F%5BAuthor%5D&cauthor=true&cauthor_uid=24803668)<span>, </span>[Salavert
@@ -888,11 +888,11 @@ associated to the phenotypelarge intestine tumor.***
</span>[Nucleic
Acids Res.](http://www.ncbi.nlm.nih.gov/pubmed/?term=BiERapp "Nucleic acids research.")<span>42 :W88-93.</span></span>
29. <span class="discreet">Landrum,M.J., Lee,J.M., Riley,G.R., Jang,W.,
- Rubinstein,W.S., Church,D.M. and Maglott,D.R. (2014) ClinVarpublic
+ Rubinstein,W.S., Church,D.M. and Maglott,D.R. (2014) ClinVar: public
archive of relationships among sequence variation and
human phenotype. Nucleic Acids Res., 42, D980–D985.</span>
30. <span class="discreet">Medina I, Salavert F, Sanchez R, de Maria A,
- Alonso R, Escobar P, Bleda M, Dopazo JGenome Maps, a new
+ Alonso R, Escobar P, Bleda M, Dopazo J: Genome Maps, a new
generation genome browser. Nucleic Acids Res 2013, 41:W41-46.</span>
Â
@@ -900,4 +900,3 @@ associated to the phenotypelarge intestine tumor.***
<span>
</span>
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.html b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.html
new file mode 100644
index 000000000..39b2f01be
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.html
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+ Priorization component (BiERApp)
+ </h1>
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+<h3 class=" ">Access</h3>
+<p>BiERApp is available at the following address :Â <a class="external-link" href="http://omics.it4i.cz/bierapp/" target="_self" title="">http://omics.it4i.cz/bierapp/</a></p>
+<p class="exclamation">The address is accessible only via <a href="../../accessing-the-cluster/vpn-access.html" title="" target="_self" class="internal-link">VPN. </a></p>
+<h3 class=" "><span>BiERApp</span></h3>
+<h3 class=" "><span>This tool is aimed to discover new disease genes or variants by studying affected families or cases and controls. It carries out a filtering process to sequentially remove:Â (i) variants which are not no compatible with the disease because are not expected to have impact on the protein function; (ii) variants that exist at frequencies incompatible with the disease; (iii) variants that do not segregate with the disease. The result is a reduced set of disease gene candidates that should be further validated experimentally.</span></h3>
+</div>
+<p class="6Tekstletter">BiERapp <span>(28)</span> efficiently helps in the identification of causative variants in family and sporadic genetic diseases. The program reads lists of predicted variants (nucleotide substitutions and indels) in affected individuals or tumor samples and controls. In family studies, different modes of inheritance can easily be defined to filter out variants that do not segregate with the disease along the family. Moreover, BiERapp integrates additional information such as allelic frequencies in the general population and the most popular damaging scores to further narrow down the number of putative variants in successive filtering steps. BiERapp provides an interactive and user-friendly interface that implements the filtering strategy used in the context of a large-scale genomic project carried out by the Spanish Network for Research, in Rare Diseases (CIBERER) and the Medical Genome Project. in which more than 800 exomes have been analyzed.</p>
+<p class="6Tekstletter"><img alt="Web interface to the prioritization tool. This figure shows the interface of the web tool for candidate gene prioritization with the filters available. The tool includes a genomic viewer (Genome Maps 30) that enables the representation of the variants in the corresponding genomic coordinates." src="images/fig6.png.1" title="fig6.png" class="image-inline" /></p>
+<p align="center" class="Default"><b><i>Figure 6</i></b>. <i>Web interface to the prioritization tool.</i> <i>This figure</i> <i>shows the interface of the web tool for candidate gene prioritization with the filters available. The tool includes a genomic viewer (Genome Maps <span>30</span>) that enables the representation of the variants in the corresponding genomic coordinates.</i></p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md
index cb68d085b..fe9b742bc 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/priorization-component-bierapp.md
@@ -45,4 +45,3 @@ the variants in the corresponding genomic coordinates.*
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.html b/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.html
new file mode 100644
index 000000000..dc09d25a9
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.html
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+ OpenFOAM
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+ A free, open source CFD software package
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+ <h2 class=" "><b>Introduction</b></h2>
+<p>OpenFOAM is a free, open source CFD software package developed by <a href="http://www.openfoam.com/about"><b>OpenCFD Ltd</b></a> at <a href="http://www.esi-group.com/"><b>ESI Group</b></a> and distributed by the <a href="http://www.openfoam.org/"><b>OpenFOAM Foundation </b></a>. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. </p>
+<p>Homepage: <a href="http://www.openfoam.com/">http://www.openfoam.com/</a></p>
+<h3 class=" "><b>Installed version</b></h3>
+<p>Currently, several version compiled by GCC/ICC compilers in single/double precision with several version of openmpi are available on Anselm.</p>
+<p>For example syntax of available OpenFOAM module is:</p>
+<p class=" "><span>< openfoam/2.2.1-icc-openmpi1.6.5-DP ></span></p>
+<p>this means openfoam version <span>2.2.1</span> compiled by <span>ICC</span> compiler with <span>openmpi1.6.5</span> in<span> double precision</span>.</p>
+<p>Naming convection of the installed versions is following:</p>
+<p><span>Â Â openfoam/<</span><span>VERSION</span><span>>-<</span><span>COMPILER</span><span>>-<</span><span>openmpiVERSION</span><span>>-<</span><span>PRECISION</span><span>></span></p>
+<ul>
+<li><span><</span><span>VERSION</span><span>> - version of openfoam</span></li>
+<li><span><<span>COMPILER</span>> - version of used compiler</span></li>
+<li><span><<span>openmpiVERSION</span>> - version of used openmpi/impi</span></li>
+<li><span><<span>PRECISION</span>> - DP/</span><span>SP – double/single precision</span></li>
+</ul>
+<h3 class=" "><b>Available OpenFOAM modules</b></h3>
+<p class=" ">To check available modules use</p>
+<div>
+<pre class=" ">$ module avail</pre>
+</div>
+<p class=" ">In /opt/modules/modulefiles/engineering you can see installed engineering softwares:</p>
+<pre class=" "><br />------------------------------------ /opt/modules/modulefiles/engineering -------------------------------------------------------------<br />ansys/14.5.x              matlab/R2013a-COM                               openfoam/2.2.1-icc-impi4.1.1.036-DP<br />comsol/43b-COM            matlab/R2013a-EDU                               openfoam/2.2.1-icc-openmpi1.6.5-DP<br />comsol/43b-EDU            openfoam/2.2.1-gcc481-openmpi1.6.5-DP           paraview/4.0.1-gcc481-bullxmpi1.2.4.1-osmesa10.0<br />lsdyna/7.x.x              openfoam/2.2.1-gcc481-openmpi1.6.5-SP<br /><br /></pre>
+<p>For information how to use modules please <a href="../environment-and-modules.html" title="Environment and Modules " target="_self" class="external-link">look here</a>.</p>
+<h2 class=" "><b>Getting Started</b></h2>
+<p>To create OpenFOAM environment on ANSELM give the commands:</p>
+<pre class=" ">$ module load openfoam/2.2.1-icc-openmpi1.6.5-DP<br /><br />$ source $FOAM_BASHRC</pre>
+<p class="callout">Pleas load correct module with your requirements “compiler - GCC/ICC, precision - DP/SP”.</p>
+<p>Create a project directory within the $HOME/OpenFOAM directory named <span><USER></span>-<OFversion> and create a directory named run within it, e.g. by typing:</p>
+<div>
+<pre class=" ">$ mkdir -p $FOAM_RUN</pre>
+</div>
+<p>Project directory is now available by typing:</p>
+<div>
+<pre class=" ">$ cd /home/<span><USER></span>/OpenFOAM/<span><USER></span>-<OFversion>/run</pre>
+<p class=" "><OFversion> - for example <2.2.1></p>
+<p class=" ">or</p>
+<div>
+<pre class=" ">$ cd $FOAM_RUN</pre>
+</div>
+<p>Copy the tutorial examples directory in the OpenFOAM distribution to the run directory:</p>
+<div>
+<pre class=" ">$ cp -r $FOAM_TUTORIALS $FOAM_RUN</pre>
+</div>
+<p>Now you can run the first case for example incompressible laminar flow in a cavity.</p>
+<h2 class=" "><b>Running Serial Applications</b></h2>
+<div>
+<p class="callout"><span>Create a Bash script </span><span>test.sh</span>Â </p>
+</div>
+<div class="visualClear"><span></span>
+<div class="visualClear"><span> </span>
+<pre class=" "><span>#!/bin/bash<br />module load openfoam/2.2.1-icc-openmpi1.6.5-DP<br />source $FOAM_BASHRC<br /><br /># source to run functions<br />. $WM_PROJECT_DIR/bin/tools/RunFunctions<br /><br />cd $FOAM_RUN/tutorials/incompressible/icoFoam/cavity<br /><br />runApplication blockMesh<br />runApplication icoFoam</span></pre>
+<span> </span></div>
+<span> </span></div>
+<p><span>Job submission</span></p>
+<div><span> </span>
+<pre class=" "><span>$ qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16,walltime=03:00:00 test.sh</span></pre>
+<span> </span></div>
+<p class=" "><span> </span>For information about job submission please <a href="../resource-allocation-and-job-execution/job-submission-and-execution.html" title="Job submission" target="_self" class="external-link">look here</a>.</p>
+<h2 class=" "><b><span>Running applications in parallel</span></b></h2>
+<div class="visualClear"><span>Run the second case for example external incompressible turbulent flow - case - motorBike.</span></div>
+<div class="visualClear"><span>First we must run serial application bockMesh and decomposePar for preparation of parallel computation.</span></div>
+<div class="visualClear"><span><br /></span></div>
+<p class="callout"><span>Create a Bash scrip test.sh:</span></p>
+<div><span> </span>
+<pre class=" "><span>#!/bin/bash<br />module load openfoam/2.2.1-icc-openmpi1.6.5-DP<br />source $FOAM_BASHRC<br /><br /># source to run functions<br />. $WM_PROJECT_DIR/bin/tools/RunFunctions<br /><br />cd $FOAM_RUN/tutorials/incompressible/simpleFoam/motorBike<br /><br />runApplication blockMesh<br />runApplication decomposePar</span></pre>
+<div class="visualClear"><span><br /></span></div>
+<span> </span></div>
+<p><span>Job submission</span></p>
+<div><span> </span>
+<pre class=" "><span>$ qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16,walltime=03:00:00 test.sh</span></pre>
+<span> </span></div>
+<p><span><span>This job create simple block mesh and domain decomposition. Check your decomposition, and submit parallel computation:</span></span></p>
+<p class="callout"><span><span>Create a PBS script<span> testParallel.pbs</span>:</span></span></p>
+<div><span> </span>
+<pre class=" "><span><span>#!/bin/bash</span><span><br /><span>#PBS -N motorBike</span></span><br /><span>#PBS -l select=2:ncpus=16</span><br /><span>#PBS -l walltime=01:00:00</span><br /><span>#PBS -q qprod<br />#PBS -A OPEN-0-0<br /></span><br /><span>module load openfoam/2.2.1-icc-openmpi1.6.5-DP</span><br /><span>source $FOAM_BASHRC</span><br /><br />cd $FOAM_RUN/tutorials/incompressible/simpleFoam/motorBike<br /><br /><span>nproc = 32</span><br /><br /><span>mpirun -hostfile ${PBS_NODEFILE} -np $nproc</span> <span>snappyHexMesh </span><span><span>-overwrite -parallel</span> | tee snappyHexMesh.log</span><br /><br /><span>mpirun -hostfile ${PBS_NODEFILE} -np $nproc</span> <span>potentialFoam </span><span><span>-noFunctionObject-writep -parallel</span> | tee potentialFoam.log</span><br /><br /><span>mpirun -hostfile ${PBS_NODEFILE} -np $nproc</span> <span>simpleFoam </span><span><span>-parallel</span> | tee simpleFoam.log </span></span></pre>
+<span> </span></div>
+<p class=" "><span>nproc – number of subdomains</span></p>
+<p><span>Job submission</span></p>
+<div><span> </span>
+<pre class=" "><span><span>$ qsub testParallel.pbs</span></span></pre>
+<span> </span></div>
+<h2 class=" "><b><span>Compile your own solver</span></b></h2>
+<p><span>Initialize OpenFOAM environment before compiling your solver </span></p>
+<div><span> </span>
+<pre class=" "><span>$ module load openfoam/2.2.1-icc-openmpi1.6.5-DP<br /><span><span>$ source $FOAM_BASHRC</span></span><br />$ cd $FOAM_RUN/</span></pre>
+<span>Create directory applications/solvers in user directory</span></div>
+<div><span> </span>
+<pre class=" "><span>$ mkdir -p applications/solvers<br />$ cd applications/solvers</span></pre>
+<span> </span></div>
+<p><span>Copy icoFoam solver’s source files</span></p>
+<div><span> </span>
+<pre class=" "><span>$ cp -r $FOAM_SOLVERS/incompressible/icoFoam/ My_icoFoam<br />$ cd My_icoFoam</span></pre>
+<div class="visualClear"></div>
+</div>
+<p><span>Rename icoFoam.C to My_icoFOAM.C</span></p>
+<div><span> </span>
+<pre class=" "><span>$ mv icoFoam.C My_icoFoam.C</span></pre>
+<span> </span></div>
+<p><span>Edit <span><i>files</i></span> file in <em>Make</em> directory:</span></p>
+<div><span> </span>
+<pre class=" "><span><span>icoFoam.C</span><br /><span>EXE = $(FOAM_APPBIN)/icoFoam</span><br /></span></pre>
+</div>
+<div>
+<div class="visualClear">
+<p class=" "><span>and change to:</span></p>
+</div>
+<pre class=" "><span><span>My_</span>icoFoam.C <br />EXE = $(<span>FOAM_USER_APPBIN</span>)/<span>My_</span>icoFoam</span></pre>
+<span></span></div>
+<p><span>In directory My_icoFoam give the compilation command:</span></p>
+<div><span> </span>
+<pre class=" "><span>$ wmake</span></pre>
+</div>
+<hr />
+<p>Â </p>
+<p><strong>Â Have a fun with OpenFOAM :)</strong></p>
+<p class=" ">Â <span id="__caret"><span id="__caret"></span></span></p>
+<p class=" ">Â </p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md b/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
index 6ed5571f5..781c001d7 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
@@ -16,7 +16,7 @@ Foundation **](http://www.openfoam.org/). It has a large user base
across most areas of engineering and science, from both commercial and
academic organisations.Â
-Homepage<http://www.openfoam.com/>
+Homepage: <http://www.openfoam.com/>
### **Installed version**
@@ -323,4 +323,3 @@ testParallel.pbs</span>:</span></span>
Â
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.html b/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.html
new file mode 100644
index 000000000..e1fb1acbf
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.html
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md b/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md
index f711e54be..d5b1b2ae7 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md
@@ -13,4 +13,3 @@ bullx Linux is based on Red Hat Enterprise Linux. bullx Linux is a Linux
distribution provided by Bull and dedicated to HPC applications.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/paraview.html b/docs.it4i.cz/anselm-cluster-documentation/software/paraview.html
new file mode 100644
index 000000000..7ac9c8799
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+ <div id="content-core">
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+
+ <div id="parent-fieldname-text-944da307e9d24e92a98476eed8c02d60" class="">
+ <h2 class=" ">Introduction</h2>
+<p><strong>ParaView</strong>Â is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities.</p>
+<p>ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of exascale size as well as on laptops for smaller data.</p>
+<p>Homepage :Â <a class="external-link" href="http://www.paraview.org/" target="_self" title="">http://www.paraview.org/</a></p>
+<h2 class=" ">Installed version</h2>
+<p class=" ">Currently, version 4.0.1 compiled with GCC 4.8.1 against Bull MPI library and OSMesa 10.0 is installed on Anselm.</p>
+<h2 class=" ">Usage</h2>
+<p>On Anselm, ParaView is to be used in client-server mode. A parallel ParaView server is launched on compute nodes by the user, and client is launched on your desktop PC to control and view the visualization. Download ParaView client application for your OS here :Â <a class="external-link" href="http://paraview.org/paraview/resources/software.php" target="_self" title="">http://paraview.org/paraview/resources/software.php</a>. Important : <strong>your version must match the version number installed on Anselm</strong> ! (currently v4.0.1)</p>
+<h3 class=" ">Launching server</h3>
+<p>To launch the server, you must first allocate compute nodes, for example :<span>Â </span></p>
+<pre class=" ">$ qsub -I -q qprod -A OPEN-0-0 -l select=2</pre>
+<p>to launch an interactive session on 2 nodes. Refer to <a href="../resource-allocation-and-job-execution/introduction.html" title="" target="_self" class="internal-link">Resource Allocation and Job Execution</a> for details.</p>
+<p>After the interactive session is opened, load the ParaView module :</p>
+<pre class=" ">$ module add paraview</pre>
+<p>Now launch the parallel server, with number of nodes times 16 processes :</p>
+<pre class=" ">$ mpirun -np 32 pvserver --use-offscreen-rendering<br /><span>Waiting for client...<br /></span><span>Connection URL: cs://cn77:11111<br /></span><span>Accepting connection(s): cn77:11111</span></pre>
+<p>Â Note the that the server is listening on compute node cn77 in this case, we shall use this information later.</p>
+<h3 class=" ">Client connection</h3>
+<p>Because a direct connection is not allowed to compute nodes on Anselm, you must establish a SSH tunnel to connect to the server. Choose a port number on your PC to be forwarded to ParaView server, for example 12345. If your PC is running Linux, use this command to estabilish a SSH tunnel :</p>
+<pre class=" ">ssh -TN -L 12345:cn77:11111 username@anselm.it4i.cz</pre>
+<p>replace <span class="monospace">username</span> with your login and cn77 with the name of compute node your ParaView server is running on (see previous step). If you use PuTTY on Windows, load Anselm connection configuration, t<span>hen go to Connection-></span><span class="highlightedSearchTerm">SSH</span><span>->Tunnels to set up the port forwarding. Click Remote radio button. Insert 12345 to Source port textbox. Insert cn77:11111. Click Add button, then Open. </span><a href="https://docs.it4i.cz/anselm-cluster-documentation/software/resolveuid/11e53ad0d2fd4c5187537f4baeedff33" title="" target="_self" class="internal-link">Read more about port forwarding.</a></p>
+<p>Now launch ParaView client installed on your desktop PC. Select File->Connect..., click Add Server. Fill in the following :</p>
+<p>Name : Anselm tunnel</p>
+<p>Server Type : Client/Server</p>
+<p>Host : localhost</p>
+<p>Port : 12345</p>
+<p>Click Configure, Save, the configuration is now saved for later use. Now click Connect to connect to the ParaView server. In your terminal where you have interactive session with ParaView server launched, you should see :</p>
+<pre class=" ">Client connected.</pre>
+<p class=" ">You can now use Parallel ParaView.</p>
+<h3 class=" ">Close server</h3>
+<p>Remember to close the interactive session after you finish working with ParaView server, as it will remain launched even after your client is disconnected and will continue to consume resources.</p>
+<h2 class=" ">GPU support</h2>
+<p>Currently, GPU acceleration is not supported in the server and ParaView will not take advantage of accelerated nodes on Anselm. Support for GPU acceleration might be added in the future.</p>
+
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md b/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md
index 3ab5ef034..78ddf47ff 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md
@@ -61,8 +61,8 @@ Now launch the parallel server, with number of nodes times 16 processes
$ mpirun -np 32 pvserver --use-offscreen-rendering
Waiting for client...
- Connection URLcs://cn77:11111
- Accepting connection(s)cn77:11111
+ Connection URL: cs://cn77:11111
+ Accepting connection(s): cn77:11111
 Note the that the server is listening on compute node cn77 in this
case, we shall use this information later.
@@ -90,13 +90,13 @@ forwarding.](https://docs.it4i.cz/anselm-cluster-documentation/software/resolveu
Now launch ParaView client installed on your desktop PC. Select
File->Connect..., click Add Server. Fill in the following :
-Name Anselm tunnel
+Name : Anselm tunnel
-Server Type Client/Server
+Server Type : Client/Server
-Host localhost
+Host : localhost
-Port 12345
+Port : 12345
Click Configure, Save, the configuration is now saved for later use. Now
click Connect to connect to the ParaView server. In your terminal where
@@ -121,4 +121,3 @@ will not take advantage of accelerated nodes on Anselm. Support for GPU
acceleration might be added in the future.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/virtualization.html b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization.html
new file mode 100644
index 000000000..c10c00840
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization.html
@@ -0,0 +1,1154 @@
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+ Running virtual machines on compute nodes
+ </div>
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+ <h2 class=" ">Introduction</h2>
+<p>There are situations when Anselm's environment is not suitable for user needs.</p>
+<ul>
+<li>Application requires different operating system (e.g Windows), application is not available for Linux</li>
+<li>Application requires different versions of base system libraries and tools</li>
+<li>Application requires specific setup (installation, configuration) of complex software stack</li>
+<li>Application requires privileged access to operating system</li>
+<li>... and combinations of above cases</li>
+</ul>
+<p style="text-align: justify; ">Â We offer solution for these cases - <strong>virtualization</strong>. Anselm's environment gives the possibility to run virtual machines on compute nodes. Users can create their own images of operating system with specific software stack and run instances of these images as virtual machines on compute nodes. Run of virtual machines is provided by standard mechanism of <a href="../resource-allocation-and-job-execution/introduction.html" title="" target="_self" class="internal-link">Resource Allocation and Job Execution</a>.</p>
+<p>Solution is based on QEMU-KVM software stack and provides hardware-assisted x86 virtualization.</p>
+<h2 class=" ">Limitations</h2>
+<p style="text-align: justify; ">Anselm's infrastructure was not designed for virtualization. Anselm's environment is not intended primary for virtualization, compute nodes, storages and all infrastructure of Anselm is intended and optimized for running HPC jobs, this implies suboptimal configuration of virtualization and limitations.</p>
+<p style="text-align: justify; ">Anselm's virtualization does not provide performance and all features of native environment. There is significant performance hit (degradation) in I/O performance (storage, network). Anselm's virtualization is not suitable for I/O (disk, network) intensive workloads.</p>
+<p>Virtualization has also some drawbacks, it is not so easy to setup efficient solution.</p>
+<p>Solution described in chapter <a class="anchor-link" href="virtualization/virtualization.html#howto" target="_self" title="">HOWTO</a><span class="anchor-link"> is suitable for </span>single node tasks, does not introduce virtual machine clustering.</p>
+<p class="exclamation">Please consider virtualization as last resort solution for your needs.</p>
+<p class="exclamation">Please consult use of virtualization with IT4Innovation's support.</p>
+<p class="exclamation">For running Windows application (when source code and Linux native application are not available) consider use of Wine, Windows compatibility layer. Many Windows applications can be run using Wine with less effort and better performance than when using virtualization.</p>
+<h2 class=" ">Licensing</h2>
+<p style="text-align: justify; ">IT4Innovations does not provide any licenses for operating systems and software of virtual machines. Users are (<span id="result_box"><span class="hps">in accordance with</span></span> <a class="external-link" href="http://www.it4i.cz/acceptable-use-policy.pdf" target="_self" title="">Acceptable use policy document</a>) fully responsible for licensing all software running in virtual machines on Anselm. Be aware of complex conditions of licensing software in virtual environments.</p>
+<p class="exclamation" style="text-align: justify; ">Users are responsible for licensing OS e.g. MS Windows and all software running in their virtual machines.</p>
+<h2 class=" "><a name="howto"></a>Â HOWTO</h2>
+<h3 class=" "><a name="virtual-machine-job-workflow"></a>Virtual Machine Job Workflow</h3>
+<p>We propose this job workflow:</p>
+<p>Â <img alt="Virtualization Job Workflow" src="virtualization/virtualization-job-workflow" title="Virtualization Job Workflow" class="image-inline" /></p>
+<p>Our recommended solution is that job script creates distinct shared job directory, which makes a central point for data exchange between Anselm's environment, compute node (host) (e.g HOME, SCRATCH, local scratch and other local or cluster filesystems) and virtual machine (guest). Job script links or copies input data and instructions what to do (run script) for virtual machine to job directory and virtual machine process input data according instructions in job directory and store output back to job directory. We recommend, that virtual machine is running in so called <a class="anchor-link" href="virtualization/virtualization.html#snapshot-mode" target="_self" title="">snapshot mode</a>, image is immutable - image does not change, so one image can be used for many concurrent jobs.</p>
+<h3 class=" ">Procedure</h3>
+<ol>
+<li>Prepare image of your virtual machine</li>
+<li>Optimize image of your virtual machine for Anselm's virtualization</li>
+<li>Modify your image for running jobs</li>
+<li>Create job script for executing virtual machine</li>
+<li>Run jobs</li>
+</ol>
+<h3 class=" ">Prepare image of your virtual machine</h3>
+<p>You can either use your existing image or create new image from scratch.</p>
+<p>QEMU currently supports these image types or formats:</p>
+<ul>
+<li>raw </li>
+<li>cloop </li>
+<li>cow </li>
+<li>qcow </li>
+<li>qcow2Â </li>
+<li class="extiw" title="w:VMware">vmdk - VMware 3 & 4, or 6 image format, for exchanging images with that product</li>
+<li>vdi - VirtualBox 1.1 compatible image format, for exchanging images with VirtualBox.</li>
+</ul>
+<p class=" ">You can convert your existing image using qemu-img convert command. Supported formats of this command are: blkdebug blkverify bochs cloop cow dmg file ftp ftps host_cdrom host_device host_floppy http https nbd parallels qcow qcow2 qed raw sheepdog tftp vdi vhdx vmdk vpc vvfat.</p>
+<p class=" ">We recommend using advanced QEMU native image format qcow2.</p>
+<p class=" "><a class="external-link" href="http://en.wikibooks.org/wiki/QEMU/Images" target="_blank" title="">More about QEMU Images</a></p>
+<h3 class=" ">Optimize image of your virtual machine</h3>
+<p>Use virtio devices (for disk/drive and network adapter) and install virtio drivers (paravirtualized drivers) into virtual machine. There is significant performance gain when using virtio drivers. For more information see <a class="external-link" href="http://www.linux-kvm.org/page/Virtio" target="_blank" title="">Virtio Linux</a> and <a class="external-link" href="http://www.linux-kvm.org/page/WindowsGuestDrivers/Download_Drivers" target="_blank" title="">Virtio Windows</a>.</p>
+<p>Disable all <span class="short_text" id="result_box"><span class="hps trans-target-highlight">unnecessary</span></span> services and tasks. Restrict all unnecessary operating system operations.</p>
+<p>Remove all <span class="short_text" id="result_box"><span class="hps trans-target-highlight">unnecessary software and files.</span></span></p>
+<p><span class="short_text" id="result_box"><span class="hps trans-target-highlight"></span></span>Remove all paging space, swap files, partitions, etc.</p>
+<p>Shrink your image. (It is recommended to zero all free space and reconvert image using qemu-img.)</p>
+<h3 class=" ">Modify your image for running jobs</h3>
+<p>Your image should run some kind of operating system startup script. Startup script should run application and when application exits run shutdown or quit virtual machine.</p>
+<p>We recommend, that startup script</p>
+<ul>
+<li>maps Job Directory from host (from compute node)</li>
+<li>runs script (we call it "run script") from Job Directory and waits for application's exit</li>
+<ul>
+<li>for management purposes if run script does not exist wait for some time period (few minutes)</li>
+</ul>
+<li>shutdowns/quits OS</li>
+</ul>
+<p>For Windows operating systems we suggest using Local Group Policy Startup script, for Linux operating systems rc.local, runlevel init script or similar service.</p>
+<p>Example startup script for Windows virtual machine:</p>
+<pre class=" ">@echo off<br />set LOG=c:\startup.log<br />set MAPDRIVE=z:<br />set SCRIPT=%MAPDRIVE%\run.bat<br />set TIMEOUT=300<br /><br />echo %DATE% %TIME% Running startup script>%LOG%<br /><br />rem Mount share<br />echo %DATE% %TIME% Mounting shared drive>>%LOG%<br />net use z: \\10.0.2.4\qemu >>%LOG% 2>&1<br />dir z:\ >>%LOG% 2>&1<br />echo. >>%LOG%<br /><br /><br />if exist %MAPDRIVE%\ (<br />Â echo %DATE% %TIME% The drive "%MAPDRIVE%" exists>>%LOG%<br /><br />Â if exist %SCRIPT% (<br />Â Â Â echo %DATE% %TIME% The script file "%SCRIPT%"exists>>%LOG%<br />Â Â Â echo %DATE% %TIME% Running script %SCRIPT%>>%LOG%<br />Â Â Â set TIMEOUT=0<br />Â Â Â call %SCRIPT%<br />Â ) else (<br />Â Â Â echo %DATE% %TIME% The script file "%SCRIPT%"does not exist>>%LOG%<br />Â )<br /><br />) else (<br />Â echo %DATE% %TIME% The drive "%MAPDRIVE%" does not exist>>%LOG%<br />)<br />echo. >>%LOG%<br /><br />timeout /T %TIMEOUT%<br /><br />echo %DATE% %TIME% Shut down>>%LOG%<br />shutdown /s /t 0</pre>
+<p class=" ">Example startup script maps shared job script as drive z: and looks for run script called run.bat. If run script is found it is run else wait for 5 minutes, then shutdown virtual machine.</p>
+<h3 class=" ">Create job script for executing virtual machine</h3>
+<p>Create job script according recommended <span class="short_text" id="result_box"><span class="hps trans-target-highlight"></span></span><a class="anchor-link" href="virtualization/virtualization.html#virtual-machine-job-workflow" target="_self" title="">Virtual Machine Job Workflow</a>.</p>
+<p>Example job for Windows virtual machine:</p>
+<pre class=" ">#/bin/sh<br /><br />JOB_DIR=/scratch/$USER/win/${PBS_JOBID}<br /><br />#Virtual machine settings<br />VM_IMAGE=~/work/img/win.img<br />VM_MEMORY=49152<br />VM_SMP=16<br /><br /># Prepare job dir<br />mkdir -p ${JOB_DIR} && cd ${JOB_DIR} || exit 1<br />ln -s ~/work/win .<br />ln -s /scratch/$USER/data .<br />ln -s ~/work/win/script/run/run-appl.bat run.bat<br /><br /># Run virtual machine<br />export TMPDIR=/lscratch/${PBS_JOBID}<br />module add qemu<br />qemu-system-x86_64 \<br />Â -enable-kvm \<br />Â -cpu host \<br />Â -smp ${VM_SMP} \<br />Â -m ${VM_MEMORY} \<br />Â -vga std \<br />Â -localtime \<br />Â -usb -usbdevice tablet \<br />Â -device virtio-net-pci,netdev=net0 \<br />Â -netdev user,id=net0,smb=${JOB_DIR},hostfwd=tcp::3389-:3389 \<br />Â -drive file=${VM_IMAGE},media=disk,if=virtio \<br />Â -snapshot \<br />Â -nographic<br /><br /></pre>
+<p class=" ">Job script links application data (win), input data (data) and run script (run.bat) into job directory and runs virtual machine.</p>
+<p class=" ">Example run script (run.bat) for Windows virtual machine:</p>
+<pre class=" ">z:<br />cd \win\appl<br />call application.bat z:\data z:\output</pre>
+<p class=" ">Run script runs application from shared job directory (mapped as drive z:), process input data (z:\data) from job directory and store output to job directory (z:\output).</p>
+<h3 class=" ">Run jobs</h3>
+<p>Run jobs as usual, see <a href="../resource-allocation-and-job-execution/introduction.html" title="" target="_self" class="internal-link">Resource Allocation and Job Execution</a>. Use only full node allocation for virtualization jobs.</p>
+<h3 class=" ">Running Virtual Machines</h3>
+<p>Virtualization is enabled only on compute nodes, virtualization does not work on login nodes.</p>
+<p>Load QEMU environment module:</p>
+<pre class=" ">$ module add qemu</pre>
+<p class=" ">Get help</p>
+<pre class=" ">$ man qemu</pre>
+<p class=" ">Run virtual machine (simple)</p>
+<pre class=" ">$ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -vnc :0<br /><br />$ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -vnc :0</pre>
+<p class=" ">You can access virtual machine by VNC viewer (option -vnc) connecting to IP address of compute node. For VNC you must use <a href="../accessing-the-cluster/vpn-access.html" title="" target="_self" class="internal-link">VPN network</a>.</p>
+<p class=" ">Install virtual machine from iso file</p>
+<pre class=" ">$ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -cdrom linux-install.iso -boot d -vnc :0<br /><br />$ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -cdrom win-install.iso -boot d -vnc :0</pre>
+<p class=" ">Run virtual machine using optimized devices, user network backend with sharing and port forwarding, in snapshot mode</p>
+<pre class=" ">$ qemu-system-x86_64 -drive file=linux.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::2222-:22 -vnc :0 -snapshot<br /><br />$ qemu-system-x86_64 -drive file=win.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::3389-:3389 -vnc :0 -snapshot</pre>
+<p class=" ">Thanks to port forwarding you can access virtual machine via SSH (Linux) or RDP (Windows) connecting to IP address of compute node (and port 2222 for SSH). You must use <a href="../accessing-the-cluster/vpn-access.html" title="" target="_self" class="internal-link">VPN network</a>.</p>
+<p class="callout">Keep in mind, that if you use virtio devices, you must have virtio drivers installed on your virtual machine.</p>
+<h3 class=" ">Networking and data sharing</h3>
+<p class=" ">For networking virtual machine we suggest to use (default) user network backend (sometimes called slirp). This network backend NATs virtual machines and provides useful services for virtual machines as DHCP, DNS, SMB sharing, port forwarding.</p>
+<p class=" ">In default configuration IP network 10.0.2.0/24 is used, host has IP address 10.0.2.2, DNS server 10.0.2.3, SMB server 10.0.2.4 and virtual machines obtain address from range 10.0.2.15-10.0.2.31. Virtual machines have access to Anselm's network via NAT on compute node (host).</p>
+<p class=" ">Simple network setup</p>
+<pre class=" ">$ qemu-system-x86_64 ... -net nic -net user</pre>
+<p class=" ">(It is default when no -net options are given.)<br /><br />Simple network setup with sharing and port forwarding (obsolete but simpler syntax, lower performance)</p>
+<pre class=" ">$ qemu-system-x86_64 ... -net nic -net user,smb=/scratch/$USER/tmp,hostfwd=tcp::3389-:3389</pre>
+<p class=" ">Optimized network setup with sharing and port forwarding</p>
+<pre class=" ">$ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::2222-:22</pre>
+<h3 class=" ">Advanced networking</h3>
+<p><strong>Internet access</strong></p>
+<p class=" ">Sometime your virtual machine needs access to internet (install software, updates, software activation, etc). We suggest solution using Virtual Distributed Ethernet (VDE) enabled QEMU with SLIRP running on login node tunnelled to compute node. Be aware, this setup has very low performance, the worst performance of all described solutions.</p>
+<p class=" ">Load VDE enabled QEMU environment module (unload standard QEMU module first if necessary).</p>
+<pre class=" ">$ module add qemu/2.1.2-vde2</pre>
+<p class=" ">Create virtual network switch.</p>
+<pre class=" ">$ vde_switch -sock /tmp/sw0 -mgmt /tmp/sw0.mgmt -daemon</pre>
+<p class=" ">Run SLIRP daemon over SSH tunnel on login node and connect it to virtual network switch.</p>
+<pre class=" ">$ dpipe vde_plug /tmp/sw0 = ssh login1 $VDE2_DIR/bin/slirpvde -s - --dhcp &</pre>
+<p class=" ">Run qemu using vde network backend, connect to created virtual switch.</p>
+<p class=" ">Basic setup (obsolete syntax)</p>
+<pre class=" ">$ qemu-system-x86_64 ... -net nic -net vde,sock=/tmp/sw0</pre>
+<p class=" ">Setup using virtio device (obsolete syntax)</p>
+<pre class=" ">$ qemu-system-x86_64 ... -net nic,model=virtio -net vde,sock=/tmp/sw0<strong></strong></pre>
+<p class=" ">Optimized setup</p>
+<pre class=" ">$ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net0 -netdev vde,id=net0,sock=/tmp/sw0</pre>
+<p class=" "><strong><br /></strong></p>
+<p class=" "><strong>TAP interconnect</strong></p>
+<p class=" ">Both user and vde network backend have low performance. For fast interconnect (10Gbps and more) of compute node (host) and virtual machine (guest) we suggest using Linux kernel TAP device.</p>
+<p class=" ">Cluster Anselm provides TAP device tap0 for your job. TAP interconnect does not provide any services (like NAT, DHCP, DNS, SMB, etc.) just raw networking, so you should provide your services if you need them.</p>
+<p class=" ">Run qemu with TAP network backend:</p>
+<pre class=" ">$ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net1 \<br /> -netdev tap,id=net1,ifname=tap0,script=no,downscript=no</pre>
+<p class=" ">Interface tap0 has IP address 192.168.1.1 and network mask 255.255.255.0 (/24). In virtual machine use IP address from range 192.168.1.2-192.168.1.254. For your convenience some ports on tap0 interface are redirected to higher numbered ports, so you as non-privileged user can provide services on these ports.</p>
+<p class=" ">Redirected ports:</p>
+<ul>
+<li>DNS udp/53->udp/3053, tcp/53->tcp3053</li>
+<li>DHCP udp/67->udp3067</li>
+<li>SMB tcp/139->tcp3139, tcp/445->tcp3445).</li>
+</ul>
+<p class=" ">You can configure IP address of virtual machine statically or dynamically. For dynamic addressing provide your DHCP server on port 3067 of tap0 interface, you can also provide your DNS server on port 3053 of tap0 interface for example:</p>
+<pre class=" ">$ dnsmasq --interface tap0 --bind-interfaces -p 3053 --dhcp-alternate-port=3067,68 --dhcp-range=192.168.1.15,192.168.1.32 --dhcp-leasefile=/tmp/dhcp.leasefile</pre>
+<p class=" ">You can also provide your SMB services (on ports 3139, 3445) to obtain high performance data sharing.</p>
+<p class=" ">Example smb.conf (not optimized)</p>
+<pre class=" ">[global]<br />socket address=192.168.1.1<br />smb ports = 3445 3139<br /><br />private dir=/tmp/qemu-smb<br />pid directory=/tmp/qemu-smb<br />lock directory=/tmp/qemu-smb<br />state directory=/tmp/qemu-smb<br />ncalrpc dir=/tmp/qemu-smb/ncalrpc<br />log file=/tmp/qemu-smb/log.smbd<br />smb passwd file=/tmp/qemu-smb/smbpasswd<br />security = user<br />map to guest = Bad User<br />unix extensions = no<br />load printers = no<br />printing = bsd<br />printcap name = /dev/null<br />disable spoolss = yes<br />log level = 1<br />guest account = USER<br />[qemu]<br />path=/scratch/USER/tmp<br />read only=no<br />guest ok=yes<br />writable=yes<br />follow symlinks=yes<br />wide links=yes<br />force user=USER</pre>
+<p class=" ">(Replace USER with your login name.)</p>
+<p class=" ">Run SMB services</p>
+<pre class=" ">smbd -s /tmp/qemu-smb/smb.conf</pre>
+<p class=" ">Â </p>
+<p class=" ">Virtual machine can of course have more than one network interface controller, virtual machine can use more than one network backend. So, you can combine for example use network backend and TAP interconnect.</p>
+<h3 class=" "><a name="snapshot-mode"></a>Snapshot mode</h3>
+<p>In snapshot mode image is not written, changes are written to temporary file (and discarded after virtual machine exits).<strong> It is strongly recommended mode for running your jobs.</strong> Set TMPDIR environment variable to local scratch directory for placement temporary files.</p>
+<pre class=" ">$ export TMPDIR=/lscratch/${PBS_JOBID}<br />$ qemu-system-x86_64 ... -snapshot</pre>
+<h3 class=" ">Windows guests</h3>
+<p>For Windows guests we recommend these options, life will be easier:</p>
+<pre class=" ">$ qemu-system-x86_64 ... -localtime -usb -usbdevice tablet</pre>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/virtualization.md b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization.md
index 335679503..77fc02199 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/virtualization.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization.md
@@ -112,7 +112,7 @@ many concurrent jobs.
You can either use your existing image or create new image from scratch.
-EMU currently supports these image types or formats:
+QEMU currently supports these image types or formats:
- rawÂ
- cloopÂ
@@ -125,7 +125,7 @@ EMU currently supports these image types or formats:
with VirtualBox.
You can convert your existing image using qemu-img convert command.
-Supported formats of this command areblkdebug blkverify bochs cloop
+Supported formats of this command are: blkdebug blkverify bochs cloop
cow dmg file ftp ftps host_cdrom host_device host_floppy http https
nbd parallels qcow qcow2 qed raw sheepdog tftp vdi vhdx vmdk vpc vvfat.
@@ -189,8 +189,8 @@ Example startup script for Windows virtual machine:
rem Mount share
echo %DATE% %TIME% Mounting shared drive>>%LOG%
- net use z10.0.2.4qemu >>%LOG% 2>&1
- dir z>>%LOG% 2>&1
+ net use z: 10.0.2.4qemu >>%LOG% 2>&1
+ dir z: >>%LOG% 2>&1
echo. >>%LOG%
@@ -216,7 +216,7 @@ Example startup script for Windows virtual machine:
echo %DATE% %TIME% Shut down>>%LOG%
shutdown /s /t 0
-Example startup script maps shared job script as drive zand looks for
+Example startup script maps shared job script as drive z: and looks for
run script called run.bat. If run script is found it is run else wait
for 5 minutes, then shutdown virtual machine.
@@ -489,4 +489,3 @@ For Windows guests we recommend these options, life will be easier:
$ qemu-system-x86_64 ... -localtime -usb -usbdevice tablet
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization.html b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization.html
new file mode 100644
index 000000000..ca8e108d9
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization.html
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+ Running virtual machines on compute nodes
+ </div>
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+ <h2 class=" ">Introduction</h2>
+<p>There are situations when Anselm's environment is not suitable for user needs.</p>
+<ul>
+<li>Application requires different operating system (e.g Windows), application is not available for Linux</li>
+<li>Application requires different versions of base system libraries and tools</li>
+<li>Application requires specific setup (installation, configuration) of complex software stack</li>
+<li>Application requires privileged access to operating system</li>
+<li>... and combinations of above cases</li>
+</ul>
+<p style="text-align: justify; ">Â We offer solution for these cases - <strong>virtualization</strong>. Anselm's environment gives the possibility to run virtual machines on compute nodes. Users can create their own images of operating system with specific software stack and run instances of these images as virtual machines on compute nodes. Run of virtual machines is provided by standard mechanism of <a href="../../resource-allocation-and-job-execution/introduction.html" title="" target="_self" class="internal-link">Resource Allocation and Job Execution</a>.</p>
+<p>Solution is based on QEMU-KVM software stack and provides hardware-assisted x86 virtualization.</p>
+<h2 class=" ">Limitations</h2>
+<p style="text-align: justify; ">Anselm's infrastructure was not designed for virtualization. Anselm's environment is not intended primary for virtualization, compute nodes, storages and all infrastructure of Anselm is intended and optimized for running HPC jobs, this implies suboptimal configuration of virtualization and limitations.</p>
+<p style="text-align: justify; ">Anselm's virtualization does not provide performance and all features of native environment. There is significant performance hit (degradation) in I/O performance (storage, network). Anselm's virtualization is not suitable for I/O (disk, network) intensive workloads.</p>
+<p>Virtualization has also some drawbacks, it is not so easy to setup efficient solution.</p>
+<p>Solution described in chapter <a class="anchor-link" href="virtualization.html#howto" target="_self" title="">HOWTO</a><span class="anchor-link"> is suitable for </span>single node tasks, does not introduce virtual machine clustering.</p>
+<p class="exclamation">Please consider virtualization as last resort solution for your needs.</p>
+<p class="exclamation">Please consult use of virtualization with IT4Innovation's support.</p>
+<p class="exclamation">For running Windows application (when source code and Linux native application are not available) consider use of Wine, Windows compatibility layer. Many Windows applications can be run using Wine with less effort and better performance than when using virtualization.</p>
+<h2 class=" ">Licensing</h2>
+<p style="text-align: justify; ">IT4Innovations does not provide any licenses for operating systems and software of virtual machines. Users are (<span id="result_box"><span class="hps">in accordance with</span></span> <a class="external-link" href="http://www.it4i.cz/acceptable-use-policy.pdf" target="_self" title="">Acceptable use policy document</a>) fully responsible for licensing all software running in virtual machines on Anselm. Be aware of complex conditions of licensing software in virtual environments.</p>
+<p class="exclamation" style="text-align: justify; ">Users are responsible for licensing OS e.g. MS Windows and all software running in their virtual machines.</p>
+<h2 class=" "><a name="howto"></a>Â HOWTO</h2>
+<h3 class=" "><a name="virtual-machine-job-workflow"></a>Virtual Machine Job Workflow</h3>
+<p>We propose this job workflow:</p>
+<p>Â <img alt="Virtualization Job Workflow" src="virtualization-job-workflow" title="Virtualization Job Workflow" class="image-inline" /></p>
+<p>Our recommended solution is that job script creates distinct shared job directory, which makes a central point for data exchange between Anselm's environment, compute node (host) (e.g HOME, SCRATCH, local scratch and other local or cluster filesystems) and virtual machine (guest). Job script links or copies input data and instructions what to do (run script) for virtual machine to job directory and virtual machine process input data according instructions in job directory and store output back to job directory. We recommend, that virtual machine is running in so called <a class="anchor-link" href="virtualization.html#snapshot-mode" target="_self" title="">snapshot mode</a>, image is immutable - image does not change, so one image can be used for many concurrent jobs.</p>
+<h3 class=" ">Procedure</h3>
+<ol>
+<li>Prepare image of your virtual machine</li>
+<li>Optimize image of your virtual machine for Anselm's virtualization</li>
+<li>Modify your image for running jobs</li>
+<li>Create job script for executing virtual machine</li>
+<li>Run jobs</li>
+</ol>
+<h3 class=" ">Prepare image of your virtual machine</h3>
+<p>You can either use your existing image or create new image from scratch.</p>
+<p>QEMU currently supports these image types or formats:</p>
+<ul>
+<li>raw </li>
+<li>cloop </li>
+<li>cow </li>
+<li>qcow </li>
+<li>qcow2Â </li>
+<li class="extiw" title="w:VMware">vmdk - VMware 3 & 4, or 6 image format, for exchanging images with that product</li>
+<li>vdi - VirtualBox 1.1 compatible image format, for exchanging images with VirtualBox.</li>
+</ul>
+<p class=" ">You can convert your existing image using qemu-img convert command. Supported formats of this command are: blkdebug blkverify bochs cloop cow dmg file ftp ftps host_cdrom host_device host_floppy http https nbd parallels qcow qcow2 qed raw sheepdog tftp vdi vhdx vmdk vpc vvfat.</p>
+<p class=" ">We recommend using advanced QEMU native image format qcow2.</p>
+<p class=" "><a class="external-link" href="http://en.wikibooks.org/wiki/QEMU/Images" target="_blank" title="">More about QEMU Images</a></p>
+<h3 class=" ">Optimize image of your virtual machine</h3>
+<p>Use virtio devices (for disk/drive and network adapter) and install virtio drivers (paravirtualized drivers) into virtual machine. There is significant performance gain when using virtio drivers. For more information see <a class="external-link" href="http://www.linux-kvm.org/page/Virtio" target="_blank" title="">Virtio Linux</a> and <a class="external-link" href="http://www.linux-kvm.org/page/WindowsGuestDrivers/Download_Drivers" target="_blank" title="">Virtio Windows</a>.</p>
+<p>Disable all <span class="short_text" id="result_box"><span class="hps trans-target-highlight">unnecessary</span></span> services and tasks. Restrict all unnecessary operating system operations.</p>
+<p>Remove all <span class="short_text" id="result_box"><span class="hps trans-target-highlight">unnecessary software and files.</span></span></p>
+<p><span class="short_text" id="result_box"><span class="hps trans-target-highlight"></span></span>Remove all paging space, swap files, partitions, etc.</p>
+<p>Shrink your image. (It is recommended to zero all free space and reconvert image using qemu-img.)</p>
+<h3 class=" ">Modify your image for running jobs</h3>
+<p>Your image should run some kind of operating system startup script. Startup script should run application and when application exits run shutdown or quit virtual machine.</p>
+<p>We recommend, that startup script</p>
+<ul>
+<li>maps Job Directory from host (from compute node)</li>
+<li>runs script (we call it "run script") from Job Directory and waits for application's exit</li>
+<ul>
+<li>for management purposes if run script does not exist wait for some time period (few minutes)</li>
+</ul>
+<li>shutdowns/quits OS</li>
+</ul>
+<p>For Windows operating systems we suggest using Local Group Policy Startup script, for Linux operating systems rc.local, runlevel init script or similar service.</p>
+<p>Example startup script for Windows virtual machine:</p>
+<pre class=" ">@echo off<br />set LOG=c:\startup.log<br />set MAPDRIVE=z:<br />set SCRIPT=%MAPDRIVE%\run.bat<br />set TIMEOUT=300<br /><br />echo %DATE% %TIME% Running startup script>%LOG%<br /><br />rem Mount share<br />echo %DATE% %TIME% Mounting shared drive>>%LOG%<br />net use z: \\10.0.2.4\qemu >>%LOG% 2>&1<br />dir z:\ >>%LOG% 2>&1<br />echo. >>%LOG%<br /><br /><br />if exist %MAPDRIVE%\ (<br />Â echo %DATE% %TIME% The drive "%MAPDRIVE%" exists>>%LOG%<br /><br />Â if exist %SCRIPT% (<br />Â Â Â echo %DATE% %TIME% The script file "%SCRIPT%"exists>>%LOG%<br />Â Â Â echo %DATE% %TIME% Running script %SCRIPT%>>%LOG%<br />Â Â Â set TIMEOUT=0<br />Â Â Â call %SCRIPT%<br />Â ) else (<br />Â Â Â echo %DATE% %TIME% The script file "%SCRIPT%"does not exist>>%LOG%<br />Â )<br /><br />) else (<br />Â echo %DATE% %TIME% The drive "%MAPDRIVE%" does not exist>>%LOG%<br />)<br />echo. >>%LOG%<br /><br />timeout /T %TIMEOUT%<br /><br />echo %DATE% %TIME% Shut down>>%LOG%<br />shutdown /s /t 0</pre>
+<p class=" ">Example startup script maps shared job script as drive z: and looks for run script called run.bat. If run script is found it is run else wait for 5 minutes, then shutdown virtual machine.</p>
+<h3 class=" ">Create job script for executing virtual machine</h3>
+<p>Create job script according recommended <span class="short_text" id="result_box"><span class="hps trans-target-highlight"></span></span><a class="anchor-link" href="virtualization.html#virtual-machine-job-workflow" target="_self" title="">Virtual Machine Job Workflow</a>.</p>
+<p>Example job for Windows virtual machine:</p>
+<pre class=" ">#/bin/sh<br /><br />JOB_DIR=/scratch/$USER/win/${PBS_JOBID}<br /><br />#Virtual machine settings<br />VM_IMAGE=~/work/img/win.img<br />VM_MEMORY=49152<br />VM_SMP=16<br /><br /># Prepare job dir<br />mkdir -p ${JOB_DIR} && cd ${JOB_DIR} || exit 1<br />ln -s ~/work/win .<br />ln -s /scratch/$USER/data .<br />ln -s ~/work/win/script/run/run-appl.bat run.bat<br /><br /># Run virtual machine<br />export TMPDIR=/lscratch/${PBS_JOBID}<br />module add qemu<br />qemu-system-x86_64 \<br />Â -enable-kvm \<br />Â -cpu host \<br />Â -smp ${VM_SMP} \<br />Â -m ${VM_MEMORY} \<br />Â -vga std \<br />Â -localtime \<br />Â -usb -usbdevice tablet \<br />Â -device virtio-net-pci,netdev=net0 \<br />Â -netdev user,id=net0,smb=${JOB_DIR},hostfwd=tcp::3389-:3389 \<br />Â -drive file=${VM_IMAGE},media=disk,if=virtio \<br />Â -snapshot \<br />Â -nographic<br /><br /></pre>
+<p class=" ">Job script links application data (win), input data (data) and run script (run.bat) into job directory and runs virtual machine.</p>
+<p class=" ">Example run script (run.bat) for Windows virtual machine:</p>
+<pre class=" ">z:<br />cd \win\appl<br />call application.bat z:\data z:\output</pre>
+<p class=" ">Run script runs application from shared job directory (mapped as drive z:), process input data (z:\data) from job directory and store output to job directory (z:\output).</p>
+<h3 class=" ">Run jobs</h3>
+<p>Run jobs as usual, see <a href="../../resource-allocation-and-job-execution/introduction.html" title="" target="_self" class="internal-link">Resource Allocation and Job Execution</a>. Use only full node allocation for virtualization jobs.</p>
+<h3 class=" ">Running Virtual Machines</h3>
+<p>Virtualization is enabled only on compute nodes, virtualization does not work on login nodes.</p>
+<p>Load QEMU environment module:</p>
+<pre class=" ">$ module add qemu</pre>
+<p class=" ">Get help</p>
+<pre class=" ">$ man qemu</pre>
+<p class=" ">Run virtual machine (simple)</p>
+<pre class=" ">$ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -vnc :0<br /><br />$ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -vnc :0</pre>
+<p class=" ">You can access virtual machine by VNC viewer (option -vnc) connecting to IP address of compute node. For VNC you must use <a href="../../accessing-the-cluster/vpn-access.html" title="" target="_self" class="internal-link">VPN network</a>.</p>
+<p class=" ">Install virtual machine from iso file</p>
+<pre class=" ">$ qemu-system-x86_64 -hda linux.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -cdrom linux-install.iso -boot d -vnc :0<br /><br />$ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -cdrom win-install.iso -boot d -vnc :0</pre>
+<p class=" ">Run virtual machine using optimized devices, user network backend with sharing and port forwarding, in snapshot mode</p>
+<pre class=" ">$ qemu-system-x86_64 -drive file=linux.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::2222-:22 -vnc :0 -snapshot<br /><br />$ qemu-system-x86_64 -drive file=win.img,media=disk,if=virtio -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::3389-:3389 -vnc :0 -snapshot</pre>
+<p class=" ">Thanks to port forwarding you can access virtual machine via SSH (Linux) or RDP (Windows) connecting to IP address of compute node (and port 2222 for SSH). You must use <a href="../../accessing-the-cluster/vpn-access.html" title="" target="_self" class="internal-link">VPN network</a>.</p>
+<p class="callout">Keep in mind, that if you use virtio devices, you must have virtio drivers installed on your virtual machine.</p>
+<h3 class=" ">Networking and data sharing</h3>
+<p class=" ">For networking virtual machine we suggest to use (default) user network backend (sometimes called slirp). This network backend NATs virtual machines and provides useful services for virtual machines as DHCP, DNS, SMB sharing, port forwarding.</p>
+<p class=" ">In default configuration IP network 10.0.2.0/24 is used, host has IP address 10.0.2.2, DNS server 10.0.2.3, SMB server 10.0.2.4 and virtual machines obtain address from range 10.0.2.15-10.0.2.31. Virtual machines have access to Anselm's network via NAT on compute node (host).</p>
+<p class=" ">Simple network setup</p>
+<pre class=" ">$ qemu-system-x86_64 ... -net nic -net user</pre>
+<p class=" ">(It is default when no -net options are given.)<br /><br />Simple network setup with sharing and port forwarding (obsolete but simpler syntax, lower performance)</p>
+<pre class=" ">$ qemu-system-x86_64 ... -net nic -net user,smb=/scratch/$USER/tmp,hostfwd=tcp::3389-:3389</pre>
+<p class=" ">Optimized network setup with sharing and port forwarding</p>
+<pre class=" ">$ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net0 -netdev user,id=net0,smb=/scratch/$USER/tmp,hostfwd=tcp::2222-:22</pre>
+<h3 class=" ">Advanced networking</h3>
+<p><strong>Internet access</strong></p>
+<p class=" ">Sometime your virtual machine needs access to internet (install software, updates, software activation, etc). We suggest solution using Virtual Distributed Ethernet (VDE) enabled QEMU with SLIRP running on login node tunnelled to compute node. Be aware, this setup has very low performance, the worst performance of all described solutions.</p>
+<p class=" ">Load VDE enabled QEMU environment module (unload standard QEMU module first if necessary).</p>
+<pre class=" ">$ module add qemu/2.1.2-vde2</pre>
+<p class=" ">Create virtual network switch.</p>
+<pre class=" ">$ vde_switch -sock /tmp/sw0 -mgmt /tmp/sw0.mgmt -daemon</pre>
+<p class=" ">Run SLIRP daemon over SSH tunnel on login node and connect it to virtual network switch.</p>
+<pre class=" ">$ dpipe vde_plug /tmp/sw0 = ssh login1 $VDE2_DIR/bin/slirpvde -s - --dhcp &</pre>
+<p class=" ">Run qemu using vde network backend, connect to created virtual switch.</p>
+<p class=" ">Basic setup (obsolete syntax)</p>
+<pre class=" ">$ qemu-system-x86_64 ... -net nic -net vde,sock=/tmp/sw0</pre>
+<p class=" ">Setup using virtio device (obsolete syntax)</p>
+<pre class=" ">$ qemu-system-x86_64 ... -net nic,model=virtio -net vde,sock=/tmp/sw0<strong></strong></pre>
+<p class=" ">Optimized setup</p>
+<pre class=" ">$ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net0 -netdev vde,id=net0,sock=/tmp/sw0</pre>
+<p class=" "><strong><br /></strong></p>
+<p class=" "><strong>TAP interconnect</strong></p>
+<p class=" ">Both user and vde network backend have low performance. For fast interconnect (10Gbps and more) of compute node (host) and virtual machine (guest) we suggest using Linux kernel TAP device.</p>
+<p class=" ">Cluster Anselm provides TAP device tap0 for your job. TAP interconnect does not provide any services (like NAT, DHCP, DNS, SMB, etc.) just raw networking, so you should provide your services if you need them.</p>
+<p class=" ">Run qemu with TAP network backend:</p>
+<pre class=" ">$ qemu-system-x86_64 ... -device virtio-net-pci,netdev=net1 \<br /> -netdev tap,id=net1,ifname=tap0,script=no,downscript=no</pre>
+<p class=" ">Interface tap0 has IP address 192.168.1.1 and network mask 255.255.255.0 (/24). In virtual machine use IP address from range 192.168.1.2-192.168.1.254. For your convenience some ports on tap0 interface are redirected to higher numbered ports, so you as non-privileged user can provide services on these ports.</p>
+<p class=" ">Redirected ports:</p>
+<ul>
+<li>DNS udp/53->udp/3053, tcp/53->tcp3053</li>
+<li>DHCP udp/67->udp3067</li>
+<li>SMB tcp/139->tcp3139, tcp/445->tcp3445).</li>
+</ul>
+<p class=" ">You can configure IP address of virtual machine statically or dynamically. For dynamic addressing provide your DHCP server on port 3067 of tap0 interface, you can also provide your DNS server on port 3053 of tap0 interface for example:</p>
+<pre class=" ">$ dnsmasq --interface tap0 --bind-interfaces -p 3053 --dhcp-alternate-port=3067,68 --dhcp-range=192.168.1.15,192.168.1.32 --dhcp-leasefile=/tmp/dhcp.leasefile</pre>
+<p class=" ">You can also provide your SMB services (on ports 3139, 3445) to obtain high performance data sharing.</p>
+<p class=" ">Example smb.conf (not optimized)</p>
+<pre class=" ">[global]<br />socket address=192.168.1.1<br />smb ports = 3445 3139<br /><br />private dir=/tmp/qemu-smb<br />pid directory=/tmp/qemu-smb<br />lock directory=/tmp/qemu-smb<br />state directory=/tmp/qemu-smb<br />ncalrpc dir=/tmp/qemu-smb/ncalrpc<br />log file=/tmp/qemu-smb/log.smbd<br />smb passwd file=/tmp/qemu-smb/smbpasswd<br />security = user<br />map to guest = Bad User<br />unix extensions = no<br />load printers = no<br />printing = bsd<br />printcap name = /dev/null<br />disable spoolss = yes<br />log level = 1<br />guest account = USER<br />[qemu]<br />path=/scratch/USER/tmp<br />read only=no<br />guest ok=yes<br />writable=yes<br />follow symlinks=yes<br />wide links=yes<br />force user=USER</pre>
+<p class=" ">(Replace USER with your login name.)</p>
+<p class=" ">Run SMB services</p>
+<pre class=" ">smbd -s /tmp/qemu-smb/smb.conf</pre>
+<p class=" ">Â </p>
+<p class=" ">Virtual machine can of course have more than one network interface controller, virtual machine can use more than one network backend. So, you can combine for example use network backend and TAP interconnect.</p>
+<h3 class=" "><a name="snapshot-mode"></a>Snapshot mode</h3>
+<p>In snapshot mode image is not written, changes are written to temporary file (and discarded after virtual machine exits).<strong> It is strongly recommended mode for running your jobs.</strong> Set TMPDIR environment variable to local scratch directory for placement temporary files.</p>
+<pre class=" ">$ export TMPDIR=/lscratch/${PBS_JOBID}<br />$ qemu-system-x86_64 ... -snapshot</pre>
+<h3 class=" ">Windows guests</h3>
+<p>For Windows guests we recommend these options, life will be easier:</p>
+<pre class=" ">$ qemu-system-x86_64 ... -localtime -usb -usbdevice tablet</pre>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization.md b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization.md
index ddf91546f..1ff0abeaa 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization.md
@@ -112,7 +112,7 @@ concurrent jobs.
You can either use your existing image or create new image from scratch.
-EMU currently supports these image types or formats:
+QEMU currently supports these image types or formats:
- rawÂ
- cloopÂ
@@ -125,7 +125,7 @@ EMU currently supports these image types or formats:
with VirtualBox.
You can convert your existing image using qemu-img convert command.
-Supported formats of this command areblkdebug blkverify bochs cloop
+Supported formats of this command are: blkdebug blkverify bochs cloop
cow dmg file ftp ftps host_cdrom host_device host_floppy http https
nbd parallels qcow qcow2 qed raw sheepdog tftp vdi vhdx vmdk vpc vvfat.
@@ -189,8 +189,8 @@ Example startup script for Windows virtual machine:
rem Mount share
echo %DATE% %TIME% Mounting shared drive>>%LOG%
- net use z10.0.2.4qemu >>%LOG% 2>&1
- dir z>>%LOG% 2>&1
+ net use z: 10.0.2.4qemu >>%LOG% 2>&1
+ dir z: >>%LOG% 2>&1
echo. >>%LOG%
@@ -216,7 +216,7 @@ Example startup script for Windows virtual machine:
echo %DATE% %TIME% Shut down>>%LOG%
shutdown /s /t 0
-Example startup script maps shared job script as drive zand looks for
+Example startup script maps shared job script as drive z: and looks for
run script called run.bat. If run script is found it is run else wait
for 5 minutes, then shutdown virtual machine.
@@ -489,4 +489,3 @@ For Windows guests we recommend these options, life will be easier:
$ qemu-system-x86_64 ... -localtime -usb -usbdevice tablet
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/storage-1.html b/docs.it4i.cz/anselm-cluster-documentation/storage-1.html
new file mode 100644
index 000000000..9b1e8c48f
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/storage-1.html
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+ <p>There are two main shared file systems on Anselm cluster, the <a class="anchor-link" href="storage.html#home" target="_self" title="">HOME</a> and <a class="anchor-link" href="storage.html#scratch" target="_self" title="">SCRATCH</a>. All login and compute nodes may access same data on shared filesystems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp filesystems.</p>
+<h2 class=" ">Archiving</h2>
+<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a href="storage-1/cesnet-data-storage.html" title="" target="_self" class="internal-link">CESNET storage service</a>, which is available via SSHFS.</p>
+<h2 class=" ">Shared Filesystems</h2>
+<p class=" ">Anselm computer provides two main shared filesystems, the <a class="anchor-link" href="storage.html#home" target="_self" title="">HOME filesystem</a> and the <a class="anchor-link" href="storage.html#scratch" target="_self" title="">SCRATCH filesystem</a>. Both HOME and SCRATCH filesystems are realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both Lustre filesystems for the purpose of sharing data with other users using fine-grained control.</p>
+<h3 class=" ">Understanding the Lustre Filesystems</h3>
+<p>(source <a class="external-link" href="http://www.nas.nasa.gov" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
+<p>A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.</p>
+<p>When a client (a <span class="glossaryItem">compute <span class="glossaryItem">node</span></span> from your job) needs to create or access a file, the client queries the metadata server (<span class="glossaryItem">MDS</span>) and the metadata target (<span class="glossaryItem">MDT</span>) for the layout and location of the <a href="http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping">file's stripes</a>. Once the file is opened and the client obtains the striping information, the <span class="glossaryItem">MDS</span> is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.</p>
+<p>If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.</p>
+<p>There is default stripe configuration for Anselm Lustre filesystems. However, users can set the following stripe parameters for their own directories or files to get optimum I/O performance:</p>
+<ol><ol>
+<li>stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre filesystems</li>
+<li>stripe_count the number of OSTs to stripe across; default is 1 for Anselm Lustre filesystems one can specify -1 to use all OSTs in the filesystem.</li>
+<li>stripe_offset The index of the <span class="glossaryItem">OST</span> where the first stripe is to be placed; default is -1 which results in random selection; using a non-default value is NOT recommended.</li>
+</ol></ol>
+<p class=" ">Â </p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<p class=" ">Use the lfs getstripe for getting the stripe parameters. Use the lfs setstripe command for setting the stripe parameters to get optimal I/O performance The correct stripe setting depends on your needs and file access patterns. </p>
+<pre class="prettyprint lang-sh"><code>$ lfs getstripe dir|filename <br />$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename </code></pre>
+<p>Example:</p>
+<pre class="prettyprint lang-sh">$ lfs getstripe /scratch/username/<br />/scratch/username/<br />stripe_count: 1 stripe_size: 1048576 stripe_offset: -1<br /><br />$ lfs setstripe -c -1 /scratch/username/<br />$ lfs getstripe /scratch/username/<br />/scratch/username/<br />stripe_count: 10 stripe_size: 1048576 stripe_offset: -1</pre>
+<p>In this example, we view current stripe setting of the /scratch/username/ directory. The stripe count is changed to all OSTs, and verified. All files written to this directory will be striped over 10 OSTs</p>
+<p>Use lfs check OSTs to see the number and status of active OSTs for each filesystem on Anselm. Learn more by reading the man page</p>
+<pre class="prettyprint lang-sh">$ lfs check osts<br />$ man lfs</pre>
+<h3 class=" ">Hints on Lustre Stripping</h3>
+<p class="callout">Increase the stripe_count for parallel I/O to the same file.</p>
+<p>When multiple processes are writing blocks of data to the same file in parallel, the I/O performance for large files will improve when the stripe_count is set to a larger value. The stripe count sets the number of OSTs the file will be written to. By default, the stripe count is set to 1. While this default setting provides for efficient access of metadata (for example to support the ls -l command), large files should use stripe counts of greater than 1. This will increase the aggregate I/O bandwidth by using multiple OSTs in parallel instead of just one. A rule of thumb is to use a stripe count approximately equal to the number of gigabytes in the file.</p>
+<p>Another good practice is to make the stripe count be an integral factor of the number of processes performing the write in parallel, so that you achieve load balance among the OSTs. For example, set the stripe count to 16 instead of 15 when you have 64 processes performing the writes.</p>
+<p class="callout">Using a large stripe size can improve performance when accessing very large files</p>
+<p>Large stripe size allows each client to have exclusive access to its own part of a file. However, it can be counterproductive in some cases if it does not match your I/O pattern. The choice of stripe size has no effect on a single-stripe file.</p>
+<p>Read more on <a class="external-link" href="http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html" target="_self" title="">http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html</a></p>
+<h3 class=" ">Lustre on Anselm</h3>
+<p>The architecture of Lustre on Anselm is composed of two metadata servers (MDS) and four data/object storage servers (OSS). Two object storage servers are used for file system HOME and another two object storage servers are used for file system SCRATCH.</p>
+<p class=" "><span class="emphasis">Configuration of the storages</span></p>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem"><span class="emphasis">HOME Lustre object storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">One disk array NetApp E5400</li>
+<li class="listitem">22 OSTs</li>
+<li class="listitem">227 2TB NL-SAS 7.2krpm disks</li>
+<li class="listitem">22 groups of 10 disks in RAID6 (8+2)</li>
+<li class="listitem">7 hot-spare disks</li>
+</ul>
+</div>
+</li>
+<li class="listitem"><span class="emphasis">SCRATCH Lustre object storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">Two disk arrays NetApp E5400</li>
+<li class="listitem">10 OSTs</li>
+<li class="listitem">106 2TB NL-SAS 7.2krpm disks</li>
+<li class="listitem">10 groups of 10 disks in RAID6 (8+2)</li>
+<li class="listitem">6 hot-spare disks</li>
+</ul>
+</div>
+</li>
+<li class="listitem"><span class="emphasis">Lustre metadata storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">One disk array NetApp E2600</li>
+<li class="listitem">12 300GB SAS 15krpm disks</li>
+<li class="listitem">2 groups of 5 disks in RAID5</li>
+<li class="listitem">2 hot-spare disks</li>
+</ul>
+</div>
+</li>
+</ul>
+</div>
+<h3 class=" "><a name="home"></a><a name="home"></a>HOME</h3>
+<p>The HOME filesystem is mounted in directory /home. Users home directories /home/username reside on this filesystem. Accessible capacity is 320TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. <span>If 250GB should prove as insufficient for particular user, please contact</span>Â <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request.</p>
+<p class="callout">The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.</p>
+<p>The HOME filesystem should not be used to archive data of past Projects or other unrelated data.</p>
+<p>The files on HOME filesystem will not be deleted until end of the <a href="../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html" title="" target="_self" class="internal-link">users lifecycle</a>.</p>
+<p class=" ">The filesystem is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files. </p>
+<p class=" ">The HOME filesystem is realized as Lustre parallel filesystem and is available on all login and computational nodes. <br />Default stripe size is 1MB, stripe count is 1. There are 22 OSTs dedicated for the HOME filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">HOME filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/home</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>320TB</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>2GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>250GB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>22</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><a name="scratch"></a><a name="scratch"></a>SCRATCH</h3>
+<p>The SCRATCH filesystem is mounted in directory /scratch. Users may freely create subdirectories and files on the filesystem. Accessible capacity is 146TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 100TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. <span>If 100TB should prove as insufficient for particular user, please contact <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request. </span></p>
+<p class="callout">The Scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the SCRATCH filesystem as their working directory.<br /><br />Users are advised to save the necessary data from the SCRATCH filesystem to HOME filesystem after the calculations and clean up the scratch files.<br /><br />Files on the SCRATCH filesystem that are <strong>not accessed for more than 90 days</strong> will be automatically <strong>deleted</strong>.</p>
+<p>The SCRATCH filesystem is realized as Lustre parallel filesystem and is available from all login and computational nodes. <br />Default stripe size is 1MB, stripe count is 1. There are 10 OSTs dedicated for the SCRATCH filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">SCRATCH filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/scratch</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>146TB</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>6GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>100TB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>10</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><span>Disk usage and quota commands</span></h3>
+<p><span>User quotas on the file systems can be checked and reviewed using following command:</span></p>
+<pre class="prettyprint lang-sh">$ lfs quota dir</pre>
+<p>Example for Lustre HOME directory:</p>
+<pre class="prettyprint lang-sh">$ lfs quota /home<br />Disk quotas for user user001 (uid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /home 300096 0 250000000 - 2102 0 500000 -<br />Disk quotas for group user001 (gid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /home 300096 0 0 - 2102 0 0 -</pre>
+<p>In this example, we view current quota size limit of 250GB and 300MB currently used by user001.</p>
+<p>Example for Lustre SCRATCH directory:</p>
+<pre class="prettyprint lang-sh">$ lfs quota /scratch<br />Disk quotas for user user001 (uid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br />  /scratch    8    0 100000000000    -    3    0    0    -<br />Disk quotas for gro<span>up user001 (gid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /scratch    8    0    0    -    3    0    0    -<br /></span></pre>
+<p>In this example, we view current quota size limit of 100TB and 8KB currently used by user001.</p>
+<p>Â </p>
+<p>To have a better understanding of where the space is exactly used, you can use following command to find out.</p>
+<pre class="prettyprint lang-sh">$ du -hs dir</pre>
+<p>Example for your HOME directory:</p>
+<pre class="prettyprint lang-sh">$ cd /home<br />$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr<br />258M cuda-samples<br />15M .cache<br />13M .mozilla<br />5,5M .eclipse<br />2,7M .idb_13.0_linux_intel64_app</pre>
+<p>This will list all directories which are having MegaBytes or GigaBytes of consumed space in your actual (in this example HOME) directory. List is sorted in descending order from largest to smallest files/directories.</p>
+<p><br /> <span>To have a better understanding of previous commands, you can read manpages.</span></p>
+<pre class="prettyprint lang-sh">$ man lfs</pre>
+<pre class="prettyprint lang-sh">$ man du </pre>
+<h3 class=" ">Extended ACLs</h3>
+<p class=" ">Extended ACLs provide another security mechanism beside the standard POSIX ACLs which are defined by three entries (for owner/group/others). Extended ACLs have more than the three basic entries. In addition, they also contain a mask entry and may contain any number of named user and named group entries.</p>
+<p class=" ">ACLs on a Lustre file system work exactly like ACLs on any Linux file system. They are manipulated with the standard tools in the standard manner. Below, we create a directory and allow a specific user access.</p>
+<pre class="prettyprint lang-sh">[vop999@login1.anselm ~]$ umask 027<br />[vop999@login1.anselm ~]$ mkdir test<br />[vop999@login1.anselm ~]$ ls -ld test<br />drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.anselm ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />group::r-x<br />other::---<br /><br />[vop999@login1.anselm ~]$ setfacl -m user:johnsm:rwx test<br />[vop999@login1.anselm ~]$ ls -ld test<br />drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.anselm ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />user:johnsm:rwx<br />group::r-x<br />mask::rwx<br />other::---</pre>
+<p class=" ">Default ACL mechanism can be used to replace setuid/setgid permissions on directories. Setting a default ACL on a directory (-d flag to setfacl) will cause the ACL permissions to be inherited by any newly created file or subdirectory within the directory. Refer to this page for more information on Linux ACL:</p>
+<p class=" "><a class="external-link" href="http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html" target="_self" title="">http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html </a></p>
+<h2 class=" ">Local Filesystems</h2>
+<h3 class=" ">Local Scratch</h3>
+<p>Every computational node is equipped with 330GB local scratch disk.</p>
+<p class="callout">Use local scratch in case you need to access large amount of small files during your calculation.</p>
+<p><a name="LocalScratch"></a>The local scratch disk is mounted as /lscratch and is accessible to user at /lscratch/$PBS_JOBID directory.</p>
+<p class=" ">The local scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs that access large number of small files within the calculation must use the local scratch filesystem as their working directory. This is required for performance reasons, as frequent access to number of small files may overload the metadata servers (MDS) of the Lustre filesystem.</p>
+<p class="callout">The local scratch directory /lscratch/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">local SCRATCH filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/lscratch</td>
+</tr>
+<tr class="odd">
+<td>Accesspoint</td>
+<td>/lscratch/$PBS_JOBID</td>
+</tr>
+<tr class="even">
+<td>Capacity</td>
+<td>330GB</td>
+</tr>
+<tr class="odd">
+<td>Throughput</td>
+<td>100MB/s</td>
+</tr>
+<tr class="even">
+<td>User quota</td>
+<td>none</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" ">RAM disk</h3>
+<p>Every computational node is equipped with filesystem realized in memory, so called RAM disk.</p>
+<p class="callout">Use RAM disk in case you need really fast access to your data of limited size during your calculation.<br />Be very careful, use of RAM disk filesystem is at the expense of operational memory.</p>
+<p><a name="LocalScratch"></a>The local RAM disk is mounted as /ramdisk and is accessible to user at /ramdisk/$PBS_JOBID directory.</p>
+<p class=" ">The local RAM disk filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. Size of RAM disk filesystem is limited. Be very careful, use of RAM disk filesystem is at the expense of operational memory. It is not recommended to allocate large amount of memory and use large amount of data in RAM disk filesystem at the same time.</p>
+<p class="callout">The local RAM disk directory /ramdisk/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">RAM disk</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td><span class="monospace">/ramdisk</span></td>
+</tr>
+<tr class="odd">
+<td>Accesspoint</td>
+<td><span class="monospace">/ramdisk/$PBS_JOBID</span></td>
+</tr>
+<tr class="even">
+<td>Capacity</td>
+<td>
+<p>60GB at compute nodes without accelerator</p>
+<p>90GB at compute nodes with accelerator</p>
+<p>500GB at fat nodes</p>
+</td>
+</tr>
+<tr class="odd">
+<td>Throughput</td>
+<td>
+<p>over 1.5 GB/s write, over 5 GB/s read, single thread<br />over 10 GB/s write, over 50 GB/s read, 16 threads</p>
+</td>
+</tr>
+<tr class="even">
+<td>User quota</td>
+<td>none</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" ">tmp</h3>
+<p>Each node is equipped with local /tmp directory of few GB capacity. The /tmp directory should be used to work with small temporary files. Old files in /tmp directory are automatically purged.</p>
+<div class="table">
+<h2 class=" "><strong>Summary<br /></strong></h2>
+<div class="table-contents">
+<table class="listing" summary="Best usage of the file systems"><colgroup><col><col><col><col><col><col><col><col></colgroup>
+<thead>
+<tr><th align="center" style="text-align: center; ">Mountpoint</th><th align="center" style="text-align: center; ">Usage</th><th align="center" style="text-align: center; ">Protocol</th><th align="center" style="text-align: center; ">Net Capacity</th><th align="center" style="text-align: center; ">Throughput</th><th align="center" style="text-align: center; ">Limitations</th><th align="center" style="text-align: center; ">Access</th><th align="center" style="text-align: center; ">Services</th></tr>
+</thead>
+<tbody>
+<tr class="even">
+<td><span class="monospace">/home</span></td>
+<td align="center">home directory</td>
+<td align="center">Lustre</td>
+<td align="center">320 TiB</td>
+<td align="center">2 GB/s</td>
+<td align="center">Quota 250GB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">backed up</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/scratch</span></td>
+<td align="center">cluster shared jobs' data</td>
+<td align="center">Lustre</td>
+<td align="center">146 TiB</td>
+<td align="center">6 GB/s</td>
+<td align="center">Quota 100TB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">files older 90 days removed</td>
+</tr>
+<tr class="even">
+<td><span class="monospace">/lscratch</span></td>
+<td align="center">node local jobs' data</td>
+<td align="center">local</td>
+<td align="center">330 GB</td>
+<td align="center">100 MB/s</td>
+<td align="center">none</td>
+<td align="center">Compute nodes</td>
+<td align="center">purged after job ends</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/ramdisk</span></td>
+<td align="center">node local jobs' data</td>
+<td align="center">local</td>
+<td align="center">60, 90, 500 GB</td>
+<td align="center">5-50 GB/s</td>
+<td align="center">none</td>
+<td align="center">Compute nodes</td>
+<td align="center">purged after job ends</td>
+</tr>
+<tr class="even">
+<td><span class="monospace">/tmp</span></td>
+<td align="center">local temporary files</td>
+<td align="center">local</td>
+<td align="center"></td>
+<td align="center">100 MB/s</td>
+<td align="center">none</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">auto purged</td>
+</tr>
+</tbody>
+</table>
+</div>
+</div>
+<p>Â </p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/storage-1.md b/docs.it4i.cz/anselm-cluster-documentation/storage-1.md
index 982a9a71f..56438ce18 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/storage-1.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/storage-1.md
@@ -61,7 +61,7 @@ There is default stripe configuration for Anselm Lustre filesystems.
However, users can set the following stripe parameters for their own
directories or files to get optimum I/O performance:
-1. stripe_sizethe size of the chunk in bytes; specify with k, m, or
+1. stripe_size: the size of the chunk in bytes; specify with k, m, or
g to use units of KB, MB, or GB, respectively; the size must be an
even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre
filesystems
@@ -93,12 +93,12 @@ Example:
```
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 1 stripe_size 1048576 stripe_offset -1
+stripe_count: 1 stripe_size: 1048576 stripe_offset: -1
$ lfs setstripe -c -1 /scratch/username/
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 10 stripe_size 1048576 stripe_offset -1
+stripe_count: 10 stripe_size: 1048576 stripe_offset: -1
```
In this example, we view current stripe setting of the
@@ -378,9 +378,9 @@ manner. Below, we create a directory and allow a specific user access.
[vop999@login1.anselm ~]$ ls -ld test
drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# filetest
-# ownervop999
-# groupvop999
+# file: test
+# owner: vop999
+# group: vop999
user::rwx
group::r-x
other::---
@@ -389,9 +389,9 @@ other::---
[vop999@login1.anselm ~]$ ls -ld test
drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# filetest
-# ownervop999
-# groupvop999
+# file: test
+# owner: vop999
+# group: vop999
user::rwx
user:johnsm:rwx
group::r-x
@@ -507,4 +507,3 @@ files in /tmp directory are automatically purged.
<span class="monospace">/tmp</span> local temporary files local 100 MB/s none Compute and login nodes auto purged
Â
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.html b/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.html
new file mode 100644
index 000000000..3c307eefa
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+ <h2 class=" ">Introduction</h2>
+<p class="external-link" title="">Do not use shared filesystems at IT4Innovations as a backup for large amount of data or long-term archiving purposes.</p>
+<p class="callout" title="">The IT4Innovations does not provide storage capacity for data archiving. Academic staff and students of research institutions in the Czech Republic can use <a class="external-link" href="https://du.cesnet.cz/" target="_self" title="">CESNET Storage service</a>.</p>
+<p class=" ">The CESNET Storage service can be used for research purposes, mainly by academic staff and students of research institutions in the Czech Republic.<br /><br />User of data storage CESNET (DU) association can become organizations or an individual person who is either in the current employment relationship (employees) or the current study relationship (students) to a legal entity (organization) that meets the “Principles for access to CESNET Large infrastructure (Access Policy)”.<br /><br />User may only use data storage CESNET for data transfer and storage which are associated with activities in science, research, development, the spread of education, culture and prosperity. In detail see “Acceptable Use Policy CESNET Large Infrastructure (Acceptable Use Policy, AUP)”.</p>
+<p class=" ">The service is documented at <a class="external-link" href="https://du.cesnet.cz/wiki/doku.php/en/start" target="_self" title="">https://du.cesnet.cz/wiki/doku.php/en/start</a>. For special requirements please contact directly CESNET Storage Department via e-mail <a class="email-link" href="mailto:du-support@cesnet.cz" target="_self" title="">du-support(at)cesnet.cz</a>.</p>
+<p class=" ">The procedure to obtain the CESNET access is quick and trouble-free.</p>
+<p class=" ">(source <a class="external-link" href="https://du.cesnet.cz/wiki/doku.php/en/start" target="_self" title="CESNET Data Storage">https://du.cesnet.cz/</a>)</p>
+<h2 class=" ">CESNET storage access</h2>
+<h3 class=" ">Understanding Cesnet storage</h3>
+<p class="callout">It is very important to understand the Cesnet storage before uploading data. Please read <a class="external-link" href="https://du.cesnet.cz/en/navody/home-migrace-plzen/start" target="_self" title="">https://du.cesnet.cz/en/navody/home-migrace-plzen/start</a> first.</p>
+<p class=" ">Once registered for CESNET Storage, you may <a class="external-link" href="https://du.cesnet.cz/en/navody/faq/start" target="_self" title="">access the storage</a> in number of ways. We recommend the SSHFS and RSYNC methods.</p>
+<h3 class=" ">SSHFS Access</h3>
+<p class="callout">SSHFS: The storage will be mounted like a local hard drive</p>
+<p>The SSHFSÂ provides a very convenient way to access the CESNET Storage. The storage will be mounted onto a local directory, exposing the vast CESNET Storage as if it was a local removable harddrive. Files can be than copied in and out in a usual fashion.</p>
+<p>First, create the mountpoint</p>
+<pre class=" ">$ mkdir cesnet</pre>
+<p>Mount the storage. Note that you can choose among the ssh.du1.cesnet.cz (Plzen), ssh.du2.cesnet.cz (Jihlava), ssh.du3.cesnet.cz (Brno)<br />Mount tier1_home <strong>(only 5120M !)</strong>:</p>
+<pre class=" ">$ sshfs username@ssh.du1.cesnet.cz:. cesnet/</pre>
+<p class=" ">For easy future access from Anselm, install your public key</p>
+<pre class=" ">$ cp .ssh/id_rsa.pub cesnet/.ssh/authorized_keys</pre>
+<p class=" ">Mount tier1_cache_tape for the Storage VO:</p>
+<pre class=" ">$ sshfs username@ssh.du1.cesnet.cz:/cache_tape/VO_storage/home/username cesnet/</pre>
+<p class=" ">View the archive, copy the files and directories in and out</p>
+<pre class=" ">$ ls cesnet/ <br />$ cp -a mydir cesnet/.<br />$ cp cesnet/myfile .</pre>
+<p class=" ">Once done, please remember to unmount the storage</p>
+<pre class=" ">$ fusermount -u cesnet</pre>
+<h3 class=" ">Rsync access</h3>
+<p class="callout">Rsync provides delta transfer for best performance, can resume interrupted transfers</p>
+<p>Rsync is a fast and extraordinarily versatile file copying tool. It is famous for its delta-transfer algorithm, which reduces the amount of data sent over the network by sending only the differences between the source files and the existing files in the destination. Rsync is widely used for backups and mirroring and as an improved copy command for everyday use.<br /><br />Rsync finds files that need to be transferred using a "quick check" algorithm (by default) that looks for files that have changed in size or in last-modified time. Any changes in the other preserved attributes (as requested by options) are made on the destination file directly when the quick check indicates that the file's data does not need to be updated.</p>
+<p class=" ">More about Rsync at <a class="external-link" href="https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele" target="_self" title="">https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele</a></p>
+<p class=" ">Transfer large files to/from Cesnet storage, assuming membership in the Storage VO</p>
+<pre class=" ">$ rsync --progress datafile username@ssh.du1.cesnet.cz:VO_storage-cache_tape/.<br />$ rsync --progress username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafile .</pre>
+<p class=" ">Transfer large directories to/from Cesnet storage, assuming membership in the Storage VO</p>
+<pre class=" ">$ rsync --progress -av datafolder username@ssh.du1.cesnet.cz:VO_storage-cache_tape/.<br />$ rsync --progress -av username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafolder .</pre>
+<p class=" ">Transfer rates of about 28MB/s can be expected.</p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md b/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md
index a8989b5f9..2f65b5a9b 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md
@@ -57,7 +57,7 @@ number of ways. We recommend the SSHFS and RSYNC methods.
### SSHFS Access
-SSHFSThe storage will be mounted like a local hard drive
+SSHFS: The storage will be mounted like a local hard drive
The SSHFSÂ provides a very convenient way to access the CESNET Storage.
The storage will be mounted onto a local directory, exposing the vast
@@ -127,4 +127,3 @@ in the Storage VO
$ rsync --progress -av username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafolder .
Transfer rates of about 28MB/s can be expected.
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.html b/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.html
new file mode 100644
index 000000000..914c89493
--- /dev/null
+++ b/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.html
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+ <p>There are two main shared file systems on Anselm cluster, the <a class="anchor-link" href="../storage.html#home" target="_self" title="">HOME</a> and <a class="anchor-link" href="../storage.html#scratch" target="_self" title="">SCRATCH</a>. All login and compute nodes may access same data on shared filesystems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp filesystems.</p>
+<h2 class=" ">Archiving</h2>
+<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a href="cesnet-data-storage.html" title="" target="_self" class="internal-link">CESNET storage service</a>, which is available via SSHFS.</p>
+<h2 class=" ">Shared Filesystems</h2>
+<p class=" ">Anselm computer provides two main shared filesystems, the <a class="anchor-link" href="../storage.html#home" target="_self" title="">HOME filesystem</a> and the <a class="anchor-link" href="../storage.html#scratch" target="_self" title="">SCRATCH filesystem</a>. Both HOME and SCRATCH filesystems are realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both Lustre filesystems for the purpose of sharing data with other users using fine-grained control.</p>
+<h3 class=" ">Understanding the Lustre Filesystems</h3>
+<p>(source <a class="external-link" href="http://www.nas.nasa.gov" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
+<p>A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.</p>
+<p>When a client (a <span class="glossaryItem">compute <span class="glossaryItem">node</span></span> from your job) needs to create or access a file, the client queries the metadata server (<span class="glossaryItem">MDS</span>) and the metadata target (<span class="glossaryItem">MDT</span>) for the layout and location of the <a href="http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping">file's stripes</a>. Once the file is opened and the client obtains the striping information, the <span class="glossaryItem">MDS</span> is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.</p>
+<p>If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.</p>
+<p>There is default stripe configuration for Anselm Lustre filesystems. However, users can set the following stripe parameters for their own directories or files to get optimum I/O performance:</p>
+<ol><ol>
+<li>stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre filesystems</li>
+<li>stripe_count the number of OSTs to stripe across; default is 1 for Anselm Lustre filesystems one can specify -1 to use all OSTs in the filesystem.</li>
+<li>stripe_offset The index of the <span class="glossaryItem">OST</span> where the first stripe is to be placed; default is -1 which results in random selection; using a non-default value is NOT recommended.</li>
+</ol></ol>
+<p class=" ">Â </p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<p class=" ">Use the lfs getstripe for getting the stripe parameters. Use the lfs setstripe command for setting the stripe parameters to get optimal I/O performance The correct stripe setting depends on your needs and file access patterns. </p>
+<pre class="prettyprint lang-sh"><code>$ lfs getstripe dir|filename <br />$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename </code></pre>
+<p>Example:</p>
+<pre class="prettyprint lang-sh">$ lfs getstripe /scratch/username/<br />/scratch/username/<br />stripe_count: 1 stripe_size: 1048576 stripe_offset: -1<br /><br />$ lfs setstripe -c -1 /scratch/username/<br />$ lfs getstripe /scratch/username/<br />/scratch/username/<br />stripe_count: 10 stripe_size: 1048576 stripe_offset: -1</pre>
+<p>In this example, we view current stripe setting of the /scratch/username/ directory. The stripe count is changed to all OSTs, and verified. All files written to this directory will be striped over 10 OSTs</p>
+<p>Use lfs check OSTs to see the number and status of active OSTs for each filesystem on Anselm. Learn more by reading the man page</p>
+<pre class="prettyprint lang-sh">$ lfs check osts<br />$ man lfs</pre>
+<h3 class=" ">Hints on Lustre Stripping</h3>
+<p class="callout">Increase the stripe_count for parallel I/O to the same file.</p>
+<p>When multiple processes are writing blocks of data to the same file in parallel, the I/O performance for large files will improve when the stripe_count is set to a larger value. The stripe count sets the number of OSTs the file will be written to. By default, the stripe count is set to 1. While this default setting provides for efficient access of metadata (for example to support the ls -l command), large files should use stripe counts of greater than 1. This will increase the aggregate I/O bandwidth by using multiple OSTs in parallel instead of just one. A rule of thumb is to use a stripe count approximately equal to the number of gigabytes in the file.</p>
+<p>Another good practice is to make the stripe count be an integral factor of the number of processes performing the write in parallel, so that you achieve load balance among the OSTs. For example, set the stripe count to 16 instead of 15 when you have 64 processes performing the writes.</p>
+<p class="callout">Using a large stripe size can improve performance when accessing very large files</p>
+<p>Large stripe size allows each client to have exclusive access to its own part of a file. However, it can be counterproductive in some cases if it does not match your I/O pattern. The choice of stripe size has no effect on a single-stripe file.</p>
+<p>Read more on <a class="external-link" href="http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html" target="_self" title="">http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html</a></p>
+<h3 class=" ">Lustre on Anselm</h3>
+<p>The architecture of Lustre on Anselm is composed of two metadata servers (MDS) and four data/object storage servers (OSS). Two object storage servers are used for file system HOME and another two object storage servers are used for file system SCRATCH.</p>
+<p class=" "><span class="emphasis">Configuration of the storages</span></p>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem"><span class="emphasis">HOME Lustre object storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">One disk array NetApp E5400</li>
+<li class="listitem">22 OSTs</li>
+<li class="listitem">227 2TB NL-SAS 7.2krpm disks</li>
+<li class="listitem">22 groups of 10 disks in RAID6 (8+2)</li>
+<li class="listitem">7 hot-spare disks</li>
+</ul>
+</div>
+</li>
+<li class="listitem"><span class="emphasis">SCRATCH Lustre object storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">Two disk arrays NetApp E5400</li>
+<li class="listitem">10 OSTs</li>
+<li class="listitem">106 2TB NL-SAS 7.2krpm disks</li>
+<li class="listitem">10 groups of 10 disks in RAID6 (8+2)</li>
+<li class="listitem">6 hot-spare disks</li>
+</ul>
+</div>
+</li>
+<li class="listitem"><span class="emphasis">Lustre metadata storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">One disk array NetApp E2600</li>
+<li class="listitem">12 300GB SAS 15krpm disks</li>
+<li class="listitem">2 groups of 5 disks in RAID5</li>
+<li class="listitem">2 hot-spare disks</li>
+</ul>
+</div>
+</li>
+</ul>
+</div>
+<h3 class=" "><a name="home"></a><a name="home"></a>HOME</h3>
+<p>The HOME filesystem is mounted in directory /home. Users home directories /home/username reside on this filesystem. Accessible capacity is 320TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. <span>If 250GB should prove as insufficient for particular user, please contact</span>Â <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request.</p>
+<p class="callout">The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.</p>
+<p>The HOME filesystem should not be used to archive data of past Projects or other unrelated data.</p>
+<p>The files on HOME filesystem will not be deleted until end of the <a href="../../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html" title="" target="_self" class="internal-link">users lifecycle</a>.</p>
+<p class=" ">The filesystem is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files. </p>
+<p class=" ">The HOME filesystem is realized as Lustre parallel filesystem and is available on all login and computational nodes. <br />Default stripe size is 1MB, stripe count is 1. There are 22 OSTs dedicated for the HOME filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">HOME filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/home</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>320TB</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>2GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>250GB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>22</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><a name="scratch"></a><a name="scratch"></a>SCRATCH</h3>
+<p>The SCRATCH filesystem is mounted in directory /scratch. Users may freely create subdirectories and files on the filesystem. Accessible capacity is 146TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 100TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. <span>If 100TB should prove as insufficient for particular user, please contact <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request. </span></p>
+<p class="callout">The Scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the SCRATCH filesystem as their working directory.<br /><br />Users are advised to save the necessary data from the SCRATCH filesystem to HOME filesystem after the calculations and clean up the scratch files.<br /><br />Files on the SCRATCH filesystem that are <strong>not accessed for more than 90 days</strong> will be automatically <strong>deleted</strong>.</p>
+<p>The SCRATCH filesystem is realized as Lustre parallel filesystem and is available from all login and computational nodes. <br />Default stripe size is 1MB, stripe count is 1. There are 10 OSTs dedicated for the SCRATCH filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">SCRATCH filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/scratch</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>146TB</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>6GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>100TB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>10</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><span>Disk usage and quota commands</span></h3>
+<p><span>User quotas on the file systems can be checked and reviewed using following command:</span></p>
+<pre class="prettyprint lang-sh">$ lfs quota dir</pre>
+<p>Example for Lustre HOME directory:</p>
+<pre class="prettyprint lang-sh">$ lfs quota /home<br />Disk quotas for user user001 (uid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /home 300096 0 250000000 - 2102 0 500000 -<br />Disk quotas for group user001 (gid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /home 300096 0 0 - 2102 0 0 -</pre>
+<p>In this example, we view current quota size limit of 250GB and 300MB currently used by user001.</p>
+<p>Example for Lustre SCRATCH directory:</p>
+<pre class="prettyprint lang-sh">$ lfs quota /scratch<br />Disk quotas for user user001 (uid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br />  /scratch    8    0 100000000000    -    3    0    0    -<br />Disk quotas for gro<span>up user001 (gid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /scratch    8    0    0    -    3    0    0    -<br /></span></pre>
+<p>In this example, we view current quota size limit of 100TB and 8KB currently used by user001.</p>
+<p>Â </p>
+<p>To have a better understanding of where the space is exactly used, you can use following command to find out.</p>
+<pre class="prettyprint lang-sh">$ du -hs dir</pre>
+<p>Example for your HOME directory:</p>
+<pre class="prettyprint lang-sh">$ cd /home<br />$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr<br />258M cuda-samples<br />15M .cache<br />13M .mozilla<br />5,5M .eclipse<br />2,7M .idb_13.0_linux_intel64_app</pre>
+<p>This will list all directories which are having MegaBytes or GigaBytes of consumed space in your actual (in this example HOME) directory. List is sorted in descending order from largest to smallest files/directories.</p>
+<p><br /> <span>To have a better understanding of previous commands, you can read manpages.</span></p>
+<pre class="prettyprint lang-sh">$ man lfs</pre>
+<pre class="prettyprint lang-sh">$ man du </pre>
+<h3 class=" ">Extended ACLs</h3>
+<p class=" ">Extended ACLs provide another security mechanism beside the standard POSIX ACLs which are defined by three entries (for owner/group/others). Extended ACLs have more than the three basic entries. In addition, they also contain a mask entry and may contain any number of named user and named group entries.</p>
+<p class=" ">ACLs on a Lustre file system work exactly like ACLs on any Linux file system. They are manipulated with the standard tools in the standard manner. Below, we create a directory and allow a specific user access.</p>
+<pre class="prettyprint lang-sh">[vop999@login1.anselm ~]$ umask 027<br />[vop999@login1.anselm ~]$ mkdir test<br />[vop999@login1.anselm ~]$ ls -ld test<br />drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.anselm ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />group::r-x<br />other::---<br /><br />[vop999@login1.anselm ~]$ setfacl -m user:johnsm:rwx test<br />[vop999@login1.anselm ~]$ ls -ld test<br />drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.anselm ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />user:johnsm:rwx<br />group::r-x<br />mask::rwx<br />other::---</pre>
+<p class=" ">Default ACL mechanism can be used to replace setuid/setgid permissions on directories. Setting a default ACL on a directory (-d flag to setfacl) will cause the ACL permissions to be inherited by any newly created file or subdirectory within the directory. Refer to this page for more information on Linux ACL:</p>
+<p class=" "><a class="external-link" href="http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html" target="_self" title="">http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html </a></p>
+<h2 class=" ">Local Filesystems</h2>
+<h3 class=" ">Local Scratch</h3>
+<p>Every computational node is equipped with 330GB local scratch disk.</p>
+<p class="callout">Use local scratch in case you need to access large amount of small files during your calculation.</p>
+<p><a name="LocalScratch"></a>The local scratch disk is mounted as /lscratch and is accessible to user at /lscratch/$PBS_JOBID directory.</p>
+<p class=" ">The local scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs that access large number of small files within the calculation must use the local scratch filesystem as their working directory. This is required for performance reasons, as frequent access to number of small files may overload the metadata servers (MDS) of the Lustre filesystem.</p>
+<p class="callout">The local scratch directory /lscratch/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">local SCRATCH filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/lscratch</td>
+</tr>
+<tr class="odd">
+<td>Accesspoint</td>
+<td>/lscratch/$PBS_JOBID</td>
+</tr>
+<tr class="even">
+<td>Capacity</td>
+<td>330GB</td>
+</tr>
+<tr class="odd">
+<td>Throughput</td>
+<td>100MB/s</td>
+</tr>
+<tr class="even">
+<td>User quota</td>
+<td>none</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" ">RAM disk</h3>
+<p>Every computational node is equipped with filesystem realized in memory, so called RAM disk.</p>
+<p class="callout">Use RAM disk in case you need really fast access to your data of limited size during your calculation.<br />Be very careful, use of RAM disk filesystem is at the expense of operational memory.</p>
+<p><a name="LocalScratch"></a>The local RAM disk is mounted as /ramdisk and is accessible to user at /ramdisk/$PBS_JOBID directory.</p>
+<p class=" ">The local RAM disk filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. Size of RAM disk filesystem is limited. Be very careful, use of RAM disk filesystem is at the expense of operational memory. It is not recommended to allocate large amount of memory and use large amount of data in RAM disk filesystem at the same time.</p>
+<p class="callout">The local RAM disk directory /ramdisk/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">RAM disk</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td><span class="monospace">/ramdisk</span></td>
+</tr>
+<tr class="odd">
+<td>Accesspoint</td>
+<td><span class="monospace">/ramdisk/$PBS_JOBID</span></td>
+</tr>
+<tr class="even">
+<td>Capacity</td>
+<td>
+<p>60GB at compute nodes without accelerator</p>
+<p>90GB at compute nodes with accelerator</p>
+<p>500GB at fat nodes</p>
+</td>
+</tr>
+<tr class="odd">
+<td>Throughput</td>
+<td>
+<p>over 1.5 GB/s write, over 5 GB/s read, single thread<br />over 10 GB/s write, over 50 GB/s read, 16 threads</p>
+</td>
+</tr>
+<tr class="even">
+<td>User quota</td>
+<td>none</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" ">tmp</h3>
+<p>Each node is equipped with local /tmp directory of few GB capacity. The /tmp directory should be used to work with small temporary files. Old files in /tmp directory are automatically purged.</p>
+<div class="table">
+<h2 class=" "><strong>Summary<br /></strong></h2>
+<div class="table-contents">
+<table class="listing" summary="Best usage of the file systems"><colgroup><col><col><col><col><col><col><col><col></colgroup>
+<thead>
+<tr><th align="center" style="text-align: center; ">Mountpoint</th><th align="center" style="text-align: center; ">Usage</th><th align="center" style="text-align: center; ">Protocol</th><th align="center" style="text-align: center; ">Net Capacity</th><th align="center" style="text-align: center; ">Throughput</th><th align="center" style="text-align: center; ">Limitations</th><th align="center" style="text-align: center; ">Access</th><th align="center" style="text-align: center; ">Services</th></tr>
+</thead>
+<tbody>
+<tr class="even">
+<td><span class="monospace">/home</span></td>
+<td align="center">home directory</td>
+<td align="center">Lustre</td>
+<td align="center">320 TiB</td>
+<td align="center">2 GB/s</td>
+<td align="center">Quota 250GB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">backed up</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/scratch</span></td>
+<td align="center">cluster shared jobs' data</td>
+<td align="center">Lustre</td>
+<td align="center">146 TiB</td>
+<td align="center">6 GB/s</td>
+<td align="center">Quota 100TB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">files older 90 days removed</td>
+</tr>
+<tr class="even">
+<td><span class="monospace">/lscratch</span></td>
+<td align="center">node local jobs' data</td>
+<td align="center">local</td>
+<td align="center">330 GB</td>
+<td align="center">100 MB/s</td>
+<td align="center">none</td>
+<td align="center">Compute nodes</td>
+<td align="center">purged after job ends</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/ramdisk</span></td>
+<td align="center">node local jobs' data</td>
+<td align="center">local</td>
+<td align="center">60, 90, 500 GB</td>
+<td align="center">5-50 GB/s</td>
+<td align="center">none</td>
+<td align="center">Compute nodes</td>
+<td align="center">purged after job ends</td>
+</tr>
+<tr class="even">
+<td><span class="monospace">/tmp</span></td>
+<td align="center">local temporary files</td>
+<td align="center">local</td>
+<td align="center"></td>
+<td align="center">100 MB/s</td>
+<td align="center">none</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">auto purged</td>
+</tr>
+</tbody>
+</table>
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+<p>Â </p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md b/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
index 33d78f293..f5cbffc4b 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
@@ -61,7 +61,7 @@ There is default stripe configuration for Anselm Lustre filesystems.
However, users can set the following stripe parameters for their own
directories or files to get optimum I/O performance:
-1. stripe_sizethe size of the chunk in bytes; specify with k, m, or
+1. stripe_size: the size of the chunk in bytes; specify with k, m, or
g to use units of KB, MB, or GB, respectively; the size must be an
even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre
filesystems
@@ -93,12 +93,12 @@ Example:
```
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 1 stripe_size 1048576 stripe_offset -1
+stripe_count: 1 stripe_size: 1048576 stripe_offset: -1
$ lfs setstripe -c -1 /scratch/username/
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 10 stripe_size 1048576 stripe_offset -1
+stripe_count: 10 stripe_size: 1048576 stripe_offset: -1
```
In this example, we view current stripe setting of the
@@ -378,9 +378,9 @@ manner. Below, we create a directory and allow a specific user access.
[vop999@login1.anselm ~]$ ls -ld test
drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# filetest
-# ownervop999
-# groupvop999
+# file: test
+# owner: vop999
+# group: vop999
user::rwx
group::r-x
other::---
@@ -389,9 +389,9 @@ other::---
[vop999@login1.anselm ~]$ ls -ld test
drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# filetest
-# ownervop999
-# groupvop999
+# file: test
+# owner: vop999
+# group: vop999
user::rwx
user:johnsm:rwx
group::r-x
@@ -507,4 +507,3 @@ files in /tmp directory are automatically purged.
<span class="monospace">/tmp</span> local temporary files local 100 MB/s none Compute and login nodes auto purged
Â
-
diff --git a/docs.it4i.cz/anselm-cluster-documentation/storage.html b/docs.it4i.cz/anselm-cluster-documentation/storage.html
new file mode 100644
index 000000000..b2ccfa507
--- /dev/null
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+ <p>There are two main shared file systems on Anselm cluster, the <a class="anchor-link" href="storage.html#home" target="_self" title="">HOME</a> and <a class="anchor-link" href="storage.html#scratch" target="_self" title="">SCRATCH</a>. All login and compute nodes may access same data on shared filesystems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp filesystems.</p>
+<h2 class=" ">Archiving</h2>
+<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a href="storage-1/cesnet-data-storage.html" title="" target="_self" class="internal-link">CESNET storage service</a>, which is available via SSHFS.</p>
+<h2 class=" ">Shared Filesystems</h2>
+<p class=" ">Anselm computer provides two main shared filesystems, the <a class="anchor-link" href="storage.html#home" target="_self" title="">HOME filesystem</a> and the <a class="anchor-link" href="storage.html#scratch" target="_self" title="">SCRATCH filesystem</a>. Both HOME and SCRATCH filesystems are realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both Lustre filesystems for the purpose of sharing data with other users using fine-grained control.</p>
+<h3 class=" ">Understanding the Lustre Filesystems</h3>
+<p>(source <a class="external-link" href="http://www.nas.nasa.gov" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
+<p>A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.</p>
+<p>When a client (a <span class="glossaryItem">compute <span class="glossaryItem">node</span></span> from your job) needs to create or access a file, the client queries the metadata server (<span class="glossaryItem">MDS</span>) and the metadata target (<span class="glossaryItem">MDT</span>) for the layout and location of the <a href="http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping">file's stripes</a>. Once the file is opened and the client obtains the striping information, the <span class="glossaryItem">MDS</span> is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.</p>
+<p>If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.</p>
+<p>There is default stripe configuration for Anselm Lustre filesystems. However, users can set the following stripe parameters for their own directories or files to get optimum I/O performance:</p>
+<ol><ol>
+<li>stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre filesystems</li>
+<li>stripe_count the number of OSTs to stripe across; default is 1 for Anselm Lustre filesystems one can specify -1 to use all OSTs in the filesystem.</li>
+<li>stripe_offset The index of the <span class="glossaryItem">OST</span> where the first stripe is to be placed; default is -1 which results in random selection; using a non-default value is NOT recommended.</li>
+</ol></ol>
+<p class=" ">Â </p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<p class=" ">Use the lfs getstripe for getting the stripe parameters. Use the lfs setstripe command for setting the stripe parameters to get optimal I/O performance The correct stripe setting depends on your needs and file access patterns. </p>
+<pre class="prettyprint lang-sh"><code>$ lfs getstripe dir|filename <br />$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename </code></pre>
+<p>Example:</p>
+<pre class="prettyprint lang-sh">$ lfs getstripe /scratch/username/<br />/scratch/username/<br />stripe_count: 1 stripe_size: 1048576 stripe_offset: -1<br /><br />$ lfs setstripe -c -1 /scratch/username/<br />$ lfs getstripe /scratch/username/<br />/scratch/username/<br />stripe_count: 10 stripe_size: 1048576 stripe_offset: -1</pre>
+<p>In this example, we view current stripe setting of the /scratch/username/ directory. The stripe count is changed to all OSTs, and verified. All files written to this directory will be striped over 10 OSTs</p>
+<p>Use lfs check OSTs to see the number and status of active OSTs for each filesystem on Anselm. Learn more by reading the man page</p>
+<pre class="prettyprint lang-sh">$ lfs check osts<br />$ man lfs</pre>
+<h3 class=" ">Hints on Lustre Stripping</h3>
+<p class="callout">Increase the stripe_count for parallel I/O to the same file.</p>
+<p>When multiple processes are writing blocks of data to the same file in parallel, the I/O performance for large files will improve when the stripe_count is set to a larger value. The stripe count sets the number of OSTs the file will be written to. By default, the stripe count is set to 1. While this default setting provides for efficient access of metadata (for example to support the ls -l command), large files should use stripe counts of greater than 1. This will increase the aggregate I/O bandwidth by using multiple OSTs in parallel instead of just one. A rule of thumb is to use a stripe count approximately equal to the number of gigabytes in the file.</p>
+<p>Another good practice is to make the stripe count be an integral factor of the number of processes performing the write in parallel, so that you achieve load balance among the OSTs. For example, set the stripe count to 16 instead of 15 when you have 64 processes performing the writes.</p>
+<p class="callout">Using a large stripe size can improve performance when accessing very large files</p>
+<p>Large stripe size allows each client to have exclusive access to its own part of a file. However, it can be counterproductive in some cases if it does not match your I/O pattern. The choice of stripe size has no effect on a single-stripe file.</p>
+<p>Read more on <a class="external-link" href="http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html" target="_self" title="">http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html</a></p>
+<h3 class=" ">Lustre on Anselm</h3>
+<p>The architecture of Lustre on Anselm is composed of two metadata servers (MDS) and four data/object storage servers (OSS). Two object storage servers are used for file system HOME and another two object storage servers are used for file system SCRATCH.</p>
+<p class=" "><span class="emphasis">Configuration of the storages</span></p>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem"><span class="emphasis">HOME Lustre object storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">One disk array NetApp E5400</li>
+<li class="listitem">22 OSTs</li>
+<li class="listitem">227 2TB NL-SAS 7.2krpm disks</li>
+<li class="listitem">22 groups of 10 disks in RAID6 (8+2)</li>
+<li class="listitem">7 hot-spare disks</li>
+</ul>
+</div>
+</li>
+<li class="listitem"><span class="emphasis">SCRATCH Lustre object storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">Two disk arrays NetApp E5400</li>
+<li class="listitem">10 OSTs</li>
+<li class="listitem">106 2TB NL-SAS 7.2krpm disks</li>
+<li class="listitem">10 groups of 10 disks in RAID6 (8+2)</li>
+<li class="listitem">6 hot-spare disks</li>
+</ul>
+</div>
+</li>
+<li class="listitem"><span class="emphasis">Lustre metadata storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">One disk array NetApp E2600</li>
+<li class="listitem">12 300GB SAS 15krpm disks</li>
+<li class="listitem">2 groups of 5 disks in RAID5</li>
+<li class="listitem">2 hot-spare disks</li>
+</ul>
+</div>
+</li>
+</ul>
+</div>
+<h3 class=" "><a name="home"></a><a name="home"></a>HOME</h3>
+<p>The HOME filesystem is mounted in directory /home. Users home directories /home/username reside on this filesystem. Accessible capacity is 320TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. <span>If 250GB should prove as insufficient for particular user, please contact</span>Â <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request.</p>
+<p class="callout">The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.</p>
+<p>The HOME filesystem should not be used to archive data of past Projects or other unrelated data.</p>
+<p>The files on HOME filesystem will not be deleted until end of the <a href="../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html" title="" target="_self" class="internal-link">users lifecycle</a>.</p>
+<p class=" ">The filesystem is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files. </p>
+<p class=" ">The HOME filesystem is realized as Lustre parallel filesystem and is available on all login and computational nodes. <br />Default stripe size is 1MB, stripe count is 1. There are 22 OSTs dedicated for the HOME filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">HOME filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/home</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>320TB</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>2GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>250GB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>22</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><a name="scratch"></a><a name="scratch"></a>SCRATCH</h3>
+<p>The SCRATCH filesystem is mounted in directory /scratch. Users may freely create subdirectories and files on the filesystem. Accessible capacity is 146TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 100TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. <span>If 100TB should prove as insufficient for particular user, please contact <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request. </span></p>
+<p class="callout">The Scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the SCRATCH filesystem as their working directory.<br /><br />Users are advised to save the necessary data from the SCRATCH filesystem to HOME filesystem after the calculations and clean up the scratch files.<br /><br />Files on the SCRATCH filesystem that are <strong>not accessed for more than 90 days</strong> will be automatically <strong>deleted</strong>.</p>
+<p>The SCRATCH filesystem is realized as Lustre parallel filesystem and is available from all login and computational nodes. <br />Default stripe size is 1MB, stripe count is 1. There are 10 OSTs dedicated for the SCRATCH filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">SCRATCH filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/scratch</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>146TB</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>6GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>100TB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>10</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><span>Disk usage and quota commands</span></h3>
+<p><span>User quotas on the file systems can be checked and reviewed using following command:</span></p>
+<pre class="prettyprint lang-sh">$ lfs quota dir</pre>
+<p>Example for Lustre HOME directory:</p>
+<pre class="prettyprint lang-sh">$ lfs quota /home<br />Disk quotas for user user001 (uid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /home 300096 0 250000000 - 2102 0 500000 -<br />Disk quotas for group user001 (gid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /home 300096 0 0 - 2102 0 0 -</pre>
+<p>In this example, we view current quota size limit of 250GB and 300MB currently used by user001.</p>
+<p>Example for Lustre SCRATCH directory:</p>
+<pre class="prettyprint lang-sh">$ lfs quota /scratch<br />Disk quotas for user user001 (uid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br />  /scratch    8    0 100000000000    -    3    0    0    -<br />Disk quotas for gro<span>up user001 (gid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /scratch    8    0    0    -    3    0    0    -<br /></span></pre>
+<p>In this example, we view current quota size limit of 100TB and 8KB currently used by user001.</p>
+<p>Â </p>
+<p>To have a better understanding of where the space is exactly used, you can use following command to find out.</p>
+<pre class="prettyprint lang-sh">$ du -hs dir</pre>
+<p>Example for your HOME directory:</p>
+<pre class="prettyprint lang-sh">$ cd /home<br />$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr<br />258M cuda-samples<br />15M .cache<br />13M .mozilla<br />5,5M .eclipse<br />2,7M .idb_13.0_linux_intel64_app</pre>
+<p>This will list all directories which are having MegaBytes or GigaBytes of consumed space in your actual (in this example HOME) directory. List is sorted in descending order from largest to smallest files/directories.</p>
+<p><br /> <span>To have a better understanding of previous commands, you can read manpages.</span></p>
+<pre class="prettyprint lang-sh">$ man lfs</pre>
+<pre class="prettyprint lang-sh">$ man du </pre>
+<h3 class=" ">Extended ACLs</h3>
+<p class=" ">Extended ACLs provide another security mechanism beside the standard POSIX ACLs which are defined by three entries (for owner/group/others). Extended ACLs have more than the three basic entries. In addition, they also contain a mask entry and may contain any number of named user and named group entries.</p>
+<p class=" ">ACLs on a Lustre file system work exactly like ACLs on any Linux file system. They are manipulated with the standard tools in the standard manner. Below, we create a directory and allow a specific user access.</p>
+<pre class="prettyprint lang-sh">[vop999@login1.anselm ~]$ umask 027<br />[vop999@login1.anselm ~]$ mkdir test<br />[vop999@login1.anselm ~]$ ls -ld test<br />drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.anselm ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />group::r-x<br />other::---<br /><br />[vop999@login1.anselm ~]$ setfacl -m user:johnsm:rwx test<br />[vop999@login1.anselm ~]$ ls -ld test<br />drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.anselm ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />user:johnsm:rwx<br />group::r-x<br />mask::rwx<br />other::---</pre>
+<p class=" ">Default ACL mechanism can be used to replace setuid/setgid permissions on directories. Setting a default ACL on a directory (-d flag to setfacl) will cause the ACL permissions to be inherited by any newly created file or subdirectory within the directory. Refer to this page for more information on Linux ACL:</p>
+<p class=" "><a class="external-link" href="http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html" target="_self" title="">http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html </a></p>
+<h2 class=" ">Local Filesystems</h2>
+<h3 class=" ">Local Scratch</h3>
+<p>Every computational node is equipped with 330GB local scratch disk.</p>
+<p class="callout">Use local scratch in case you need to access large amount of small files during your calculation.</p>
+<p><a name="LocalScratch"></a>The local scratch disk is mounted as /lscratch and is accessible to user at /lscratch/$PBS_JOBID directory.</p>
+<p class=" ">The local scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs that access large number of small files within the calculation must use the local scratch filesystem as their working directory. This is required for performance reasons, as frequent access to number of small files may overload the metadata servers (MDS) of the Lustre filesystem.</p>
+<p class="callout">The local scratch directory /lscratch/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">local SCRATCH filesystem</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td>/lscratch</td>
+</tr>
+<tr class="odd">
+<td>Accesspoint</td>
+<td>/lscratch/$PBS_JOBID</td>
+</tr>
+<tr class="even">
+<td>Capacity</td>
+<td>330GB</td>
+</tr>
+<tr class="odd">
+<td>Throughput</td>
+<td>100MB/s</td>
+</tr>
+<tr class="even">
+<td>User quota</td>
+<td>none</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" ">RAM disk</h3>
+<p>Every computational node is equipped with filesystem realized in memory, so called RAM disk.</p>
+<p class="callout">Use RAM disk in case you need really fast access to your data of limited size during your calculation.<br />Be very careful, use of RAM disk filesystem is at the expense of operational memory.</p>
+<p><a name="LocalScratch"></a>The local RAM disk is mounted as /ramdisk and is accessible to user at /ramdisk/$PBS_JOBID directory.</p>
+<p class=" ">The local RAM disk filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. Size of RAM disk filesystem is limited. Be very careful, use of RAM disk filesystem is at the expense of operational memory. It is not recommended to allocate large amount of memory and use large amount of data in RAM disk filesystem at the same time.</p>
+<p class="callout">The local RAM disk directory /ramdisk/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">RAM disk</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td><span class="monospace">/ramdisk</span></td>
+</tr>
+<tr class="odd">
+<td>Accesspoint</td>
+<td><span class="monospace">/ramdisk/$PBS_JOBID</span></td>
+</tr>
+<tr class="even">
+<td>Capacity</td>
+<td>
+<p>60GB at compute nodes without accelerator</p>
+<p>90GB at compute nodes with accelerator</p>
+<p>500GB at fat nodes</p>
+</td>
+</tr>
+<tr class="odd">
+<td>Throughput</td>
+<td>
+<p>over 1.5 GB/s write, over 5 GB/s read, single thread<br />over 10 GB/s write, over 50 GB/s read, 16 threads</p>
+</td>
+</tr>
+<tr class="even">
+<td>User quota</td>
+<td>none</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" ">tmp</h3>
+<p>Each node is equipped with local /tmp directory of few GB capacity. The /tmp directory should be used to work with small temporary files. Old files in /tmp directory are automatically purged.</p>
+<div class="table">
+<h2 class=" "><strong>Summary<br /></strong></h2>
+<div class="table-contents">
+<table class="listing" summary="Best usage of the file systems"><colgroup><col><col><col><col><col><col><col><col></colgroup>
+<thead>
+<tr><th align="center" style="text-align: center; ">Mountpoint</th><th align="center" style="text-align: center; ">Usage</th><th align="center" style="text-align: center; ">Protocol</th><th align="center" style="text-align: center; ">Net Capacity</th><th align="center" style="text-align: center; ">Throughput</th><th align="center" style="text-align: center; ">Limitations</th><th align="center" style="text-align: center; ">Access</th><th align="center" style="text-align: center; ">Services</th></tr>
+</thead>
+<tbody>
+<tr class="even">
+<td><span class="monospace">/home</span></td>
+<td align="center">home directory</td>
+<td align="center">Lustre</td>
+<td align="center">320 TiB</td>
+<td align="center">2 GB/s</td>
+<td align="center">Quota 250GB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">backed up</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/scratch</span></td>
+<td align="center">cluster shared jobs' data</td>
+<td align="center">Lustre</td>
+<td align="center">146 TiB</td>
+<td align="center">6 GB/s</td>
+<td align="center">Quota 100TB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">files older 90 days removed</td>
+</tr>
+<tr class="even">
+<td><span class="monospace">/lscratch</span></td>
+<td align="center">node local jobs' data</td>
+<td align="center">local</td>
+<td align="center">330 GB</td>
+<td align="center">100 MB/s</td>
+<td align="center">none</td>
+<td align="center">Compute nodes</td>
+<td align="center">purged after job ends</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/ramdisk</span></td>
+<td align="center">node local jobs' data</td>
+<td align="center">local</td>
+<td align="center">60, 90, 500 GB</td>
+<td align="center">5-50 GB/s</td>
+<td align="center">none</td>
+<td align="center">Compute nodes</td>
+<td align="center">purged after job ends</td>
+</tr>
+<tr class="even">
+<td><span class="monospace">/tmp</span></td>
+<td align="center">local temporary files</td>
+<td align="center">local</td>
+<td align="center"></td>
+<td align="center">100 MB/s</td>
+<td align="center">none</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">auto purged</td>
+</tr>
+</tbody>
+</table>
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+<p>Â </p>
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diff --git a/docs.it4i.cz/anselm-cluster-documentation/storage.md b/docs.it4i.cz/anselm-cluster-documentation/storage.md
index 982a9a71f..56438ce18 100644
--- a/docs.it4i.cz/anselm-cluster-documentation/storage.md
+++ b/docs.it4i.cz/anselm-cluster-documentation/storage.md
@@ -61,7 +61,7 @@ There is default stripe configuration for Anselm Lustre filesystems.
However, users can set the following stripe parameters for their own
directories or files to get optimum I/O performance:
-1. stripe_sizethe size of the chunk in bytes; specify with k, m, or
+1. stripe_size: the size of the chunk in bytes; specify with k, m, or
g to use units of KB, MB, or GB, respectively; the size must be an
even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre
filesystems
@@ -93,12 +93,12 @@ Example:
```
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 1 stripe_size 1048576 stripe_offset -1
+stripe_count: 1 stripe_size: 1048576 stripe_offset: -1
$ lfs setstripe -c -1 /scratch/username/
$ lfs getstripe /scratch/username/
/scratch/username/
-stripe_count 10 stripe_size 1048576 stripe_offset -1
+stripe_count: 10 stripe_size: 1048576 stripe_offset: -1
```
In this example, we view current stripe setting of the
@@ -378,9 +378,9 @@ manner. Below, we create a directory and allow a specific user access.
[vop999@login1.anselm ~]$ ls -ld test
drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# filetest
-# ownervop999
-# groupvop999
+# file: test
+# owner: vop999
+# group: vop999
user::rwx
group::r-x
other::---
@@ -389,9 +389,9 @@ other::---
[vop999@login1.anselm ~]$ ls -ld test
drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.anselm ~]$ getfacl test
-# filetest
-# ownervop999
-# groupvop999
+# file: test
+# owner: vop999
+# group: vop999
user::rwx
user:johnsm:rwx
group::r-x
@@ -507,4 +507,3 @@ files in /tmp directory are automatically purged.
<span class="monospace">/tmp</span> local temporary files local 100 MB/s none Compute and login nodes auto purged
Â
-
diff --git a/docs.it4i.cz/anselm.html b/docs.it4i.cz/anselm.html
new file mode 100644
index 000000000..c277b9009
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+ <p>Welcome to Anselm supercomputer cluster. The Anselm cluster consists of 209 compute nodes, totaling 3344 compute cores with 15TB RAM and giving over 94 Tflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 16 cores, at least 64GB RAM, and 500GB harddrive. Nodes are interconnected by fully non-blocking fat-tree Infiniband network and equipped with Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in <a href="anselm-cluster-documentation/hardware-overview.html" title="" target="_self" class="internal-link">Hardware Overview</a>.</p>
+<p>The cluster runs bullx Linux <a class="external-link" href="http://www.bull.com/bullx-logiciels/systeme-exploitation.html" target="_self" title=""><span class="WYSIWYG_LINK"></span></a><a href="anselm-cluster-documentation/software/operating-system.html" title="" target="_self" class="internal-link">operating system</a>, which is compatible with the <span class="WYSIWYG_LINK">RedHat</span> <a class="external-link" href="http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg" target="_self" title=""><span class="WYSIWYG_LINK">Linux family.</span></a> We have installed a wide range of <a href="anselm-cluster-documentation/software.1.html" title="" target="_self" class="internal-link">software</a> packages targeted at different scientific domains. These packages are accessible via the <a href="anselm-cluster-documentation/environment-and-modules.html" title="" target="_self" class="internal-link">modules environment</a>.</p>
+<p>User data shared file-system (HOME, 320TB) and job data shared file-system (SCRATCH, 146TB) are available to users.</p>
+<p>The PBS Professional workload manager provides <a href="anselm-cluster-documentation/resource-allocation-and-job-execution.html" title="" target="_self" class="internal-link">computing resources allocations and job execution</a>.</p>
+<p>Read more on how to <a href="get-started-with-it4innovations/applying-for-resources.html" title="" target="_self" class="internal-link">apply for resources</a>, <a href="get-started-with-it4innovations/obtaining-login-credentials.html" title="" target="_self" class="internal-link">obtain login credentials,</a> and <a href="anselm-cluster-documentation/accessing-the-cluster.html" title="" target="_self" class="internal-link">access the cluster</a>.</p>
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diff --git a/docs.it4i.cz/anselm.md b/docs.it4i.cz/anselm.md
index 6ff741f5e..7d0f0258c 100644
--- a/docs.it4i.cz/anselm.md
+++ b/docs.it4i.cz/anselm.md
@@ -40,4 +40,3 @@ resources](get-started-with-it4innovations/applying-for-resources.html),
credentials,](get-started-with-it4innovations/obtaining-login-credentials.html)
and [access the
cluster](anselm-cluster-documentation/accessing-the-cluster.html).
-
diff --git a/docs.it4i.cz/changelog.html b/docs.it4i.cz/changelog.html
new file mode 100644
index 000000000..e3df35145
--- /dev/null
+++ b/docs.it4i.cz/changelog.html
@@ -0,0 +1,806 @@
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+
+
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+ <p>The IT4Innovations clusters are accessed by SSH protocol via login nodes.</p>
+<p class="callout">Read more on <a href="../salomon/accessing-the-cluster.html" title="" target="_self" class="internal-link">Accessing the Salomon Cluste</a>r or <a href="../anselm-cluster-documentation/accessing-the-cluster.html" title="" target="_self" class="internal-link">Accessing the Anselm Cluster</a> pages.</p>
+<h3 class=" ">PuTTY</h3>
+<p>On <strong>Windows</strong>, use <a href="accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html" title="" target="_self" class="internal-link">PuTTY ssh client</a>.</p>
+<h3 class=" " id="parent-fieldname-title">SSH keys</h3>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters.md
index bcf136329..5616c4d47 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters.md
@@ -19,4 +19,3 @@ client](accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
Read more about [SSH keys
management](accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html).
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html
new file mode 100644
index 000000000..7ee5bdd5e
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.html
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+<p>The X Window system is a principal way to get GUI access to the clusters.</p>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.md
index 02639ef8a..fea06f988 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface.md
@@ -28,4 +28,3 @@ class="link-external">[computer](http://en.wikipedia.org/wiki/Computer "Computer
Read more about configuring
**[VNC](../../salomon/accessing-the-cluster/graphical-user-interface/vnc.html)**.
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.html
new file mode 100644
index 000000000..c91218bf1
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.html
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+<p>Read more about configuring <a href="x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link"><b>X Window System</b></a>.</p>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
index d389946f9..7f4f4a334 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
@@ -30,4 +30,3 @@ Read more about configuring
**[VNC](../../../salomon/accessing-the-cluster/graphical-user-interface/vnc.html)**.
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmscreensaver.png/@@images/44048cfa-e854-4cb4-902b-c173821c2db1.png b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmscreensaver.png/@@images/8e80a92f-f691-4d92-8e62-344128dcc00b.png
similarity index 100%
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rename to docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmscreensaver.png/@@images/8e80a92f-f691-4d92-8e62-344128dcc00b.png
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+ <p>The <b>Virtual Network Computing</b> (<b>VNC</b>) is a graphical <a href="http://en.wikipedia.org/wiki/Desktop_sharing" title="Desktop sharing">desktop sharing</a> system that uses the <a href="http://en.wikipedia.org/wiki/RFB_protocol" title="RFB protocol">Remote Frame Buffer protocol (RFB)</a> to remotely control another <a href="http://en.wikipedia.org/wiki/Computer" title="Computer">computer</a>. It transmits the <a href="http://en.wikipedia.org/wiki/Computer_keyboard" title="Computer keyboard">keyboard</a> and <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Computer_mouse" title="Computer mouse">mouse</a> events from one computer to another, relaying the graphical <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Computer_screen" title="Computer screen">screen</a> updates back in the other direction, over a <a href="http://en.wikipedia.org/wiki/Computer_network" title="Computer network">network</a>.<sup class="reference" id="cite_ref-1"><a href="http://en.wikipedia.org/wiki/Virtual_Network_Computing#cite_note-1"><span>[</span>1<span>]</span></a></sup></p>
+<p>The recommended clients are <a class="external-link" href="http://www.tightvnc.com" target="_self" title="">TightVNC</a> or <a class="external-link" href="http://sourceforge.net/apps/mediawiki/tigervnc/index.php?title=Main_Page" target="_self" title="">TigerVNC</a> (free, open source, available for almost any platform).</p>
+<h2 class=" ">Create VNC password</h2>
+<p class="callout">Local VNC password should be set before the first login. Do use a strong password.</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">~]</span><span class="pln">$ vncpasswd</span><br /><span class="typ">Password</span><span class="pun">:</span><br /><span class="typ">Verify</span><span class="pun">:</span></pre>
+<h2 class=" ">Start vncserver</h2>
+<p class="callout">To access VNC a local vncserver must be started first and also a tunnel using SSH port forwarding must be established.<br /><a class="anchor-link" href="vnc.html#linux-example-of-creating-a-tunnel" target="_self" title="">See below</a> for the details on SSH tunnels. In this example we use port 61.</p>
+<p class=" ">You can find ports which are already occupied. Here you can see that ports "<span class="pln">/usr/bin/Xvnc :79"</span> and "<span class="pln">/usr/bin/Xvnc :60" are occupied.</span></p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">~]</span><span class="pln">$ </span>ps aux | grep Xvnc<br /><span class="pln"><span class="pln"><span class="pln">username</span></span></span>   5971 0.0 0.0 201072 92564 ?       SN  Sep22  4:19 /usr/bin/Xvnc :79 -desktop login2:79 (<span class="pln"><span class="pln"><span class="pln">username</span></span></span>) -auth /home/gre196/.Xauthority -geometry 1024x768 -rfbwait 30000 -rfbauth /home/<span class="pln"><span class="pln"><span class="pln">username</span></span></span>/.vnc/passwd -rfbport 5979 -fp catalogue:/etc/X11/fontpath.d -pn<br /><span class="pln"><span class="pln"><span class="pln">username</span>   </span>10296 0.0 0.0 131772 21076 pts/29  SN  13:01  0:01 /usr/bin/Xvnc :60 -desktop login2:61 (<span class="pln">username</span>) -auth /home/<span class="pln">username</span>/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/jir13/.vnc/passwd -rfbport 5960 -fp catalogue:/etc/X11/fontpath.d -pn<br />.....<br /></span></pre>
+<p class=" ">Choose free port e.g. 61 and start your VNC server:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">~]</span><span class="pln">$ vncserver </span><span class="pln">:61 </span><span class="pun">-</span><span class="pln">geometry </span><strong><span class="lit">1600</span></strong><span class="lit">x900</span><span class="pln"> </span><span class="pun">-</span><span class="pln">depth </span><span class="lit">16</span><br /><br /><span class="typ">New</span><span class="pln"> </span><span class="str">'login2:1 (username)'</span><span class="pln"> desktop is login2</span><span class="pun">:</span><span class="lit">1</span><br /><br /><span class="typ">Starting</span><span class="pln"> applications specified </span><span class="kwd">in</span><span class="pln"> </span><span class="pun">/</span><span class="pln">home</span><span class="pun">/</span><span class="pln">username</span><span class="pun">/.</span><span class="pln">vnc</span><span class="pun">/</span><span class="pln">xstartup</span><br /><span class="typ">Log</span><span class="pln"> file is </span><span class="pun">/</span><span class="pln">home</span><span class="pun">/</span><span class="pln">username</span><span class="pun">/.</span><span class="pln">vnc</span><span class="pun">/</span><span class="pln">login2</span><span class="pun">:</span><span class="lit">1.log</span><br /><span class="pun"></span></pre>
+<p>Check if VNC server is started on the port (in this example 61):</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ vncserver </span><span class="pun">-</span><span class="pln">list</span><br /><br /><span class="typ">TigerVNC</span><span class="pln"> server sessions</span><span class="pun">:</span><br /><br /><span class="pln">X DISPLAY </span><span class="com">#Â Â Â Â PROCESS ID</span><br /><span class="pun">:<span class="pun"></span><span class="lit">6</span></span><span class="lit">1</span><span class="pln">Â Â Â Â Â Â Â Â Â Â Â Â Â </span><span class="lit">18437</span></pre>
+<p>Another command:<span class="pln"></span></p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ Â ps aux | grep Xvnc<br /><br /><span class="pln">username</span>Â Â Â 10296Â 0.0Â 0.0 131772 21076 pts/29Â Â SNÂ Â 13:01Â Â 0:01 /usr/bin/Xvnc :61 -desktop login2:61 (<span class="pln">username</span>) -auth /home/jir13/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/<span class="pln"><span class="pln">username</span></span>/.vnc/passwd -rfbport 5961 -fp catalogue:/etc/X11/fontpath.d -pn<br /></span></pre>
+<p>To access the VNC server you have to create a tunnel between the login node using TCP <strong>port 5961</strong> and your machine using a free TCP port (for simplicity the very same, in this case).</p>
+<p class="exclamation">The tunnel must point to the same login node where you launched the VNC server, eg. login2. If you use just cluster-name.it4i.cz, the tunnel might point to a different node due to DNS round robin.</p>
+<h3 class=" "><a name="linux-example-of-creating-a-tunnel"></a><a name="linux-example"></a>Linux/Mac OS example of creating a tunnel</h3>
+<p>At your machine, create the tunnel:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $Â ssh </span><span class="pun">-</span><span class="pln">TN </span><span class="pun">-</span><span class="pln">f username@login2.cluster-name</span><span class="pun">.</span><span class="pln">it4i</span><span class="pun">.</span><span class="pln">cz </span><span class="pun">-</span><span class="pln">L </span><span class="lit">5961</span><span class="pun">:</span><span class="pln">localhost</span><span class="pun">:</span><span class="lit">5961</span></pre>
+<p>Issue the following command to check the tunnel is established (please note the PID 2022 in the last column, you'll need it for closing the tunnel):</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ netstat </span><span class="pun">-</span><span class="pln">natp </span><span class="pun">|</span><span class="pln"> grep </span><span class="lit">5961</span><br /><span class="pun">(</span><span class="typ">Not</span><span class="pln"> all processes could be identified</span><span class="pun">,</span><span class="pln"> non</span><span class="pun">-</span><span class="pln">owned process info</span><br /><span class="pln"> will not be shown</span><span class="pun">,</span><span class="pln"> you would have to be root to see it all</span><span class="pun">.)</span><br /><span class="pln">tcp       </span><span class="lit">0</span><span class="pln">     </span><span class="lit">0</span><span class="pln"> </span><span class="lit">127.0</span><span class="pun">.</span><span class="lit">0.1</span><span class="pun">:</span><span class="lit">5961</span><span class="pln">         </span><span class="lit">0.0</span><span class="pun">.</span><span class="lit">0.0</span><span class="pun">:*</span><span class="pln">              LISTEN     </span><span class="lit">2022</span><span class="pun">/</span><span class="pln">ssh       </span><br /><span class="pln">tcp6      </span><span class="lit">0</span><span class="pln">     </span><span class="lit">0</span><span class="pln"> </span><span class="pun">::</span><span class="lit">1</span><span class="pun">:</span><span class="lit">5961</span><span class="pln">               </span><span class="pun">:::*</span><span class="pln">                   LISTEN     </span><span class="lit">2022</span><span class="pun">/</span><span class="pln">ssh </span></pre>
+<p>Or on Mac OS use this command:</p>
+<pre class="prettyprint lang-sh">local-mac $ lsof -n -i4TCP:5961 | grep LISTEN<br />ssh 75890 sta545 7u IPv4 0xfb062b5c15a56a3b 0t0 TCP 127.0.0.1:5961 (LISTEN)</pre>
+<p>Connect with the VNC client:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ vncviewer </span><span class="lit">127.0</span><span class="pun">.</span><span class="lit">0.1</span><span class="pun">:</span><span class="lit">5961</span></pre>
+<p>In this example, we connect to VNC server on port 5961, via the ssh tunnel. The connection is encrypted and secured. The VNC server listening on port 5961 provides screen of 1600x900 pixels.</p>
+<p>You have to destroy the SSH tunnel which is still running at the background after you finish the work. Use the following command (PID 2022 in this case, see the netstat command above):</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">kill </span><span class="lit">2022</span></pre>
+<h3 class=" ">Windows example of creating a tunnel</h3>
+<p>Use PuTTY to log in on cluster.</p>
+<p>Start vncserver using command vncserver described above.</p>
+<p>Search for the localhost and port number (in this case 127.0.0.1:5961).<strong><br /></strong></p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ netstat </span><span class="pun">-</span><span class="pln">tanp </span><span class="pun">|</span><span class="pln"> grep </span><span class="typ">Xvnc</span><br /><span class="pun">(</span><span class="typ">Not</span><span class="pln"> all processes could be identified</span><span class="pun">,</span><span class="pln"> non</span><span class="pun">-</span><span class="pln">owned process info</span><br /><span class="pln"> will not be shown</span><span class="pun">,</span><span class="pln"> you would have to be root to see it all</span><span class="pun">.)</span><br /><span class="pln">tcp       </span><span class="lit">0</span><span class="pln">     </span><span class="lit">0</span><span class="pln"> </span><span class="lit">127.0</span><span class="pun">.</span><span class="lit">0.1</span><span class="pun">:</span><span class="lit">5961</span><span class="pln">             </span><span class="lit">0.0</span><span class="pun">.</span><span class="lit">0.0</span><span class="pun">:*</span><span class="pln">                  LISTEN     </span><span class="lit">24031</span><span class="pun">/</span><span class="typ">Xvnc</span></pre>
+<p>On the PuTTY Configuration screen go to Connection->SSH->Tunnels to set up the tunnel.</p>
+<p>Fill the Source port and Destination fields. <strong>Do not forget to click the Add button</strong>.<br /><br /> <a href="putty-tunnel.png" title="" target="_blank" class="internal-link"><img alt="PuTTY - Create tunnel" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png/@@images/4c66cd51-c858-473b-98c2-8d901aea7118.png" title="PuTTY Tunnel" class="image-inline" /></a></p>
+<p>Run the VNC client of your choice, select VNC server 127.0.0.1, port 5961 and connect using VNC password.</p>
+<h3 class=" ">Example of starting TigerVNC viewer</h3>
+<p><img alt="TigerVNC vncviewer" src="../../../../anselm-cluster-documentation/vncviewer.png/@@images/bb4cedff-4cb6-402b-ac79-039186fe5df3.png" title="Vncviewer" class="image-inline" /></p>
+<p>In this example, we connect to VNC server on port 5961, via the ssh tunnel, using TigerVNC viewer. The connection is encrypted and secured. The VNC server listening on port 5961 provides screen of 1600x900 pixels.</p>
+<h3 class=" ">Example of starting TightVNC Viewer</h3>
+<p>Use your VNC password to log using TightVNC Viewer and start a Gnome Session on the login node.</p>
+<p><a href="TightVNC_login.png" title="" target="_blank" class="internal-link"><strong><img alt="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png/@@images/e53354d8-a2e8-4947-92b3-dd107d498408.png" title="" class="image-inline" /></strong></a></p>
+<h2 class=" ">Gnome session</h2>
+<p>You should see after the successful login.</p>
+<p><a href="https://docs.it4i.cz/get-started-with-it4innovations/gnome_screen.jpg" title="" target="_blank" class="internal-link"><img alt="Default Gnome session" src="../../../../salomon/gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-618cda100fda.png" title="Default Gnome session" class="image-inline" /></a></p>
+<h3 class=" "><strong>Disable your Gnome session screensaver<br /></strong></h3>
+<p>Open Screensaver preferences dialog:</p>
+<p><a href="../../../../salomon/gnome_screen.jpg.1" title="" target="_blank" class="internal-link"><img alt="Screensaver Preferences" src="gdmscreensaver.png/@@images/8e80a92f-f691-4d92-8e62-344128dcc00b.png" title="Screensaver Preferences" class="image-inline" /></a></p>
+<p>Uncheck both options below the slider:</p>
+<p><a href="gdmdisablescreensaver.png" title="" target="_blank" class="internal-link"><img alt="Disable lock screen and screensaver" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png/@@images/8a4758d9-3027-4ce4-9a90-2d5e88197451.png" title="Disable lock screen and screensaver" class="image-inline" /></a></p>
+<h3 class=" ">Kill screensaver if locked screen</h3>
+<p>If the screen gets locked you have to kill the screensaver. Do not to forget to disable the screensaver then.</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ ps aux </span><span class="pun">|</span><span class="pln"> grep screen</span><br /><span class="pln">username    </span><span class="lit">1503</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">103244</span><span class="pln">  </span><span class="lit">892</span><span class="pln"> pts</span><span class="pun">/</span><span class="lit">4</span><span class="pln">   S</span><span class="pun">+</span><span class="pln">  </span><span class="lit">14</span><span class="pun">:</span><span class="lit">37</span><span class="pln">  </span><span class="lit">0</span><span class="pun">:</span><span class="lit">00</span><span class="pln"> grep screen</span><br /><span class="pln">username    </span><span class="lit">24316</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">270564</span><span class="pln"> </span><span class="lit">3528</span><span class="pln"> </span><span class="pun">?</span><span class="pln">       </span><span class="typ">Ss</span><span class="pln">  </span><span class="lit">14</span><span class="pun">:</span><span class="lit">12</span><span class="pln">  </span><span class="lit">0</span><span class="pun">:</span><span class="lit">00</span><span class="pln"> gnome</span><span class="pun">-</span><span class="pln">screensaver</span><br /><br /><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ kill </span><span class="lit">24316</span></pre>
+<h3 class=" ">Kill vncserver after finished work</h3>
+<p>You should kill your VNC server using command:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ </span><span class="pln">vncserver -kill :61<br />Killing Xvnc process ID 7074<br />Xvnc process ID 7074 already killed<br /></span><span class="pun"></span></pre>
+<p>Or this way:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$Â p</span><span class="pln">kill vnc</span></pre>
+<h2 class=" ">GUI applications on compute nodes over VNC</h2>
+<p>The very <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc#gui-applications-on-compute-nodes" title="" target="_self" class="anchor-link">same methods as described above</a>, may be used to run the GUI applications on compute nodes. However, for <strong>maximum performance</strong>, proceed following these steps:</p>
+<p>Open a Terminal (Applications -> System Tools -> Terminal). Run all the next commands in the terminal.<br /><br /><a href="gnome-terminal.png" title="" target="_blank" class="internal-link"><img alt="gnome-terminal.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png/@@images/b44f5d8c-156d-4041-9bb0-973996413834.png" title="gnome-terminal.png" class="image-inline" /></a></p>
+<p>Allow incoming X11 graphics from the compute nodes at the login node:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ xhost </span><span class="pun">+</span></pre>
+<p>Get an interactive session on a compute node (for more detailed info <a href="../../../../anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_self" class="internal-link">look here</a>). Use the <strong>-v DISPLAY</strong> option to propagate the DISPLAY on the compute node. In this example, we want a complete node (24 cores in this example) from the production queue:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ qsub </span><span class="pun">-</span><span class="pln">I </span><span class="pun">-</span><span class="pln">v DISPLAY</span><span class="pun">=</span><span class="pln">$</span><span class="pun">(</span><span class="pln">uname </span><span class="pun">-</span><span class="pln">n</span><span class="pun">):</span><span class="pln">$</span><span class="pun">(</span><span class="pln">echo $DISPLAY </span><span class="pun">|</span><span class="pln"> cut </span><span class="pun">-</span><span class="pln">d </span><span class="str">':'</span><span class="pln"> </span><span class="pun">-</span><span class="pln">f </span><span class="lit">2</span><span class="pun">)</span><span class="pln"> </span><span class="pun">-</span><span class="pln">A PROJECT_ID </span><span class="pun">-</span><span class="pln">q qprod </span><span class="pun">-</span><span class="pln">l select</span><span class="pun">=</span><span class="lit">1</span><span class="pun">:</span><span class="pln">ncpus</span><span class="pun">=24</span><span class="lit"></span></pre>
+<p>Test that the DISPLAY redirection into your VNC session works, by running a X11 application (e. g. XTerm) on the assigned compute node:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ xterm<br /></span></pre>
+<p>Example described above:</p>
+<p><a href="gnome-compute-nodes-over-vnc.png" title="" target="_blank" class="internal-link"><img alt="gnome-compute-nodes-over-vnc.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png/@@images/90ca3609-a3ff-4867-9019-954c74224961.png" title="gnome-compute-nodes-over-vnc.png" class="image-inline" /></a></p>
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+ </div>
+
+ <!-- TODO -->
+ <!-- nagios_check_http_expect_string -->
+ <!-- TODO -->
+
+</div>
+</body>
+</html>
+
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/vnc.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/vnc.md
index 230ae392f..6fe47bc4e 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/vnc.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/vnc.md
@@ -199,12 +199,12 @@ session](../../../../salomon/gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-6
Open Screensaver preferences dialog:
[](../../../../salomon/gnome_screen.jpg.1)
+Preferences](gdmscreensaver.png/@@images/8e80a92f-f691-4d92-8e62-344128dcc00b.png "Screensaver Preferences")](../../../../salomon/gnome_screen.jpg.1)
Uncheck both options below the slider:
[](gdmdisablescreensaver.png)
+screensaver](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png/@@images/8a4758d9-3027-4ce4-9a90-2d5e88197451.png "Disable lock screen and screensaver")](gdmdisablescreensaver.png)
### Kill screensaver if locked screen
@@ -277,4 +277,3 @@ Example described above:
[](gnome-compute-nodes-over-vnc.png)
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1.html
new file mode 100644
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+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1.html
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+ <p>The X Window system is a principal way to get GUI access to the clusters. The <b>X Window System</b> (commonly known as <b>X11</b>, based on its current major version being 11, or shortened to simply <b>X</b>, and sometimes informally <b>X-Windows</b>) is a computer software system and network <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Protocol_%28computing%29" title="Protocol (computing)">protocol</a> that provides a basis for <a href="http://en.wikipedia.org/wiki/Graphical_user_interface" title="Graphical user interface">graphical user interfaces</a> (GUIs) and rich input device capability for <a href="http://en.wikipedia.org/wiki/Computer_network" title="Computer network">networked computers</a>.</p>
+<p class="callout">The X display forwarding must be activated and the X server running on client side</p>
+<h3 class=" ">X display</h3>
+<p>In order to display graphical user interface GUI of various software tools, you need to enable the X display forwarding. On Linux and Mac, log in using the -X option tho ssh client:</p>
+<pre class="prettyprint lang-sh"> local $ ssh -X username@cluster-name.it4i.cz</pre>
+<h3 class=" ">X Display Forwarding on Windows</h3>
+<p class=" ">On Windows use the PuTTY client to enable X11 forwarding. Â In PuTTY menu, go to Connection->SSH->X11, mark the Enable X11 forwarding checkbox before logging in. Then log in as usual.</p>
+<p class=" ">To verify the forwarding, type</p>
+<pre class="prettyprint lang-sh">$ echo $DISPLAY</pre>
+<p>if you receive something like</p>
+<pre class="prettyprint lang-sh">localhost:10.0</pre>
+<p class=" ">then the X11 forwarding is enabled.</p>
+<h3 class=" ">X Server</h3>
+<p>In order to display graphical user interface GUI of various software tools, you need running X server on your desktop computer. For Linux users, no action is required as the X server is the default GUI environment on most Linux distributions. Mac and Windows users need to install and run the X server on their workstations.</p>
+<h3 class=" ">X Server on OS X</h3>
+<p>Mac OS users need to install <a class="external-link" href="http://xquartz.macosforge.org/landing/" target="_self" title="">XQuartz server</a>.</p>
+<h3 class=" ">X Server on Windows</h3>
+<p>There are variety of X servers available for Windows environment. The commercial Xwin32 is very stable and rich featured. The Cygwin environment provides fully featured open-source XWin X server. For simplicity, we recommend open-source X server by the <a class="external-link" href="http://sourceforge.net/projects/xming/" target="_self" title="">Xming project</a>. For stability and full features we recommend the <a class="external-link" href="http://x.cygwin.com/" target="_self" title="">XWin</a> X server by Cygwin</p>
+<table class="listing">
+<tbody>
+<tr><th style="text-align: center; ">How to use Xwin</th><th style="text-align: center; ">How to use Xming</th></tr>
+<tr>
+<td>
+<p><a class="external-link" href="http://x.cygwin.com/" target="_self" title="">Install Cygwin</a></p>
+<p>Find and execute XWin.exe<br />to start the X server on Windows desktop computer.</p>
+<p><a href="x-window-system/cygwin-and-x11-forwarding.html" title="" target="_self" class="internal-link">If no able to forward X11 using PuTTY to CygwinX</a></p>
+</td>
+<td>
+<p>Use Xlaunch to configure the Xming.</p>
+<p>Run Xming <br />to start the X server on Windows desktop computer.</p>
+</td>
+</tr>
+</tbody>
+</table>
+<p>Read more on <a class="external-link" href="http://www.math.umn.edu/systems_guide/putty_xwin32.shtml" target="_self" title="">http://www.math.umn.edu/systems_guide/putty_xwin32.html</a></p>
+<h3 class=" ">Running GUI Enabled Applications</h3>
+<p class="callout">Make sure that X forwarding is activated and the X server is running.</p>
+<p>Then launch the application as usual. Use the & to run the application in background.</p>
+<pre class="prettyprint lang-sh">$ module load intel (idb and gvim not installed yet)<br />$ gvim &</pre>
+<pre class="prettyprint lang-sh">$ xterm</pre>
+<p>In this example, we activate the intel programing environment tools, then start the graphical gvim editor.</p>
+<h3 class=" "><a name="gui-applications-on-compute-nodes"></a>GUI Applications on Compute Nodes</h3>
+<p>Allocate the compute nodes using -X option on the qsub command</p>
+<pre class="prettyprint lang-sh">$ qsub -q qexp -l select=2:ncpus=24 -X -I</pre>
+<p>In this example, we allocate 2 nodes via qexp queue, interactively. We request X11 forwarding with the -X option. It will be possible to run the GUI enabled applications directly on the first compute node.</p>
+<p><strong>Better performance</strong> is obtained by logging on the allocated compute node via ssh, using the -X option.</p>
+<pre class="prettyprint lang-sh">$ ssh -X r24u35n680</pre>
+<p>In this example, we log in on the r24u35n680 compute node, with the X11 forwarding enabled.</p>
+<p class="hiddenForView">HTML commented section #1 (no GUI on Compute nodes - Xvfb)</p>
+
+<h3 class=" ">The Gnome GUI Environment</h3>
+<p>The Gnome 2.28 GUI environment is available on the clusters. We recommend to use separate X server window for displaying the Gnome environment.</p>
+<h3 class=" ">Gnome on Linux and OS X</h3>
+<p>To run the remote Gnome session in a window on Linux/OS X computer, you need to install Xephyr. Ubuntu package is <span class="monospace">xserver-xephyr</span>, on OS X it is part of <a class="external-link" href="http://xquartz.macosforge.org/landing/" target="_self" title="">XQuartz</a>. First, launch Xephyr on local machine:</p>
+<pre class="prettyprint lang-sh">local $ Xephyr -ac -screen 1024x768 -br -reset -terminate :1 &</pre>
+<p class=" ">This will open a new X window with size 1024x768 at DISPLAY :1. Next, ssh to the cluster with DISPLAY environment variable set and launch <span class="monospace">gnome-session</span></p>
+<pre class=" ">local $ DISPLAY=:1.0 ssh -XC yourname@cluster-name.it4i.cz -i ~/.ssh/path_to_your_key<br />... cluster-name MOTD...<br />yourname@login1.cluster-namen.it4i.cz $Â gnome-session &</pre>
+<p class=" ">On older systems where Xephyr is not available, you may also try Xnest instead of Xephyr. Another option is to launch a new X server in a separate console, via:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">xinit </span><span class="pun">/</span><span class="pln">usr</span><span class="pun">/</span><span class="pln">bin</span><span class="pun">/</span><span class="pln">ssh </span><span class="pun">-</span><span class="pln">XT </span><span class="pun">-</span><span class="pln">i </span><span class="pun">.</span><span class="pln">ssh</span><span class="pun">/</span><span class="pln">path_to_your_key yourname@cluster-namen</span><span class="pun">.</span><span class="pln">it4i</span><span class="pun">.</span><span class="pln">cz gnome</span><span class="pun">-</span><span class="pln">session </span><span class="pun">--</span><span class="pln"> </span><span class="pun">:</span><span class="lit">1</span><span class="pln"> vt12</span></pre>
+<p>However this method does not seem to work with recent Linux distributions and you will need to manually source <span class="monospace">/etc/profile</span> to properly set environment variables for PBS.</p>
+<h3 class=" ">Gnome on Windows<strong><br /></strong></h3>
+<p>Use Xlaunch to start the Xming server or run the XWin.exe. Select the ''One window" mode.</p>
+<p>Log in to the cluster, using PuTTY. On the cluster, run the gnome-session command.</p>
+<pre class="prettyprint lang-sh">$ gnome-session &</pre>
+<p>In this way, we run remote gnome session on the cluster, displaying it in the local X server</p>
+<p>Use System->Log Out to close the gnome-session</p>
+
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1.md
index cd1435966..7762da1c7 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.1.md
@@ -200,4 +200,3 @@ in the local X server
Use System->Log Out to close the gnome-session
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.html
new file mode 100644
index 000000000..7fc785d0d
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.html
@@ -0,0 +1,705 @@
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+ <h3 class=" ">If <span style="text-align: left; float: none; ">no able to forward X11 using PuTTY to CygwinX</span></h3>
+<pre class="prettyprint lang-sh"><span style="text-align: left; float: none; ">[usename@login1.anselm ~]$ gnome-session &<br />[1] 23691<br />[<span style="text-align: left; float: none; ">usename</span>@login1.anselm ~]$ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br />PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br /><br />** (gnome-session:23691): WARNING **: Cannot open display:<br /></span></pre>
+<p><span style="text-align: left; float: none; ">Â </span></p>
+<ol>
+<li><span style="text-align: left; float: none; ">Locate and modify <span style="text-align: left; float: none; ">Cygwin shortcut that uses<span class="Apple-converted-space">Â </span></span><a href="http://x.cygwin.com/docs/man1/startxwin.1.html" rel="nofollow" style="text-align: left; ">startxwin</a><br />locate<br />C:\cygwin64\bin\XWin.exe<br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">change it to</span></span></span><br />C:\<i class="moz-txt-slash">cygwin64\bin\XWin.exe -listen tcp</i><br /><br /><img alt="XWin-listen-tcp.png" src="cygwin-and-x11-forwarding/XWinlistentcp.png" title="XWin-listen-tcp.png" class="image-inline" /><br /></span><br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span></span></li>
+<li><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">Check Putty settings:<br /><span style="text-align: left; float: none; ">Enable X11 forwarding</span><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span><span class="Apple-converted-space"><br /></span></span><br /><a href="cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.html" title="" target="_self" class="internal-link"><img alt="" src="cygwin-and-x11-forwarding/cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.png" title="" class="image-inline" /></a><br /></span></span></li>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.md
index 2cdf7d60b..f99e4d95a 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding.md
@@ -1,40 +1,40 @@
Cygwin and X11 forwarding
=========================
-### If <span style="text-alignleft; floatnone; ">no able to forward X11 using PuTTY to CygwinX</span>
+### If <span style="text-align: left; float: none; ">no able to forward X11 using PuTTY to CygwinX</span>
```
[usename@login1.anselm ~]$ gnome-session &
[1] 23691
-[usename@login1.anselm ~]$ PuTTY X11 proxyunable to connect to forwarded X serverNetwork errorConnection refused
-PuTTY X11 proxyunable to connect to forwarded X serverNetwork errorConnection refused
+[usename@login1.anselm ~]$ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused
+PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused
-** (gnome-session:23691)WARNING **Cannot open display:
+** (gnome-session:23691): WARNING **: Cannot open display:
```
-<span style="text-alignleft; floatnone; ">Â </span>
+<span style="text-align: left; float: none; ">Â </span>
-1. <span style="text-alignleft; floatnone; ">Locate and modify
- <span style="text-alignleft; floatnone; ">Cygwin shortcut that
+1. <span style="text-align: left; float: none; ">Locate and modify
+ <span style="text-align: left; float: none; ">Cygwin shortcut that
uses<span
class="Apple-converted-space">Â </span></span>[startxwin](http://x.cygwin.com/docs/man1/startxwin.1.html)
locate
C:cygwin64binXWin.exe
- <span style="text-alignleft; floatnone; "><span
- style="text-alignleft; floatnone; "><span
- style="text-alignleft; floatnone; ">change it
+ <span style="text-align: left; float: none; "><span
+ style="text-align: left; float: none; "><span
+ style="text-align: left; float: none; ">change it
to</span></span></span>
C:*cygwin64binXWin.exe -listen tcp*
</span>
- <span style="text-alignleft; floatnone; "><span
- style="text-alignleft; floatnone; "></span></span>
-2. <span style="text-alignleft; floatnone; "><span
- style="text-alignleft; floatnone; ">Check Putty settings:
- <span style="text-alignleft; floatnone; ">Enable X11
- forwarding</span><span style="text-alignleft; floatnone; "><span
- style="text-alignleft; floatnone; "></span><span
+ <span style="text-align: left; float: none; "><span
+ style="text-align: left; float: none; "></span></span>
+2. <span style="text-align: left; float: none; "><span
+ style="text-align: left; float: none; ">Check Putty settings:
+ <span style="text-align: left; float: none; ">Enable X11
+ forwarding</span><span style="text-align: left; float: none; "><span
+ style="text-align: left; float: none; "></span><span
class="Apple-converted-space">
</span></span>
[](cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.html)
@@ -43,4 +43,3 @@ PuTTY X11 proxyunable to connect to forwarded X serverNetwork errorConnection re
Â
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.html
new file mode 100644
index 000000000..ea3781d03
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.html
@@ -0,0 +1,705 @@
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+ <h3 class=" ">If <span style="text-align: left; float: none; ">no able to forward X11 using PuTTY to CygwinX</span></h3>
+<pre class="prettyprint lang-sh"><span style="text-align: left; float: none; ">[usename@login1.anselm ~]$ gnome-session &<br />[1] 23691<br />[<span style="text-align: left; float: none; ">usename</span>@login1.anselm ~]$ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br />PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused<br /><br />** (gnome-session:23691): WARNING **: Cannot open display:<br /></span></pre>
+<p><span style="text-align: left; float: none; ">Â </span></p>
+<ol>
+<li><span style="text-align: left; float: none; ">Locate and modify <span style="text-align: left; float: none; ">Cygwin shortcut that uses<span class="Apple-converted-space">Â </span></span><a href="http://x.cygwin.com/docs/man1/startxwin.1.html" rel="nofollow" style="text-align: left; ">startxwin</a><br />locate<br />C:\cygwin64\bin\XWin.exe<br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">change it to</span></span></span><br />C:\<i class="moz-txt-slash">cygwin64\bin\XWin.exe -listen tcp</i><br /><br /><img alt="XWin-listen-tcp.png" src="XWinlistentcp.png" title="XWin-listen-tcp.png" class="image-inline" /><br /></span><br /><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span></span></li>
+<li><span style="text-align: left; float: none; "><span style="text-align: left; float: none; ">Check Putty settings:<br /><span style="text-align: left; float: none; ">Enable X11 forwarding</span><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "></span><span class="Apple-converted-space"><br /></span></span><br /><a href="cygwin-and-x11-forwarding.html" title="" target="_self" class="internal-link"><img alt="" src="cygwinX11forwarding.png/@@images/0f5b58e3-253c-4f87-a3b2-16f75cbf090f.png" title="" class="image-inline" /></a><br /></span></span></li>
+</ol>
+<p>Â </p>
+
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.md
index 80aa46df5..e652cf79c 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwin-and-x11-forwarding.md
@@ -1,40 +1,40 @@
Cygwin and X11 forwarding
=========================
-### If <span style="text-alignleft; floatnone; ">no able to forward X11 using PuTTY to CygwinX</span>
+### If <span style="text-align: left; float: none; ">no able to forward X11 using PuTTY to CygwinX</span>
```
[usename@login1.anselm ~]$ gnome-session &
[1] 23691
-[usename@login1.anselm ~]$ PuTTY X11 proxyunable to connect to forwarded X serverNetwork errorConnection refused
-PuTTY X11 proxyunable to connect to forwarded X serverNetwork errorConnection refused
+[usename@login1.anselm ~]$ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused
+PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused
-** (gnome-session:23691)WARNING **Cannot open display:
+** (gnome-session:23691): WARNING **: Cannot open display:
```
-<span style="text-alignleft; floatnone; ">Â </span>
+<span style="text-align: left; float: none; ">Â </span>
-1. <span style="text-alignleft; floatnone; ">Locate and modify
- <span style="text-alignleft; floatnone; ">Cygwin shortcut that
+1. <span style="text-align: left; float: none; ">Locate and modify
+ <span style="text-align: left; float: none; ">Cygwin shortcut that
uses<span
class="Apple-converted-space">Â </span></span>[startxwin](http://x.cygwin.com/docs/man1/startxwin.1.html)
locate
C:cygwin64binXWin.exe
- <span style="text-alignleft; floatnone; "><span
- style="text-alignleft; floatnone; "><span
- style="text-alignleft; floatnone; ">change it
+ <span style="text-align: left; float: none; "><span
+ style="text-align: left; float: none; "><span
+ style="text-align: left; float: none; ">change it
to</span></span></span>
C:*cygwin64binXWin.exe -listen tcp*
</span>
- <span style="text-alignleft; floatnone; "><span
- style="text-alignleft; floatnone; "></span></span>
-2. <span style="text-alignleft; floatnone; "><span
- style="text-alignleft; floatnone; ">Check Putty settings:
- <span style="text-alignleft; floatnone; ">Enable X11
- forwarding</span><span style="text-alignleft; floatnone; "><span
- style="text-alignleft; floatnone; "></span><span
+ <span style="text-align: left; float: none; "><span
+ style="text-align: left; float: none; "></span></span>
+2. <span style="text-align: left; float: none; "><span
+ style="text-align: left; float: none; ">Check Putty settings:
+ <span style="text-align: left; float: none; ">Enable X11
+ forwarding</span><span style="text-align: left; float: none; "><span
+ style="text-align: left; float: none; "></span><span
class="Apple-converted-space">
</span></span>
[](cygwin-and-x11-forwarding.html)
@@ -43,4 +43,3 @@ PuTTY X11 proxyunable to connect to forwarded X serverNetwork errorConnection re
Â
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html
new file mode 100644
index 000000000..87298469c
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html
@@ -0,0 +1,757 @@
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+ <p>The X Window system is a principal way to get GUI access to the clusters. The <b>X Window System</b> (commonly known as <b>X11</b>, based on its current major version being 11, or shortened to simply <b>X</b>, and sometimes informally <b>X-Windows</b>) is a computer software system and network <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Protocol_%28computing%29" title="Protocol (computing)">protocol</a> that provides a basis for <a href="http://en.wikipedia.org/wiki/Graphical_user_interface" title="Graphical user interface">graphical user interfaces</a> (GUIs) and rich input device capability for <a href="http://en.wikipedia.org/wiki/Computer_network" title="Computer network">networked computers</a>.</p>
+<p class="callout">The X display forwarding must be activated and the X server running on client side</p>
+<h3 class=" ">X display</h3>
+<p>In order to display graphical user interface GUI of various software tools, you need to enable the X display forwarding. On Linux and Mac, log in using the -X option tho ssh client:</p>
+<pre class="prettyprint lang-sh"> local $ ssh -X username@cluster-name.it4i.cz</pre>
+<h3 class=" ">X Display Forwarding on Windows</h3>
+<p class=" ">On Windows use the PuTTY client to enable X11 forwarding. Â In PuTTY menu, go to Connection->SSH->X11, mark the Enable X11 forwarding checkbox before logging in. Then log in as usual.</p>
+<p class=" ">To verify the forwarding, type</p>
+<pre class="prettyprint lang-sh">$ echo $DISPLAY</pre>
+<p>if you receive something like</p>
+<pre class="prettyprint lang-sh">localhost:10.0</pre>
+<p class=" ">then the X11 forwarding is enabled.</p>
+<h3 class=" ">X Server</h3>
+<p>In order to display graphical user interface GUI of various software tools, you need running X server on your desktop computer. For Linux users, no action is required as the X server is the default GUI environment on most Linux distributions. Mac and Windows users need to install and run the X server on their workstations.</p>
+<h3 class=" ">X Server on OS X</h3>
+<p>Mac OS users need to install <a class="external-link" href="http://xquartz.macosforge.org/landing/" target="_self" title="">XQuartz server</a>.</p>
+<h3 class=" ">X Server on Windows</h3>
+<p>There are variety of X servers available for Windows environment. The commercial Xwin32 is very stable and rich featured. The Cygwin environment provides fully featured open-source XWin X server. For simplicity, we recommend open-source X server by the <a class="external-link" href="http://sourceforge.net/projects/xming/" target="_self" title="">Xming project</a>. For stability and full features we recommend the <a class="external-link" href="http://x.cygwin.com/" target="_self" title="">XWin</a> X server by Cygwin</p>
+<table class="listing">
+<tbody>
+<tr><th style="text-align: center; ">How to use Xwin</th><th style="text-align: center; ">How to use Xming</th></tr>
+<tr>
+<td>
+<p><a class="external-link" href="http://x.cygwin.com/" target="_self" title="">Install Cygwin</a></p>
+<p>Find and execute XWin.exe<br />to start the X server on Windows desktop computer.</p>
+<p><a href="cygwin-and-x11-forwarding.html" title="" target="_self" class="internal-link">If no able to forward X11 using PuTTY to CygwinX</a></p>
+</td>
+<td>
+<p>Use Xlaunch to configure the Xming.</p>
+<p>Run Xming <br />to start the X server on Windows desktop computer.</p>
+</td>
+</tr>
+</tbody>
+</table>
+<p>Read more on <a class="external-link" href="http://www.math.umn.edu/systems_guide/putty_xwin32.shtml" target="_self" title="">http://www.math.umn.edu/systems_guide/putty_xwin32.html</a></p>
+<h3 class=" ">Running GUI Enabled Applications</h3>
+<p class="callout">Make sure that X forwarding is activated and the X server is running.</p>
+<p>Then launch the application as usual. Use the & to run the application in background.</p>
+<pre class="prettyprint lang-sh">$ module load intel (idb and gvim not installed yet)<br />$ gvim &</pre>
+<pre class="prettyprint lang-sh">$ xterm</pre>
+<p>In this example, we activate the intel programing environment tools, then start the graphical gvim editor.</p>
+<h3 class=" "><a name="gui-applications-on-compute-nodes"></a>GUI Applications on Compute Nodes</h3>
+<p>Allocate the compute nodes using -X option on the qsub command</p>
+<pre class="prettyprint lang-sh">$ qsub -q qexp -l select=2:ncpus=24 -X -I</pre>
+<p>In this example, we allocate 2 nodes via qexp queue, interactively. We request X11 forwarding with the -X option. It will be possible to run the GUI enabled applications directly on the first compute node.</p>
+<p><strong>Better performance</strong> is obtained by logging on the allocated compute node via ssh, using the -X option.</p>
+<pre class="prettyprint lang-sh">$ ssh -X r24u35n680</pre>
+<p>In this example, we log in on the r24u35n680 compute node, with the X11 forwarding enabled.</p>
+<p class="hiddenForView">HTML commented section #1 (no GUI on Compute nodes - Xvfb)</p>
+
+<h3 class=" ">The Gnome GUI Environment</h3>
+<p>The Gnome 2.28 GUI environment is available on the clusters. We recommend to use separate X server window for displaying the Gnome environment.</p>
+<h3 class=" ">Gnome on Linux and OS X</h3>
+<p>To run the remote Gnome session in a window on Linux/OS X computer, you need to install Xephyr. Ubuntu package is <span class="monospace">xserver-xephyr</span>, on OS X it is part of <a class="external-link" href="http://xquartz.macosforge.org/landing/" target="_self" title="">XQuartz</a>. First, launch Xephyr on local machine:</p>
+<pre class="prettyprint lang-sh">local $ Xephyr -ac -screen 1024x768 -br -reset -terminate :1 &</pre>
+<p class=" ">This will open a new X window with size 1024x768 at DISPLAY :1. Next, ssh to the cluster with DISPLAY environment variable set and launch <span class="monospace">gnome-session</span></p>
+<pre class=" ">local $ DISPLAY=:1.0 ssh -XC yourname@cluster-name.it4i.cz -i ~/.ssh/path_to_your_key<br />... cluster-name MOTD...<br />yourname@login1.cluster-namen.it4i.cz $Â gnome-session &</pre>
+<p class=" ">On older systems where Xephyr is not available, you may also try Xnest instead of Xephyr. Another option is to launch a new X server in a separate console, via:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">xinit </span><span class="pun">/</span><span class="pln">usr</span><span class="pun">/</span><span class="pln">bin</span><span class="pun">/</span><span class="pln">ssh </span><span class="pun">-</span><span class="pln">XT </span><span class="pun">-</span><span class="pln">i </span><span class="pun">.</span><span class="pln">ssh</span><span class="pun">/</span><span class="pln">path_to_your_key yourname@cluster-namen</span><span class="pun">.</span><span class="pln">it4i</span><span class="pun">.</span><span class="pln">cz gnome</span><span class="pun">-</span><span class="pln">session </span><span class="pun">--</span><span class="pln"> </span><span class="pun">:</span><span class="lit">1</span><span class="pln"> vt12</span></pre>
+<p>However this method does not seem to work with recent Linux distributions and you will need to manually source <span class="monospace">/etc/profile</span> to properly set environment variables for PBS.</p>
+<h3 class=" ">Gnome on Windows<strong><br /></strong></h3>
+<p>Use Xlaunch to start the Xming server or run the XWin.exe. Select the ''One window" mode.</p>
+<p>Log in to the cluster, using PuTTY. On the cluster, run the gnome-session command.</p>
+<pre class="prettyprint lang-sh">$ gnome-session &</pre>
+<p>In this way, we run remote gnome session on the cluster, displaying it in the local X server</p>
+<p>Use System->Log Out to close the gnome-session</p>
+
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.md
index 64a5688b2..38b843be1 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.md
@@ -200,4 +200,3 @@ in the local X server
Use System->Log Out to close the gnome-session
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/accessing-the-clusters.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/accessing-the-clusters.html
new file mode 100644
index 000000000..8bca76967
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/accessing-the-clusters.html
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/accessing-the-clusters.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/accessing-the-clusters.md
index 3f5be332a..10f87cdf2 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/accessing-the-clusters.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/accessing-the-clusters.md
@@ -18,4 +18,3 @@ client](putty/putty.html).
### SSH keys
Read more about [SSH keys management](ssh-keys.html).
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.html
new file mode 100644
index 000000000..a512fdbfc
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.html
@@ -0,0 +1,736 @@
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+
+
+ <h1 id="parent-fieldname-title" class="documentFirstHeading">
+ PuTTY
+ </h1>
+
+
+
+
+ <div id="viewlet-below-content-title">
+</div>
+
+
+
+
+
+
+
+
+
+
+
+ <div id="viewlet-above-content-body">
+<dl id="document-toc" class="portlet toc" style="display: none">
+ <dt class="portletHeader">Obsah</dt>
+ <dd class="portletItem">
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+ <div id="parent-fieldname-text-7963ffe5309646e29c3de629f9e0d2e9" class="">
+ <h2 class=" " style="text-align: start; ">PuTTY -<span class="Apple-converted-space"> </span>before we start SSH connection</h2>
+<h3 class=" ">Windows PuTTY Installer</h3>
+<p>We recommned you to download "<b style="text-align: start; ">A Windows installer for everything except PuTTYtel</b>" with <strong><em>Pageant</em> </strong>(SSH authentication agent) and <strong>PuTTYgen</strong> (PuTTY key generator) which is available <a class="external-link" href="http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html" target="_self" title="">here</a>.</p>
+<p class="callout"><span class="internal-link">After installation you can proceed directly to private keys authentication using <a class="internal-link" href="putty/putty.html#putty" target="_self" title="">"Putty"</a>.</span><br />"Change Password for Existing Private Key" is optional.<br />"Generate a New Public/Private key pair" is intended for users without Public/Private key in the initial email containing login credentials.<br />"Pageant" is optional.</p>
+<h3 class=" ">PuTTYgen</h3>
+<p>PuTTYgen is the PuTTY key generator. Read more how to load in an existing private key and change your passphrase or generate a new public/private key pair using <a href="putty/puttygen.html" title="" target="_self" class="internal-link">PuTTYgen</a> if needed.</p>
+<h3 class=" ">Pageant SSH agent</h3>
+<p><a href="putty/pageant.html" title="" target="_self" class="internal-link">Pageant</a> holds your private key in memory without needing to retype a passphrase on every login. We recommend its usage.</p>
+<h2 class=" "><a name="putty"></a>PuTTY - how to connect to the IT4Innovations cluster</h2>
+<ul>
+<li>Run PuTTY</li>
+<li>Enter Host name and Save session fields with <a href="../../../salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html" title="" target="_self" class="internal-link">Login address</a> and browse Connection - > SSH -> Auth menu.<br />The <em>Host Name</em> input may be in the format <strong>"username@clustername.it4i.cz"</strong> so you don't have to type your login each time.<br />In this example we will connect to the Salomon cluster using  <strong>"salomon.it4i.cz"</strong>.<br /><br /><a href="putty/PuTTY_host_Salomon.png" title="" target="_self" class="internal-link"><img alt="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_host_Salomon.png/@@images/c24acdc5-21eb-47aa-b412-75849ccd2e82.png" title="" class="image-inline" /></a></li>
+</ul>
+<p class=" ">Â </p>
+<ul>
+<li>Category -> Connection - > SSH -> Auth:<br />Select Attempt authentication using Pageant.<br />Select Allow agent forwarding.<br />Browse and select your <a href="ssh-keys.html" title="" target="_self" class="internal-link">private key</a> file.<br /><br /><a href="putty/PuTTY_keyV.png" title="" target="_self" class="internal-link"><img alt="PuttyKey" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_keyV.png/@@images/9f161548-31a6-42a7-ad61-4e885e4b4664.png" title="PuttyKey" class="image-inline" /></a><br /><br /></li>
+<li>Return to Session page and Save selected configuration with <em>Save</em> button.<br /><br /><a href="putty/PuTTY_save_Salomon.png" title="" target="_self" class="internal-link"><img alt="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_save_Salomon.png/@@images/0eeeb971-b295-4780-88e7-7557da05a1cb.png" title="" class="image-inline" /></a><br /><br /></li>
+<li>Now you can log in using <em>Open</em> button.<br /><br /><a href="putty/PuTTY_open_Salomon.png" title="" target="_self" class="internal-link"><img alt="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_open_Salomon.png/@@images/741d3e56-d9b3-48fd-838f-90ad6c1bf8eb.png" title="" class="image-inline" /></a><br /><br /></li>
+<li>Enter your username if the <em>Host Name</em> input is not in the format "username@salomon.it4i.cz".<br /><br /></li>
+<li>Enter passphrase for selected <a href="ssh-keys.html" title="" target="_self" class="internal-link">private key</a> file if Pageant <strong></strong>SSH authentication agent is not used.<br /><br /></li>
+</ul>
+<h2 class=" ">Another PuTTY Settings</h2>
+<ul>
+<li>Category -> Windows -> Translation -> Remote character set and select <strong>UTF-8</strong>.</li>
+</ul>
+<ul>
+<li>Category -> Terminal -> Features and select <strong>Disable application keypad mode</strong> (enable numpad)</li>
+<li>Save your configuration on Session page in to Default Settings with <em>Save</em> button .</li>
+</ul>
+
+ </div>
+
+
+ <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
+
+ <div id="plone-discussions">
+ <hr />
+ <b><a id="plone-discussions-href" href="putty/putty.html#plone-discussions">Komentáře</a></b>
+ </div>
+
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+<li class="navTreeItem visualNoMarker section-pageant">
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.md
index b45b7ac76..2ba252f55 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.md
@@ -5,7 +5,7 @@ PuTTY
-PuTTY -<span class="Apple-converted-space"> </span>before we start SSH connection {#putty---before-we-start-ssh-connection style="text-alignstart; "}
+PuTTY -<span class="Apple-converted-space"> </span>before we start SSH connection ssh-connection style="text-align: start; "}
---------------------------------------------------------------------------------
### Windows PuTTY Installer
@@ -93,4 +93,3 @@ Another PuTTY Settings
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant.html
new file mode 100644
index 000000000..229268203
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant.html
@@ -0,0 +1,725 @@
+
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+ <span id="breadcrumbs-current">Pageant SSH agent</span>
+
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+ <dl class="portalMessage info" id="kssPortalMessage" style="display:none">
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+ </h1>
+
+
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+ <div id="viewlet-below-content-title">
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+ <p>Pageant holds your private key in memory without needing to retype a passphrase on every login.</p>
+<ul>
+<li>Run Pageant.</li>
+<li>On Pageant Key List press <em>Add key</em> and select your private key (id_rsa.ppk).</li>
+<li>Enter your passphrase.</li>
+<li>Now you have your private key in memory without needing to retype a passphrase on every login.<br /><br /><a href="PageantV.png" title="" target="_self" class="internal-link"><img alt="Pageant" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PageantV.png/@@images/b82926bc-3890-49b9-b5be-a673975e442b.png" title="Pageant" class="image-inline" /></a></li>
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+<li class="navTreeItem visualNoMarker navTreeItemInPath navTreeFolderish section-accessing-the-clusters">
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+<li class="navTreeItem visualNoMarker section-puttygen">
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant.md
index 6108599dc..d6e3c3b8d 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/pageant.md
@@ -18,4 +18,3 @@ passphrase on every login.
[](PageantV.png)
Â
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html
new file mode 100644
index 000000000..21ec014fa
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html
@@ -0,0 +1,736 @@
+
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+<div class="cell width-full position-0">
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+ <p class="hiddenStructure">
+ <a accesskey="2" href="putty.html#content">PĹ™ejĂt na obsah</a> |
+
+ <a accesskey="6" href="putty.html#portal-globalnav">PĹ™ejĂt na navigaci</a>
+</p>
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+ <label for="searchbox_currentfolder_only" style="cursor: pointer">pouze v aktuálnà sekci</label>
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+ <div class="LSResult" id="LSResult"><div class="LSShadow" id="LSShadow"></div></div>
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+ <h2 class=" " style="text-align: start; ">PuTTY -<span class="Apple-converted-space"> </span>before we start SSH connection</h2>
+<h3 class=" ">Windows PuTTY Installer</h3>
+<p>We recommned you to download "<b style="text-align: start; ">A Windows installer for everything except PuTTYtel</b>" with <strong><em>Pageant</em> </strong>(SSH authentication agent) and <strong>PuTTYgen</strong> (PuTTY key generator) which is available <a class="external-link" href="http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html" target="_self" title="">here</a>.</p>
+<p class="callout"><span class="internal-link">After installation you can proceed directly to private keys authentication using <a class="internal-link" href="putty.html#putty" target="_self" title="">"Putty"</a>.</span><br />"Change Password for Existing Private Key" is optional.<br />"Generate a New Public/Private key pair" is intended for users without Public/Private key in the initial email containing login credentials.<br />"Pageant" is optional.</p>
+<h3 class=" ">PuTTYgen</h3>
+<p>PuTTYgen is the PuTTY key generator. Read more how to load in an existing private key and change your passphrase or generate a new public/private key pair using <a href="puttygen.html" title="" target="_self" class="internal-link">PuTTYgen</a> if needed.</p>
+<h3 class=" ">Pageant SSH agent</h3>
+<p><a href="pageant.html" title="" target="_self" class="internal-link">Pageant</a> holds your private key in memory without needing to retype a passphrase on every login. We recommend its usage.</p>
+<h2 class=" "><a name="putty"></a>PuTTY - how to connect to the IT4Innovations cluster</h2>
+<ul>
+<li>Run PuTTY</li>
+<li>Enter Host name and Save session fields with <a href="../../../../salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html" title="" target="_self" class="internal-link">Login address</a> and browse Connection - > SSH -> Auth menu.<br />The <em>Host Name</em> input may be in the format <strong>"username@clustername.it4i.cz"</strong> so you don't have to type your login each time.<br />In this example we will connect to the Salomon cluster using  <strong>"salomon.it4i.cz"</strong>.<br /><br /><a href="PuTTY_host_Salomon.png" title="" target="_self" class="internal-link"><img alt="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_host_Salomon.png/@@images/c24acdc5-21eb-47aa-b412-75849ccd2e82.png" title="" class="image-inline" /></a></li>
+</ul>
+<p class=" ">Â </p>
+<ul>
+<li>Category -> Connection - > SSH -> Auth:<br />Select Attempt authentication using Pageant.<br />Select Allow agent forwarding.<br />Browse and select your <a href="../ssh-keys.html" title="" target="_self" class="internal-link">private key</a> file.<br /><br /><a href="PuTTY_keyV.png" title="" target="_self" class="internal-link"><img alt="PuttyKey" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_keyV.png/@@images/9f161548-31a6-42a7-ad61-4e885e4b4664.png" title="PuttyKey" class="image-inline" /></a><br /><br /></li>
+<li>Return to Session page and Save selected configuration with <em>Save</em> button.<br /><br /><a href="PuTTY_save_Salomon.png" title="" target="_self" class="internal-link"><img alt="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_save_Salomon.png/@@images/0eeeb971-b295-4780-88e7-7557da05a1cb.png" title="" class="image-inline" /></a><br /><br /></li>
+<li>Now you can log in using <em>Open</em> button.<br /><br /><a href="PuTTY_open_Salomon.png" title="" target="_self" class="internal-link"><img alt="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuTTY_open_Salomon.png/@@images/741d3e56-d9b3-48fd-838f-90ad6c1bf8eb.png" title="" class="image-inline" /></a><br /><br /></li>
+<li>Enter your username if the <em>Host Name</em> input is not in the format "username@salomon.it4i.cz".<br /><br /></li>
+<li>Enter passphrase for selected <a href="../ssh-keys.html" title="" target="_self" class="internal-link">private key</a> file if Pageant <strong></strong>SSH authentication agent is not used.<br /><br /></li>
+</ul>
+<h2 class=" ">Another PuTTY Settings</h2>
+<ul>
+<li>Category -> Windows -> Translation -> Remote character set and select <strong>UTF-8</strong>.</li>
+</ul>
+<ul>
+<li>Category -> Terminal -> Features and select <strong>Disable application keypad mode</strong> (enable numpad)</li>
+<li>Save your configuration on Session page in to Default Settings with <em>Save</em> button .</li>
+</ul>
+
+ </div>
+
+
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.md
index 9461b0121..31f03e8a3 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.md
@@ -5,7 +5,7 @@ PuTTY
-PuTTY -<span class="Apple-converted-space"> </span>before we start SSH connection {#putty---before-we-start-ssh-connection style="text-alignstart; "}
+PuTTY -<span class="Apple-converted-space"> </span>before we start SSH connection ssh-connection style="text-align: start; "}
---------------------------------------------------------------------------------
### Windows PuTTY Installer
@@ -90,4 +90,3 @@ Another PuTTY Settings
application keypad mode** (enable numpad)
- Save your configuration on Session page in to Default Settings with
*Save* button .
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html
new file mode 100644
index 000000000..802c8e06e
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html
@@ -0,0 +1,739 @@
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+ <dl class="portalMessage info" id="kssPortalMessage" style="display:none">
+ <dt>Info</dt>
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+ PuTTY key generator
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+ <p>PuTTYgen is the PuTTY key generator. You can load in an existing private key and change your passphrase or generate a new public/private key pair.</p>
+<h3 class=" ">Change Password for Existing Private Key</h3>
+<p>You can change the password of your SSH key with "PuTTY Key Generator". Make sure to backup the key.</p>
+<ul>
+<li>Load your <a href="../ssh-keys.html" title="" target="_self" class="internal-link">private key</a> file with <em>Load</em> button.</li>
+<li>Enter your current passphrase.</li>
+<li>Change key passphrase.</li>
+<li>Confirm key passphrase.</li>
+<li>Save your private key with <em>Save private key</em> button.<br /><br /><a href="PuttyKeygeneratorV.png" title="" target="_self" class="internal-link"><img alt="PuttyKeygenerator" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygeneratorV.png/@@images/22954eec-6127-4d42-b159-9bebacb3223d.png" title="PuttyKeygenerator" class="image-inline" /></a></li>
+</ul>
+<p>Â </p>
+<h3 class=" ">Generate a New Public/Private key pair</h3>
+<p>You can generate an additional public/private key pair and insert public key into authorized_keys file for authentication with your own private <span>key. </span></p>
+<ul>
+<li>Start with <em>Generate</em> button.<br /><br /><a href="PuttyKeygenerator_001V.png" title="" target="_self" class="internal-link"><img alt="PuttyKeygenerator_001" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_001V.png/@@images/f7c1889f-605f-4c5c-8904-d962ec4531a2.png" title="PuttyKeygenerator_001" class="image-inline" /></a><br /><br /></li>
+<li>Generate some randomness.<br /><br /><a href="PuttyKeygenerator_002V.png" title="" target="_self" class="internal-link"><img alt="PuttyKeygenerator_002" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_002V.png/@@images/13b88922-8c1d-47b2-b3e6-043c18b11d86.png" title="PuttyKeygenerator_002" class="image-inline" /></a><br /><br /></li>
+<li>Wait.<br /><br /><a href="20150312_143443.png" title="" target="_self" class="internal-link"><img alt="PuttyKeygenerator_003" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/20150312_143443.png/@@images/29ff0f89-8203-4777-9a00-c068d3188fd0.png" title="PuttyKeygenerator_003" class="image-inline" /></a><br /><br /></li>
+<li>Enter a <em>comment</em> for your key using format 'username@organization.example.com'.<br />Enter key passphrase.<br />Confirm key passphrase.<br />Save your new private key <code>in "*.ppk" </code>format with <em>Save private key</em> button.<br /><br /><a href="PuttyKeygenerator_004V.png" title="" target="_self" class="internal-link"><img alt="PuttyKeygenerator_004" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_004V.png/@@images/8ef00e6b-0155-4dc2-82e6-7141a15f282c.png" title="PuttyKeygenerator_004" class="image-inline" /></a><br /><br /></li>
+<li>Save the public key with <em>Save public key</em> button.<br />You can copy public key out of the â€Public key for pasting into authorized_keys file’ box.<br /><br /><a href="PuttyKeygenerator_005V.png" title="" target="_self" class="internal-link"><img alt="PuttyKeygenerator_005" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_005V.png/@@images/929621fe-45f7-45c8-9ed0-c34d430d65f4.png" title="PuttyKeygenerator_005" class="image-inline" /></a><br /><br /></li>
+<li>Export private key in OpenSSH format "id_rsa" using Conversion -> Export OpenSSH key<br /><br /><a href="PuttyKeygenerator_006V.png" title="" target="_self" class="internal-link"><img alt="PuttyKeygenerator_006" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/PuttyKeygenerator_006V.png/@@images/de851079-6ed4-440a-b270-77dd6a0a950c.png" title="PuttyKeygenerator_006" class="image-inline" /></a><br /><br /></li>
+<li>Now you can insert additional public key into authorized_keys file for authentication with your own private <span>key. <br />You must log in using ssh key received after registration. Then proceed to <a href="../ssh-keys.html" title="" target="_self" class="internal-link">How to add your own key</a>.<br /></span></li>
+</ul>
+
+ </div>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.md
index 0d8d612d6..628cc640c 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.md
@@ -69,4 +69,3 @@ key into authorized_keys file for authentication with your own private
proceed to [How to add your own
key](../ssh-keys.html).
</span>
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html
new file mode 100644
index 000000000..6b25902d3
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html
@@ -0,0 +1,696 @@
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+ <h2 class=" "><span class="mw-headline" id="Key_management">Key management</span></h2>
+<p>After logging in, you can see .ssh/ directory with SSH keys and authorized_keys file:</p>
+<pre class=" ">$ cd /home/username/<br />$ ls -la .ssh/<br />total 24<br />drwx------ 2 username username 4096 May 13 15:12 .<br />drwxr-x---22 username username 4096 May 13 07:22 ..<br />-rw-r--r-- 1 username username 392 May 21 2014 authorized_keys<br />-rw------- 1 username username 1675 May 21 2014 id_rsa<br />-rw------- 1 username username 1460 May 21 2014 id_rsa.ppk<br />-rw-r--r-- 1 username username 392 May 21 2014 id_rsa.pub<br /><br /></pre>
+<p class="callout"><span class="visualHighlight"></span>Please note that private keys in .ssh directory are without passphrase and allow you to connect within the cluster.</p>
+<h3 class=" ">Access privileges on .ssh folder</h3>
+<ul>
+<li><code style="text-align: left; ">.ssh</code><span style="text-align: left; float: none; "><span class="Apple-converted-space">Â </span>directory:</span> <span style="text-align: left; float: none; ">700 (drwx------)</span></li>
+<li><span style="text-align: left; float: none; ">Authorized_keys, <span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span class="Apple-converted-space">known_hosts</span></span></span> and <span style="text-align: left; float: none; ">public key <span style="text-align: left; float: none; ">(</span><code style="text-align: left; ">.pub</code><span style="text-align: left; float: none; "><span class="Apple-converted-space"> </span>file): <span class="Apple-converted-space"> </span></span><code style="text-align: left; ">644 (-rw-r--r--)</code></span></span></li>
+<li><span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><code style="text-align: left; "></code><span class="Apple-converted-space"> <span style="text-align: left; float: none; ">Private key (</span><code style="text-align: left; ">id_rsa/id_rsa.ppk</code><span style="text-align: left; float: none; ">): <span class="Apple-converted-space"></span></span><code style="text-align: left; ">600 (-rw-------)</code><br class="Apple-converted-space" /></span></span><br /></span></li>
+</ul>
+<pre class=" ">cd /home/username/<br />chmod 700 .ssh/<br />chmod 644 .ssh/authorized_keys<br />chmod 644 .ssh/id_rsa.pub<br />chmod 644 .ssh/<span style="text-align: left; float: none; "><span style="text-align: left; float: none; "><span class="Apple-converted-space">known_hosts</span></span></span><br />chmod 600 .ssh/id_rsa<br />chmod 600Â .ssh/id_rsa.ppk</pre>
+<h2 class=" ">Private key</h2>
+<p class="exclamation">The path to a private key is usually /home/username/.ssh/</p>
+<p>Private key file in "id_rsa" or <code>"*.ppk" </code>format is used to authenticate with the servers. <span style="text-align: start; float: none; ">Private key is present locally on local side and used for example in SSH agent <a href="putty/PageantV.png" title="" target="_self" class="internal-link">Pageant (for Windows users)</a>. The private key should always be kept in a safe place.</span></p>
+<p><span style="text-align: start; float: none; ">An example of private key format:</span></p>
+<pre class=" "><span style="text-align: start; float: none; ">-----BEGIN RSA PRIVATE KEY-----<br />MIIEpAIBAAKCAQEAqbo7jokygnBpG2wYa5NB45ns6+UKTNLMLHF0BO3zmRtKEElE<br />aGqXfbYwvXlcuRb2d9/Y5dVpCZHV0kbY3NhtVOcEIe+1ROaiU9BEsUAhMNEvgiLV<br />gSql4QvRO4BWPlM8+WAWXDp3oeoBh8glXyuh9teb8yq98fv1r1peYGRrW3/s4V+q<br />O1SQ0XY2T7rWCYRLIP6rTMXArTI35v3WU513mn7nm1fJ7oN0QgVH5b0W9V1Kyc4l<br />9vILHeMXxvz+i/5jTEfLOJpiRGYZYcaYrE4dIiHPl3IlbV7hlkK23Xb1US8QJr5G<br />ADxp1VTkHjY+mKagEfxl1hQIb42JLHhKMEGqNQIDAQABAoIBAQCkypPuxZjL+vai<br />UGa5dAWiRZ46P2yrwHPKpvEdpCdDPbLAc1K/CtdBkHZsUPxNHVV6eFWweW99giIY<br />Av+mFWC58X8asBHQ7xkmxW0cqAZRzpkRAl9IBS9/fKjO28Fgy/p+suOi8oWbKIgJ<br />3LMkX0nnT9oz1AkOfTNC6Tv+3SE7eTj1RPcMjur4W1Cd1N3EljLszdVk4tLxlXBS<br /><span style="text-align: start; float: none; ">yl9NzVnJJbJR4t01l45VfFECgYEAno1WJSB/SwdZvS9GkfhvmZd3r4vyV9Bmo3dn<br /></span>XZAh8HRW13imOnpklDR4FRe98D9A7V3yh9h60Co4oAUd6N+Oc68/qnv/8O9efA+M<br />/neI9ANYFo8F0+yFCp4Duj7zPV3aWlN/pd8TNzLqecqh10uZNMy8rAjCxybeZjWd<br />DyhgywXhAoGBAN3BCazNefYpLbpBQzwes+f2oStvwOYKDqySWsYVXeVgUI+OWTVZ<br />eZ26Y86E8MQO+q0TIxpwou+TEaUgOSqCX40Q37rGSl9K+rjnboJBYNCmwVp9bfyj<br />kCLL/3g57nTSqhgHNa1xwemePvgNdn6FZteA8sXiCg5ZzaISqWAffek5AoGBAMPw<br />V/vwQ96C8E3l1cH5cUbmBCCcfXM2GLv74bb1V3SvCiAKgOrZ8gEgUiQ0+TfcbAbe<br />7MM20vRNQjaLTBpai/BTbmqM1Q+r1KNjq8k5bfTdAoGANgzlNM9omM10rd9WagL5<br />yuJcal/03p048mtB4OI4Xr5ZJISHze8fK4jQ5veUT9Vu2Fy/w6QMsuRf+qWeCXR5<br /><span style="text-align: start; float: none; ">RPC2H0JzkS+2uZp8BOHk1iDPqbxWXJE9I57CxBV9C/tfzo2IhtOOcuJ4LY+sw+y/<br /></span>ocKpJbdLTWrTLdqLHwicdn8OxeWot1mOukyK2l0UeDkY6H5pYPtHTpAZvRBd7ETL<br />Zs2RP3KFFvho6aIDGrY0wee740/jWotx7fbxxKwPyDRsbH3+1Wx/eX2RND4OGdkH<br />gejJEzpk/7y/P/hCad7bSDdHZwO+Z03HIRC0E8yQz+JYatrqckaRCtd7cXryTmTR<br />FbvLJmECgYBDpfno2CzcFJCTdNBZFi34oJRiDb+HdESXepk58PcNcgK3R8PXf+au<br />OqDBtZIuFv9U1WAg0gzGwt/0Y9u2c8m0nXziUS6AePxy5sBHs7g9C9WeZRz/nCWK<br />+cHIm7XOwBEzDKz5f9eBqRGipm0skDZNKl8X/5QMTT5K3Eci2n+lTw==<br />-----END RSA PRIVATE KEY-----</span></pre>
+<h2 class=" ">Public key</h2>
+<p>Public key file in "*.pub" format is used to <span style="text-align: start; float: none; ">verify a<span class="Apple-converted-space">Â </span></span><span style="text-align: start; ">digital signature</span>. Public <span style="text-align: start; float: none; ">key is present on the remote side and <span style="text-align: start; float: none; ">allows access to the owner of the matching private key</span>.</span></p>
+<p><span style="text-align: start; float: none; ">An example of public key format:</span></p>
+<pre class=" "><span style="text-align: start; float: none; ">ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCpujuOiTKCcGkbbBhrk0Hjmezr5QpM0swscXQE7fOZG0oQSURoapd9tjC9eVy5FvZ339jl1WkJkdXSRtjc2G1U5wQh77VE5qJT0ESxQCEw0S+CItWBKqXhC9E7gFY+UyP5YBZcOneh6gGHyCVfK6H215vzKr3x+/WvWl5gZGtbf+zhX6o4RJDRdjZPutYJhEsg/qtMxcCtMjfm/dZTnXeafuebV8nug3RCBUflvRb1XUrJuiX28gsd4xfG/P6L/mNMR8s4kmJEZhlhxpj8Th0iIc+XciVtXuGWQrbddcVRLxAmvkYAPGnVVOQeNj69pqAR/GXaFAhvjYkseEowQao1 username@organization.example.com</span></pre>
+<h3 class=" ">How to add your own key</h3>
+<p>First, generate a new keypair of your public and private key:</p>
+<pre class=" ">local $ ssh-keygen -C 'username@organization.example.com' -f additional_key</pre>
+<p class="exclamation">Please, enter <strong>strong</strong> <strong>passphrase</strong> for securing your private key.</p>
+<p>You can insert additional public key into authorized_keys file for authentication with your own private <span>key. Additional records in authorized_keys file must be delimited by new line</span>. Users are not advised to remove the default public key from authorized_keys file.</p>
+<p>Example:</p>
+<pre class=" ">$ cat additional_key.pub >> ~/.ssh/authorized_keys</pre>
+<p>In this example, we add an additional public key, stored in file additional_key.pub into the authorized_keys. Next time we log in, we will be able to use the private addtional_key key to log in.</p>
+<h3 class=" ">How to remove your own key</h3>
+<p>Removing your key from authorized_keys can be done simply by deleting the corresponding public key which can be identified by a comment at the end of line (eg. username@organization.example.com).</p>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
index 34845d405..e3ad6a6fe 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
@@ -27,28 +27,28 @@ the cluster.
### Access privileges on .ssh folder
-- `.ssh`{style="text-alignleft; "}<span
- style="text-alignleft; floatnone; "><span
+- `.ssh`<span
+ style="text-align: left; float: none; "><span
class="Apple-converted-space">Â </span>directory:</span> <span
- style="text-alignleft; floatnone; ">700 (drwx------)</span>
+ style="text-align: left; float: none; ">700 (drwx------)</span>
- <span
- style="text-alignleft; floatnone; ">Authorized_keys, <span
- style="text-alignleft; floatnone; "><span
- style="text-alignleft; floatnone; "><span
+ style="text-align: left; float: none; ">Authorized_keys, <span
+ style="text-align: left; float: none; "><span
+ style="text-align: left; float: none; "><span
class="Apple-converted-space">known_hosts</span></span></span> and
- <span style="text-alignleft; floatnone; ">public key <span
- style="text-alignleft; floatnone; ">(</span>`.pub`{style="text-alignleft; "}<span
- style="text-alignleft; floatnone; "><span
+ <span style="text-align: left; float: none; ">public key <span
+ style="text-align: left; float: none; ">(</span>`.pub`<span
+ style="text-align: left; float: none; "><span
class="Apple-converted-space">Â </span>file):Â <span
class="Apple-converted-space">
- </span></span>`644 (-rw-r--r--)`{style="text-alignleft; "}</span></span>
-- <span style="text-alignleft; floatnone; "><span
- style="text-alignleft; floatnone; ">``{style="text-alignleft; "}<span
+ </span></span>`644 (-rw-r--r--)`</span></span>
+- <span style="text-align: left; float: none; "><span
+ style="text-align: left; float: none; ">``<span
class="Apple-converted-space"> <span
- style="text-alignleft; floatnone; ">Private key
- (</span>`id_rsa/id_rsa.ppk`{style="text-alignleft; "}<span
- style="text-alignleft; floatnone; ">)<span
- class="Apple-converted-space"></span></span>`600 (-rw-------)`{style="text-alignleft; "}
+ style="text-align: left; float: none; ">Private key
+ (</span>`id_rsa/id_rsa.ppk`<span
+ style="text-align: left; float: none; ">): <span
+ class="Apple-converted-space"></span></span>`600 (-rw-------)`
</span></span>
</span>
@@ -69,12 +69,12 @@ The path to a private key is usually /home/username/.ssh/
Private key file in "id_rsa" or `"*.ppk" `format is used to
authenticate with the servers. <span
-style="text-alignstart; floatnone; ">Private key is present locally
+style="text-align: start; float: none; ">Private key is present locally
on local side and used for example in SSH agent [Pageant (for Windows
users)](putty/PageantV.png). The private key should
always be kept in a safe place.</span>
-<span style="text-alignstart; floatnone; ">An example of private key
+<span style="text-align: start; float: none; ">An example of private key
format:</span>
-----BEGIN RSA PRIVATE KEY-----
@@ -109,14 +109,14 @@ Public key
----------
Public key file in "*.pub" format is used to <span
-style="text-alignstart; floatnone; ">verify a<span
+style="text-align: start; float: none; ">verify a<span
class="Apple-converted-space">Â </span></span><span
-style="text-alignstart; ">digital signature</span>. Public <span
-style="text-alignstart; floatnone; ">key is present on the remote
-side and <span style="text-alignstart; floatnone; ">allows access to
+style="text-align: start; ">digital signature</span>. Public <span
+style="text-align: start; float: none; ">key is present on the remote
+side and <span style="text-align: start; float: none; ">allows access to
the owner of the matching private key</span>.</span>
-<span style="text-alignstart; floatnone; ">An example of public key
+<span style="text-align: start; float: none; ">An example of public key
format:</span>
ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCpujuOiTKCcGkbbBhrk0Hjmezr5QpM0swscXQE7fOZG0oQSURoapd9tjC9eVy5FvZ339jl1WkJkdXSRtjc2G1U5wQh77VE5qJT0ESxQCEw0S+CItWBKqXhC9E7gFY+UyP5YBZcOneh6gGHyCVfK6H215vzKr3x+/WvWl5gZGtbf+zhX6o4RJDRdjZPutYJhEsg/qtMxcCtMjfm/dZTnXeafuebV8nug3RCBUflvRb1XUrJuiX28gsd4xfG/P6L/mNMR8s4kmJEZhlhxpj8Th0iIc+XciVtXuGWQrbddcVRLxAmvkYAPGnVVOQeNj69pqAR/GXaFAhvjYkseEowQao1 username@organization.example.com
@@ -147,3 +147,7 @@ will be able to use the private addtional_key key to log in.
Removing your key from authorized_keys can be done simply by deleting
the corresponding public key which can be identified by a comment at the
end of line (eg. username@organization.example.com).
+
+
+
+
diff --git a/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.html b/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.html
new file mode 100644
index 000000000..6927679ce
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.html
@@ -0,0 +1,570 @@
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md b/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
index f54782816..2e9159d4e 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
@@ -37,4 +37,3 @@ and [Obtaining Login
Credentials](obtaining-login-credentials.html) page.
Â
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/changelog.html b/docs.it4i.cz/get-started-with-it4innovations/changelog.html
new file mode 100644
index 000000000..d76d34f21
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/changelog.html
@@ -0,0 +1,799 @@
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+ <div id="content-core">
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+ <thead>
+ <tr>
+ <th class="listing-header-ModificationDate">Datum Ăşpravy</th>
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+
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+ <tr class="odd">
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+ <td class="listing-body-ModificationDate">
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+
+
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+
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+ <tr class="even">
+
+
+
+
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+ <td class="listing-body-ModificationDate">
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+<h2><span class="link-external"><span class="WYSIWYG_LINK">How to read the documentation</span></span></h2>
+<ol>
+<li>Read the list in the left column. Select the subject of interest. Alternatively, use the Search box in the upper right corner.</li>
+<li>Read the CONTENTS in the upper right corner.</li>
+<li>Scan for all the yellow bulb call-outs on the page.</li>
+<li>Read the details if still more information is needed. <strong>Look for examples</strong> illustrating the concepts.</li>
+</ol>
+<p>Â </p>
+<p class="callout">The call-out. Â Focus on the call-outs before reading full details.</p>
+<p>Â </p>
+<ul>
+<li>Read the <a href="changelog.html" title="" target="_self" class="external-link">Changelog</a> to keep up to date.</li>
+</ul>
+<h2 class=" ">Getting Help and Support</h2>
+<p class="callout" title="">Contact <a class="email-link" href="mailto:support%20[at]%20it4i.cz" target="_self" title="">support [at] it4i.cz</a> for help and support regarding the cluster technology at IT4Innovations.<br />Please use <strong>Czech</strong>, <strong>Slovak</strong> or <strong>English</strong> language for communication with us.<br />Follow the status of your request to IT4Innovations at <a class="external-link" href="http://support.it4i.cz/rt" target="_self" title="">support.it4i.cz/rt</a>.</p>
+<p class="external-link" title="">Â </p>
+<p class="external-link" title="">Use your IT4Innotations username and password to log in to the <a class="external-link" href="http://support.it4i.cz/" target="_self" title="">support</a> portal.</p>
+<h2 class=" ">Required Proficiency</h2>
+<p class="callout">You need basic proficiency in Linux environment.</p>
+<p>Â </p>
+<p>In order to use the system for your calculations, you need basic proficiency in Linux environment. To gain the proficiency, we recommend you reading the <a class="external-link" href="http://www.tldp.org/LDP/intro-linux/html/" target="_self" title=""><span class="WYSIWYG_LINK">introduction to Linux</span></a> operating system environment and installing a Linux distribution on your personal computer. A good choice might be the <a class="external-link" href="http://fedoraproject.org/" target="_self" title=""><span class="WYSIWYG_LINK">Fedora</span></a> distribution, as it is similar to systems on the clusters at IT4Innovations. It's easy to install and use. In fact, any distribution would do.</p>
+<p>Â </p>
+<p class="callout">Learn how to parallelize your code!</p>
+<p>Â </p>
+<p>In many cases, you will run your own code on the cluster. In order to fully exploit the cluster, you will need to carefully consider how to utilize all the cores available on the node and how to use multiple nodes at the same time. You need to <b>parallelize</b> your code. Proficieny in MPI, OpenMP, CUDA, UPC or GPI2 programming may be gained via the <a class="external-link" href="http://prace.it4i.cz" target="_self" title="">training provided by IT4Innovations.</a></p>
+<h2 class=" ">Terminology Frequently Used on These Pages</h2>
+<ul>
+<ul>
+<li><strong>node:</strong> a computer, interconnected by network to other computers - Computational nodes are powerful computers, designed and dedicated for executing demanding scientific computations.</li>
+<li><strong>core:</strong> processor core, a unit of processor, executing computations</li>
+<li><strong>corehours:</strong> wall clock hours of processor core time - Each node is equipped with <strong>X</strong> processor cores, provides <strong>X</strong> corehours per 1 wall clock hour.</li>
+<li><strong><a name="job"></a>job:</strong> a calculation running on the supercomputer - The job allocates and utilizes resources of the supercomputer for certain time.</li>
+<li><strong>HPC:</strong> High Performance Computing</li>
+<li><a name="HPC_resources"></a><strong>HPC (computational) resources:</strong> corehours, storage capacity, software licences</li>
+<li><strong>code:</strong> a program</li>
+<li><strong>primary investigator (PI):</strong> a person responsible for execution of computational project and utilization of computational resources allocated to that project</li>
+<li><strong>collaborator:</strong> a person participating on execution of computational project and utilization of computational resources allocated to that project</li>
+<li><strong><a name="Project"></a>project:</strong> a computational project under investigation by the PI - The project is identified by the project ID. The computational resources are allocated and charged per project.</li>
+<li><strong><a name="Jobscript"></a>jobscript:</strong> a script to be executed by the PBS Professional workload manager</li>
+</ul>
+</ul>
+<h2 class=" ">Conventions</h2>
+<p class=" ">In this documentation, you will find a number of pages containing examples. We use the following conventions:<br /><br />Â Cluster command prompt</p>
+<pre class="prettyprint lang-sh">$</pre>
+<p>Your local linux host command prompt</p>
+<pre class="prettyprint lang-sh">local $</pre>
+<h2 class=" ">Â Errata</h2>
+<p>Although we have taken every care to ensure the accuracy of our content, mistakes do happen. If you find a mistake in the text or the code we would be grateful if you would report this to us. By doing so, you can save other readers from frustration and help us improve subsequent versions of this documentation. If you find any errata, please report them by visiting http://support.it4i.cz/rt, creating a new ticket, and entering the details of your errata. Once your errata are verified, your submission will be accepted and the errata will be uploaded on our website.</p>
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+ <a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
+ <a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
+ </p>
+ <!-- nagios_check_http_expect_string -->
+</div>
+
+ </div>
+ </div>
+
+ <!-- TODO -->
+ <!-- nagios_check_http_expect_string -->
+ <!-- TODO -->
+
+</div>
+</body>
+</html>
+
diff --git a/docs.it4i.cz/get-started-with-it4innovations/introduction.md b/docs.it4i.cz/get-started-with-it4innovations/introduction.md
index 66c4410c6..25dac76a5 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/introduction.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/introduction.md
@@ -143,4 +143,3 @@ entering the details of your errata. Once your errata are verified, your
submission will be accepted and the errata will be uploaded on our
website.
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials.html b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials.html
new file mode 100644
index 000000000..efd2d9c63
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials.html
@@ -0,0 +1,660 @@
+
+<!DOCTYPE html>
+
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+
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+ </h1>
+
+
+
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+
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+ </a>
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+
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+
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+
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+ </a>
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+
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+
+ <span>PBSPro Documentation</span>
+ </a>
+
+
+
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+
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+
+
+ </ul>
+ <span class="portletBottomLeft"></span>
+ <span class="portletBottomRight"></span>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.html b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.html
new file mode 100644
index 000000000..2bf60bf8f
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.html
@@ -0,0 +1,706 @@
+
+<!DOCTYPE html>
+
+<html xmlns="http://www.w3.org/1999/xhtml" lang="cs">
+
+
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+
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+
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+
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+<h2>Q: What are certificates?</h2>
+<p>IT4Innovations employs X.509 certificates for secure communication (e. g. credentials exchange) and for grid services related to PRACE, as they present a single method of authentication for all PRACE services, where only one password is required.</p>
+<p>There are different kinds of certificates, each with a different scope of use. We mention here:</p>
+<ul>
+<li>User (Private) certificates</li>
+</ul>
+<ul>
+<li>Certificate Authority (CA) certificates</li>
+</ul>
+<ul>
+<li>Host certificates</li>
+</ul>
+<ul>
+<li>Service certificates</li>
+</ul>
+<p>Â </p>
+<p>However, users need only manage User and CA certificates. Note that your user certificate is protected by an associated private key, and this <strong>private key must never be disclosed</strong>.</p>
+<h2>Q: Which X.509 certificates are recognised by IT4Innovations?</h2>
+<p>Any certificate that has been issued by a Certification Authority (CA) from a member of the IGTF (<a href="http://www.igtf.net/">http:www.igtf.net</a>) is recognised by IT4Innovations: European certificates are issued by members of the EUGridPMA (<a href="https://www.eugridpma.org/">https://www.eugridmpa.org</a>), which is part of the IGTF and coordinates the trust fabric for e-Science Grid authentication within Europe. Further the Czech<em> "Qualified certificate" (Kvalifikovaný certifikát</em><em>)</em> (provided by <a href="http://www.postsignum.cz/">http://www.postsignum.cz/</a> or <a href="http://www.ica.cz/Kvalifikovany-certifikat.aspx">http://www.ica.cz/Kvalifikovany-certifikat.aspx</a>), that is used in electronic contact with Czech public authorities is accepted.</p>
+<h2>Q: How do I get a User Certificate that can be used with IT4Innovations?</h2>
+<p>To get a certificate, you must make a request to your local, IGTF approved, Certificate Authority (CA). Usually you then must visit, in person, your nearest Registration Authority (RA) to verify your affiliation and identity (photo identification is required). Usually, you will then be emailed details on how to retrieve your certificate, although procedures can vary between CAs. If you are in Europe, you can locate your trusted CA via <a href="http://www.eugridpma.org/members/worldmap">http://www.eugridpma.org/members/worldmap</a>.</p>
+<p>In some countries certificates can also be retrieved using the TERENA Certificate Service, see the FAQ below for the link.</p>
+<h2>Q: Does IT4Innovations support short lived certificates (SLCS)?</h2>
+<p>Yes, provided that the CA which provides this service is also a member of IGTF.</p>
+<h2>Q: Does IT4Innovations support the TERENA certificate service?</h2>
+<p>Yes, ITInnovations supports TERENA eScience personal certificates. For more information, please visit <a class="spip_url spip_out" href="https://tcs-escience-portal.terena.org/" rel="nofollow external">https://tcs-escience-portal.terena.org</a>, where you also can find if your organisation/country can use this service</p>
+<h2>Q: What format should my certificate take?</h2>
+<p>User Certificates come in many formats, the three most common being the ’PKCS12’, ’PEM’ and the JKS formats.</p>
+<p>The PKCS12 (often abbreviated to ’p12’) format stores your user certificate, along with your associated private key, in a single file. This form of your certificate is typically employed by web browsers, mail clients, and grid services like UNICORE, DART, gsissh-term and Globus toolkit (GSI-SSH, GridFTP and GRAM5).</p>
+<p>The PEM format (*.pem) stores your user certificate and your associated private key in two separate files. This form of your certificate can be used by PRACE’s gsissh-term and with the grid related services like Globus toolkit (GSI-SSH, GridFTP and GRAM5).</p>
+<p>To convert your Certificate from PEM to p12 formats, and <i>vice versa</i>, IT4Innovations recommends using the openssl tool (see separate FAQ entry).</p>
+<p>JKS is the Java KeyStore and may contain both your personal certificate with your private key and a list of your trusted CA certificates. This form of your certificate can be used by grid services like DART and UNICORE6.</p>
+<p>To convert your Certificate from p12 to JKS, IT4Innovations recommends using the keytool utiliy (see separate FAQ entry).</p>
+<h2>Q: What are CA certificates?</h2>
+<p>Certification Authority (CA) certificates are used to verify the link between your user certificate and the authority which issued it. They are also used to verify the link between the host certificate of a IT4Innovations server and the CA which issued that certificate. In essence they establish a chain of trust between you and the target server. Thus, for some grid services, users must have a copy of all the CA certificates.</p>
+<p>To assist users, SURFsara (a member of PRACE) provides a complete and up-to-date bundle of all the CA certificates that any PRACE user (or IT4Innovations grid services user) will require. Bundle of certificates, in either p12, PEM or JKS formats, are available from <a href="http://winnetou.sara.nl/prace/certs/">http://winnetou.sara.nl/prace/certs/</a>.</p>
+<p>It is worth noting that gsissh-term and DART automatically updates their CA certificates from this SURFsara website. In other cases, if you receive a warning that a server’s certificate can not be validated (not trusted), then please update your CA certificates via the SURFsara website. If this fails, then please contact the IT4Innovations helpdesk.</p>
+<p>Lastly, if you need the CA certificates for a personal Globus 5 installation, then you can install the CA certificates from a MyProxy server with the following command.</p>
+<pre>myproxy-get-trustroots -s myproxy-prace.lrz.de</pre>
+<p>If you run this command as ’root’, then it will install the certificates into /etc/grid-security/certificates. If you run this not as ’root’, then the certificates will be installed into $HOME/.globus/certificates. For Globus, you can download the globuscerts.tar.gz packet from <a href="http://winnetou.sara.nl/prace/certs/">http://winnetou.sara.nl/prace/certs/</a>.</p>
+<h2>Q: What is a DN and how do I find mine?</h2>
+<p>DN stands for Distinguished Name and is part of your user certificate. IT4Innovations needs to know your DN to enable your account to use the grid services. You may use openssl (see below) to determine your DN or, if your browser contains your user certificate, you can extract your DN from your browser.</p>
+<p>For Internet Explorer users, the DN is referred to as the "subject" of your certificate. Tools->Internet Options->Content->Certificates->View->Details->Subject.</p>
+<p>For users running Firefox under Windows, the DN is referred to as the "subject" of your certificate. Tools->Options->Advanced->Encryption->View Certificates. Highlight your name and then Click View->Details->Subject.</p>
+<h2>Q: How do I use the openssl tool?</h2>
+<p>The following examples are for Unix/Linux operating systems only.</p>
+<p>To convert from PEM to p12, enter the following command:</p>
+<pre>openssl pkcs12 -export -in usercert.pem -inkey userkey.pem -out
+username.p12</pre>
+<p>To convert from p12 to PEM, type the following <i>four</i> commands:</p>
+<pre>openssl pkcs12 -in username.p12 -out usercert.pem -clcerts -nokeys
+openssl pkcs12 -in username.p12 -out userkey.pem -nocerts
+chmod 444 usercert.pem
+chmod 400 userkey.pem</pre>
+<p>To check your Distinguished Name (DN), enter the following command:</p>
+<pre>openssl x509 -in usercert.pem -noout -subject -nameopt
+RFC2253</pre>
+<p>To check your certificate (e.g., DN, validity, issuer, public key algorithm, etc.), enter the following command:</p>
+<pre>openssl x509 -in usercert.pem -text -noout</pre>
+<p>To download openssl for both Linux and Windows, please visit <a href="http://www.openssl.org/related/binaries.html">http://www.openssl.org/related/binaries.html</a>. On Macintosh Mac OS X computers openssl is already pre-installed and can be used immediately.</p>
+<h2>Q: How do I create and then manage a keystore?</h2>
+<p>IT4innovations recommends the java based keytool utility to create and manage keystores, which themselves are stores of keys and certificates. For example if you want to convert your pkcs12 formatted key pair into a java keystore you can use the following command.</p>
+<pre>keytool -importkeystore -srckeystore $my_p12_cert -destkeystore
+$my_keystore -srcstoretype pkcs12 -deststoretype jks -alias
+$my_nickname -destalias $my_nickname</pre>
+<p>where $my_p12_cert is the name of your p12 (pkcs12) certificate, $my_keystore is the name that you give to your new java keystore and $my_nickname is the alias name that the p12 certificate was given and is used also for the new keystore.</p>
+<p>You also can import CA certificates into your java keystore with the tool, e.g.:</p>
+<pre>keytool -import -trustcacerts -alias $mydomain -file $mydomain.crt -keystore $my_keystore</pre>
+<p>where $mydomain.crt is the certificate of a trusted signing authority (CA) and $mydomain is the alias name that you give to the entry.</p>
+<p>More information on the tool can be found at:<a class="external-link" href="http://docs.oracle.com/javase/7/docs/technotes/tools/solaris/keytool.html" target="_self" title="">http://docs.oracle.com/javase/7/docs/technotes/tools/solaris/keytool.html</a></p>
+<h2>Q: How do I use my certificate to access the different grid Services?</h2>
+<p>Most grid services require the use of your certificate; however, the format of your certificate depends on the grid Service you wish to employ.</p>
+<p>If employing the PRACE version of GSISSH-term (also a Java Web Start Application), you may use either the PEM or p12 formats. Note that this service automatically installs up-to-date PRACE CA certificates.</p>
+<p>If the grid service is UNICORE, then you bind your certificate, in either the p12 format or JKS, to UNICORE during the installation of the client on your local machine. For more information, please visit <a class="spip_in external-link" href="http://www.prace-ri.eu/UNICORE6-in-PRACE" target="_self" title="">UNICORE6 in PRACE</a></p>
+<p>If the grid service is part of Globus, such as GSI-SSH, GriFTP or GRAM5, then the certificates can be in either p12 or PEM format and must reside in the "$HOME/.globus" directory for Linux and Mac users or %HOMEPATH%\.globus for Windows users. (Windows users will have to use the DOS command ’cmd’ to create a directory which starts with a ’.’). Further, user certificates should be named either "usercred.p12" or "usercert.pem" and "userkey.pem", and the CA certificates must be kept in a pre-specified directory as follows. For Linux and Mac users, this directory is either $HOME/.globus/certificates or /etc/grid-security/certificates. For Windows users, this directory is %HOMEPATH%\.globus\certificates. (If you are using GSISSH-Term from prace-ri.eu then you do not have to create the .globus directory nor install CA certificates to use this tool alone).</p>
+<h2>Q: How do I manually import my certificate into my browser?</h2>
+<p>If you employ the Firefox browser, then you can import your certificate by first choosing the "Preferences" window. For Windows, this is Tools->Options. For Linux, this is Edit->Preferences. For Mac, this is Firefox->Preferences. Then, choose the "Advanced" button; followed by the "Encryption" tab. Then, choose the "Certificates" panel; select the option <a></a>"Select one automatically" if you have only one certificate, or "Ask me every time" if you have more then one. Then click on the "View Certificates" button to open the "Certificate Manager" window. You can then select the "Your Certificates" tab and click on button "Import". Then locate the PKCS12 (.p12) certificate you wish to import, and employ its associated password.</p>
+<p>If you are a Safari user, then simply open the "Keychain Access" application and follow "File->Import items".</p>
+<p>If you are an Internet Explorer user, click Start->Settings->Control Panel and then double-click on Internet. On the Content tab, click Personal, and then click Import. In the Password box, type your password. NB you may be prompted multiple times for your password. In the "Certificate File To Import" box, type the filename of the certificate you wish to import, and then click OK. Click Close, and then click OK.</p>
+<h2>Q: What is a proxy certificate?</h2>
+<p>A proxy certificate is a short-lived certificate which may be employed by UNICORE and the Globus services. The proxy certificate consists of a new user certificate and a newly generated proxy private key. This proxy typically has a rather short lifetime (normally 12 hours) and often only allows a limited delegation of rights. Its default location, for Unix/Linux, is /tmp/x509_u<i>uid</i> but can be set via the $X509_USER_PROXY environment variable.</p>
+<h2>Q: What is the MyProxy service?</h2>
+<p><a class="spip_in external-link" href="http://grid.ncsa.illinois.edu/myproxy/" target="_self" title="">The MyProxy Service</a>, can be employed by gsissh-term and Globus tools, and is an online repository that allows users to store long lived proxy certificates remotely, which can then be retrieved for use at a later date. Each proxy is protected by a password provided by the user at the time of storage. This is beneficial to Globus users as they do not have to carry their private keys and certificates when travelling; nor do users have to install private keys and certificates on possibly insecure computers.</p>
+<h2>Q: Someone may have copied or had access to the private key of my certificate either in a separate file or in the browser. What should I do?</h2>
+<p>Please ask the CA that issued your certificate to revoke this certifcate and to supply you with a new one. In addition, please report this to IT4Innovations by contacting <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">the support team</a>.</p>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
index 1b905bcd7..b1d4ad3e6 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
@@ -7,7 +7,7 @@ FAQ about certificates in general
-What are certificates?
+Q: What are certificates?
-------------------------
IT4Innovations employs X.509 certificates for secure communication (e.
@@ -38,12 +38,12 @@ However, users need only manage User and CA certificates. Note that your
user certificate is protected by an associated private key, and this
**private key must never be disclosed**.
-Which X.509 certificates are recognised by IT4Innovations?
+Q: Which X.509 certificates are recognised by IT4Innovations?
-------------------------------------------------------------
Any certificate that has been issued by a Certification Authority (CA)
from a member of the IGTF ([http:www.igtf.net](http://www.igtf.net/)) is
-recognised by IT4InnovationsEuropean certificates are issued by
+recognised by IT4Innovations: European certificates are issued by
members of the EUGridPMA
([https://www.eugridmpa.org](https://www.eugridpma.org/)), which is part
of the IGTF and coordinates the trust fabric for e-Science Grid
@@ -52,7 +52,7 @@ authentication within Europe. Further the Czech *"Qualified certificate"
<http://www.ica.cz/Kvalifikovany-certifikat.aspx>), that is used in
electronic contact with Czech public authorities is accepted.
-How do I get a User Certificate that can be used with IT4Innovations?
+Q: How do I get a User Certificate that can be used with IT4Innovations?
------------------------------------------------------------------------
To get a certificate, you must make a request to your local, IGTF
@@ -66,13 +66,13 @@ locate your trusted CA via <http://www.eugridpma.org/members/worldmap>.
In some countries certificates can also be retrieved using the TERENA
Certificate Service, see the FAQ below for the link.
-Does IT4Innovations support short lived certificates (SLCS)?
+Q: Does IT4Innovations support short lived certificates (SLCS)?
---------------------------------------------------------------
Yes, provided that the CA which provides this service is also a member
of IGTF.
-Does IT4Innovations support the TERENA certificate service?
+Q: Does IT4Innovations support the TERENA certificate service?
--------------------------------------------------------------
Yes, ITInnovations supports TERENA eScience personal certificates. For
@@ -81,7 +81,7 @@ more information, please visit
.spip_out}, where you also can find if your organisation/country can use
this service
-What format should my certificate take?
+Q: What format should my certificate take?
------------------------------------------
User Certificates come in many formats, the three most common being the
@@ -110,7 +110,7 @@ UNICORE6.
To convert your Certificate from p12 to JKS, IT4Innovations recommends
using the keytool utiliy (see separate FAQ entry).
-What are CA certificates?
+Q: What are CA certificates?
----------------------------
Certification Authority (CA) certificates are used to verify the link
@@ -145,7 +145,7 @@ then the certificates will be installed into
$HOME/.globus/certificates. For Globus, you can download the
globuscerts.tar.gz packet from <http://winnetou.sara.nl/prace/certs/>.
-What is a DN and how do I find mine?
+Q: What is a DN and how do I find mine?
---------------------------------------
DN stands for Distinguished Name and is part of your user certificate.
@@ -163,7 +163,7 @@ For users running Firefox under Windows, the DN is referred to as the
Tools->Options->Advanced->Encryption->View Certificates.
Highlight your name and then Click View->Details->Subject.
-How do I use the openssl tool?
+Q: How do I use the openssl tool?
---------------------------------
The following examples are for Unix/Linux operating systems only.
@@ -194,7 +194,7 @@ To download openssl for both Linux and Windows, please visit
<http://www.openssl.org/related/binaries.html>. On Macintosh Mac OS X
computers openssl is already pre-installed and can be used immediately.
-How do I create and then manage a keystore?
+Q: How do I create and then manage a keystore?
----------------------------------------------
IT4innovations recommends the java based keytool utility to create and
@@ -222,7 +222,7 @@ where $mydomain.crt is the certificate of a trusted signing authority
More information on the tool can be found
at:<http://docs.oracle.com/javase/7/docs/technotes/tools/solaris/keytool.html>
-How do I use my certificate to access the different grid Services?
+Q: How do I use my certificate to access the different grid Services?
---------------------------------------------------------------------
Most grid services require the use of your certificate; however, the
@@ -253,7 +253,7 @@ directory is either $HOME/.globus/certificates or
prace-ri.eu then you do not have to create the .globus directory nor
install CA certificates to use this tool alone).
-How do I manually import my certificate into my browser?
+Q: How do I manually import my certificate into my browser?
-----------------------------------------------------------
If you employ the Firefox browser, then you can import your certificate
@@ -279,7 +279,7 @@ for your password. In the "Certificate File To Import" box, type the
filename of the certificate you wish to import, and then click OK. Click
Close, and then click OK.
-What is a proxy certificate?
+Q: What is a proxy certificate?
-------------------------------
A proxy certificate is a short-lived certificate which may be employed
@@ -290,7 +290,7 @@ allows a limited delegation of rights. Its default location, for
Unix/Linux, is /tmp/x509_u*uid* but can be set via the
$X509_USER_PROXY environment variable.
-What is the MyProxy service?
+Q: What is the MyProxy service?
-------------------------------
[The MyProxy Service](http://grid.ncsa.illinois.edu/myproxy/){.spip_in
@@ -303,7 +303,7 @@ to carry their private keys and certificates when travelling; nor do
users have to install private keys and certificates on possibly insecure
computers.
-Someone may have copied or had access to the private key of my certificate either in a separate file or in the browser. What should I do?
+Q: Someone may have copied or had access to the private key of my certificate either in a separate file or in the browser. What should I do?
--------------------------------------------------------------------------------------------------------------------------------------------
Please ask the CA that issued your certificate to revoke this certifcate
@@ -313,4 +313,3 @@ team](https://support.it4i.cz/rt).
-
diff --git a/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html
new file mode 100644
index 000000000..d1673d120
--- /dev/null
+++ b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html
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+ <h2 class=" ">Obtaining Authorization</h2>
+<p>The computational resources of IT4I  are allocated by the Allocation Committee to a <a href="../introduction.html" title="" target="_self" class="internal-link">Project</a>, investigated by a Primary Investigator. By allocating the computational resources, the Allocation Committee is authorizing the PI to access and use the clusters. The PI may decide to authorize a number of her/his Collaborators to access and use the clusters, to consume the resources allocated to her/his Project. These collaborators will be associated to the Project. The Figure below is depicting the authorization chain:</p>
+<div class="wide-view-wrapper">
+<p><img alt="The Authorization chain for access and utilization of computational resources on Anselm" src="../../anselm-cluster-documentation/Authorization_chain.png" title="Authorization chain" class="image-inline" /></p>
+</div>
+<p class="callout">Â You need to either <a href="../applying-for-resources.html" title="" target="_self" class="internal-link">become the PI</a> or <a class="anchor-link" href="obtaining-login-credentials.html#authorization-of-collaborator-by-pi" target="_self" title="">be named as a collaborator</a> by a PI in order to access and use the clusters.</p>
+<p>Head of Supercomputing Services acts as a PI of a project DD-13-5. Joining this project, you may <strong>access and explore the clusters</strong>, use software, development environment and computers via the qexp and qfree queues. You may use these resources for own education/research, no paperwork is required. All IT4I employees may contact the Head of Supercomputing Services in order to obtain <strong>free access to the clusters</strong>.</p>
+<h3 class=" "><a name="authorization-of-collaborator-by-pi"></a>Authorization of PI by Allocation Committee</h3>
+<p>The PI is authorized to use the clusters by the allocation decision issued by the Allocation Committee.The PI will be informed by IT4I about the Allocation Committee decision.</p>
+<h3 class=" ">Authorization by web</h3>
+<p class="callout">This is a preferred way of granting access to project resources.<br />Please, use this method whenever it's possible.</p>
+<p>Log in to the <a class="external-link" href="https://extranet.it4i.cz" target="_self" title="">IT4I Extranet portal</a> using IT4I credentials and go to the <strong>Projects</strong> section.</p>
+<ul>
+<li><strong>Users:</strong> Please, submit your requests for becoming a project member.</li>
+<li><strong>Primary Investigators:</strong> Please, approve or deny users' requests in the same section.</li>
+</ul>
+<h3 class=" ">Authorization by e-mail (an alternative approach)</h3>
+<p>Â In order to authorize a Collaborator to utilize the allocated resources, the PI should contact the <a class="external-link" href="https://support.it4i.cz/rt/" target="_self" title="">IT4I support</a> (E-mail: <a href="mailto:support%20[at]%20it4i.cz">support [at] it4i.cz</a>) and provide following information:</p>
+<ol>
+<li>Identify your project by project ID</li>
+<li>Provide list of people, including himself, who are authorized to use the resources allocated to the project. The list must include full name, e-mail and affiliation. Provide usernames as well, if collaborator login access already exists on the IT4I systems.</li>
+<li>Include "Authorization to IT4Innovations" into the subject line.</li>
+</ol>
+<p>Example (except the subject line which must be in English, you may use Czech or Slovak language for communication with us):</p>
+<pre class=" ">Subject: Authorization to IT4Innovations<br /><br />Dear support,<br /><br />Please include my collaborators to project OPEN-0-0.<br /><br />John Smith, john.smith@myemail.com, Department of Chemistry, MIT, US<br />Jonas Johansson, jjohansson@otheremail.se, Department of Physics, Royal Institute of Technology, Sweden<br />Luisa Fibonacci, lf@emailitalia.it, Department of Mathematics, National Research Council, Italy<br /><br />Thank you,<br />PI<br />(Digitally signed)</pre>
+<p class=" ">Should the above information be provided by e-mail, the e-mail <strong>must be</strong> digitally signed. Read more on <a class="anchor-link" href="obtaining-login-credentials.html#the-certificates-for-digital-signatures" target="_self" title="">digital signatures</a> below.</p>
+<h2 class=" "><a name="the-login-credentials"></a>The Login Credentials</h2>
+<p>Once authorized by PI, every person (PI or Collaborator) wishing to access the clusters, should contact the <a class="external-link" href="https://support.it4i.cz/rt/" target="_self" title="">IT4I support</a> (E-mail: <a href="mailto:support%20[at]%20it4i.cz">support [at] it4i.cz</a>) providing following information:</p>
+<ol>
+<li>Project ID</li>
+<li>Full name and affiliation</li>
+<li>Statement that you have read and accepted the <a class="external-link" href="http://www.it4i.cz/acceptable-use-policy.pdf" target="_self" title="">Acceptable use policy document</a> (AUP).</li>
+<li>Attach the AUP file.</li>
+<li>Your preferred username, max 8 characters long. The preferred username must associate your surname and name or be otherwise derived from it. Only alphanumeric sequences, dash and underscore signs are allowed.</li>
+<li>In case you choose <a class="anchor-link" href="obtaining-login-credentials.html#alternative-way-of-getting-personal-certificate" target="_self" title="">Alternative way to personal certificate</a>, a <strong>scan of photo ID</strong> (personal ID or passport or driver license) is required</li>
+</ol>
+<p class=" ">Example (except the subject line which must be in English, you may use Czech or Slovak language for communication with us):</p>
+<pre class=" ">Subject: Access to IT4Innovations<br /><br />Dear support,<br /><br />Please open the user account for me and attach the account to OPEN-0-0<br />Name and affiliation: John Smith, john.smith@myemail.com, Department of Chemistry, MIT, US<br />I have read and accept the Acceptable use policy document (attached)<br /><br />Preferred username: johnsm<br /><br />Thank you,<br />John Smith<br />(Digitally signed)</pre>
+<p>Should the above information be provided by e-mail, the e-mail <strong>must be</strong> digitally signed. To sign an e-mail, you need digital certificate. Read more on <a class="anchor-link" href="obtaining-login-credentials.html#the-certificates-for-digital-signatures" target="_self" title="">digital signatures</a> below.</p>
+<p class="callout">Digital signature allows us to confirm your identity in remote electronic communication and provides an encrypted channel to exchange sensitive information such as login credentials. After receiving your signed e-mail with the requested information, we will send you your login credentials (user name, key, passphrase and password) to access the IT4I systems.<br /><br />We accept certificates issued by any widely respected certification authority.</p>
+<p class="callout"><strong>For various reasons we do not accept PGP keys.</strong> Please, use only X.509 PKI certificates for communication with us.</p>
+<p>You will receive your personal login credentials by protected e-mail. The login credentials include:</p>
+<ol>
+<li>username</li>
+<li>ssh private key and private key passphrase</li>
+<li>system password</li>
+</ol>
+<p class="callout">The clusters are accessed by the <a href="../accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html" title="" target="_self" class="internal-link">private key</a> and username.<br />Username and password is used for login to the information systems listed on <a class="external-link" href="http://support.it4i.cz/" target="_self" title="">http://support.it4i.cz/</a>.</p>
+<h3 class=" ">Change Passphrase</h3>
+<p>On Linux, use</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ </span><span class="pln"><span style="text-align: start; float: none; ">ssh-keygen -f id_rsa -p</span></span></pre>
+<p>On Windows, use <a href="../accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html" title="" target="_self" class="internal-link">PuTTY Key Generator</a>.</p>
+<h3 class=" ">Change Password</h3>
+<p>Change password in your user profile at <a class="external-link" href="https://extranet.it4i.cz/user/" target="_self" title="extranet.it4i.cz/user/">https://extranet.it4i.cz/user/</a></p>
+<h2 class=" "><a name="the-certificates-for-digital-signatures"></a>The Certificates for Digital Signatures</h2>
+<p>We accept personal certificates issued by any widely respected certification authority (CA). This includes certificates by CAs organized in International Grid Trust Federation (<a class="moz-txt-link-freetext" href="http://www.igtf.net/">http://www.igtf.net/</a>), its European branch EUGridPMA - <a class="moz-txt-link-freetext" href="https://www.eugridpma.org/">https://www.eugridpma.org/</a> and its member organizations, e.g. the CESNET certification authority - <a class="external-link" href="https://tcs-p.cesnet.cz/confusa/" target="_self" title="">https://tcs-p.cesnet.cz/confusa/</a>. The Czech<em> "Qualified certificate" (Kvalifikovaný certifikát</em><em>)</em> (provided by <a href="http://www.postsignum.cz/">http://www.postsignum.cz/</a> or <a href="http://www.ica.cz/Kvalifikovany-certifikat.aspx">http://www.ica.cz/Kvalifikovany-certifikat.aspx</a>), that is used in electronic contact with Czech authorities is accepted as well.</p>
+<p>Certificate generation process is well-described here:</p>
+<ul>
+<li><a class="external-link" href="http://idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/moz-cert-gen" target="_self" title="">How to generate a personal TCS certificate in Mozilla Firefox web browser (in Czech)</a></li>
+</ul>
+<p>Â </p>
+<p>A FAQ about certificates can be found here: <span><a href="certificates-faq.html" title="" target="_self" class="internal-link">Certificates FAQ</a>.</span></p>
+<h2 class=" "><a name="alternative-way-of-getting-personal-certificate"></a>Alternative Way to Personal Certificate</h2>
+<p class="callout">Follow these steps <strong>only</strong> if you can not obtain your certificate in a standard way.<br />In case you choose this procedure, please attach a <strong>scan of photo ID</strong> (personal ID or passport or drivers license) when applying for <a class="anchor-link" href="obtaining-login-credentials.html#the-login-credentials" target="_self" title="">login credentials</a>.</p>
+<ol>
+<li>Go to <a class="external-link" href="https://www.cacert.org/" target="_self" title="">https://www.cacert.org/</a>.<br />
+<ul>
+<li>If there's a security warning, just acknowledge it.</li>
+</ul>
+</li>
+<li>Click <em>Join</em>.</li>
+<li>Fill in the form and submit it by the <em>Next</em> button.<br />
+<ul>
+<li>Type in the e-mail address which you use for communication with us.</li>
+<li>Don't forget your chosen <em>Pass Phrase</em>.</li>
+</ul>
+</li>
+<li>You will receive an e-mail verification link. Follow it.</li>
+<li>After verifying, go to the CAcert's homepage and login using <em>Password Login</em>.</li>
+<li>Go to <em>Client Certificates</em> -> <em>New</em>.</li>
+<li>Tick <em>Add</em> for your e-mail address and click the <em>Next</em> button.</li>
+<li>Click the <em>Create Certificate Request</em> button.</li>
+<li>You'll be redirected to a page from where you can download/install your certificate.<br />
+<ul>
+<li>Simultaneously you'll get an e-mail with a link to the certificate.</li>
+</ul>
+</li>
+</ol>
+<h2 class=" ">Installation of the Certificate Into Your Mail Client</h2>
+<p>The procedure is similar to the following guides:</p>
+<ul>
+<li>MS Outlook 2010<br />
+<ul>
+<li><a class="external-link" href="http://support.microsoft.com/kb/179380" target="_self" title="">How to Remove, Import, and Export Digital Certificates</a></li>
+<li><a class="external-link" href="http://idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/outl-cert-imp" target="_self" title="">Importing a PKCS #12 certificate (in Czech)</a></li>
+</ul>
+</li>
+<li>Mozilla Thudnerbird<br />
+<ul>
+<li><a class="external-link" href="http://kb.mozillazine.org/Installing_an_SMIME_certificate" target="_self" title="">Installing an SMIME certificate</a></li>
+<li><a class="external-link" href="http://idoc.vsb.cz/xwiki/wiki/infra/view/uzivatel/moz-cert-imp" target="_self" title="">Importing a PKCS #12 certificate (in Czech)</a></li>
+</ul>
+</li>
+</ul>
+<h2 class=" ">End of User Account Lifecycle</h2>
+<p>User accounts are supported by membership in active Project(s) or by affiliation to IT4Innovations. User accounts, that loose the support (meaning, are not attached to an active project and are not affiliated with IT4I), will be deleted 1 year after the last project to which they were attached expires.</p>
+<p>User will get 3 automatically generated warning e-mail messages of the pending removal:.</p>
+<ul>
+<li>First message will be sent 3 months before the removal</li>
+<li>Second message will be sent 1 month before the removal</li>
+<li>Third message will be sent 1 week before the removal.</li>
+</ul>
+<p>The messages will inform about the projected removal date and will challenge the user to migrate her/his data</p>
+
+ </div>
+
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+ </a>
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+
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+<li class="navTreeItem visualNoMarker section-certificates-faq">
+
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+ </a>
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+ <a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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diff --git a/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
index 4c19a0014..752bd57eb 100644
--- a/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
+++ b/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
@@ -61,7 +61,7 @@ and go to the **Projects** section.
 In order to authorize a Collaborator to utilize the allocated
resources, the PI should contact the [IT4I
-support](https://support.it4i.cz/rt/) (E-mail[support
+support](https://support.it4i.cz/rt/) (E-mail: [support
[at] it4i.cz](mailto:support%20%5Bat%5D%20it4i.cz)) and provide
following information:
@@ -75,7 +75,7 @@ following information:
Example (except the subject line which must be in English, you may use
Czech or Slovak language for communication with us):
- SubjectAuthorization to IT4Innovations
+ Subject: Authorization to IT4Innovations
Dear support,
@@ -99,7 +99,7 @@ below.
Once authorized by PI, every person (PI or Collaborator) wishing to
access the clusters, should contact the [IT4I
-support](https://support.it4i.cz/rt/) (E-mail[support
+support](https://support.it4i.cz/rt/) (E-mail: [support
[at] it4i.cz](mailto:support%20%5Bat%5D%20it4i.cz)) providing
following information:
@@ -120,15 +120,15 @@ following information:
Example (except the subject line which must be in English, you may use
Czech or Slovak language for communication with us):
- SubjectAccess to IT4Innovations
+ Subject: Access to IT4Innovations
Dear support,
Please open the user account for me and attach the account to OPEN-0-0
- Name and affiliationJohn Smith, john.smith@myemail.com, Department of Chemistry, MIT, US
+ Name and affiliation: John Smith, john.smith@myemail.com, Department of Chemistry, MIT, US
I have read and accept the Acceptable use policy document (attached)
- Preferred usernamejohnsm
+ Preferred username: johnsm
Thank you,
John Smith
@@ -204,7 +204,7 @@ Certificate generation process is well-described here:
Â
-A FAQ about certificates can be found here<span>[Certificates
+A FAQ about certificates can be found here: <span>[Certificates
FAQ](certificates-faq.html).</span>
[]()Alternative Way to Personal Certificate
@@ -270,4 +270,3 @@ pending removal:.
The messages will inform about the projected removal date and will
challenge the user to migrate her/his data
-
diff --git a/docs.it4i.cz/heartbleed-bug.md b/docs.it4i.cz/heartbleed-bug.md
deleted file mode 100644
index 4bfac0660..000000000
--- a/docs.it4i.cz/heartbleed-bug.md
+++ /dev/null
@@ -1,81 +0,0 @@
-Heartbleed bug
-==============
-
-
-
-
-
-Last update2014-04-16 12:20:32
-
-Introduction
-------------
-
-A serious bug in the OpenSSL library, known as the "Heartbleed bug" has
-been recently discovered.
-
-The bug in OpenSSL library affected many sites worldwide for nearly two
-years.<span> Although the Anselm cluster itself was exposed only for two
-weeks and other systems for approximately three months, IT4I didn't take
-this situation lightly and with full responsibility responded
-immediately.</span> At this moment, there is no evidence that any abuse
-of data took place at IT4I.
-
-<span>For more information about the Heartbleed bug, please see:
-<http://heartbleed.com/></span>
-
-Response
---------
-
-### <span>OpenSSL fix
-</span>
-
-<span>IT4I has taken all necessary steps to fix the OpenSSL library on
-all it's systems.</span>
-
-### <span>Server keys change</span>
-
-Due to a safety preventive action, the fingerprint of Anselm login nodes
-has changed.
-
-You are advised to remove the deprecated fingerprint from your local SSH
-known_hosts file:
-
- local $ ssh-keygen -R anselm.it4i.cz
- local $ ssh-keygen -R login1.anselm.it4i.cz
- local $ ssh-keygen -R login2.anselm.it4i.cz
- local $ ssh-keygen -R 195.113.250.82
- local $ ssh-keygen -R 195.113.250.83
-
-new fingerprints for both login nodes are:
-<span
-class="monospace">29:b3:f4:64:b0:73:f5:6f:a7:85:0f:e0:0d:be:76:bf (DSA)
-d4:6f:5c:18:f4:3f:70:ef:bc:fc:cc:2b:fd:13:36:b7Â (RSA)</span>
-
-You have to reconnect on Anselm to apply this change.
-
-### Login credentials change
-
-There is no evidence that any abuse of data took place at IT4I, however
-as a safety preventive action, all users will be issued new login
-credentials.
-
-In order to ensure the security and integrity of IT4I systems, all users
-will be issued new login credentials, including password and ssh kyes.
-
-We will use your original digital signatures to deliver the login
-credential in a secure way.
-
-In case that you're using a new digital signature since getting access
-to Anselm, please let us know by writing to <span
-class="moz-txt-link-abbreviated">[support [at]
-it4i.cz](mailto:support%20%5Bat%5D%20it4i.cz)</span> .
-Don't forget to digitally sign your message and please include the
-string "**Digital Signature Change**" in the subject line.
-
-We'll be collecting new digital signatures till Friday, 18th April.
-<span>[](http://heartbleed.com/)</span>
-
-Â
-
-
-
diff --git a/docs.it4i.cz/index.html b/docs.it4i.cz/index.html
new file mode 100644
index 000000000..42076f9fd
--- /dev/null
+++ b/docs.it4i.cz/index.html
@@ -0,0 +1,586 @@
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+ <p>Welcome to IT4Innovations documentation pages. The IT4Innovations national supercomputing center operates supercomputers <a href="salomon.html" title="" target="_self" class="internal-link">Salomon</a> and <a href="anselm.html" title="" target="_self" class="internal-link">Anselm</a>. The supercomputers are <a href="get-started-with-it4innovations/applying-for-resources.html" title="" target="_self" class="internal-link"><span class="external-link">available</span></a> to academic community within the Czech Republic and Europe and industrial community worldwide. The purpose of these pages is to provide a comprehensive documentation on hardware, software and usage of the computers.</p>
+<h2><span class="link-external"><span class="WYSIWYG_LINK">How to read the documentation</span></span></h2>
+<ol>
+<li>Read the list in the left column. Select the subject of interest. Alternatively, use the Search box in the upper right corner.</li>
+<li>Read the CONTENTS in the upper right corner.</li>
+<li>Scan for all the yellow bulb call-outs on the page.</li>
+<li>Read the details if still more information is needed. <strong>Look for examples</strong> illustrating the concepts.</li>
+</ol>
+<p>Â </p>
+<p class="callout">The call-out. Â Focus on the call-outs before reading full details.</p>
+<p>Â </p>
+<ul>
+<li>Read the <a href="get-started-with-it4innovations/changelog.html" title="" target="_self" class="external-link">Changelog</a> to keep up to date.</li>
+</ul>
+<h2 class=" ">Getting Help and Support</h2>
+<p class="callout" title="">Contact <a class="email-link" href="mailto:support%20[at]%20it4i.cz" target="_self" title="">support [at] it4i.cz</a> for help and support regarding the cluster technology at IT4Innovations.<br />Please use <strong>Czech</strong>, <strong>Slovak</strong> or <strong>English</strong> language for communication with us.<br />Follow the status of your request to IT4Innovations at <a class="external-link" href="http://support.it4i.cz/rt" target="_self" title="">support.it4i.cz/rt</a>.</p>
+<p class="external-link" title="">Â </p>
+<p class="external-link" title="">Use your IT4Innotations username and password to log in to the <a class="external-link" href="http://support.it4i.cz/" target="_self" title="">support</a> portal.</p>
+<h2 class=" ">Required Proficiency</h2>
+<p class="callout">You need basic proficiency in Linux environment.</p>
+<p>Â </p>
+<p>In order to use the system for your calculations, you need basic proficiency in Linux environment. To gain the proficiency, we recommend you reading the <a class="external-link" href="http://www.tldp.org/LDP/intro-linux/html/" target="_self" title=""><span class="WYSIWYG_LINK">introduction to Linux</span></a> operating system environment and installing a Linux distribution on your personal computer. A good choice might be the <a class="external-link" href="http://fedoraproject.org/" target="_self" title=""><span class="WYSIWYG_LINK">Fedora</span></a> distribution, as it is similar to systems on the clusters at IT4Innovations. It's easy to install and use. In fact, any distribution would do.</p>
+<p>Â </p>
+<p class="callout">Learn how to parallelize your code!</p>
+<p>Â </p>
+<p>In many cases, you will run your own code on the cluster. In order to fully exploit the cluster, you will need to carefully consider how to utilize all the cores available on the node and how to use multiple nodes at the same time. You need to <b>parallelize</b> your code. Proficieny in MPI, OpenMP, CUDA, UPC or GPI2 programming may be gained via the <a class="external-link" href="http://prace.it4i.cz" target="_self" title="">training provided by IT4Innovations.</a></p>
+<h2 class=" ">Terminology Frequently Used on These Pages</h2>
+<ul>
+<ul>
+<li><strong>node:</strong> a computer, interconnected by network to other computers - Computational nodes are powerful computers, designed and dedicated for executing demanding scientific computations.</li>
+<li><strong>core:</strong> processor core, a unit of processor, executing computations</li>
+<li><strong>corehours:</strong> wall clock hours of processor core time - Each node is equipped with <strong>X</strong> processor cores, provides <strong>X</strong> corehours per 1 wall clock hour.</li>
+<li><strong><a name="job"></a>job:</strong> a calculation running on the supercomputer - The job allocates and utilizes resources of the supercomputer for certain time.</li>
+<li><strong>HPC:</strong> High Performance Computing</li>
+<li><a name="HPC_resources"></a><strong>HPC (computational) resources:</strong> corehours, storage capacity, software licences</li>
+<li><strong>code:</strong> a program</li>
+<li><strong>primary investigator (PI):</strong> a person responsible for execution of computational project and utilization of computational resources allocated to that project</li>
+<li><strong>collaborator:</strong> a person participating on execution of computational project and utilization of computational resources allocated to that project</li>
+<li><strong><a name="Project"></a>project:</strong> a computational project under investigation by the PI - The project is identified by the project ID. The computational resources are allocated and charged per project.</li>
+<li><strong><a name="Jobscript"></a>jobscript:</strong> a script to be executed by the PBS Professional workload manager</li>
+</ul>
+</ul>
+<h2 class=" ">Conventions</h2>
+<p class=" ">In this documentation, you will find a number of pages containing examples. We use the following conventions:<br /><br />Â Cluster command prompt</p>
+<pre class="prettyprint lang-sh">$</pre>
+<p>Your local linux host command prompt</p>
+<pre class="prettyprint lang-sh">local $</pre>
+<h2 class=" ">Â Errata</h2>
+<p>Although we have taken every care to ensure the accuracy of our content, mistakes do happen. If you find a mistake in the text or the code we would be grateful if you would report this to us. By doing so, you can save other readers from frustration and help us improve subsequent versions of this documentation. If you find any errata, please report them by visiting http://support.it4i.cz/rt, creating a new ticket, and entering the details of your errata. Once your errata are verified, your submission will be accepted and the errata will be uploaded on our website.</p>
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diff --git a/docs.it4i.cz/index.md b/docs.it4i.cz/index.md
index cb0f04f1b..69233f4f7 100644
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@@ -143,4 +143,3 @@ them by visiting http://support.it4i.cz/rt, creating a new ticket, and
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diff --git a/docs.it4i.cz/links.html b/docs.it4i.cz/links.html
new file mode 100644
index 000000000..8c233c172
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diff --git a/docs.it4i.cz/links.md b/docs.it4i.cz/links.md
index bea8ab456..e6a35b388 100644
--- a/docs.it4i.cz/links.md
+++ b/docs.it4i.cz/links.md
@@ -22,4 +22,3 @@ Links
<span class="WYSIWYG_LINK">
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diff --git a/docs.it4i.cz/pbspro-documentation.html b/docs.it4i.cz/pbspro-documentation.html
new file mode 100644
index 000000000..ca1202336
--- /dev/null
+++ b/docs.it4i.cz/pbspro-documentation.html
@@ -0,0 +1,668 @@
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+</div>
+
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+ <a href="pbspro-documentation/pbspro-programmers-guide/view.html" class="contenttype-file state-missing-value url">PBSPro Programmer's Guide</a>
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+
+ <span class="documentByLine">
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+ </dt>
+
+ <dd>
+ <span class="description">Version 12.</span>
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+ <span class="description">Version 12.</span>
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+ <span class="portletTopLeft"></span>
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+ <ul class="navTree navTreeLevel0">
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+ <p>Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24 cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced hypercube Infiniband network and equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in <a href="salomon/hardware-overview-1/hardware-overview.html" title="" target="_self" class="internal-link">Hardware Overview</a>.</p>
+<p>The cluster runs CentOS Linux <a class="external-link" href="http://www.bull.com/bullx-logiciels/systeme-exploitation.html" target="_self" title=""><span class="WYSIWYG_LINK"></span></a><span class="internal-link">operating system</span>, which is compatible with the <span class="WYSIWYG_LINK">RedHat</span> <a class="external-link" href="http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg" target="_self" title=""><span class="WYSIWYG_LINK">Linux family.</span></a></p>
+<p style="padding-left: 30px; "><strong>Water-cooled Compute Nodes With MIC Accelerator</strong></p>
+<p style="padding-left: 30px; "><a href="salomon/salomon" title="" target="_self" class="internal-link"><img alt="Salomon" src="https://docs.it4i.cz/salomon/salomon/@@images/8fe6c2ad-25f3-48cf-abbb-6f8ba653b93e.jpeg" title="Salomon" class="image-inline" /></a></p>
+<p style="padding-left: 30px; "><img alt="Salomon" src="salomon/salomon-1/@@images/ba2c321e-1554-4826-b6ec-3c68d370cd9f.jpeg" title="Salomon" class="image-inline" /></p>
+<p style="padding-left: 30px; "><strong>Tape Library T950B</strong></p>
+<p style="padding-left: 30px; "><img alt="Salomon" src="salomon/salomon-3/@@images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpeg" title="Salomon" class="image-inline" /></p>
+<p style="padding-left: 30px; "><img alt="Salomon" src="salomon/salomon-4/@@images/82997462-cd88-49eb-aad5-71d77903d903.jpeg" title="Salomon" class="image-inline" /></p>
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+ <h2 class=" ">Interactive Login</h2>
+<p>The Salomon cluster is accessed by SSH protocol via login nodes login1, login2, login3 and login4 at address salomon.it4i.cz. The login nodes may be addressed specifically, by prepending the login node name to the address.</p>
+<p class="exclamation">The alias <span>salomon.it4i.cz is currently not available through VPN connection. Please use loginX.salomon.it4i.cz when connected to VPN.</span></p>
+<table class="listing">
+<tbody>
+<tr><th>Login address</th><th>Port</th><th>Protocol</th><th>Login node</th></tr>
+<tr class="even">
+<td>salomon.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>round-robin DNS record for login[1-4]</td>
+</tr>
+<tr class="odd">
+<td>login1.salomon.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login1</td>
+</tr>
+<tr class="even">
+<td>login2.salomon.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login2</td>
+</tr>
+<tr class="even">
+<td>login3.salomon.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login3</td>
+</tr>
+<tr class="even">
+<td>login4.salomon.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login4</td>
+</tr>
+</tbody>
+</table>
+<p>The authentication is by the <a href="../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html" title="" target="_self" class="internal-link">private key</a></p>
+<p class="callout">Please verify SSH fingerprints during the first logon. They are identical on all login nodes:<span class="monospace"><br />f6:28:98:e4:f9:b2:a6:8f:f2:f4:2d:0a:09:67:69:80 (DSA)<br />70:01:c9:9a:5d:88:91:c7:1b:c0:84:d1:fa:4e:83:5c (RSA)</span></p>
+<p>Â </p>
+<p>Private keys authentication:</p>
+<p>On <strong>Linux</strong> or <strong>Mac</strong>, use</p>
+<pre class="prettyprint lang-sh">local $ ssh -i /path/to/id_rsa username@salomon.it4i.cz</pre>
+<p>If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this command to set lower permissions to private key file.</p>
+<pre class="prettyprint lang-sh">local $ chmod 600 /path/to/id_rsa</pre>
+<p>On <strong>Windows</strong>, use <a href="../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html" title="" target="_self" class="internal-link">PuTTY ssh client</a>.</p>
+<p>After logging in, you will see the command prompt:</p>
+<pre class=" ">Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â _____Â Â Â Â Â Â _Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â / ____|Â Â Â Â | |Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â | (___Â Â __ _| | ___Â _ __ ___Â Â ___Â _ __ Â <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â \___ \ / _` | |/ _ \| '_ ` _ \ / _ \| '_ \ <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â ____) | (_| | | (_) | | | | | | (_) | | | |<br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â |_____/ \__,_|_|\___/|_| |_| |_|\___/|_| |_|<br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â <br /><br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http://www.it4i.cz/?lang=en<br /><br /><br />Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com<br />[username@login2.salomon ~]$</pre>
+<p class="callout">The environment is <strong>not</strong> shared between login nodes, except for <a href="storage/storage.html" title="" target="_self" class="internal-link">shared filesystems</a>.</p>
+<h2 class=" ">Data Transfer</h2>
+<p>Data in and out of the system may be transferred by the <a class="external-link" href="http://en.wikipedia.org/wiki/Secure_copy" target="_self" title="">scp</a> and sftp protocols.</p>
+<p class="hiddenForView">In case large volumes of data are transferred, use dedicated data mover nodes cedge[1-3].salomon.it4i.cz for increased performance.</p>
+<p class="hiddenForView">Â </p>
+<p class="hiddenForView">HTML commented section #1 (removed cedge servers from the table)</p>
+<table class="listing">
+<tbody>
+<tr><th>Address</th><th>Port</th><th>Protocol</th></tr>
+<tr class="even">
+<td>salomon.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="odd">
+<td>login1.salomon.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="even">
+<td>login2.salomon.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="odd">
+<td><span class="discreet"></span>login3.salomon.it4i.cz</td>
+<td>22</td>
+<td><span class="discreet"></span>scp, sftp</td>
+</tr>
+<tr class="odd">
+<td>login4.salomon.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+</tbody>
+</table>
+<p>Â The authentication is by the <a href="../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html" title="" target="_self" class="internal-link">private key</a></p>
+<p class="hiddenForView">HTML commented section #2 (ssh transfer performance data need to be verified)</p>
+
+<p>On linux or Mac, use scp or sftp client to transfer the data to Salomon:</p>
+<pre class="prettyprint lang-sh">local $ scp -i /path/to/id_rsa my-local-file username@salomon.it4i.cz:directory/file</pre>
+<pre class="prettyprint lang-sh">local $ scp -i /path/to/id_rsa -r my-local-dir username@salomon.it4i.cz:directory</pre>
+<blockquote>or</blockquote>
+<pre class="prettyprint lang-sh">local $ sftp -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz</pre>
+<p>Very convenient way to transfer files in and out of the Salomon computer is via the fuse filesystem <a class="external-link" href="http://linux.die.net/man/1/sshfs" target="_self" title="">sshfs</a></p>
+<pre class="prettyprint lang-sh">local $ sshfs -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz:. mountpoint</pre>
+<p>Using sshfs, the users Salomon home directory will be mounted on your local computer, just like an external disk.</p>
+<p>Learn more on ssh, scp and sshfs by reading the manpages</p>
+<pre class="prettyprint lang-sh">$ man ssh<br />$ man scp<br />$ man sshfs</pre>
+<p><span>On Windows</span>, use <a class="external-link" href="http://winscp.net/eng/download.php" target="_self" title="">WinSCP client</a> to transfer the data. The <a class="external-link" href="http://code.google.com/p/win-sshfs/" target="_self" title="">win-sshfs client</a> provides a way to mount the Salomon filesystems directly as an external disc.</p>
+<p>More information about the shared file systems is available <a href="storage/storage.html" title="" target="_self" class="internal-link">here</a>.</p>
+
+
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+<li class="navTreeItem visualNoMarker section-vpn-access">
+
+
+
+
+ <a href="accessing-the-cluster/vpn-access.html" title="" class="state-published contenttype-document">
+
+ <span>VPN Access</span>
+ </a>
+
+
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+
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+ <a href="accessing-the-cluster/outgoing-connections.html" title="" class="state-published contenttype-document">
+
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+ </a>
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diff --git a/docs.it4i.cz/salomon/accessing-the-cluster.md b/docs.it4i.cz/salomon/accessing-the-cluster.md
index 3974eb55d..a1d96c626 100644
--- a/docs.it4i.cz/salomon/accessing-the-cluster.md
+++ b/docs.it4i.cz/salomon/accessing-the-cluster.md
@@ -66,7 +66,7 @@ After logging in, you will see the command prompt:
                       http://www.it4i.cz/?lang=en
- Last loginTue Jul 9 15:57:38 2013 from your-host.example.com
+ Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com
[username@login2.salomon ~]$
The environment is **not** shared between login nodes, except for
diff --git a/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface.html b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface.html
new file mode 100644
index 000000000..2afd73faf
--- /dev/null
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface.html
@@ -0,0 +1,662 @@
+
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+
+
+<title> Graphical User Interface — IT4I Docs</title>
+
+ <link rel="canonical" href="../../anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.html" />
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+ Graphical User Interface
+ </h1>
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+</div>
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+ <div id="content-core">
+
+
+
+ <div id="parent-fieldname-text-0088a96108124c8b932ad89062d8b4dd" class="">
+ <h2 class=" ">X Window System</h2>
+<p>The X Window system is a principal way to get GUI access to the clusters.</p>
+<p>Read more about configuring <a href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link"><b>X Window System</b></a>.</p>
+<h2>VNC</h2>
+<p>The <b>Virtual Network Computing</b> (<b>VNC</b>) is a graphical <span class="link-external"><a href="http://en.wikipedia.org/wiki/Desktop_sharing" title="Desktop sharing">desktop sharing</a></span> system that uses the <span class="link-external"><a href="http://en.wikipedia.org/wiki/RFB_protocol" title="RFB protocol">Remote Frame Buffer protocol (RFB)</a></span> to remotely control another <span class="link-external"><a href="http://en.wikipedia.org/wiki/Computer" title="Computer">computer</a></span>.</p>
+<p>Read more about configuring <strong><a href="graphical-user-interface/vnc.html" title="" target="_self" class="internal-link">VNC</a></strong>.</p>
+
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+
+
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diff --git a/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface.md b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface.md
index c07285098..e5dc5cd4f 100644
--- a/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface.md
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@@ -28,3 +28,7 @@ class="link-external">[computer](http://en.wikipedia.org/wiki/Computer "Computer
Read more about configuring
**[VNC](graphical-user-interface/vnc.html)**.
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diff --git a/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc.html b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc.html
new file mode 100644
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+ <p>The <b>Virtual Network Computing</b> (<b>VNC</b>) is a graphical <a href="http://en.wikipedia.org/wiki/Desktop_sharing" title="Desktop sharing">desktop sharing</a> system that uses the <a href="http://en.wikipedia.org/wiki/RFB_protocol" title="RFB protocol">Remote Frame Buffer protocol (RFB)</a> to remotely control another <a href="http://en.wikipedia.org/wiki/Computer" title="Computer">computer</a>. It transmits the <a href="http://en.wikipedia.org/wiki/Computer_keyboard" title="Computer keyboard">keyboard</a> and <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Computer_mouse" title="Computer mouse">mouse</a> events from one computer to another, relaying the graphical <a class="mw-redirect" href="http://en.wikipedia.org/wiki/Computer_screen" title="Computer screen">screen</a> updates back in the other direction, over a <a href="http://en.wikipedia.org/wiki/Computer_network" title="Computer network">network</a>.<sup class="reference" id="cite_ref-1"><a href="http://en.wikipedia.org/wiki/Virtual_Network_Computing#cite_note-1"><span>[</span>1<span>]</span></a></sup></p>
+<p>The recommended clients are <a class="external-link" href="http://www.tightvnc.com" target="_self" title="">TightVNC</a> or <a class="external-link" href="http://sourceforge.net/apps/mediawiki/tigervnc/index.php?title=Main_Page" target="_self" title="">TigerVNC</a> (free, open source, available for almost any platform).</p>
+<h2 class=" ">Create VNC password</h2>
+<p class="callout">Local VNC password should be set before the first login. Do use a strong password.</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">~]</span><span class="pln">$ vncpasswd</span><br /><span class="typ">Password</span><span class="pun">:</span><br /><span class="typ">Verify</span><span class="pun">:</span></pre>
+<h2 class=" ">Start vncserver</h2>
+<p class="callout">To access VNC a local vncserver must be started first and also a tunnel using SSH port forwarding must be established.<br /><a class="anchor-link" href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/vnc.html#linux-example-of-creating-a-tunnel" target="_self" title="">See below</a> for the details on SSH tunnels. In this example we use port 61.</p>
+<p class=" ">You can find ports which are already occupied. Here you can see that ports "<span class="pln">/usr/bin/Xvnc :79"</span> and "<span class="pln">/usr/bin/Xvnc :60" are occupied.</span></p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">~]</span><span class="pln">$ </span>ps aux | grep Xvnc<br /><span class="pln"><span class="pln"><span class="pln">username</span></span></span>   5971 0.0 0.0 201072 92564 ?       SN  Sep22  4:19 /usr/bin/Xvnc :79 -desktop login2:79 (<span class="pln"><span class="pln"><span class="pln">username</span></span></span>) -auth /home/gre196/.Xauthority -geometry 1024x768 -rfbwait 30000 -rfbauth /home/<span class="pln"><span class="pln"><span class="pln">username</span></span></span>/.vnc/passwd -rfbport 5979 -fp catalogue:/etc/X11/fontpath.d -pn<br /><span class="pln"><span class="pln"><span class="pln">username</span>   </span>10296 0.0 0.0 131772 21076 pts/29  SN  13:01  0:01 /usr/bin/Xvnc :60 -desktop login2:61 (<span class="pln">username</span>) -auth /home/<span class="pln">username</span>/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/jir13/.vnc/passwd -rfbport 5960 -fp catalogue:/etc/X11/fontpath.d -pn<br />.....<br /></span></pre>
+<p class=" ">Choose free port e.g. 61 and start your VNC server:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">~]</span><span class="pln">$ vncserver </span><span class="pln">:61 </span><span class="pun">-</span><span class="pln">geometry </span><strong><span class="lit">1600</span></strong><span class="lit">x900</span><span class="pln"> </span><span class="pun">-</span><span class="pln">depth </span><span class="lit">16</span><br /><br /><span class="typ">New</span><span class="pln"> </span><span class="str">'login2:1 (username)'</span><span class="pln"> desktop is login2</span><span class="pun">:</span><span class="lit">1</span><br /><br /><span class="typ">Starting</span><span class="pln"> applications specified </span><span class="kwd">in</span><span class="pln"> </span><span class="pun">/</span><span class="pln">home</span><span class="pun">/</span><span class="pln">username</span><span class="pun">/.</span><span class="pln">vnc</span><span class="pun">/</span><span class="pln">xstartup</span><br /><span class="typ">Log</span><span class="pln"> file is </span><span class="pun">/</span><span class="pln">home</span><span class="pun">/</span><span class="pln">username</span><span class="pun">/.</span><span class="pln">vnc</span><span class="pun">/</span><span class="pln">login2</span><span class="pun">:</span><span class="lit">1.log</span><br /><span class="pun"></span></pre>
+<p>Check if VNC server is started on the port (in this example 61):</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ vncserver </span><span class="pun">-</span><span class="pln">list</span><br /><br /><span class="typ">TigerVNC</span><span class="pln"> server sessions</span><span class="pun">:</span><br /><br /><span class="pln">X DISPLAY </span><span class="com">#Â Â Â Â PROCESS ID</span><br /><span class="pun">:<span class="pun"></span><span class="lit">6</span></span><span class="lit">1</span><span class="pln">Â Â Â Â Â Â Â Â Â Â Â Â Â </span><span class="lit">18437</span></pre>
+<p>Another command:<span class="pln"></span></p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ Â ps aux | grep Xvnc<br /><br /><span class="pln">username</span>Â Â Â 10296Â 0.0Â 0.0 131772 21076 pts/29Â Â SNÂ Â 13:01Â Â 0:01 /usr/bin/Xvnc :61 -desktop login2:61 (<span class="pln">username</span>) -auth /home/jir13/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/<span class="pln"><span class="pln">username</span></span>/.vnc/passwd -rfbport 5961 -fp catalogue:/etc/X11/fontpath.d -pn<br /></span></pre>
+<p>To access the VNC server you have to create a tunnel between the login node using TCP <strong>port 5961</strong> and your machine using a free TCP port (for simplicity the very same, in this case).</p>
+<p class="exclamation">The tunnel must point to the same login node where you launched the VNC server, eg. login2. If you use just cluster-name.it4i.cz, the tunnel might point to a different node due to DNS round robin.</p>
+<h3 class=" "><a name="linux-example-of-creating-a-tunnel"></a><a name="linux-example"></a>Linux/Mac OS example of creating a tunnel</h3>
+<p>At your machine, create the tunnel:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $Â ssh </span><span class="pun">-</span><span class="pln">TN </span><span class="pun">-</span><span class="pln">f username@login2.cluster-name</span><span class="pun">.</span><span class="pln">it4i</span><span class="pun">.</span><span class="pln">cz </span><span class="pun">-</span><span class="pln">L </span><span class="lit">5961</span><span class="pun">:</span><span class="pln">localhost</span><span class="pun">:</span><span class="lit">5961</span></pre>
+<p>Issue the following command to check the tunnel is established (please note the PID 2022 in the last column, you'll need it for closing the tunnel):</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ netstat </span><span class="pun">-</span><span class="pln">natp </span><span class="pun">|</span><span class="pln"> grep </span><span class="lit">5961</span><br /><span class="pun">(</span><span class="typ">Not</span><span class="pln"> all processes could be identified</span><span class="pun">,</span><span class="pln"> non</span><span class="pun">-</span><span class="pln">owned process info</span><br /><span class="pln"> will not be shown</span><span class="pun">,</span><span class="pln"> you would have to be root to see it all</span><span class="pun">.)</span><br /><span class="pln">tcp       </span><span class="lit">0</span><span class="pln">     </span><span class="lit">0</span><span class="pln"> </span><span class="lit">127.0</span><span class="pun">.</span><span class="lit">0.1</span><span class="pun">:</span><span class="lit">5961</span><span class="pln">         </span><span class="lit">0.0</span><span class="pun">.</span><span class="lit">0.0</span><span class="pun">:*</span><span class="pln">              LISTEN     </span><span class="lit">2022</span><span class="pun">/</span><span class="pln">ssh       </span><br /><span class="pln">tcp6      </span><span class="lit">0</span><span class="pln">     </span><span class="lit">0</span><span class="pln"> </span><span class="pun">::</span><span class="lit">1</span><span class="pun">:</span><span class="lit">5961</span><span class="pln">               </span><span class="pun">:::*</span><span class="pln">                   LISTEN     </span><span class="lit">2022</span><span class="pun">/</span><span class="pln">ssh </span></pre>
+<p>Or on Mac OS use this command:</p>
+<pre class="prettyprint lang-sh">local-mac $ lsof -n -i4TCP:5961 | grep LISTEN<br />ssh 75890 sta545 7u IPv4 0xfb062b5c15a56a3b 0t0 TCP 127.0.0.1:5961 (LISTEN)</pre>
+<p>Connect with the VNC client:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ vncviewer </span><span class="lit">127.0</span><span class="pun">.</span><span class="lit">0.1</span><span class="pun">:</span><span class="lit">5961</span></pre>
+<p>In this example, we connect to VNC server on port 5961, via the ssh tunnel. The connection is encrypted and secured. The VNC server listening on port 5961 provides screen of 1600x900 pixels.</p>
+<p>You have to destroy the SSH tunnel which is still running at the background after you finish the work. Use the following command (PID 2022 in this case, see the netstat command above):</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">kill </span><span class="lit">2022</span></pre>
+<h3 class=" ">Windows example of creating a tunnel</h3>
+<p>Use PuTTY to log in on cluster.</p>
+<p>Start vncserver using command vncserver described above.</p>
+<p>Search for the localhost and port number (in this case 127.0.0.1:5961).<strong><br /></strong></p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ netstat </span><span class="pun">-</span><span class="pln">tanp </span><span class="pun">|</span><span class="pln"> grep </span><span class="typ">Xvnc</span><br /><span class="pun">(</span><span class="typ">Not</span><span class="pln"> all processes could be identified</span><span class="pun">,</span><span class="pln"> non</span><span class="pun">-</span><span class="pln">owned process info</span><br /><span class="pln"> will not be shown</span><span class="pun">,</span><span class="pln"> you would have to be root to see it all</span><span class="pun">.)</span><br /><span class="pln">tcp       </span><span class="lit">0</span><span class="pln">     </span><span class="lit">0</span><span class="pln"> </span><span class="lit">127.0</span><span class="pun">.</span><span class="lit">0.1</span><span class="pun">:</span><span class="lit">5961</span><span class="pln">             </span><span class="lit">0.0</span><span class="pun">.</span><span class="lit">0.0</span><span class="pun">:*</span><span class="pln">                  LISTEN     </span><span class="lit">24031</span><span class="pun">/</span><span class="typ">Xvnc</span></pre>
+<p>On the PuTTY Configuration screen go to Connection->SSH->Tunnels to set up the tunnel.</p>
+<p>Fill the Source port and Destination fields. <strong>Do not forget to click the Add button</strong>.<br /><br /> <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png" title="" target="_blank" class="internal-link"><img alt="PuTTY - Create tunnel" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png/@@images/4c66cd51-c858-473b-98c2-8d901aea7118.png" title="PuTTY Tunnel" class="image-inline" /></a></p>
+<p>Run the VNC client of your choice, select VNC server 127.0.0.1, port 5961 and connect using VNC password.</p>
+<h3 class=" ">Example of starting TigerVNC viewer</h3>
+<p><img alt="TigerVNC vncviewer" src="../../../anselm-cluster-documentation/vncviewer.png/@@images/bb4cedff-4cb6-402b-ac79-039186fe5df3.png" title="Vncviewer" class="image-inline" /></p>
+<p>In this example, we connect to VNC server on port 5961, via the ssh tunnel, using TigerVNC viewer. The connection is encrypted and secured. The VNC server listening on port 5961 provides screen of 1600x900 pixels.</p>
+<h3 class=" ">Example of starting TightVNC Viewer</h3>
+<p>Use your VNC password to log using TightVNC Viewer and start a Gnome Session on the login node.</p>
+<p><a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png" title="" target="_blank" class="internal-link"><strong><img alt="" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/TightVNC_login.png/@@images/e53354d8-a2e8-4947-92b3-dd107d498408.png" title="" class="image-inline" /></strong></a></p>
+<h2 class=" ">Gnome session</h2>
+<p>You should see after the successful login.</p>
+<p><a href="https://docs.it4i.cz/get-started-with-it4innovations/gnome_screen.jpg" title="" target="_blank" class="internal-link"><img alt="Default Gnome session" src="../../gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-618cda100fda.png" title="Default Gnome session" class="image-inline" /></a></p>
+<h3 class=" "><strong>Disable your Gnome session screensaver<br /></strong></h3>
+<p>Open Screensaver preferences dialog:</p>
+<p><a href="../../gnome_screen.jpg.1" title="" target="_blank" class="internal-link"><img alt="Screensaver Preferences" src="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmscreensaver.png/@@images/8e80a92f-f691-4d92-8e62-344128dcc00b.png" title="Screensaver Preferences" class="image-inline" /></a></p>
+<p>Uncheck both options below the slider:</p>
+<p><a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png" title="" target="_blank" class="internal-link"><img alt="Disable lock screen and screensaver" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png/@@images/8a4758d9-3027-4ce4-9a90-2d5e88197451.png" title="Disable lock screen and screensaver" class="image-inline" /></a></p>
+<h3 class=" ">Kill screensaver if locked screen</h3>
+<p>If the screen gets locked you have to kill the screensaver. Do not to forget to disable the screensaver then.</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ ps aux </span><span class="pun">|</span><span class="pln"> grep screen</span><br /><span class="pln">username    </span><span class="lit">1503</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">103244</span><span class="pln">  </span><span class="lit">892</span><span class="pln"> pts</span><span class="pun">/</span><span class="lit">4</span><span class="pln">   S</span><span class="pun">+</span><span class="pln">  </span><span class="lit">14</span><span class="pun">:</span><span class="lit">37</span><span class="pln">  </span><span class="lit">0</span><span class="pun">:</span><span class="lit">00</span><span class="pln"> grep screen</span><br /><span class="pln">username    </span><span class="lit">24316</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">0.0</span><span class="pln"> </span><span class="lit">270564</span><span class="pln"> </span><span class="lit">3528</span><span class="pln"> </span><span class="pun">?</span><span class="pln">       </span><span class="typ">Ss</span><span class="pln">  </span><span class="lit">14</span><span class="pun">:</span><span class="lit">12</span><span class="pln">  </span><span class="lit">0</span><span class="pun">:</span><span class="lit">00</span><span class="pln"> gnome</span><span class="pun">-</span><span class="pln">screensaver</span><br /><br /><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ kill </span><span class="lit">24316</span></pre>
+<h3 class=" ">Kill vncserver after finished work</h3>
+<p>You should kill your VNC server using command:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$ </span><span class="pln">vncserver -kill :61<br />Killing Xvnc process ID 7074<br />Xvnc process ID 7074 already killed<br /></span><span class="pun"></span></pre>
+<p>Or this way:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pun">[</span><span class="pln">username@login2 </span><span class="pun">.</span><span class="pln">vnc</span><span class="pun">]</span><span class="pln">$Â p</span><span class="pln">kill vnc</span></pre>
+<h2 class=" ">GUI applications on compute nodes over VNC</h2>
+<p>The very <a href="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc#gui-applications-on-compute-nodes" title="" target="_self" class="anchor-link">same methods as described above</a>, may be used to run the GUI applications on compute nodes. However, for <strong>maximum performance</strong>, proceed following these steps:</p>
+<p>Open a Terminal (Applications -> System Tools -> Terminal). Run all the next commands in the terminal.<br /><br /><a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png" title="" target="_blank" class="internal-link"><img alt="gnome-terminal.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png/@@images/b44f5d8c-156d-4041-9bb0-973996413834.png" title="gnome-terminal.png" class="image-inline" /></a></p>
+<p>Allow incoming X11 graphics from the compute nodes at the login node:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ xhost </span><span class="pun">+</span></pre>
+<p>Get an interactive session on a compute node (for more detailed info <a href="../../../anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_self" class="internal-link">look here</a>). Use the <strong>-v DISPLAY</strong> option to propagate the DISPLAY on the compute node. In this example, we want a complete node (24 cores in this example) from the production queue:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ qsub </span><span class="pun">-</span><span class="pln">I </span><span class="pun">-</span><span class="pln">v DISPLAY</span><span class="pun">=</span><span class="pln">$</span><span class="pun">(</span><span class="pln">uname </span><span class="pun">-</span><span class="pln">n</span><span class="pun">):</span><span class="pln">$</span><span class="pun">(</span><span class="pln">echo $DISPLAY </span><span class="pun">|</span><span class="pln"> cut </span><span class="pun">-</span><span class="pln">d </span><span class="str">':'</span><span class="pln"> </span><span class="pun">-</span><span class="pln">f </span><span class="lit">2</span><span class="pun">)</span><span class="pln"> </span><span class="pun">-</span><span class="pln">A PROJECT_ID </span><span class="pun">-</span><span class="pln">q qprod </span><span class="pun">-</span><span class="pln">l select</span><span class="pun">=</span><span class="lit">1</span><span class="pun">:</span><span class="pln">ncpus</span><span class="pun">=24</span><span class="lit"></span></pre>
+<p>Test that the DISPLAY redirection into your VNC session works, by running a X11 application (e. g. XTerm) on the assigned compute node:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ xterm<br /></span></pre>
+<p>Example described above:</p>
+<p><a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png" title="" target="_blank" class="internal-link"><img alt="gnome-compute-nodes-over-vnc.png" src="https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png/@@images/90ca3609-a3ff-4867-9019-954c74224961.png" title="gnome-compute-nodes-over-vnc.png" class="image-inline" /></a></p>
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diff --git a/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc.md b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc.md
index 4d232ffa7..2bcd60f9a 100644
--- a/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc.md
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface/vnc.md
@@ -200,12 +200,12 @@ session](../../gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-618cda100fda.pn
Open Screensaver preferences dialog:
[](../../gnome_screen.jpg.1)
+Preferences](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmscreensaver.png/@@images/8e80a92f-f691-4d92-8e62-344128dcc00b.png "Screensaver Preferences")](../../gnome_screen.jpg.1)
Uncheck both options below the slider:
[](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png)
+screensaver](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png/@@images/8a4758d9-3027-4ce4-9a90-2d5e88197451.png "Disable lock screen and screensaver")](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png)
### Kill screensaver if locked screen
@@ -276,3 +276,7 @@ $ xterm
Example described above:
[](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png)
+
+
+
+
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index 000000000..f10f6f51e
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+ <h2 class=" ">Connection restrictions</h2>
+<p>Outgoing connections, from Salomon Cluster login nodes to the outside world, are restricted to following ports:</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>Port</th><th>Protocol</th></tr>
+<tr class="even">
+<td>22</td>
+<td>ssh</td>
+</tr>
+<tr class="odd">
+<td>80</td>
+<td>http</td>
+</tr>
+<tr class="even">
+<td>443</td>
+<td>https</td>
+</tr>
+<tr class="odd">
+<td>9418</td>
+<td>git</td>
+</tr>
+</tbody>
+</table>
+<p class="callout">Please use<strong> ssh port forwarding</strong> and proxy servers to connect from Salomon to all other remote ports.</p>
+<p class=" ">Outgoing connections, from Salomon Cluster compute nodes are restricted to the internal network. Direct connections form compute nodes to outside world are cut.</p>
+<h2 class=" ">Port forwarding</h2>
+<h3 class=" "><a name="port-forwarding-from-login-nodes"></a>Port forwarding from login nodes</h3>
+<p class="callout">Port forwarding allows an application running on Salomon to connect to arbitrary remote host and port.</p>
+<p class=" ">It works by tunneling the connection from Salomon back to users workstation and forwarding from the workstation to the remote host.</p>
+<p>Pick some unused port on Salomon login node (for example 6000) and establish the port forwarding:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ ssh </span><span class="pun">-</span><span class="pln">R </span><span class="lit">6000</span><span class="pun">:</span><span class="pln">remote</span><span class="pun">.</span><span class="pln">host</span><span class="pun">.</span><span class="pln">com</span><span class="pun">:</span><span class="lit">1234</span><span class="pln"> salomon</span><span class="pun">.</span><span class="pln">it4i</span><span class="pun">.</span><span class="pln">cz</span></pre>
+<p>In this example, we establish port forwarding between port 6000 on Salomon and port 1234 on the remote.host.com. By accessing localhost:6000 on Salomon, an application will see response of remote.host.com:1234. The traffic will run via users local workstation.</p>
+<p class=" ">Port forwarding may be done<strong> using PuTTY</strong> as well. On the PuTTY Configuration screen, load your Salomon configuration first. Then go to Connection->SSH->Tunnels to set up the port forwarding. Click Remote radio button. Insert 6000 to Source port textbox. Insert remote.host.com:1234. Click Add button, then Open.</p>
+<p class=" ">Port forwarding may be established directly to the remote host. However, this requires that user has ssh access to remote.host.com</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ ssh </span><span class="pun">-</span><span class="pln">L </span><span class="lit">6000</span><span class="pun">:</span><span class="pln">localhost</span><span class="pun">:</span><span class="lit">1234</span><span class="pln"> remote</span><span class="pun">.</span><span class="pln">host</span><span class="pun">.</span><span class="pln">com</span></pre>
+<p class=" ">Note: Port number 6000 is chosen as an example only. Pick any free port.</p>
+<h3 class=" "><a name="port-forwarding-from-compute-nodes"></a>Port forwarding from compute nodes</h3>
+<p class=" ">Remote port forwarding from compute nodes allows applications running on the compute nodes to access hosts outside Salomon Cluster.</p>
+<p class=" ">First, establish the remote port forwarding form the login node, as <a class="anchor-link" href="outgoing-connections.html#port-forwarding-from-login-nodes" target="_self" title="">described above</a>.</p>
+<p class=" ">Second, invoke port forwarding from the compute node to the login node. Insert following line into your jobscript or interactive shell</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ ssh </span><span class="pun">-</span><span class="pln">TN </span><span class="pun">-</span><span class="pln">f </span><span class="pun">-</span><span class="pln">L </span><span class="lit">6000</span><span class="pun">:</span><span class="pln">localhost</span><span class="pun">:</span><span class="lit">6000</span><span class="pln"> login1</span></pre>
+<p>In this example, we assume that port forwarding from login1:6000 to remote.host.com:1234 has been established beforehand. By accessing localhost:6000, an application running on a compute node will see response of remote.host.com:1234</p>
+<h3 class=" ">Using proxy servers</h3>
+<p>Port forwarding is static, each single port is mapped to a particular port on remote host. Connection to other remote host, requires new forward.</p>
+<p class="callout">Applications with inbuilt proxy support, experience unlimited access to remote hosts, via single proxy server.</p>
+<p>To establish local proxy server on your workstation, install and run SOCKS proxy server software. On Linux, sshd demon provides the functionality. To establish SOCKS proxy server listening on port 1080 run:</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ ssh </span><span class="pun">-</span><span class="pln">D </span><span class="lit">1080</span><span class="pln"> localhost</span></pre>
+<p>On Windows, install and run the free, open source <a class="external-link" href="http://sockspuppet.com/" target="_self" title="">Sock Puppet</a> server.</p>
+<p>Once the proxy server is running, establish ssh port forwarding from Salomon to the proxy server, port 1080, exactly as <a class="anchor-link" href="outgoing-connections.html#port-forwarding-from-login-nodes" target="_self" title="">described above</a>.</p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="kwd">local</span><span class="pln"> $ ssh </span><span class="pun">-</span><span class="pln">R </span><span class="lit">6000</span><span class="pun">:</span><span class="pln">localhost</span><span class="pun">:</span><span class="lit">1080</span><span class="pln"> salomon</span><span class="pun">.</span><span class="pln">it4i</span><span class="pun">.</span><span class="pln">cz</span></pre>
+<p>Now, configure the applications proxy settings to <strong>localhost:6000</strong>. Use port forwarding to access the <a class="anchor-link" href="outgoing-connections.html#port-forwarding-from-compute-nodes" target="_self" title="">proxy server from compute nodes</a> as well .</p>
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diff --git a/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md b/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
index 168df3de2..7da426aab 100644
--- a/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
@@ -61,7 +61,7 @@ this requires that user has ssh access to remote.host.com
$ ssh -L 6000:localhost:1234 remote.host.com
```
-NotePort number 6000 is chosen as an example only. Pick any free port.
+Note: Port number 6000 is chosen as an example only. Pick any free port.
### []()Port forwarding from compute nodes
@@ -117,3 +117,7 @@ Now, configure the applications proxy settings to **localhost:6000**.
Use port forwarding to access the [proxy server from compute
nodes](outgoing-connections.html#port-forwarding-from-compute-nodes)
as well .
+
+
+
+
diff --git a/docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html b/docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html
new file mode 100644
index 000000000..edbb15d9c
--- /dev/null
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html
@@ -0,0 +1,863 @@
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+ <div id="parent-fieldname-text-ee0eabe3d22344259bc4a66b354691ab" class="">
+ <h2 class=" ">Interactive Login</h2>
+<p>The Salomon cluster is accessed by SSH protocol via login nodes login1, login2, login3 and login4 at address salomon.it4i.cz. The login nodes may be addressed specifically, by prepending the login node name to the address.</p>
+<p class="exclamation">The alias <span>salomon.it4i.cz is currently not available through VPN connection. Please use loginX.salomon.it4i.cz when connected to VPN.</span></p>
+<table class="listing">
+<tbody>
+<tr><th>Login address</th><th>Port</th><th>Protocol</th><th>Login node</th></tr>
+<tr class="even">
+<td>salomon.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>round-robin DNS record for login[1-4]</td>
+</tr>
+<tr class="odd">
+<td>login1.salomon.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login1</td>
+</tr>
+<tr class="even">
+<td>login2.salomon.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login2</td>
+</tr>
+<tr class="even">
+<td>login3.salomon.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login3</td>
+</tr>
+<tr class="even">
+<td>login4.salomon.it4i.cz</td>
+<td>22</td>
+<td>ssh</td>
+<td>login4</td>
+</tr>
+</tbody>
+</table>
+<p>The authentication is by the <a href="../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html" title="" target="_self" class="internal-link">private key</a></p>
+<p class="callout">Please verify SSH fingerprints during the first logon. They are identical on all login nodes:<span class="monospace"><br />f6:28:98:e4:f9:b2:a6:8f:f2:f4:2d:0a:09:67:69:80 (DSA)<br />70:01:c9:9a:5d:88:91:c7:1b:c0:84:d1:fa:4e:83:5c (RSA)</span></p>
+<p>Â </p>
+<p>Private keys authentication:</p>
+<p>On <strong>Linux</strong> or <strong>Mac</strong>, use</p>
+<pre class="prettyprint lang-sh">local $ ssh -i /path/to/id_rsa username@salomon.it4i.cz</pre>
+<p>If you see warning message "UNPROTECTED PRIVATE KEY FILE!", use this command to set lower permissions to private key file.</p>
+<pre class="prettyprint lang-sh">local $ chmod 600 /path/to/id_rsa</pre>
+<p>On <strong>Windows</strong>, use <a href="../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html" title="" target="_self" class="internal-link">PuTTY ssh client</a>.</p>
+<p>After logging in, you will see the command prompt:</p>
+<pre class=" ">Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â _____Â Â Â Â Â Â _Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â / ____|Â Â Â Â | |Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â | (___Â Â __ _| | ___Â _ __ ___Â Â ___Â _ __ Â <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â \___ \ / _` | |/ _ \| '_ ` _ \ / _ \| '_ \ <br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â ____) | (_| | | (_) | | | | | | (_) | | | |<br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â |_____/ \__,_|_|\___/|_| |_| |_|\___/|_| |_|<br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â <br /><br />Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â http://www.it4i.cz/?lang=en<br /><br /><br />Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com<br />[username@login2.salomon ~]$</pre>
+<p class="callout">The environment is <strong>not</strong> shared between login nodes, except for <a href="../../storage/storage.html" title="" target="_self" class="internal-link">shared filesystems</a>.</p>
+<h2 class=" ">Data Transfer</h2>
+<p>Data in and out of the system may be transferred by the <a class="external-link" href="http://en.wikipedia.org/wiki/Secure_copy" target="_self" title="">scp</a> and sftp protocols.</p>
+<p class="hiddenForView">In case large volumes of data are transferred, use dedicated data mover nodes cedge[1-3].salomon.it4i.cz for increased performance.</p>
+<p class="hiddenForView">Â </p>
+<p class="hiddenForView">HTML commented section #1 (removed cedge servers from the table)</p>
+<table class="listing">
+<tbody>
+<tr><th>Address</th><th>Port</th><th>Protocol</th></tr>
+<tr class="even">
+<td>salomon.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="odd">
+<td>login1.salomon.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="even">
+<td>login2.salomon.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+<tr class="odd">
+<td><span class="discreet"></span>login3.salomon.it4i.cz</td>
+<td>22</td>
+<td><span class="discreet"></span>scp, sftp</td>
+</tr>
+<tr class="odd">
+<td>login4.salomon.it4i.cz</td>
+<td>22</td>
+<td>scp, sftp</td>
+</tr>
+</tbody>
+</table>
+<p>Â The authentication is by the <a href="../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html" title="" target="_self" class="internal-link">private key</a></p>
+<p class="hiddenForView">HTML commented section #2 (ssh transfer performance data need to be verified)</p>
+
+<p>On linux or Mac, use scp or sftp client to transfer the data to Salomon:</p>
+<pre class="prettyprint lang-sh">local $ scp -i /path/to/id_rsa my-local-file username@salomon.it4i.cz:directory/file</pre>
+<pre class="prettyprint lang-sh">local $ scp -i /path/to/id_rsa -r my-local-dir username@salomon.it4i.cz:directory</pre>
+<blockquote>or</blockquote>
+<pre class="prettyprint lang-sh">local $ sftp -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz</pre>
+<p>Very convenient way to transfer files in and out of the Salomon computer is via the fuse filesystem <a class="external-link" href="http://linux.die.net/man/1/sshfs" target="_self" title="">sshfs</a></p>
+<pre class="prettyprint lang-sh">local $ sshfs -o IdentityFile=/path/to/id_rsa username@salomon.it4i.cz:. mountpoint</pre>
+<p>Using sshfs, the users Salomon home directory will be mounted on your local computer, just like an external disk.</p>
+<p>Learn more on ssh, scp and sshfs by reading the manpages</p>
+<pre class="prettyprint lang-sh">$ man ssh<br />$ man scp<br />$ man sshfs</pre>
+<p><span>On Windows</span>, use <a class="external-link" href="http://winscp.net/eng/download.php" target="_self" title="">WinSCP client</a> to transfer the data. The <a class="external-link" href="http://code.google.com/p/win-sshfs/" target="_self" title="">win-sshfs client</a> provides a way to mount the Salomon filesystems directly as an external disc.</p>
+<p>More information about the shared file systems is available <a href="../../storage/storage.html" title="" target="_self" class="internal-link">here</a>.</p>
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diff --git a/docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md b/docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
index c39429882..7907e5915 100644
--- a/docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
@@ -66,7 +66,7 @@ After logging in, you will see the command prompt:
                       http://www.it4i.cz/?lang=en
- Last loginTue Jul 9 15:57:38 2013 from your-host.example.com
+ Last login: Tue Jul 9 15:57:38 2013 from your-host.example.com
[username@login2.salomon ~]$
The environment is **not** shared between login nodes, except for
@@ -143,3 +143,7 @@ way to mount the Salomon filesystems directly as an external disc.
More information about the shared file systems is available
[here](../../storage/storage.html).
+
+
+
+
diff --git a/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.html b/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.html
new file mode 100644
index 000000000..cfa0064d5
--- /dev/null
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.html
@@ -0,0 +1,804 @@
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+
+
+<title>VPN Access — IT4I Docs</title>
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+ <div class="">
+
+
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+ <dl class="portalMessage info" id="kssPortalMessage" style="display:none">
+ <dt>Info</dt>
+ <dd></dd>
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+ <div id="viewlet-above-content-title"></div>
+
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+ <h1 id="parent-fieldname-title" class="documentFirstHeading">
+ VPN Access
+ </h1>
+
+
+
+
+ <div id="viewlet-below-content-title">
+</div>
+
+
+
+
+
+
+
+
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+ <div id="viewlet-above-content-body">
+<dl id="document-toc" class="portlet toc" style="display: none">
+ <dt class="portletHeader">Obsah</dt>
+ <dd class="portletItem">
+ </dd>
+</dl>
+</div>
+ <div id="content-core">
+
+
+
+ <div id="parent-fieldname-text-1dec66fad166419fa3f2d32bd7bce79b" class="">
+ <h2 class=" ">Accessing IT4Innovations internal resources via VPN</h2>
+<p class=" ">For using resources and licenses which are located at IT4Innovations local network, it is necessary to VPN connect to this network.<br />We use Cisco AnyConnect Secure Mobility Client, which is supported on the following operating systems:</p>
+<ul>
+<li><span>Windows XP</span></li>
+<li><span>Windows Vista</span></li>
+<li><span>Windows 7</span></li>
+<li><span>Windows 8</span></li>
+<li><span>Linux</span></li>
+<li><span>MacOS</span></li>
+</ul>
+<p class=" ">It is impossible to connect to VPN from other operating systems.</p>
+<h2 class=" "><span>VPN client installation</span></h2>
+<p class=" ">You can install VPN client from web interface after successful login with LDAP credentials on address <a class="external-link" href="https://vpn.it4i.cz/user" target="_blank" title="">https://vpn.it4i.cz/user</a></p>
+<p class=" "><a href="../vpn_web_login.png" title="" target="_blank" class="internal-link"><img alt="VPN Install" src="https://docs.it4i.cz/salomon/vpn_web_login.png/@@images/5eac6b9c-22e4-4abe-ab38-e4ccbe87b710.png" title="VPN Install" class="image-inline" /></a></p>
+<p class=" ">According to the Java settings after login, the client either automatically installs, or downloads installation file for your operating system. It is necessary to allow start of installation tool for automatic installation.</p>
+<p class=" "><a href="../vpn_web_login_2.png" title="" target="_blank" class="internal-link"><img alt="VPN Install" src="https://docs.it4i.cz/salomon/vpn_web_login_2.png/@@images/be923364-0175-4099-a363-79229b88e252.png" title="VPN Install" class="image-inline" /></a></p>
+<p class=" "><a href="../vpn_web_install_2.png" title="" target="_blank" class="internal-link"><img alt="VPN Install" src="https://docs.it4i.cz/salomon/vpn_web_install_2.png/@@images/c2baba93-824b-418d-b548-a73af8030320.png" title="VPN Install" class="image-inline" /></a><a href="../copy_of_vpn_web_install_3.png" title="" target="_blank" class="internal-link"><img alt="VPN Install" src="https://docs.it4i.cz/salomon/copy_of_vpn_web_install_3.png/@@images/9c34e8ad-64b1-4e1d-af3a-13c7a18fbca4.png" title="VPN Install" class="image-inline" /></a></p>
+<p class=" ">After successful installation, VPN connection will be established and you can use available resources from IT4I network.</p>
+<p class=" "><a href="../vpn_web_install_4.png" title="" target="_blank" class="internal-link"><img alt="VPN Install" src="https://docs.it4i.cz/salomon/vpn_web_install_4.png/@@images/4cc26b3b-399d-413b-9a6c-82ec47899585.png" title="VPN Install" class="image-inline" /></a></p>
+<p class=" ">If your Java setting doesn't allow automatic installation, you can download installation file and install VPN client manually.</p>
+<p class=" "><a href="../vpn_web_download.png" title="" target="_blank" class="internal-link"><img alt="VPN Install" src="https://docs.it4i.cz/salomon/vpn_web_download.png/@@images/06a88cce-5f51-42d3-8f0a-f615a245beef.png" title="VPN Install" class="image-inline" /></a></p>
+<p class=" ">After you click on the link, download of installation file will start.</p>
+<p class=" "><a href="../vpn_web_download_2.png" title="" target="_blank" class="internal-link"><img alt="VPN Install" src="https://docs.it4i.cz/salomon/vpn_web_download_2.png/@@images/3358d2ce-fe4d-447b-9e6c-b82285f9796e.png" title="VPN Install" class="image-inline" /></a></p>
+<p class=" ">After successful download of installation file, you have to execute this tool with administrator's rights and install VPN client manually.</p>
+<h2 class=" ">Working with VPN client</h2>
+<p class=" ">You can use graphical user interface or command line interface to run VPN client on all supported operating systems. We suggest using GUI.</p>
+<p class=" "><img alt="Icon" src="https://docs.it4i.cz/anselm-cluster-documentation/icon.jpg/@@images/56ee3417-80b8-4988-b9d5-8cda3f894963.jpeg" title="Icon" class="image-inline" /></p>
+<p>Before the first login to VPN, you have to fill URLÂ <strong>https://vpn.it4i.cz/user </strong>into the text field.</p>
+<p><a href="../vpn_contacting_https_cluster.png" title="" target="_blank" class="internal-link"><img alt="VPN Contacting Cluster" src="https://docs.it4i.cz/salomon/vpn_contacting_https_cluster.png/@@images/22b15d8c-5d5f-4c5c-8973-fbc4e9a32128.png" title="VPN Contacting Cluster" class="image-inline" /></a></p>
+<p>After you click on the Connect button, you must fill your login credentials.</p>
+<p><a href="../vpn_contacting_https.png" title="" target="_blank" class="internal-link"><img alt="VPN Contacting Cluster" src="https://docs.it4i.cz/salomon/vpn_contacting_https.png/@@images/ff365499-d07c-4baf-abb8-ce3e15559210.png" title="VPN Contacting Cluster" class="image-inline" /></a></p>
+<p>After a successful login, the client will minimize to the system tray. If everything works, you can see a lock in the Cisco tray icon.</p>
+<p><a href="../../anselm-cluster-documentation/anyconnecticon.jpg" title="" target="_blank" class="internal-link"><img alt="Successfull connection" src="https://docs.it4i.cz/anselm-cluster-documentation/anyconnecticon.jpg/@@images/ebdd0e41-e839-497e-ab33-45162d00b03b.jpeg" title="Successfull connection" class="image-inline" /></a></p>
+<p>If you right-click on this icon, you will see a context menu in which you can control the VPN connection.</p>
+<p><a href="../../anselm-cluster-documentation/anyconnectcontextmenu.jpg" title="" target="_blank" class="internal-link"><img alt="Context menu" src="https://docs.it4i.cz/anselm-cluster-documentation/anyconnectcontextmenu.jpg/@@images/9655f6a6-cd7b-4462-90d6-480d43c8cc0c.jpeg" title="Context menu" class="image-inline" /></a></p>
+<p>When you connect to the VPN for the first time, the client downloads the profile and creates a new item "IT4I cluster" in the connection list. For subsequent connections, it is not necessary to re-enter the URL address, but just select the corresponding item.</p>
+<p><a href="../vpn_contacting.png" title="" target="_blank" class="internal-link"><img alt="VPN Contacting Cluster" src="https://docs.it4i.cz/salomon/vpn_contacting.png/@@images/9ccabccf-581a-476a-8c24-ce9842c3e657.png" title="VPN Contacting Cluster" class="image-inline" /></a></p>
+<p>Then AnyConnect automatically proceeds like in the case of first logon.</p>
+<p><a href="../vpn_login.png" title="" target="_blank" class="internal-link"><img alt="VPN login" src="https://docs.it4i.cz/salomon/vpn_login.png/@@images/5102f29d-93cf-4cfd-8f55-c99c18f196ea.png" title="VPN login" class="image-inline" /></a></p>
+<p>After a successful logon, you can see a green circle with a tick mark on the lock icon.</p>
+<p><a href="../vpn_successfull_connection.png" title="" target="_blank" class="internal-link"><img alt="VPN Succesfull Connection" src="https://docs.it4i.cz/salomon/vpn_successfull_connection.png/@@images/45537053-a47f-48b2-aacd-3b519d6770e6.png" title="VPN Succesfull Connection" class="image-inline" /></a></p>
+<p>For disconnecting, right-click on the AnyConnect client icon in the system tray and select <strong>VPN Disconnect</strong>.</p>
+
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diff --git a/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md b/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
index 9f3a20865..6093d132d 100644
--- a/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
+++ b/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
@@ -116,3 +116,7 @@ Connection](https://docs.it4i.cz/salomon/vpn_successfull_connection.png/@@images
For disconnecting, right-click on the AnyConnect client icon in the
system tray and select **VPN Disconnect**.
+
+
+
+
diff --git a/docs.it4i.cz/salomon/compute-nodes.html b/docs.it4i.cz/salomon/compute-nodes.html
new file mode 100644
index 000000000..e49ffd92b
--- /dev/null
+++ b/docs.it4i.cz/salomon/compute-nodes.html
@@ -0,0 +1,905 @@
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+ Compute Nodes
+ </h1>
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+ <div id="parent-fieldname-text-3028a7e1f7024efda22efc53bd8237f0" class="">
+ <h2 class=" ">Nodes Configuration</h2>
+<p>Salomon is cluster of x86-64 Intel based nodes. The cluster contains two types of compute nodes of the same processor type and memory size. Compute nodes with MIC accelerator<strong></strong> contains two Intel Xeon Phi 7120P accelerators.</p>
+<p><a href="network-1/ib-single-plane-topology.html" title="" target="_self" class="internal-link">More about schematic representation of the Salomon cluster compute nodes IB topology</a>.</p>
+<h3 class=" "><strong>Compute Nodes Without Accelerator</strong></h3>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li><span>codename "grafton"</span></li>
+<li><span>576Â nodes</span></li>
+<li class="listitem">
+<div class="itemizedlist">13Â 824 cores in total</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">two Intel Xeon E5-2680v3, 12-core, 2.5GHz processors per node</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">128 GB of physical memory per node</div>
+</li>
+</ul>
+<p style="padding-left: 30px; "><a href="cn_m_cell" title="" target="_blank" class="internal-link"><img alt="cn_m_cell" src="https://docs.it4i.cz/salomon/cn_m_cell/@@images/8294d5d2-3fec-47d2-a467-10f66d048891.jpeg" title="cn_m_cell" class="image-inline" /></a></p>
+<h3 class=" "><strong>Compute Nodes With MIC Accelerator</strong></h3>
+<div class="itemizedlist">
+<ul>
+<li>codename "perrin"</li>
+<li><span>432Â nodes</span></li>
+</ul>
+</div>
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">
+<div class="itemizedlist"><span>10Â 368Â cores in total</span></div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">two Intel Xeon E5-2680v3, 12-core, 2.5GHz processors per node</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">128 GB of physical memory per node</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">MIC accelerator 2x Intel Xeon Phi 7120P per node, 61-cores, 16GB per accelerator</div>
+</li>
+</ul>
+</div>
+<p style="padding-left: 30px; "><a href="cn_mic-1" title="" target="_blank" class="internal-link"><img alt="cn_mic" src="https://docs.it4i.cz/salomon/cn_mic-1/@@images/44cb01e0-2d67-4ea1-883c-d06919fbf351.jpeg" title="cn_mic" class="image-inline" /></a></p>
+<p style="padding-left: 30px; "><a class="external-link" href="https://www.sgi.com/products/servers/rackable/1u_intel.html#v3" target="_self" title="(source Silicon Graphics International Corp.)"><img alt="(source Silicon Graphics International Corp.)" src="sgi-c1104-gp1/@@images/c1109cbb-9bf4-4f0a-8b0f-a1e464fed0c4.jpeg" title="SGI-C1104-GP1" class="image-inline" /> </a><a href="cn_mic" title="" target="_blank" class="internal-link"><img src="https://docs.it4i.cz/salomon/cn_mic/@@images/46081fb2-10d0-43b3-b32f-9650bedf107a.jpeg" width="87" title="cn_mic" class="image-inline" alt="cn_mic" height="122" /></a></p>
+<div class="figure">
+<h3 class=" ">UV 2000</h3>
+<div class="itemizedlist">
+<ul>
+<li>codename "UV2000"</li>
+<li><span>1 node</span></li>
+</ul>
+</div>
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">
+<div class="itemizedlist"><span>112 cores in total</span></div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">14x Intel Xeon E5-4627v2, 8-core, 3.3GHz processors, in 14 NUMA nodes</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">3328 GB of physical memory per node</div>
+</li>
+<li class="listitem">
+<div class="itemizedlist">1x NVIDIA GM200 (GeForce GTX TITAN X), 12GB RAM</div>
+</li>
+</ul>
+<img alt="UV 2000" src="uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpeg" title="UV 2000" class="image-inline" /><br />
+<h3 class=" ">Compute Nodes Summary<strong><strong></strong></strong></h3>
+<table class="listing">
+<tbody>
+<tr><th>Node type</th><th>Count</th><th>Memory</th><th>Cores</th></tr>
+<tr class="even">
+<td>Nodes without accelerator</td>
+<td>576</td>
+<td>128GB</td>
+<td>24 @ 2.5Ghz</td>
+</tr>
+<tr class="odd">
+<td>Nodes with MIC accelerator</td>
+<td>432</td>
+<td>
+<p>128GB</p>
+<p>32GB</p>
+</td>
+<td>
+<p>24 @ 2.5Ghz</p>
+<p>61 @ <span style="text-align: start; float: none; ">1.238GHz</span></p>
+</td>
+</tr>
+<tr class="odd">
+<td>UV2000 SMP node</td>
+<td>1</td>
+<td>
+<p>3328GB</p>
+</td>
+<td>
+<p>112 @ 3.3GHz</p>
+</td>
+</tr>
+</tbody>
+</table>
+</div>
+<div class="simplesect">
+<div class="titlepage">
+<div>
+<div>
+<h2 class=" ">Processor Architecture</h2>
+</div>
+</div>
+</div>
+<p>Salomon is equipped with Intel Xeon processors Intel Xeon E5-2680v3. Processors support Advanced Vector Extensions 2.0 (AVX2) 256-bit instruction set.</p>
+<div class="simplesect">
+<div class="titlepage">
+<div>
+<div>
+<h3 class=" ">Intel Xeon E5-2680v3 Processor</h3>
+</div>
+</div>
+</div>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">12-core</li>
+<li class="listitem">speed: 2.5 GHz, up to <span style="text-align: start; float: none; ">3.3</span> GHz using Turbo Boost Technology</li>
+<li class="listitem">peak performance: <span class="emphasis">19.2 Gflop/s</span> per core</li>
+<li class="listitem">caches:
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem"><span style="text-align: start; float: none; ">Intel® Smart Cache</span>: <span style="text-align: start; float: none; ">30 MB</span></li>
+</ul>
+</div>
+</li>
+<li class="listitem">memory bandwidth at the level of the processor: <span style="text-align: start; float: none; ">68 GB/s</span></li>
+</ul>
+</div>
+</div>
+<div class="section">
+<div class="titlepage">
+<div>
+<div>
+<h3 class=" ">MIC Accelerator Intel Xeon Phi 7120PÂ Processor</h3>
+</div>
+</div>
+</div>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">61-core</li>
+<li class="listitem">speed: <span style="text-align: start; float: none; ">1.238</span> GHz, up to <span style="text-align: start; float: none; ">1.333</span> GHz using Turbo Boost Technology</li>
+<li class="listitem">peak performance: <span class="emphasis">18.4 Gflop/s</span> per core</li>
+<li class="listitem">caches:
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">L2: <span style="text-align: start; float: none; ">30.5 MB</span></li>
+</ul>
+</div>
+</li>
+<li class="listitem">memory bandwidth at the level of the processor: <span style="text-align: start; float: none; ">352 GB/s</span></li>
+</ul>
+</div>
+<p>Â </p>
+<h2 class=" ">Memory Architecture</h2>
+<p>Memory is equally distributed across all CPUs and cores for optimal performance. Memory is composed of memory modules of the same size and evenly distributed across all memory controllers and memory channels.</p>
+<div class="simplesect">
+<div class="titlepage">
+<div>
+<div>
+<h3 class=" ">Compute Node Without Accelerator</h3>
+</div>
+</div>
+</div>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">2 sockets</li>
+<li class="listitem">Memory Controllers are integrated into processors.
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">8Â DDR4 DIMMS per node</li>
+<li class="listitem">4Â DDR4 DIMMS per CPU</li>
+<li class="listitem"><span>1Â DDR4 DIMMS per channel</span></li>
+</ul>
+</div>
+</li>
+<li class="listitem">Populated memory: 8x 16GB DDR4 DIMM <span>2133MHz</span></li>
+</ul>
+</div>
+</div>
+<div class="simplesect">
+<div class="titlepage">
+<div>
+<div>
+<h3 class=" ">Compute Node With MIC Accelerator</h3>
+</div>
+</div>
+</div>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem">2 sockets</li>
+<li class="listitem">Memory Controllers are integrated into processors.
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">8Â DDR4 DIMMS per node</li>
+<li class="listitem">4Â DDR4 DIMMS per CPU</li>
+<li class="listitem"><span>1Â DDR4 DIMMS per channel</span></li>
+</ul>
+</div>
+</li>
+<li class="listitem"><span>Populated memory: 8x 16GB DDR4 DIMM 2133MHz</span></li>
+<li class="listitem">
+<p class=" ">MIC Accelerator Intel Xeon Phi 7120P Processor</p>
+</li>
+<ul>
+<li class="listitem">2 sockets</li>
+<li class="listitem"><span><span>Memory Controllers are are connected via an Interprocessor Network (IPN) ring.</span></span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">16 GDDR5 DIMMS per node</li>
+<li class="listitem">8Â GDDR5 DIMMS per CPU</li>
+<li class="listitem">2Â GDDR5 DIMMS per channel</li>
+</ul>
+</div>
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diff --git a/docs.it4i.cz/salomon/compute-nodes.md b/docs.it4i.cz/salomon/compute-nodes.md
index b83281bd6..0e4efa0d0 100644
--- a/docs.it4i.cz/salomon/compute-nodes.md
+++ b/docs.it4i.cz/salomon/compute-nodes.md
@@ -40,7 +40,7 @@ topology](network-1/ib-single-plane-topology.html).
-[](cn_m_cell)
+[](cn_m_cell)
### **Compute Nodes With MIC Accelerator**
@@ -77,7 +77,7 @@ topology](network-1/ib-single-plane-topology.html).
-[](cn_mic-1)
+[](cn_mic-1)
[](https://www.sgi.com/products/servers/rackable/1u_intel.html#v3 "(source Silicon Graphics International Corp.)")[{.image-inline
@@ -149,7 +149,7 @@ width="87" height="122"}](cn_mic)
<td align="left"><p>128GB</p>
<p>32GB</p></td>
<td align="left"><p>24 @ 2.5Ghz</p>
-<p>61 @ <span style="text-alignstart; floatnone; ">1.238GHz</span></p></td>
+<p>61 @ <span style="text-align: start; float: none; ">1.238GHz</span></p></td>
</tr>
<tr class="odd">
<td align="left">UV2000 SMP node</td>
@@ -173,41 +173,41 @@ instruction set.
### Intel Xeon E5-2680v3 Processor
- 12-core
-- speed2.5 GHz, up to <span
- style="text-alignstart; floatnone; ">3.3</span> GHz using Turbo
+- speed: 2.5 GHz, up to <span
+ style="text-align: start; float: none; ">3.3</span> GHz using Turbo
Boost Technology
-- peak performance<span class="emphasis">19.2 Gflop/s</span> per
+- peak performance: <span class="emphasis">19.2 Gflop/s</span> per
core
- caches:
<div class="itemizedlist">
- - <span style="text-alignstart; floatnone; ">Intel® Smart
- Cache</span>:Â <span style="text-alignstart; floatnone; ">30
+ - <span style="text-align: start; float: none; ">Intel® Smart
+ Cache</span>:Â <span style="text-align: start; float: none; ">30
MB</span>
-- memory bandwidth at the level of the processor<span
- style="text-alignstart; floatnone; ">68 GB/s</span>
+- memory bandwidth at the level of the processor: <span
+ style="text-align: start; float: none; ">68 GB/s</span>
### MIC Accelerator Intel Xeon Phi 7120PÂ Processor
- 61-core
-- speed:Â <span style="text-alignstart; floatnone; ">1.238</span>
+- speed:Â <span style="text-align: start; float: none; ">1.238</span>
GHz, up to <span
- style="text-alignstart; floatnone; ">1.333</span> GHz using
+ style="text-align: start; float: none; ">1.333</span> GHz using
Turbo Boost Technology
-- peak performance<span class="emphasis">18.4 Gflop/s</span> per
+- peak performance: <span class="emphasis">18.4 Gflop/s</span> per
core
- caches:
<div class="itemizedlist">
- - L2<span style="text-alignstart; floatnone; ">30.5
+ - L2: <span style="text-align: start; float: none; ">30.5
MB</span>
-- memory bandwidth at the level of the processor<span
- style="text-alignstart; floatnone; ">352 GB/s</span>
+- memory bandwidth at the level of the processor: <span
+ style="text-align: start; float: none; ">352 GB/s</span>
@@ -231,7 +231,7 @@ evenly distributed across all memory controllers and memory channels.
-- Populated memory8x 16GB DDR4 DIMM <span>2133MHz</span>
+- Populated memory: 8x 16GB DDR4 DIMM <span>2133MHz</span>
### Compute Node With MIC Accelerator
2 sockets
@@ -243,7 +243,7 @@ Memory Controllers are integrated into processors.
-<span>Populated memory8x 16GB DDR4 DIMM 2133MHz</span>
+<span>Populated memory: 8x 16GB DDR4 DIMM 2133MHz</span>
MIC Accelerator Intel Xeon Phi 7120P Processor
- 2 sockets
@@ -258,4 +258,3 @@ MIC Accelerator Intel Xeon Phi 7120P Processor
-
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+ <h3 class=" ">Environment Customization</h3>
+<p>After logging in, you may want to configure the environment. Write your preferred path definitions, aliases, functions and module loads in the .bashrc file</p>
+<pre class="prettyprint lang-sh"># ./bashrc<br /><br /># Source global definitions<br />if [ -f /etc/bashrc ]; then<br /> . /etc/bashrc<br />fi<br /><br /># User specific aliases and functions<br />alias qs='qstat -a'<br />module load intel/2015b<br /><br /># Display informations to standard output - only in interactive ssh session<br />if [ -n "$SSH_TTY" ]<br />then<br /> module list # Display loaded modules<br />fi</pre>
+<p class="callout">Do not run commands outputing to standard output (echo, module list, etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental functionality (scp, PBS) of your account! Take care for SSH session interactivity for such commands as <span class="short_text" id="result_box"><span class="hps alt-edited">stated</span> <span class="hps">in the previous example.</span></span></p>
+<h3 class=" ">Application Modules</h3>
+<p class=" ">In order to configure your shell for running particular application on Salomon we use Module package interface.</p>
+<p class=" ">Application modules on Salomon cluster are built using <a class="external-link" href="http://hpcugent.github.io/easybuild/" target="_self" title="EasyBuild">EasyBuild</a>. The modules are divided into the following structure:</p>
+<pre class="prettyprint"> base: Default module class<br /> bio: Bioinformatics, biology and biomedical<br /> cae: Computer Aided Engineering (incl. CFD)<br /> chem: Chemistry, Computational Chemistry and Quantum Chemistry<br /> compiler: Compilers<br /> data: Data management & processing tools<br /> debugger: Debuggers<br /> devel: Development tools<br /> geo: Earth Sciences<br /> ide: Integrated Development Environments (e.g. editors)<br /> lang: Languages and programming aids<br /> lib: General purpose libraries<br /> math: High-level mathematical software<br /> mpi: MPI stacks<br /> numlib: Numerical Libraries<br /> perf: Performance tools<br /> phys: Physics and physical systems simulations<br /> system: System utilities (e.g. highly depending on system OS and hardware)<br /> toolchain: EasyBuild toolchains<br /> tools: General purpose tools<br /> vis: Visualization, plotting, documentation and typesetting</pre>
+<p class="callout">The modules set up the application paths, library paths and environment variables for running particular application.</p>
+<p class=" ">The modules may be loaded, unloaded and switched, according to momentary needs.</p>
+<p class=" ">To check available modules use</p>
+<pre class="prettyprint lang-sh">$ module avail</pre>
+<p class=" ">To load a module, for example the OpenMPI module use</p>
+<pre class="prettyprint lang-sh">$ module load OpenMPI</pre>
+<p>loading the OpenMPI module will set up paths and environment variables of your active shell such that you are ready to run the OpenMPI software</p>
+<p class=" ">To check loaded modules use</p>
+<pre class="prettyprint lang-sh">$ module list</pre>
+<p>Â To unload a module, for example the OpenMPI module use</p>
+<pre class="prettyprint lang-sh">$ module unload OpenMPI</pre>
+<p class=" ">Learn more on modules by reading the module man page</p>
+<pre class="prettyprint lang-sh">$ man module</pre>
+<h3 class=" ">EasyBuild Toolchains</h3>
+<p>As we wrote earlier, we are using EasyBuild for automatised software installation and module creation. </p>
+<p>EasyBuild employs so-called <strong>compiler toolchains</strong> or, simply <cite>toolchains</cite> for short, which are a major concept in handling the build and installation processes.</p>
+<p>A typical toolchain consists of one or more compilers, usually put together with some libraries for specific functionality, e.g., for using an MPI stack for distributed computing, or which provide optimized routines for commonly used math operations, e.g., the well-known BLAS/LAPACK APIs for linear algebra routines.</p>
+<p>For each software package being built, the toolchain to be used must be specified in some way.</p>
+<p>The EasyBuild framework prepares the <cite>build environment</cite> for the different toolchain components, by loading their respective modules and defining environment variables to specify compiler commands (e.g., via <code class="docutils literal"><span class="pre">$F90</span></code>), compiler and linker options (e.g., via <code class="docutils literal"><span class="pre">$CFLAGS</span></code> and <code class="docutils literal"><span class="pre">$LDFLAGS</span></code>), the list of library names to supply to the linker (via <code class="docutils literal"><span class="pre">$LIBS</span></code>), etc. This enables making easyblocks largely <cite>toolchain-agnostic</cite> since they can simply rely on these environment variables; that is, unless they need to be aware of, for example, the particular compiler being used to determine the build configuration options.</p>
+<p>Recent releases of EasyBuild include out-of-the-box toolchain support for:</p>
+<ul class="simple">
+<li>various compilers, including GCC, Intel, Clang, CUDA</li>
+<li>common MPI libraries, such as Intel MPI, MPICH, MVAPICH2, OpenMPI</li>
+<li>various numerical libraries, including ATLAS, Intel MKL, OpenBLAS, ScalaPACK, FFTW</li>
+</ul>
+<p>Â </p>
+<p>On Salomon, we have currently following toolchains installed:</p>
+<table class="plain">
+<tbody>
+<tr><th>Toolchain</th><th>Module(s)</th></tr>
+<tr>
+<td>GCC</td>
+<td>GCC</td>
+</tr>
+<tr>
+<td>ictce</td>
+<td>icc, ifort, imkl, impi</td>
+</tr>
+<tr>
+<td>intel</td>
+<td>GCC, icc, ifort, imkl, impi</td>
+</tr>
+<tr>
+<td>gompi</td>
+<td>GCC, OpenMPI</td>
+</tr>
+<tr>
+<td>goolf</td>
+<td>BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK</td>
+</tr>
+<tr>
+<td><span>iompi</span></td>
+<td>OpenMPI, icc, ifort</td>
+</tr>
+<tr>
+<td>iccifort</td>
+<td>icc, ifort</td>
+</tr>
+</tbody>
+</table>
+
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+<li class="navTreeItem visualNoMarker navTreeFolderish section-accessing-the-cluster">
+
+
+
+
+ <a href="accessing-the-cluster.html" title="" class="state-published navTreeFolderish contenttype-folder">
+
+ <span>Accessing the Cluster</span>
+ </a>
+
+
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+<li class="navTreeItem visualNoMarker navTreeCurrentNode section-environment-and-modules">
+
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+
+
+<li class="navTreeItem visualNoMarker section-list_of_modules">
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diff --git a/docs.it4i.cz/salomon/environment-and-modules.md b/docs.it4i.cz/salomon/environment-and-modules.md
index 30dae0287..957d43f2c 100644
--- a/docs.it4i.cz/salomon/environment-and-modules.md
+++ b/docs.it4i.cz/salomon/environment-and-modules.md
@@ -47,27 +47,27 @@ Application modules on Salomon cluster are built using
modules are divided into the following structure:
```
- baseDefault module class
- bioBioinformatics, biology and biomedical
- caeComputer Aided Engineering (incl. CFD)
- chemChemistry, Computational Chemistry and Quantum Chemistry
- compilerCompilers
- dataData management & processing tools
- debuggerDebuggers
- develDevelopment tools
- geoEarth Sciences
- ideIntegrated Development Environments (e.g. editors)
- langLanguages and programming aids
- libGeneral purpose libraries
- mathHigh-level mathematical software
- mpiMPI stacks
- numlibNumerical Libraries
- perfPerformance tools
- physPhysics and physical systems simulations
- systemSystem utilities (e.g. highly depending on system OS and hardware)
- toolchainEasyBuild toolchains
- toolsGeneral purpose tools
- visVisualization, plotting, documentation and typesetting
+ base: Default module class
+ bio: Bioinformatics, biology and biomedical
+ cae: Computer Aided Engineering (incl. CFD)
+ chem: Chemistry, Computational Chemistry and Quantum Chemistry
+ compiler: Compilers
+ data: Data management & processing tools
+ debugger: Debuggers
+ devel: Development tools
+ geo: Earth Sciences
+ ide: Integrated Development Environments (e.g. editors)
+ lang: Languages and programming aids
+ lib: General purpose libraries
+ math: High-level mathematical software
+ mpi: MPI stacks
+ numlib: Numerical Libraries
+ perf: Performance tools
+ phys: Physics and physical systems simulations
+ system: System utilities (e.g. highly depending on system OS and hardware)
+ toolchain: EasyBuild toolchains
+ tools: General purpose tools
+ vis: Visualization, plotting, documentation and typesetting
```
The modules set up the application paths, library paths and environment
diff --git a/docs.it4i.cz/salomon/hardware-overview-1.1.html b/docs.it4i.cz/salomon/hardware-overview-1.1.html
new file mode 100644
index 000000000..c6d2da764
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+ <div id="parent-fieldname-text-e3d9b88c840a474ea3bbc24a1dc19bed" class="">
+ <h2 class=" ">Introduction</h2>
+<p>The Salomon cluster consists of 1008 computational nodes of which 576 are regular compute nodes and 432 accelerated nodes. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24 cores (two twelve-core Intel Xeon processors) and 128GB RAM. The nodes are interlinked by high speed InfiniBand and Ethernet networks. All nodes share 0.5PB /home NFS disk storage to store the user files. Users may use a DDN Lustre shared storage with capacity of 1.69 PB which is available for the scratch project data. The user access to the Salomon cluster is provided by four login nodes.</p>
+<p><a href="network-1/ib-single-plane-topology.html" title="" target="_self" class="internal-link">More about schematic representation of the Salomon cluster compute nodes IB topology</a>.<span class="internal-link"></span></p>
+<p style="padding-left: 30px; "><a href="salomon-2" title="" target="_self" class="internal-link"><img alt="Salomon" src="https://docs.it4i.cz/salomon/salomon-2/@@images/25c7db03-5c44-4981-9e19-07c1c23fcf1e.jpeg" title="Salomon" class="image-inline" /></a></p>
+<p>The parameters are summarized in the following tables:</p>
+<h2 class=" ">General information</h2>
+<table class="listing">
+<tbody>
+<tr><th colspan="2"><strong>In general</strong></th></tr>
+<tr class="even">
+<td>Primary purpose</td>
+<td>High Performance Computing</td>
+</tr>
+<tr class="odd">
+<td>Architecture of compute nodes</td>
+<td>x86-64</td>
+</tr>
+<tr class="even">
+<td>Operating system</td>
+<td>CentOS 6.7 Linux</td>
+</tr>
+<tr><th colspan="2"><a href="compute-nodes.html" title="" target="_self" class="internal-link"><strong>Compute nodes</strong></a></th></tr>
+<tr class="even">
+<td>Totally</td>
+<td>1008</td>
+</tr>
+<tr class="odd">
+<td>Processor</td>
+<td>2x Intel Xeon E5-2680v3, 2.5GHz, 12cores</td>
+</tr>
+<tr class="even">
+<td>RAM</td>
+<td>128GB, 5.3GB per core, DDR4@2133 MHz</td>
+</tr>
+<tr class="odd">
+<td>Local disk drive</td>
+<td>no</td>
+</tr>
+<tr class="even">
+<td>Compute network / Topology</td>
+<td>InfiniBand FDR56 / 7D Enhanced hypercube</td>
+</tr>
+<tr class="odd">
+<td>w/o accelerator</td>
+<td>576</td>
+</tr>
+<tr class="even">
+<td>MIC accelerated</td>
+<td>432</td>
+</tr>
+<tr><th colspan="2"><strong>In total</strong></th></tr>
+<tr class="even">
+<td>Total theoretical peak performance (Rpeak)</td>
+<td>2011 Tflop/s</td>
+</tr>
+<tr class="even">
+<td>Total amount of RAM</td>
+<td><span>129.024 TB</span></td>
+</tr>
+</tbody>
+</table>
+<h2 class=" ">Compute nodes</h2>
+<table class="listing">
+<tbody>
+<tr><th>Node</th><th>Count</th><th>Processor</th><th>Cores</th><th>Memory</th><th>Accelerator</th></tr>
+<tr class="even">
+<td>w/o accelerator</td>
+<td>576</td>
+<td>2x Intel Xeon E5-2680v3, 2.5GHz</td>
+<td>24</td>
+<td>128GB</td>
+<td>-</td>
+</tr>
+<tr class="odd">
+<td>MIC accelerated</td>
+<td>432</td>
+<td>2x Intel Xeon E5-2680v3, 2.5GHz </td>
+<td>24</td>
+<td>128GB</td>
+<td>2x Intel Xeon Phi 7120P, 61cores, 16GB RAM</td>
+</tr>
+</tbody>
+</table>
+<p class="internal-link" title="">For more details please refer to the <a href="compute-nodes.html" title="" target="_self" class="internal-link">Compute nodes</a>.</p>
+<h2 class=" ">Remote visualization nodes</h2>
+<p class="internal-link" title="">For remote visualization two nodes with NICE DCV software are available each configured:</p>
+<table class="listing">
+<tbody>
+<tr><th>Node</th><th>Count</th><th>Processor</th><th>Cores</th><th>Memory</th><th>GPU Accelerator</th></tr>
+<tr class="even">
+<td>visualization</td>
+<td>2</td>
+<td>2x Intel Xeon E5-2695v3, 2.3GHz</td>
+<td>28</td>
+<td>512GB</td>
+<td>NVIDIA QUADRO K5000, 4GB RAM</td>
+</tr>
+</tbody>
+</table>
+<h2 class=" ">SGI UV 2000</h2>
+<p class="internal-link" title="">For large memory computations a special SMP/NUMA SGI UV 2000 server is available:</p>
+<table class="listing">
+<tbody>
+<tr><th>Node</th><th>Count</th><th>Processor</th><th>Cores</th><th>Memory</th><th>Extra HW</th></tr>
+<tr class="even">
+<td>UV2000</td>
+<td>1</td>
+<td>14x Intel Xeon E5-4627v2, 3.3GHz, 8cores</td>
+<td>112</td>
+<td>3328GB DDR3@1866MHz</td>
+<td>
+<p>2x 400GB local SSD<br />1x NVIDIA GM200 <br />(GeForce GTX TITAN X), <br />12GB RAM</p>
+</td>
+</tr>
+</tbody>
+</table>
+<p style="padding-left: 30px; "><img alt="UV 2000" src="uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpeg" title="UV 2000" class="image-inline" /></p>
+
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+
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+ <div id="parent-fieldname-text-e3d9b88c840a474ea3bbc24a1dc19bed" class="">
+ <h2 class=" ">Introduction</h2>
+<p>The Salomon cluster consists of 1008 computational nodes of which 576 are regular compute nodes and 432 accelerated nodes. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24 cores (two twelve-core Intel Xeon processors) and 128GB RAM. The nodes are interlinked by high speed InfiniBand and Ethernet networks. All nodes share 0.5PB /home NFS disk storage to store the user files. Users may use a DDN Lustre shared storage with capacity of 1.69 PB which is available for the scratch project data. The user access to the Salomon cluster is provided by four login nodes.</p>
+<p><a href="../network-1/ib-single-plane-topology.html" title="" target="_self" class="internal-link">More about schematic representation of the Salomon cluster compute nodes IB topology</a>.<span class="internal-link"></span></p>
+<p style="padding-left: 30px; "><a href="../salomon-2" title="" target="_self" class="internal-link"><img alt="Salomon" src="https://docs.it4i.cz/salomon/salomon-2/@@images/25c7db03-5c44-4981-9e19-07c1c23fcf1e.jpeg" title="Salomon" class="image-inline" /></a></p>
+<p>The parameters are summarized in the following tables:</p>
+<h2 class=" ">General information</h2>
+<table class="listing">
+<tbody>
+<tr><th colspan="2"><strong>In general</strong></th></tr>
+<tr class="even">
+<td>Primary purpose</td>
+<td>High Performance Computing</td>
+</tr>
+<tr class="odd">
+<td>Architecture of compute nodes</td>
+<td>x86-64</td>
+</tr>
+<tr class="even">
+<td>Operating system</td>
+<td>CentOS 6.7 Linux</td>
+</tr>
+<tr><th colspan="2"><a href="../compute-nodes.html" title="" target="_self" class="internal-link"><strong>Compute nodes</strong></a></th></tr>
+<tr class="even">
+<td>Totally</td>
+<td>1008</td>
+</tr>
+<tr class="odd">
+<td>Processor</td>
+<td>2x Intel Xeon E5-2680v3, 2.5GHz, 12cores</td>
+</tr>
+<tr class="even">
+<td>RAM</td>
+<td>128GB, 5.3GB per core, DDR4@2133 MHz</td>
+</tr>
+<tr class="odd">
+<td>Local disk drive</td>
+<td>no</td>
+</tr>
+<tr class="even">
+<td>Compute network / Topology</td>
+<td>InfiniBand FDR56 / 7D Enhanced hypercube</td>
+</tr>
+<tr class="odd">
+<td>w/o accelerator</td>
+<td>576</td>
+</tr>
+<tr class="even">
+<td>MIC accelerated</td>
+<td>432</td>
+</tr>
+<tr><th colspan="2"><strong>In total</strong></th></tr>
+<tr class="even">
+<td>Total theoretical peak performance (Rpeak)</td>
+<td>2011 Tflop/s</td>
+</tr>
+<tr class="even">
+<td>Total amount of RAM</td>
+<td><span>129.024 TB</span></td>
+</tr>
+</tbody>
+</table>
+<h2 class=" ">Compute nodes</h2>
+<table class="listing">
+<tbody>
+<tr><th>Node</th><th>Count</th><th>Processor</th><th>Cores</th><th>Memory</th><th>Accelerator</th></tr>
+<tr class="even">
+<td>w/o accelerator</td>
+<td>576</td>
+<td>2x Intel Xeon E5-2680v3, 2.5GHz</td>
+<td>24</td>
+<td>128GB</td>
+<td>-</td>
+</tr>
+<tr class="odd">
+<td>MIC accelerated</td>
+<td>432</td>
+<td>2x Intel Xeon E5-2680v3, 2.5GHz </td>
+<td>24</td>
+<td>128GB</td>
+<td>2x Intel Xeon Phi 7120P, 61cores, 16GB RAM</td>
+</tr>
+</tbody>
+</table>
+<p class="internal-link" title="">For more details please refer to the <a href="../compute-nodes.html" title="" target="_self" class="internal-link">Compute nodes</a>.</p>
+<h2 class=" ">Remote visualization nodes</h2>
+<p class="internal-link" title="">For remote visualization two nodes with NICE DCV software are available each configured:</p>
+<table class="listing">
+<tbody>
+<tr><th>Node</th><th>Count</th><th>Processor</th><th>Cores</th><th>Memory</th><th>GPU Accelerator</th></tr>
+<tr class="even">
+<td>visualization</td>
+<td>2</td>
+<td>2x Intel Xeon E5-2695v3, 2.3GHz</td>
+<td>28</td>
+<td>512GB</td>
+<td>NVIDIA QUADRO K5000, 4GB RAM</td>
+</tr>
+</tbody>
+</table>
+<h2 class=" ">SGI UV 2000</h2>
+<p class="internal-link" title="">For large memory computations a special SMP/NUMA SGI UV 2000 server is available:</p>
+<table class="listing">
+<tbody>
+<tr><th>Node</th><th>Count</th><th>Processor</th><th>Cores</th><th>Memory</th><th>Extra HW</th></tr>
+<tr class="even">
+<td>UV2000</td>
+<td>1</td>
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+<td>112</td>
+<td>3328GB DDR3@1866MHz</td>
+<td>
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+ <p>Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24 cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced hypercube Infiniband network and equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in <a href="hardware-overview-1/hardware-overview.html" title="" target="_self" class="internal-link">Hardware Overview</a>.</p>
+<p>The cluster runs CentOS Linux <a class="external-link" href="http://www.bull.com/bullx-logiciels/systeme-exploitation.html" target="_self" title=""><span class="WYSIWYG_LINK"></span></a><span class="internal-link">operating system</span>, which is compatible with the <span class="WYSIWYG_LINK">RedHat</span> <a class="external-link" href="http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg" target="_self" title=""><span class="WYSIWYG_LINK">Linux family.</span></a></p>
+<p style="padding-left: 30px; "><strong>Water-cooled Compute Nodes With MIC Accelerator</strong></p>
+<p style="padding-left: 30px; "><a href="salomon" title="" target="_self" class="internal-link"><img alt="Salomon" src="https://docs.it4i.cz/salomon/salomon/@@images/8fe6c2ad-25f3-48cf-abbb-6f8ba653b93e.jpeg" title="Salomon" class="image-inline" /></a></p>
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+<p style="padding-left: 30px; "><strong>Tape Library T950B</strong></p>
+<p style="padding-left: 30px; "><img alt="Salomon" src="salomon-3/@@images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpeg" title="Salomon" class="image-inline" /></p>
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+ <p>Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totaling 24192 compute cores with 129TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a <span class="WYSIWYG_LINK">powerful</span> x86-64 computer, equipped with 24 cores, at least 128GB RAM. Nodes are interconnected by 7D Enhanced hypercube Infiniband network and equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in <a href="hardware-overview-1/hardware-overview.html" title="" target="_self" class="internal-link">Hardware Overview</a>.</p>
+<p>The cluster runs CentOS Linux <a class="external-link" href="http://www.bull.com/bullx-logiciels/systeme-exploitation.html" target="_self" title=""><span class="WYSIWYG_LINK"></span></a><span class="internal-link">operating system</span>, which is compatible with the <span class="WYSIWYG_LINK">RedHat</span> <a class="external-link" href="http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg" target="_self" title=""><span class="WYSIWYG_LINK">Linux family.</span></a></p>
+<p style="padding-left: 30px; "><strong>Water-cooled Compute Nodes With MIC Accelerator</strong></p>
+<p style="padding-left: 30px; "><a href="salomon" title="" target="_self" class="internal-link"><img alt="Salomon" src="https://docs.it4i.cz/salomon/salomon/@@images/8fe6c2ad-25f3-48cf-abbb-6f8ba653b93e.jpeg" title="Salomon" class="image-inline" /></a></p>
+<p style="padding-left: 30px; "><img alt="Salomon" src="salomon-1/@@images/ba2c321e-1554-4826-b6ec-3c68d370cd9f.jpeg" title="Salomon" class="image-inline" /></p>
+<p style="padding-left: 30px; "><strong>Tape Library T950B</strong></p>
+<p style="padding-left: 30px; "><img alt="Salomon" src="salomon-3/@@images/d2a6de55-62fc-454f-adda-a6a25e3f44dd.jpeg" title="Salomon" class="image-inline" /></p>
+<p style="padding-left: 30px; "><img alt="Salomon" src="salomon-4/@@images/82997462-cd88-49eb-aad5-71d77903d903.jpeg" title="Salomon" class="image-inline" /></p>
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+ <a href="list_of_modules.html#base">base</a><br />
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+ <a href="list_of_modules.html#bio">bio</a><br />
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+ <a href="list_of_modules.html#tools">tools</a><br />
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+ <a href="list_of_modules.html#vis">vis</a><br />
+ </li>
+ </ul>
+
+ <div>
+ <h2 id="base"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">base</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>EasyBuild</b><br />
+ <a href="http://hpcugent.github.com/easybuild/">http://hpcugent.github.com/easybuild/</a>
+ </td>
+ <td>EasyBuild is a software build and installation framework
+written in Python that allows you to install software in a structured,
+repeatable and robust way.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.1.1</li>
+ <li style="white-space: nowrap;">2.2.0</li>
+ <li style="white-space: nowrap;">2.3.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Python</b><br />
+ <a href="http://python.org/">http://python.org/</a>
+ </td>
+ <td>Python is a programming language that lets you work more quickly and integrate your systems more effectively.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.4.3-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="bio"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">bio</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>Amber</b><br />
+ <a href="http://ambermd.org">http://ambermd.org</a>
+ </td>
+ <td>A set of molecular mechanical force fields for the simulation of biomolecules</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">14</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>BCFtools</b><br />
+ <a href="http://www.htslib.org/">http://www.htslib.org/</a>
+ </td>
+ <td>Samtools is a suite of programs for interacting with high-throughput sequencing data.
+ BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.3-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>BWA</b><br />
+ <a href="http://bio-bwa.sourceforge.net/">http://bio-bwa.sourceforge.net/</a>
+ </td>
+ <td>Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
+ relatively short nucleotide sequences against a long reference sequence such as the human genome.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.7.5a-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>FastQC</b><br />
+ <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/">http://www.bioinformatics.babraham.ac.uk/projects/fastqc/</a>
+ </td>
+ <td>FastQC is a quality control application for high throughput sequence data.
+ It reads in sequence data in a variety of formats and can either provide an interactive
+ application to review the results of several different QC checks, or create an HTML based
+ report which can be integrated into a pipeline.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.11.3</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>GATK</b><br />
+ <a href="http://www.broadinstitute.org/gatk/">http://www.broadinstitute.org/gatk/</a>
+ </td>
+ <td>The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute
+ to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,
+ with a primary focus on variant discovery and genotyping as well as strong emphasis on
+ data quality assurance. Its robust architecture, powerful processing engine and
+ high-performance computing features make it capable of taking on projects of any size.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.6-5-Java-1.7.0_79</li>
+ <li style="white-space: nowrap;">3.5-Java-1.7.0_79</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>GROMACS</b><br />
+ <a href="http://www.gromacs.org">http://www.gromacs.org</a>
+ </td>
+ <td>GROMACS is a versatile package to perform molecular dynamics,
+ i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.6.7-foss-2015g-hybrid-single-PLUMED</li>
+ <li style="white-space: nowrap;">5.0.4-foss-2015e-hybrid-single-PLUMED</li>
+ <li style="white-space: nowrap;">5.0.4-foss-2015g-hybrid-single</li>
+ <li style="white-space: nowrap;">5.0.4-foss-2015g-hybrid-single-PLUMED</li>
+ <li style="white-space: nowrap;">5.0.4-ictce-7.3.5-hybrid-single</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>HTSlib</b><br />
+ <a href="http://www.htslib.org/">http://www.htslib.org/</a>
+ </td>
+ <td> A C library for reading/writing high-throughput sequencing data.
+ This package includes the utilities bgzip and tabix </td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.3-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>PLUMED</b><br />
+ <a href="http://www.plumed-code.org">http://www.plumed-code.org</a>
+ </td>
+ <td>PLUMED is an open source library for free energy calculations
+ in molecular systems which works together with some of the most popular molecular
+ dynamics engines. Free energy calculations can be performed as a function of many
+ order parameters with a particular focus on biological problems, using state of
+ the art methods such as metadynamics, umbrella sampling and Jarzynski-equation
+ based steered MD. The software, written in C++, can be easily interfaced with
+ both fortran and C/C++ codes.
+ </td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.1.3-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>RELION</b><br />
+ <a href="http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page">http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page</a>
+ </td>
+ <td>RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer
+ program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class
+ averages in electron cryo-microscopy (cryo-EM).</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.3-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>SAMtools</b><br />
+ <a href="http://www.htslib.org/">http://www.htslib.org/</a>
+ </td>
+ <td>SAM Tools provide various utilities for manipulating alignments in the SAM format,
+ including sorting, merging, indexing and generating alignments in a per-position format.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.3-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>SnpEff</b><br />
+ <a href="http://snpeff.sourceforge.net/">http://snpeff.sourceforge.net/</a>
+ </td>
+ <td>Genetic variant annotation and effect prediction toolbox.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.1_G</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Trimmomatic</b><br />
+ <a href="http://www.usadellab.org/cms/?page=trimmomatic">http://www.usadellab.org/cms/?page=trimmomatic</a>
+ </td>
+ <td>Trimmomatic performs a variety of useful trimming tasks for illumina
+ paired-end and single ended data.The selection of trimming steps and their associated
+ parameters are supplied on the command line. </td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.35-Java-1.7.0_79</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>almost</b><br />
+ <a href="http://www-almost.ch.cam.ac.uk/site">http://www-almost.ch.cam.ac.uk/site</a>
+ </td>
+ <td>all atom molecular simulation toolkit
+ - is a fast and flexible molecular modeling environment
+ that provides powerful and efficient algorithms for molecular
+ simulation, homology modeling, de novo design and ab-initio
+ calculations.
+ </td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.1.0-foss-2015b</li>
+ <li style="white-space: nowrap;">2.1.0-foss-2015g</li>
+ <li style="white-space: nowrap;">2.1.0-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>picard</b><br />
+ <a href="http://sourceforge.net/projects/picard">http://sourceforge.net/projects/picard</a>
+ </td>
+ <td>A set of tools (in Java) for working with next generation sequencing data in the BAM format.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.119</li>
+ <li style="white-space: nowrap;">2.1.0</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="cae"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">cae</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>ANSYS</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">16.1</li>
+ <li style="white-space: nowrap;">17.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Adams</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2013.2</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>COMSOL</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">51-COM</li>
+ <li style="white-space: nowrap;">51-EDU</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Digimat</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.0.1-COM</li>
+ <li style="white-space: nowrap;">5.0.1-EDU</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>FreeFem++</b><br />
+ <a href="http://www.freefem.org">http://www.freefem.org</a>
+ </td>
+ <td>FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D.
+Problems involving PDE (2d, 3d) from several branches of physics such as fluid-structure interactions require interpolations of data on several meshes and their manipulation within one program. FreeFem++ includes a fast 2^d-tree-based interpolation algorithm and a language for the manipulation of data on multiple meshes (as a follow up of bamg (now a part of FreeFem++ ).
+
+FreeFem++ is written in C++ and the FreeFem++ language is a C++ idiom. It runs on Macs, Windows, Unix machines. FreeFem++ replaces the older freefem and freefem+.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.45-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>HyperWorks</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">13.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Marc</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2013.1.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>OpenFOAM</b><br />
+ <a href="http://www.openfoam.com/">http://www.openfoam.com/</a>
+ </td>
+ <td>OpenFOAM is a free, open source CFD software package.
+ OpenFOAM has an extensive range of features to solve anything from complex fluid flows
+ involving chemical reactions, turbulence and heat transfer,
+ to solid dynamics and electromagnetics.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.2.2-intel-2015b</li>
+ <li style="white-space: nowrap;">2.3.0-intel-2015b</li>
+ <li style="white-space: nowrap;">3.0.0-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="chem"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">chem</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>ABINIT</b><br />
+ <a href="http://www.abinit.org/">http://www.abinit.org/</a>
+ </td>
+ <td>Abinit is a plane wave pseudopotential code for doing
+ condensed phase electronic structure calculations using DFT.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">7.10.1-foss-2015b</li>
+ <li style="white-space: nowrap;">7.10.1-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>CP2K</b><br />
+ <a href="http://www.cp2k.org/">http://www.cp2k.org/</a>
+ </td>
+ <td>CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular
+ simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different
+ methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and
+ classical pair and many-body potentials. </td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.6.0-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>LAMMPS</b><br />
+ <a href="http://lammps.sandia.gov">http://lammps.sandia.gov</a>
+ </td>
+ <td>LAMMPS is a classical molecular dynamics code,
+and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
+Has potentials for solid-state materials (metals, semiconductors) and soft
+matter (biomolecules, polymers) and coarse-grained or mesoscopic systems.
+It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic,
+meso, or continuum scale.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">28Jun14-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Libint</b><br />
+ <a href="https://sourceforge.net/p/libint/">https://sourceforge.net/p/libint/</a>
+ </td>
+ <td>Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body
+matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.1.4-foss-2015b</li>
+ <li style="white-space: nowrap;">1.1.4-gompi-2015b</li>
+ <li style="white-space: nowrap;">1.1.4-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Molpro</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2010.1-patch-57-intel2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>NAMD</b><br />
+ <a href="http://www.ks.uiuc.edu/Research/namd/">http://www.ks.uiuc.edu/Research/namd/</a>
+ </td>
+ <td>NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.9-mpi</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>NWChem</b><br />
+ <a href="http://www.nwchem-sw.org">http://www.nwchem-sw.org</a>
+ </td>
+ <td>NWChem aims to provide its users with computational chemistry tools that are scalable both in
+ their ability to treat large scientific computational chemistry problems efficiently, and in their use of available
+ parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
+ NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all
+ combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties
+ and relativity.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">6.3.revision2-2013-10-17-Python-2.7.8</li>
+ <li style="white-space: nowrap;">6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>S4MPLE</b><br />
+ <a href="http://infochim.u-strasbg.fr/spip.php?rubrique152">http://infochim.u-strasbg.fr/spip.php?rubrique152</a>
+ </td>
+ <td>S4MPLE (Sampler For Multiple Protein-Ligand Entities) is a flexible molecular modeling tool, supporting empirical
+force field-driven conformational sampling and geometry optimization heuristics using a hybrid genetic algorithm (GA).
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.0.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libctl</b><br />
+ <a href="http://ab-initio.mit.edu/libctl">http://ab-initio.mit.edu/libctl</a>
+ </td>
+ <td>libctl is a free Guile-based library implementing flexible control files for scientific simulations.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.2.2-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libxc</b><br />
+ <a href="http://www.tddft.org/programs/octopus/wiki/index.php/Libxc">http://www.tddft.org/programs/octopus/wiki/index.php/Libxc</a>
+ </td>
+ <td>Libxc is a library of exchange-correlation functionals for density-functional theory.
+ The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.2.0-foss-2015b</li>
+ <li style="white-space: nowrap;">2.2.0-gompi-2015b</li>
+ <li style="white-space: nowrap;">2.2.1-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="compiler"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">compiler</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>BerkeleyUPC</b><br />
+ <a href="http://upc.lbl.gov">http://upc.lbl.gov</a>
+ </td>
+ <td>The goal of the Berkeley UPC compiler group is to develop a portable,
+high performance implementation of UPC for large-scale multiprocessors, PC clusters,
+and clusters of shared memory multiprocessors.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.16.2-gompi-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Clang</b><br />
+ <a href="http://clang.llvm.org/">http://clang.llvm.org/</a>
+ </td>
+ <td>C, C++, Objective-C compiler, based on LLVM. Does not
+ include C++ standard library -- use libstdc++ from GCC.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.7.0-GNU-5.1.0-2.25</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>GCC</b><br />
+ <a href="http://gcc.gnu.org/">http://gcc.gnu.org/</a>
+ </td>
+ <td>The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...).</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.4.7-system</li>
+ <li style="white-space: nowrap;">4.7.4</li>
+ <li style="white-space: nowrap;">4.8.3</li>
+ <li style="white-space: nowrap;">4.9.2-binutils-2.25</li>
+ <li style="white-space: nowrap;">4.9.3</li>
+ <li style="white-space: nowrap;">4.9.3-2.25</li>
+ <li style="white-space: nowrap;">4.9.3-binutils-2.25</li>
+ <li style="white-space: nowrap;">5.1.0-binutils-2.25</li>
+ <li style="white-space: nowrap;">5.2.0</li>
+ <li style="white-space: nowrap;">5.3.0-2.25</li>
+ <li style="white-space: nowrap;">5.3.0-2.26</li>
+ <li style="white-space: nowrap;">5.3.0-binutils-2.25</li>
+ <li style="white-space: nowrap;">5.3.1-snapshot-20160419-2.25</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>GCCcore</b><br />
+ <a href="http://gcc.gnu.org/">http://gcc.gnu.org/</a>
+ </td>
+ <td>The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
+ as well as libraries for these languages (libstdc++, libgcj,...).</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.9.3</li>
+ <li style="white-space: nowrap;">5.3.0</li>
+ <li style="white-space: nowrap;">5.3.1-snapshot-20160419</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>LLVM</b><br />
+ <a href="http://llvm.org/">http://llvm.org/</a>
+ </td>
+ <td>The LLVM Core libraries provide a modern source- and target-independent
+ optimizer, along with code generation support for many popular CPUs
+ (as well as some less common ones!) These libraries are built around a well
+ specified code representation known as the LLVM intermediate representation
+ ("LLVM IR"). The LLVM Core libraries are well documented, and it is
+ particularly easy to invent your own language (or port an existing compiler)
+ to use LLVM as an optimizer and code generator.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.7.1-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>OpenCoarrays</b><br />
+ <a href="http://www.opencoarrays.org/">http://www.opencoarrays.org/</a>
+ </td>
+ <td>A transport layer for coarray Fortran compilers.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.4.0-GCC-5.3.0-2.25</li>
+ <li style="white-space: nowrap;">1.4.0-GCC-5.3.1-snapshot-20160419-2.25</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>PGI</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">15.7</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>icc</b><br />
+ <a href="http://software.intel.com/en-us/intel-compilers/">http://software.intel.com/en-us/intel-compilers/</a>
+ </td>
+ <td>C and C++ compiler from Intel</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2013.5.192</li>
+ <li style="white-space: nowrap;">2013.5.192-GCC-4.8.3</li>
+ <li style="white-space: nowrap;">2015.3.187</li>
+ <li style="white-space: nowrap;">2015.3.187-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2015.3.187-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">2016.0.109-GCC-4.9.3</li>
+ <li style="white-space: nowrap;">2016.1.150</li>
+ <li style="white-space: nowrap;">2016.1.150-GCC-4.9.3</li>
+ <li style="white-space: nowrap;">2016.1.150-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2016.3.210-GCC-5.3.0-2.26</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>ifort</b><br />
+ <a href="http://software.intel.com/en-us/intel-compilers/">http://software.intel.com/en-us/intel-compilers/</a>
+ </td>
+ <td>Fortran compiler from Intel</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2013.5.192</li>
+ <li style="white-space: nowrap;">2013.5.192-GCC-4.8.3</li>
+ <li style="white-space: nowrap;">2015.3.187</li>
+ <li style="white-space: nowrap;">2015.3.187-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2015.3.187-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">2016.0.109-GCC-4.9.3</li>
+ <li style="white-space: nowrap;">2016.1.150</li>
+ <li style="white-space: nowrap;">2016.1.150-GCC-4.9.3</li>
+ <li style="white-space: nowrap;">2016.1.150-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2016.3.210-GCC-5.3.0-2.26</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="data"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">data</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>GDAL</b><br />
+ <a href="http://www.gdal.org/">http://www.gdal.org/</a>
+ </td>
+ <td>GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
+ Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
+ to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for
+ data translation and processing.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.9.2-foss-2015g</li>
+ <li style="white-space: nowrap;">2.0.1-foss-2015b</li>
+ <li style="white-space: nowrap;">2.1.0-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">2.1.0-GNU-5.1.0-2.25-intel-2015b</li>
+ <li style="white-space: nowrap;">2.1.0-foss-2015g</li>
+ <li style="white-space: nowrap;">2.1.0-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>HDF5</b><br />
+ <a href="http://www.hdfgroup.org/HDF5/">http://www.hdfgroup.org/HDF5/</a>
+ </td>
+ <td>HDF5 is a unique technology suite that makes possible the management of
+ extremely large and complex data collections.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.10.0-patch1-intel-2016.01-mic</li>
+ <li style="white-space: nowrap;">1.8.13-foss-2015g</li>
+ <li style="white-space: nowrap;">1.8.13-intel-2015b</li>
+ <li style="white-space: nowrap;">1.8.13-intel-2015b-no-mpi</li>
+ <li style="white-space: nowrap;">1.8.13-intel-2016.01</li>
+ <li style="white-space: nowrap;">1.8.14-ictce-7.3.5-serial</li>
+ <li style="white-space: nowrap;">1.8.15-patch1-foss-2015b</li>
+ <li style="white-space: nowrap;">1.8.16-foss-2015g</li>
+ <li style="white-space: nowrap;">1.8.16-intel-2015b</li>
+ <li style="white-space: nowrap;">1.8.16-intel-2015b-threadsafe</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>h5py</b><br />
+ <a href="http://www.h5py.org/">http://www.h5py.org/</a>
+ </td>
+ <td>HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library,
+ version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous
+ amounts of data.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.4.0-ictce-7.3.5-Python-2.7.9-serial</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>netCDF</b><br />
+ <a href="http://www.unidata.ucar.edu/software/netcdf/">http://www.unidata.ucar.edu/software/netcdf/</a>
+ </td>
+ <td>NetCDF (network Common Data Form) is a set of software libraries
+ and machine-independent data formats that support the creation, access, and sharing of array-oriented
+ scientific data.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.3.2-foss-2015g</li>
+ <li style="white-space: nowrap;">4.3.2-intel-2015b</li>
+ <li style="white-space: nowrap;">4.3.2-intel-2016.01</li>
+ <li style="white-space: nowrap;">4.3.3.1-foss-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>netCDF-Fortran</b><br />
+ <a href="http://www.unidata.ucar.edu/software/netcdf/">http://www.unidata.ucar.edu/software/netcdf/</a>
+ </td>
+ <td>NetCDF (network Common Data Form) is a set of software libraries
+ and machine-independent data formats that support the creation, access, and sharing of array-oriented
+ scientific data.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.4.0-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="debugger"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">debugger</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>DDT</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.2</li>
+ <li style="white-space: nowrap;">5.0.1</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Forge</b><br />
+ <a href="http://www.allinea.com/products/develop-allinea-forge">http://www.allinea.com/products/develop-allinea-forge</a>
+ </td>
+ <td>Allinea Forge is the complete toolsuite for software development
+- with everything needed to debug, profile, optimize, edit and build C, C++
+and FORTRAN applications on Linux for high performance - from single threads through
+to complex parallel HPC codes with MPI, OpenMP, threads or CUDA.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.1-43967</li>
+ <li style="white-space: nowrap;">6.0.5</li>
+ <li style="white-space: nowrap;">6.0.6</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>PerformanceReports</b><br />
+ <a href="http://www.allinea.com/products/allinea-performance-reports">http://www.allinea.com/products/allinea-performance-reports</a>
+ </td>
+ <td>Allinea Performance Reports are the most effective way
+to characterize and understand the performance of HPC application runs.
+One single-page HTML report elegantly answers a range of vital questions for any HPC site.
+ - Is this application well-optimized for the system and the processors it is running on?
+ - Does it benefit from running at this scale?
+ - Are there I/O, networking or threading bottlenecks affecting performance?
+ - Which hardware, software or configuration changes can we make to improve performance further.
+ - How much energy did this application use?
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.1-43967</li>
+ <li style="white-space: nowrap;">6.0.6</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>TotalView</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">8.15.4-6-linux-x86-64</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Valgrind</b><br />
+ <a href="http://valgrind.org/downloads/">http://valgrind.org/downloads/</a>
+ </td>
+ <td>Valgrind: Debugging and profiling tools</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.11.0-foss-2015b</li>
+ <li style="white-space: nowrap;">3.11.0-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>aislinn</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">20160105-Python-2.7.9-gompi-2015e</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="devel"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">devel</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>Autoconf</b><br />
+ <a href="http://www.gnu.org/software/autoconf/">http://www.gnu.org/software/autoconf/</a>
+ </td>
+ <td>Autoconf is an extensible package of M4 macros that produce shell scripts
+ to automatically configure software source code packages. These scripts can adapt the
+ packages to many kinds of UNIX-like systems without manual user intervention. Autoconf
+ creates a configuration script for a package from a template file that lists the
+ operating system features that the package can use, in the form of M4 macro calls.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.69</li>
+ <li style="white-space: nowrap;">2.69-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2.69-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2.69-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">2.69-foss-2015g</li>
+ <li style="white-space: nowrap;">2.69-intel-2015b</li>
+ <li style="white-space: nowrap;">2.69-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Automake</b><br />
+ <a href="http://www.gnu.org/software/automake/automake.html">http://www.gnu.org/software/automake/automake.html</a>
+ </td>
+ <td>Automake: GNU Standards-compliant Makefile generator</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.15</li>
+ <li style="white-space: nowrap;">1.15-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">1.15-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">1.15-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">1.15-foss-2015g</li>
+ <li style="white-space: nowrap;">1.15-intel-2015b</li>
+ <li style="white-space: nowrap;">1.15-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Autotools</b><br />
+ <a href="http://autotools.io">http://autotools.io</a>
+ </td>
+ <td>This bundle collect the standard GNU build tools: Autoconf, Automake and libtool</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">20150215</li>
+ <li style="white-space: nowrap;">20150215-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">20150215-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">20150215-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">20150215-intel-2015b</li>
+ <li style="white-space: nowrap;">20150215-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Boost</b><br />
+ <a href="http://www.boost.org/">http://www.boost.org/</a>
+ </td>
+ <td>Boost provides free peer-reviewed portable C++ source libraries.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.58.0-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.58.0-foss-2015g-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.58.0-gompi-2015e-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.58.0-ictce-7.3.5-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.58.0-intel-2015b-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.58.0-intel-2016.01-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.59.0-intel-2015b-Python-2.7.11</li>
+ <li style="white-space: nowrap;">1.59.0-intel-2016.01</li>
+ <li style="white-space: nowrap;">1.60.0-foss-2015g-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>CMake</b><br />
+ <a href="http://www.cmake.org">http://www.cmake.org</a>
+ </td>
+ <td>CMake, the cross-platform, open-source build system.
+ CMake is a family of tools designed to build, test and package software.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.0.0-foss-2015g</li>
+ <li style="white-space: nowrap;">3.0.0-ictce-7.3.5</li>
+ <li style="white-space: nowrap;">3.0.0-intel-2015b</li>
+ <li style="white-space: nowrap;">3.0.0-intel-2016.01</li>
+ <li style="white-space: nowrap;">3.3.1-GCC-5.3.0-2.25</li>
+ <li style="white-space: nowrap;">3.3.1-GCC-5.3.1-snapshot-20160419-2.25</li>
+ <li style="white-space: nowrap;">3.3.1-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">3.3.1-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">3.3.1-foss-2015g</li>
+ <li style="white-space: nowrap;">3.3.1-intel-2016.01</li>
+ <li style="white-space: nowrap;">3.3.2-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">3.3.2-intel-2016.01</li>
+ <li style="white-space: nowrap;">3.4.1-GCCcore-4.9.3</li>
+ <li style="white-space: nowrap;">3.4.1-foss-2015b</li>
+ <li style="white-space: nowrap;">3.4.1-intel-2015b</li>
+ <li style="white-space: nowrap;">3.5.2</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Doxygen</b><br />
+ <a href="http://www.doxygen.org">http://www.doxygen.org</a>
+ </td>
+ <td>Doxygen is a documentation system for C++, C, Java, Objective-C, Python,
+ IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.8.10-foss-2015b</li>
+ <li style="white-space: nowrap;">1.8.11</li>
+ <li style="white-space: nowrap;">1.8.7-foss-2015g</li>
+ <li style="white-space: nowrap;">1.8.7-intel-2015b</li>
+ <li style="white-space: nowrap;">1.8.7-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>JUnit</b><br />
+ <a href="http://sourceforge.net/projects/junit">http://sourceforge.net/projects/junit</a>
+ </td>
+ <td>A programmer-oriented testing framework for Java.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.11-Java-1.7.0_79</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>M4</b><br />
+ <a href="http://www.gnu.org/software/m4/m4.html">http://www.gnu.org/software/m4/m4.html</a>
+ </td>
+ <td>GNU M4 is an implementation of the traditional Unix macro processor.
+ It is mostly SVR4 compatible although it has some extensions
+ (for example, handling more than 9 positional parameters to macros).
+ GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.4.16-foss-2015g</li>
+ <li style="white-space: nowrap;">1.4.16-intel-2015b</li>
+ <li style="white-space: nowrap;">1.4.17</li>
+ <li style="white-space: nowrap;">1.4.17-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">1.4.17-GCC-4.9.3-binutils-2.25</li>
+ <li style="white-space: nowrap;">1.4.17-GCC-5.1.0-binutils-2.25</li>
+ <li style="white-space: nowrap;">1.4.17-GCCcore-4.9.3</li>
+ <li style="white-space: nowrap;">1.4.17-GCCcore-5.3.0</li>
+ <li style="white-space: nowrap;">1.4.17-GCCcore-5.3.1-snapshot-20160419</li>
+ <li style="white-space: nowrap;">1.4.17-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">1.4.17-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">1.4.17-foss-2015b</li>
+ <li style="white-space: nowrap;">1.4.17-foss-2015g</li>
+ <li style="white-space: nowrap;">1.4.17-intel-2015b</li>
+ <li style="white-space: nowrap;">1.4.17-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Maven</b><br />
+ <a href="http://maven.apache.org/index.html">http://maven.apache.org/index.html</a>
+ </td>
+ <td>Binary maven install, Apache Maven is a software project management and comprehension tool. Based on
+the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a
+central piece of information.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.3.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>PCRE</b><br />
+ <a href="http://www.pcre.org/">http://www.pcre.org/</a>
+ </td>
+ <td>
+ The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax
+ and semantics as Perl 5.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">8.36-foss-2015g</li>
+ <li style="white-space: nowrap;">8.36-intel-2015b</li>
+ <li style="white-space: nowrap;">8.36-intel-2016.01</li>
+ <li style="white-space: nowrap;">8.37</li>
+ <li style="white-space: nowrap;">8.37-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Qt</b><br />
+ <a href="http://qt-project.org/">http://qt-project.org/</a>
+ </td>
+ <td>Qt is a comprehensive cross-platform C++ application framework.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.8.6</li>
+ <li style="white-space: nowrap;">4.8.6-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>SCons</b><br />
+ <a href="http://www.scons.org/">http://www.scons.org/</a>
+ </td>
+ <td>SCons is a software construction tool.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.3.6-Python-2.7.9</li>
+ <li style="white-space: nowrap;">2.3.6-foss-2015g-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>SQLite</b><br />
+ <a href="http://www.sqlite.org/">http://www.sqlite.org/</a>
+ </td>
+ <td>SQLite: SQL Database Engine in a C Library</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.10.1-foss-2015g</li>
+ <li style="white-space: nowrap;">3.8.10.2-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">3.8.10.2-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">3.8.8.1</li>
+ <li style="white-space: nowrap;">3.8.8.1-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">3.8.8.1-foss-2015b</li>
+ <li style="white-space: nowrap;">3.8.8.1-foss-2015g</li>
+ <li style="white-space: nowrap;">3.8.8.1-gompi-2015e</li>
+ <li style="white-space: nowrap;">3.8.8.1-ictce-7.3.5</li>
+ <li style="white-space: nowrap;">3.8.8.1-intel-2015b</li>
+ <li style="white-space: nowrap;">3.8.8.1-intel-2016.01</li>
+ <li style="white-space: nowrap;">3.9.2-foss-2015g</li>
+ <li style="white-space: nowrap;">3.9.2-intel-2015b</li>
+ <li style="white-space: nowrap;">3.9.2-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>SWIG</b><br />
+ <a href="http://www.swig.org/">http://www.swig.org/</a>
+ </td>
+ <td>SWIG is a software development tool that connects programs written in C and C++ with
+ a variety of high-level programming languages.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.0.12-Python-2.7.9</li>
+ <li style="white-space: nowrap;">2.0.12-intel-2015b-Python-2.7.9</li>
+ <li style="white-space: nowrap;">3.0.7-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Spark</b><br />
+ <a href="http://spark.apache.org">http://spark.apache.org</a>
+ </td>
+ <td>Spark is Hadoop MapReduce done in memory</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.5.2</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>ant</b><br />
+ <a href="http://ant.apache.org/">http://ant.apache.org/</a>
+ </td>
+ <td>Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
+ as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.9.3-Java-1.7.0_79</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>fontsproto</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X11 font extension wire protocol</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.1.3-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>glproto</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X protocol and ancillary headers</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.4.16-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>gperf</b><br />
+ <a href="http://www.gnu.org/software/gperf/">http://www.gnu.org/software/gperf/</a>
+ </td>
+ <td>GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash
+ function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash
+ function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single
+ string comparison only.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.0.4-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>guile</b><br />
+ <a href="http://www.gnu.org/software/guile">http://www.gnu.org/software/guile</a>
+ </td>
+ <td>Guile is the GNU Ubiquitous Intelligent Language for Extensions,
+ the official extension language for the GNU operating system.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.8.8</li>
+ <li style="white-space: nowrap;">1.8.8-foss-2015b</li>
+ <li style="white-space: nowrap;">1.8.8-foss-2015g</li>
+ <li style="white-space: nowrap;">1.8.8-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libSM</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X11 Session Management library, which allows for applications to both manage sessions,
+ and make use of session managers to save and restore their state for later use.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.2.2</li>
+ <li style="white-space: nowrap;">1.2.2-foss-2015g</li>
+ <li style="white-space: nowrap;">1.2.2-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>make</b><br />
+ <a href="http://www.gnu.org/software/make/make.html">http://www.gnu.org/software/make/make.html</a>
+ </td>
+ <td>make-3.82: GNU version of make utility</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.82</li>
+ <li style="white-space: nowrap;">3.82-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>makedepend</b><br />
+ <a href="http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html">http://www.linuxfromscratch.org/blfs/view/svn/x/makedepend.html</a>
+ </td>
+ <td>The makedepend package contains a C-preprocessor like utility to determine build-time dependencies.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.0.4</li>
+ <li style="white-space: nowrap;">1.0.4-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>ncurses</b><br />
+ <a href="http://www.gnu.org/software/ncurses/">http://www.gnu.org/software/ncurses/</a>
+ </td>
+ <td>The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0,
+ and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and
+ function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.9</li>
+ <li style="white-space: nowrap;">5.9-GCC-5.3.0-2.25</li>
+ <li style="white-space: nowrap;">5.9-GCC-5.3.1-snapshot-20160419-2.25</li>
+ <li style="white-space: nowrap;">5.9-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">5.9-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">5.9-foss-2015b</li>
+ <li style="white-space: nowrap;">5.9-foss-2015g</li>
+ <li style="white-space: nowrap;">5.9-gompi-2015e</li>
+ <li style="white-space: nowrap;">5.9-ictce-5.5.0</li>
+ <li style="white-space: nowrap;">5.9-ictce-7.3.5</li>
+ <li style="white-space: nowrap;">5.9-intel-2015b</li>
+ <li style="white-space: nowrap;">5.9-intel-2016.01</li>
+ <li style="white-space: nowrap;">6.0</li>
+ <li style="white-space: nowrap;">6.0-GCCcore-4.9.3</li>
+ <li style="white-space: nowrap;">6.0-foss-2015b</li>
+ <li style="white-space: nowrap;">6.0-foss-2015g</li>
+ <li style="white-space: nowrap;">6.0-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>pkg-config</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/pkg-config/">http://www.freedesktop.org/wiki/Software/pkg-config/</a>
+ </td>
+ <td>pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the
+ correct compiler options on the command line so an application can use
+ gcc -o test test.c `pkg-config --libs --cflags glib-2.0`
+ for instance, rather than hard-coding values on where to find glib (or other libraries).</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.27.1</li>
+ <li style="white-space: nowrap;">0.27.1-foss-2015b</li>
+ <li style="white-space: nowrap;">0.27.1-foss-2015g</li>
+ <li style="white-space: nowrap;">0.27.1-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>python-meep</b><br />
+ <a href="https://code.launchpad.net/python-meep">https://code.launchpad.net/python-meep</a>
+ </td>
+ <td>Python wrapper for the Meep FDTD solver.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.4.2-intel-2015b-Python-2.7.9-Meep-1.3</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>renderproto</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>Xrender protocol and ancillary headers</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.11</li>
+ <li style="white-space: nowrap;">0.11-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>xbitmaps</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>provides bitmaps for x</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.1.1</li>
+ <li style="white-space: nowrap;">1.1.1-foss-2015g</li>
+ <li style="white-space: nowrap;">1.1.1-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>xcb-proto</b><br />
+ <a href="http://xcb.freedesktop.org/">http://xcb.freedesktop.org/</a>
+ </td>
+ <td>The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint,
+latency hiding, direct access to the protocol, improved threading support, and extensibility.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.10-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.11-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.11-foss-2015g-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.11-intel-2015b-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>xextproto</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>XExtProto protocol headers.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">7.3.0</li>
+ <li style="white-space: nowrap;">7.3.0-foss-2015g</li>
+ <li style="white-space: nowrap;">7.3.0-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>xineramaproto</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X protocol and ancillary headers for xinerama</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.2.1</li>
+ <li style="white-space: nowrap;">1.2.1-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>xorg-macros</b><br />
+ <a href="http://cgit.freedesktop.org/xorg/util/macros">http://cgit.freedesktop.org/xorg/util/macros</a>
+ </td>
+ <td>X.org macros utilities.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.17</li>
+ <li style="white-space: nowrap;">1.17-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>xproto</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X protocol and ancillary headers</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">7.0.26</li>
+ <li style="white-space: nowrap;">7.0.26-foss-2015g</li>
+ <li style="white-space: nowrap;">7.0.26-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>xtrans</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>xtrans includes a number of routines to make X implementations transport-independent;
+ at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.3.4-intel-2015b</li>
+ <li style="white-space: nowrap;">1.3.5</li>
+ <li style="white-space: nowrap;">1.3.5-foss-2015g</li>
+ <li style="white-space: nowrap;">1.3.5-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="geo"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">geo</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>DCW</b><br />
+ <a href="http://gmt.soest.hawaii.edu/projects/gmt">http://gmt.soest.hawaii.edu/projects/gmt</a>
+ </td>
+ <td>country polygons for GMT</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.1.2</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>GMT</b><br />
+ <a href="http://gmt.soest.hawaii.edu/">http://gmt.soest.hawaii.edu/</a>
+ </td>
+ <td>GMT is an open source collection of about 80 command-line tools for manipulating
+ geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting,
+ etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps
+ to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another
+ 40 more specialized and discipline-specific tools. </td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.2.1-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>PROJ_4</b><br />
+ <a href="http://proj.osgeo.org">http://proj.osgeo.org</a>
+ </td>
+ <td>PROJ.4 - Cartographic Projections Library originally written by Gerald Evenden then of the USGS.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.9.2-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="lang"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">lang</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>Bison</b><br />
+ <a href="http://www.gnu.org/software/bison">http://www.gnu.org/software/bison</a>
+ </td>
+ <td>Bison is a general-purpose parser generator that converts an annotated context-free grammar
+ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.5-intel-2015b</li>
+ <li style="white-space: nowrap;">2.7-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">2.7-foss-2015b</li>
+ <li style="white-space: nowrap;">2.7-foss-2015g</li>
+ <li style="white-space: nowrap;">2.7-intel-2015b</li>
+ <li style="white-space: nowrap;">3.0.2</li>
+ <li style="white-space: nowrap;">3.0.2-foss-2015g</li>
+ <li style="white-space: nowrap;">3.0.2-intel-2015b</li>
+ <li style="white-space: nowrap;">3.0.2-intel-2016.01</li>
+ <li style="white-space: nowrap;">3.0.4</li>
+ <li style="white-space: nowrap;">3.0.4-GCC-4.9.3-binutils-2.25</li>
+ <li style="white-space: nowrap;">3.0.4-GCC-5.1.0-binutils-2.25</li>
+ <li style="white-space: nowrap;">3.0.4-GCCcore-4.9.3</li>
+ <li style="white-space: nowrap;">3.0.4-GCCcore-5.3.0</li>
+ <li style="white-space: nowrap;">3.0.4-GCCcore-5.3.1-snapshot-20160419</li>
+ <li style="white-space: nowrap;">3.0.4-foss-2015b</li>
+ <li style="white-space: nowrap;">3.0.4-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Java</b><br />
+ <a href="http://java.com/">http://java.com/</a>
+ </td>
+ <td>Java Platform, Standard Edition (Java SE) lets you develop and deploy
+ Java applications on desktops and servers.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.7.0_79</li>
+ <li style="white-space: nowrap;">1.8.0_51</li>
+ <li style="white-space: nowrap;">1.8.0_72</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Mono</b><br />
+ <a href="http://www.mono-project.com">http://www.mono-project.com</a>
+ </td>
+ <td>Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards
+for C# and the Common Language Runtime.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.12.1</li>
+ <li style="white-space: nowrap;">3.12.1-GCC-4.4.7-system</li>
+ <li style="white-space: nowrap;">4.0.3.20-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">4.2.2.10-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>NASM</b><br />
+ <a href="http://www.nasm.us/">http://www.nasm.us/</a>
+ </td>
+ <td>NASM: General-purpose x86 assembler</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.11.05</li>
+ <li style="white-space: nowrap;">2.11.05-foss-2015b</li>
+ <li style="white-space: nowrap;">2.11.05-foss-2015g</li>
+ <li style="white-space: nowrap;">2.11.05-intel-2015b</li>
+ <li style="white-space: nowrap;">2.11.06-intel-2015b</li>
+ <li style="white-space: nowrap;">2.11.08-foss-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>OpenCL-builder</b><br />
+ <a href="https://software.intel.com/en-us/intel-opencl">https://software.intel.com/en-us/intel-opencl</a>
+ </td>
+ <td>OpenCL™ is the first open, royalty-free standard for cross-platform,
+parallel programming of modern processors found in personal computers, servers and handheld/embedded devices.
+OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications
+in numerous market categories from gaming and entertainment to scientific and medical software.
+
+This is builder (formerly runtime) package.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2015</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>OpenCL-runtime</b><br />
+ <a href="https://software.intel.com/en-us/intel-opencl">https://software.intel.com/en-us/intel-opencl</a>
+ </td>
+ <td>OpenCL™ is the first open, royalty-free standard for cross-platform,
+parallel programming of modern processors found in personal computers, servers and handheld/embedded devices.
+OpenCL (Open Computing Language) greatly improves speed and responsiveness for a wide spectrum of applications
+in numerous market categories from gaming and entertainment to scientific and medical software.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">15.1</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Perl</b><br />
+ <a href="http://www.perl.org/">http://www.perl.org/</a>
+ </td>
+ <td>Larry Wall's Practical Extraction and Report Language</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.16.3-intel-2015b</li>
+ <li style="white-space: nowrap;">5.20.2-GNU-4.9.3-2.25-bare</li>
+ <li style="white-space: nowrap;">5.20.2-bare</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Python</b><br />
+ <a href="http://python.org/">http://python.org/</a>
+ </td>
+ <td>Python is a programming language that lets you work more quickly and integrate your systems more effectively.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.7.10-GCC-4.9.3-2.25-bare</li>
+ <li style="white-space: nowrap;">2.7.10-GNU-4.9.3-2.25-bare</li>
+ <li style="white-space: nowrap;">2.7.11-intel-2015b</li>
+ <li style="white-space: nowrap;">2.7.8-intel-2015b</li>
+ <li style="white-space: nowrap;">2.7.8-intel-2016.01</li>
+ <li style="white-space: nowrap;">2.7.9</li>
+ <li style="white-space: nowrap;">2.7.9-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">2.7.9-foss-2015b</li>
+ <li style="white-space: nowrap;">2.7.9-foss-2015g</li>
+ <li style="white-space: nowrap;">2.7.9-gompi-2015e</li>
+ <li style="white-space: nowrap;">2.7.9-ictce-7.3.5</li>
+ <li style="white-space: nowrap;">2.7.9-intel-2015b</li>
+ <li style="white-space: nowrap;">2.7.9-intel-2016.01</li>
+ <li style="white-space: nowrap;">3.5.1-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>R</b><br />
+ <a href="http://www.r-project.org/">http://www.r-project.org/</a>
+ </td>
+ <td>R is a free software environment for statistical computing and graphics.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.1.1-intel-2015b</li>
+ <li style="white-space: nowrap;">3.2.3-foss-2015b</li>
+ <li style="white-space: nowrap;">3.2.3-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Racket</b><br />
+ <a href="http://racket-lang.org">http://racket-lang.org</a>
+ </td>
+ <td>Racket is a full-spectrum programming language. It goes
+beyond Lisp and Scheme with dialects that support objects, types,
+laziness, and more.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">6.1.1-GNU-5.1.0-2.25</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Ruby</b><br />
+ <a href="https://www.ruby-lang.org">https://www.ruby-lang.org</a>
+ </td>
+ <td>Ruby is a dynamic, open source programming language with
+ a focus on simplicity and productivity. It has an elegant syntax that is
+ natural to read and easy to write.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.1.5-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>SIP</b><br />
+ <a href="http://www.riverbankcomputing.com/software/sip/">http://www.riverbankcomputing.com/software/sip/</a>
+ </td>
+ <td>SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.16.4-foss-2015g-Python-2.7.9</li>
+ <li style="white-space: nowrap;">4.17-foss-2015g-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>SnuCL</b><br />
+ <a href="http://snucl.snu.ac.kr">http://snucl.snu.ac.kr</a>
+ </td>
+ <td>An OpenCL Framework for Heterogeneous Clusters</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.3.3-gompi-2015e</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Tcl</b><br />
+ <a href="http://www.tcl.tk/">http://www.tcl.tk/</a>
+ </td>
+ <td>Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language,
+suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">8.5.12-intel-2015b</li>
+ <li style="white-space: nowrap;">8.6.3</li>
+ <li style="white-space: nowrap;">8.6.3-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">8.6.3-foss-2015b</li>
+ <li style="white-space: nowrap;">8.6.3-foss-2015g</li>
+ <li style="white-space: nowrap;">8.6.3-gompi-2015e</li>
+ <li style="white-space: nowrap;">8.6.3-ictce-7.3.5</li>
+ <li style="white-space: nowrap;">8.6.3-intel-2015b</li>
+ <li style="white-space: nowrap;">8.6.3-intel-2016.01</li>
+ <li style="white-space: nowrap;">8.6.4</li>
+ <li style="white-space: nowrap;">8.6.4-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">8.6.4-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">8.6.4-foss-2015b</li>
+ <li style="white-space: nowrap;">8.6.4-foss-2015g</li>
+ <li style="white-space: nowrap;">8.6.4-intel-2015b</li>
+ <li style="white-space: nowrap;">8.6.4-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>byacc</b><br />
+ <a href="http://invisible-island.net/byacc/byacc.html">http://invisible-island.net/byacc/byacc.html</a>
+ </td>
+ <td>Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available.
+ In contrast to bison, it is written to avoid dependencies upon a particular compiler.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">20120526</li>
+ <li style="white-space: nowrap;">20120526-foss-2015b</li>
+ <li style="white-space: nowrap;">20120526-foss-2015g</li>
+ <li style="white-space: nowrap;">20120526-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>flex</b><br />
+ <a href="http://flex.sourceforge.net/">http://flex.sourceforge.net/</a>
+ </td>
+ <td>Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner,
+ sometimes called a tokenizer, is a program which recognizes lexical patterns in text.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.5.35-intel-2015b</li>
+ <li style="white-space: nowrap;">2.5.37-intel-2015b</li>
+ <li style="white-space: nowrap;">2.5.38-GCC-4.8.3</li>
+ <li style="white-space: nowrap;">2.5.39</li>
+ <li style="white-space: nowrap;">2.5.39-GCC-4.9.3-binutils-2.25</li>
+ <li style="white-space: nowrap;">2.5.39-GCC-5.1.0-binutils-2.25</li>
+ <li style="white-space: nowrap;">2.5.39-GCCcore-4.9.3</li>
+ <li style="white-space: nowrap;">2.5.39-GCCcore-5.3.0</li>
+ <li style="white-space: nowrap;">2.5.39-GCCcore-5.3.1-snapshot-20160419</li>
+ <li style="white-space: nowrap;">2.5.39-foss-2015b</li>
+ <li style="white-space: nowrap;">2.5.39-foss-2015g</li>
+ <li style="white-space: nowrap;">2.5.39-intel-2015b</li>
+ <li style="white-space: nowrap;">2.5.39-intel-2016.01</li>
+ <li style="white-space: nowrap;">2.6.0</li>
+ <li style="white-space: nowrap;">2.6.0-GCCcore-5.3.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libgdiplus</b><br />
+ <a href="https://github.com/mono/libgdiplus">https://github.com/mono/libgdiplus</a>
+ </td>
+ <td>An Open Source implementation of the GDI+ API.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.12</li>
+ <li style="white-space: nowrap;">3.12-GCC-4.4.7-system</li>
+ <li style="white-space: nowrap;">3.12-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">3.12-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="lib"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">lib</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>FOX</b><br />
+ <a href="http://fox-toolkit.org">http://fox-toolkit.org</a>
+ </td>
+ <td>FOX is a C++ based Toolkit for developing Graphical User Interfaces easily and effectively.
+It offers a wide, and growing, collection of Controls, and provides state of the art facilities such as
+drag and drop, selection, as well as OpenGL widgets for 3D graphical manipulation.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.6.51-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>LibTIFF</b><br />
+ <a href="http://www.remotesensing.org/libtiff/">http://www.remotesensing.org/libtiff/</a>
+ </td>
+ <td>tiff: Library and tools for reading and writing TIFF data files</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.0.3-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>OpenCoarrays</b><br />
+ <a href="http://www.opencoarrays.org">http://www.opencoarrays.org</a>
+ </td>
+ <td>OpenCoarrays is an open-source software project for developing,
+porting and tuning transport layers that support coarray Fortran
+compilers.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.0.0-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">1.0.1-GNU-5.1.0-2.25</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>PROJ</b><br />
+ <a href="http://trac.osgeo.org/proj/">http://trac.osgeo.org/proj/</a>
+ </td>
+ <td>Program proj is a standard Unix filter function which converts
+geographic longitude and latitude coordinates into cartesian coordinates</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.8.0-foss-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>QCA</b><br />
+ <a href="http://delta.affinix.com/qca/">http://delta.affinix.com/qca/</a>
+ </td>
+ <td>QCA aims to provide a straightforward and cross-platform crypto API,
+using Qt datatypes and conventions. QCA separates the API from the implementation,
+using plugins known as Providers</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.1.0-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>QGIS</b><br />
+ <a href="http://www.qgis.org">http://www.qgis.org</a>
+ </td>
+ <td>A Free and Open Source Geographic Information System</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.12.3-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Qwt</b><br />
+ <a href="http://qwt.sourceforge.net/index.html">http://qwt.sourceforge.net/index.html</a>
+ </td>
+ <td>The Qwt library contains GUI Components and utility classes which are primarily
+useful for programs with a technical background. Beside a framework for 2D plots it provides scales,
+sliders, dials, compasses, thermometers, wheels and knobs to control or display values, arrays,
+or ranges of type double.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">6.1.2-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>SpatiaLite</b><br />
+ <a href="https://www.gaia-gis.it/fossil/libspatialite/index">https://www.gaia-gis.it/fossil/libspatialite/index</a>
+ </td>
+ <td>SpatiaLite is an open source library intended to extend the SQLite core to support
+fully fledged Spatial SQL capabilities.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.3.0a-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libMesh</b><br />
+ <a href="http://libmesh.github.io/">http://libmesh.github.io/</a>
+ </td>
+ <td>The libMesh library provides a framework for the numerical simulation of partial differential equations
+ using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to
+ provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist
+ to focus on the physics they are modeling.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.9.5-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libdrm</b><br />
+ <a href="http://dri.freedesktop.org">http://dri.freedesktop.org</a>
+ </td>
+ <td>Direct Rendering Manager runtime library.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.4.27-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libffi</b><br />
+ <a href="http://sourceware.org/libffi/">http://sourceware.org/libffi/</a>
+ </td>
+ <td>The libffi library provides a portable, high level programming interface to various calling
+conventions. This allows a programmer to call any function specified by a call interface description at run-time.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.0.13</li>
+ <li style="white-space: nowrap;">3.0.13-foss-2015b</li>
+ <li style="white-space: nowrap;">3.0.13-foss-2015g</li>
+ <li style="white-space: nowrap;">3.0.13-intel-2015b</li>
+ <li style="white-space: nowrap;">3.1-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">3.1-foss-2015b</li>
+ <li style="white-space: nowrap;">3.1-intel-2015b</li>
+ <li style="white-space: nowrap;">3.1-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libfontenc</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs/">http://www.freedesktop.org/wiki/Software/xlibs/</a>
+ </td>
+ <td>X11 font encoding library</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.1.3-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libjpeg-turbo</b><br />
+ <a href="http://sourceforge.net/libjpeg-turbo/">http://sourceforge.net/libjpeg-turbo/</a>
+ </td>
+ <td>libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG
+compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.3.1-foss-2015b</li>
+ <li style="white-space: nowrap;">1.3.1-intel-2015b</li>
+ <li style="white-space: nowrap;">1.4.0</li>
+ <li style="white-space: nowrap;">1.4.0-foss-2015g</li>
+ <li style="white-space: nowrap;">1.4.0-intel-2015b</li>
+ <li style="white-space: nowrap;">1.4.1-foss-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libmatheval</b><br />
+ <a href="http://www.gnu.org/software/libmatheval/">http://www.gnu.org/software/libmatheval/</a>
+ </td>
+ <td>GNU libmatheval is a library (callable from C and Fortran) to parse
+ and evaluate symbolic expressions input as text.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.1.8-foss-2015b</li>
+ <li style="white-space: nowrap;">1.1.8-foss-2015g</li>
+ <li style="white-space: nowrap;">1.1.8-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libpng</b><br />
+ <a href="http://www.libpng.org/pub/png/libpng.html">http://www.libpng.org/pub/png/libpng.html</a>
+ </td>
+ <td>libpng is the official PNG reference library</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.6.12</li>
+ <li style="white-space: nowrap;">1.6.12-foss-2015b</li>
+ <li style="white-space: nowrap;">1.6.12-foss-2015g</li>
+ <li style="white-space: nowrap;">1.6.12-intel-2015b</li>
+ <li style="white-space: nowrap;">1.6.12-intel-2016.01</li>
+ <li style="white-space: nowrap;">1.6.17-foss-2015b</li>
+ <li style="white-space: nowrap;">1.6.21-foss-2015b</li>
+ <li style="white-space: nowrap;">1.6.21-foss-2015g</li>
+ <li style="white-space: nowrap;">1.6.9-ictce-5.5.0</li>
+ <li style="white-space: nowrap;">1.6.9-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libpthread-stubs</b><br />
+ <a href="http://xcb.freedesktop.org/">http://xcb.freedesktop.org/</a>
+ </td>
+ <td>The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint,
+latency hiding, direct access to the protocol, improved threading support, and extensibility.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.3</li>
+ <li style="white-space: nowrap;">0.3-foss-2015g</li>
+ <li style="white-space: nowrap;">0.3-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libreadline</b><br />
+ <a href="http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html">http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html</a>
+ </td>
+ <td>The GNU Readline library provides a set of functions for use by applications that
+ allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available.
+ The Readline library includes additional functions to maintain a list of previously-entered command lines,
+ to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">6.2-ictce-5.5.0</li>
+ <li style="white-space: nowrap;">6.2-intel-2015b</li>
+ <li style="white-space: nowrap;">6.3</li>
+ <li style="white-space: nowrap;">6.3-GCCcore-4.9.3</li>
+ <li style="white-space: nowrap;">6.3-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">6.3-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">6.3-foss-2015b</li>
+ <li style="white-space: nowrap;">6.3-foss-2015g</li>
+ <li style="white-space: nowrap;">6.3-gompi-2015e</li>
+ <li style="white-space: nowrap;">6.3-ictce-7.3.5</li>
+ <li style="white-space: nowrap;">6.3-intel-2015b</li>
+ <li style="white-space: nowrap;">6.3-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libtool</b><br />
+ <a href="http://www.gnu.org/software/libtool">http://www.gnu.org/software/libtool</a>
+ </td>
+ <td>GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries
+ behind a consistent, portable interface.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.4.2</li>
+ <li style="white-space: nowrap;">2.4.2-foss-2015b</li>
+ <li style="white-space: nowrap;">2.4.2-foss-2015g</li>
+ <li style="white-space: nowrap;">2.4.2-intel-2015b</li>
+ <li style="white-space: nowrap;">2.4.6</li>
+ <li style="white-space: nowrap;">2.4.6-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2.4.6-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2.4.6-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">2.4.6-foss-2015g</li>
+ <li style="white-space: nowrap;">2.4.6-intel-2015b</li>
+ <li style="white-space: nowrap;">2.4.6-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libunistring</b><br />
+ <a href="http://www.gnu.org/software/libunistring/">http://www.gnu.org/software/libunistring/</a>
+ </td>
+ <td>This library provides functions for manipulating Unicode strings and for manipulating C strings
+ according to the Unicode standard.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.9.3</li>
+ <li style="white-space: nowrap;">0.9.3-foss-2015b</li>
+ <li style="white-space: nowrap;">0.9.3-foss-2015g</li>
+ <li style="white-space: nowrap;">0.9.3-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libxcb</b><br />
+ <a href="http://xcb.freedesktop.org/">http://xcb.freedesktop.org/</a>
+ </td>
+ <td>The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint,
+latency hiding, direct access to the protocol, improved threading support, and extensibility.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.10-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.11-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.11-foss-2015g-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.11-intel-2015b-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libxml2</b><br />
+ <a href="http://xmlsoft.org/">http://xmlsoft.org/</a>
+ </td>
+ <td>Libxml2 is the XML C parser and
+toolchain developed for the Gnome project
+ (but usable outside of the Gnome platform).</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.9.2-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2.9.2-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2.9.2-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">2.9.2-foss-2015b</li>
+ <li style="white-space: nowrap;">2.9.2-foss-2015g</li>
+ <li style="white-space: nowrap;">2.9.2-foss-2015g-Python-2.7.9</li>
+ <li style="white-space: nowrap;">2.9.2-gompi-2015e</li>
+ <li style="white-space: nowrap;">2.9.2-ictce-7.3.5</li>
+ <li style="white-space: nowrap;">2.9.2-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>spatialindex</b><br />
+ <a href="https://libspatialindex.github.io/index.html">https://libspatialindex.github.io/index.html</a>
+ </td>
+ <td>The purpose of this library is to provide:
+ * An extensible framework that will support robust spatial indexing methods.
+ * Support for sophisticated spatial queries. Range, point location, nearest
+ neighbor and k-nearest neighbor as well as parametric queries (defined by spatial
+ constraints) should be easy to deploy and run.
+ * Easy to use interfaces for inserting, deleting and updating information.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.8.5-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>tbb</b><br />
+ <a href="http://software.intel.com/en-us/articles/intel-tbb/">http://software.intel.com/en-us/articles/intel-tbb/</a>
+ </td>
+ <td>Intel Threading Building Blocks 4.0 (Intel TBB)
+ is a widely used, award-winning C++ template library for creating reliable,
+ portable, and scalable parallel applications.
+ Use Intel TBB for a simple and rapid way of developing robust task-based
+ parallel applications that scale to available processor cores, are compatible
+ with multiple environments, and are easier to maintain.
+ Intel TBB is the most proficient way to implement future-proof parallel applications
+ that tap into the power and performance of multicore and manycore hardware platforms.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.3.5.187</li>
+ <li style="white-space: nowrap;">4.4.2.152</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>zlib</b><br />
+ <a href="http://www.zlib.net/">http://www.zlib.net/</a>
+ </td>
+ <td>zlib is designed to be a free, general-purpose, legally unencumbered -- that is,
+ not covered by any patents -- lossless data-compression library for use on virtually any
+ computer hardware and operating system.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.2.7-foss-2015b</li>
+ <li style="white-space: nowrap;">1.2.7-ictce-5.5.0</li>
+ <li style="white-space: nowrap;">1.2.7-intel-2015b</li>
+ <li style="white-space: nowrap;">1.2.8</li>
+ <li style="white-space: nowrap;">1.2.8-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">1.2.8-GCC-4.9.3-binutils-2.25</li>
+ <li style="white-space: nowrap;">1.2.8-GCC-5.1.0-binutils-2.25</li>
+ <li style="white-space: nowrap;">1.2.8-GCCcore-4.9.3</li>
+ <li style="white-space: nowrap;">1.2.8-GCCcore-5.3.0</li>
+ <li style="white-space: nowrap;">1.2.8-GCCcore-5.3.1-snapshot-20160419</li>
+ <li style="white-space: nowrap;">1.2.8-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">1.2.8-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">1.2.8-GNU-5.1.0-2.25-intel-2015b</li>
+ <li style="white-space: nowrap;">1.2.8-foss-2015b</li>
+ <li style="white-space: nowrap;">1.2.8-foss-2015g</li>
+ <li style="white-space: nowrap;">1.2.8-gompi-2015e</li>
+ <li style="white-space: nowrap;">1.2.8-ictce-7.3.5</li>
+ <li style="white-space: nowrap;">1.2.8-intel-2015b</li>
+ <li style="white-space: nowrap;">1.2.8-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="math"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">math</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>FIAT</b><br />
+ <a href="https://bitbucket.org/fenics-project/fiat">https://bitbucket.org/fenics-project/fiat</a>
+ </td>
+ <td>The FInite element Automatic Tabulator FIAT supports generation of arbitrary order
+instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating
+arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.6.0-intel-2015b-Python-2.7.11</li>
+ <li style="white-space: nowrap;">1.6.0-intel-2015b-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.6.0-intel-2016.01-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>GEOS</b><br />
+ <a href="http://trac.osgeo.org/geos">http://trac.osgeo.org/geos</a>
+ </td>
+ <td>GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.5.0-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>GMP</b><br />
+ <a href="http://gmplib.org/">http://gmplib.org/</a>
+ </td>
+ <td>GMP is a free library for arbitrary precision arithmetic,
+ operating on signed integers, rational numbers, and floating point numbers. </td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.0.5</li>
+ <li style="white-space: nowrap;">5.0.5-foss-2015b</li>
+ <li style="white-space: nowrap;">5.0.5-foss-2015g</li>
+ <li style="white-space: nowrap;">5.0.5-intel-2015b</li>
+ <li style="white-space: nowrap;">6.0.0a-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">6.0.0a-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">6.0.0a-foss-2015b</li>
+ <li style="white-space: nowrap;">6.1.0-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">6.1.0-intel-2015b</li>
+ <li style="white-space: nowrap;">6.1.0-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Harminv</b><br />
+ <a href="http://ab-initio.mit.edu/wiki/index.php/Harminv">http://ab-initio.mit.edu/wiki/index.php/Harminv</a>
+ </td>
+ <td>Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given
+ a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying)
+ in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.4-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>ISL</b><br />
+ <a href="http://isl.gforge.inria.fr/">http://isl.gforge.inria.fr/</a>
+ </td>
+ <td>isl is a library for manipulating sets and relations of integer points bounded by linear constraints.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.14-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">0.15-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">0.15-GNU-4.9.3-2.25</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>METIS</b><br />
+ <a href="http://glaros.dtc.umn.edu/gkhome/metis/metis/overview">http://glaros.dtc.umn.edu/gkhome/metis/metis/overview</a>
+ </td>
+ <td>METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes,
+and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the
+multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.1.0-intel-2015b</li>
+ <li style="white-space: nowrap;">5.1.0-intel-2016.01</li>
+ <li style="white-space: nowrap;">5.1.0-intel-2016.01-32bitIDX</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Octave</b><br />
+ <a href="http://www.gnu.org/software/octave/">http://www.gnu.org/software/octave/</a>
+ </td>
+ <td>GNU Octave is a high-level interpreted language, primarily intended for numerical computations.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.8.2-foss-2015g</li>
+ <li style="white-space: nowrap;">3.8.2-intel-2015b</li>
+ <li style="white-space: nowrap;">4.0.0-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>ParMETIS</b><br />
+ <a href="http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview">http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview</a>
+ </td>
+ <td>ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs,
+ meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes
+ routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in
+ ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning
+ schemes.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.0.3-intel-2015b</li>
+ <li style="white-space: nowrap;">4.0.3-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>SCOTCH</b><br />
+ <a href="http://gforge.inria.fr/projects/scotch/">http://gforge.inria.fr/projects/scotch/</a>
+ </td>
+ <td>Software package and libraries for sequential and parallel graph partitioning,
+static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.1.12b_esmumps-foss-2015b</li>
+ <li style="white-space: nowrap;">6.0.0_esmumps-intel-2015b</li>
+ <li style="white-space: nowrap;">6.0.3-intel-2015b</li>
+ <li style="white-space: nowrap;">6.0.3-intel-2016.01</li>
+ <li style="white-space: nowrap;">6.0.4-intel-2015b</li>
+ <li style="white-space: nowrap;">6.0.4-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>ScientificPython</b><br />
+ <a href="https://sourcesup.cru.fr/projects/scientific-py/">https://sourcesup.cru.fr/projects/scientific-py/</a>
+ </td>
+ <td>ScientificPython is a collection of Python modules for scientific computing.
+ It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization,
+ and parallelization.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.9.4-intel-2015b-Python-2.7.11</li>
+ <li style="white-space: nowrap;">2.9.4-intel-2015b-Python-2.7.9</li>
+ <li style="white-space: nowrap;">2.9.4-intel-2016.01-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>numpy</b><br />
+ <a href="http://www.numpy.org">http://www.numpy.org</a>
+ </td>
+ <td>NumPy is the fundamental package for scientific computing with Python. It contains among other things:
+ a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran
+ code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses,
+ NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be
+ defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.8.2-intel-2015b-Python-2.7.11</li>
+ <li style="white-space: nowrap;">1.8.2-intel-2015b-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.8.2-intel-2016.01-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.9.1-intel-2015b-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>sympy</b><br />
+ <a href="http://sympy.org/">http://sympy.org/</a>
+ </td>
+ <td>SymPy is a Python library for symbolic mathematics. It aims to
+ become a full-featured computer algebra system (CAS) while keeping the code as
+ simple as possible in order to be comprehensible and easily extensible. SymPy
+ is written entirely in Python and does not require any external libraries.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.7.6-intel-2015b-Python-2.7.9</li>
+ <li style="white-space: nowrap;">0.7.6-intel-2016.01-Python-2.7.9</li>
+ <li style="white-space: nowrap;">0.7.6.1-intel-2015b-Python-2.7.11</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="mpi"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">mpi</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>MPICH</b><br />
+ <a href="http://www.mpich.org/">http://www.mpich.org/</a>
+ </td>
+ <td>MPICH v3.x is an open source high-performance MPI 3.0 implementation.
+It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.2-GCC-5.3.0-2.25</li>
+ <li style="white-space: nowrap;">3.2-GCC-5.3.1-snapshot-20160419-2.25</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>MPI_NET</b><br />
+ <a href="http://www.osl.iu.edu/research/mpi.net/">http://www.osl.iu.edu/research/mpi.net/</a>
+ </td>
+ <td>MPI.NET is a high-performance, easy-to-use implementation of the Message Passing Interface (MPI)
+for Microsoft's .NET environment</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.2.0-gompi-2015e</li>
+ <li style="white-space: nowrap;">1.2.0-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>MVAPICH2</b><br />
+ <a href="http://mvapich.cse.ohio-state.edu/overview/mvapich2/">http://mvapich.cse.ohio-state.edu/overview/mvapich2/</a>
+ </td>
+ <td>This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.1-GCC-4.4.7-system</li>
+ <li style="white-space: nowrap;">2.1-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">2.1-iccifort-2015.3.187-GNU-5.1.0-2.25</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>OpenMPI</b><br />
+ <a href="http://www.open-mpi.org/">http://www.open-mpi.org/</a>
+ </td>
+ <td>The Open MPI Project is an open source MPI-2 implementation.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.10.1-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">1.10.2-GCC-5.3.0-2.26</li>
+ <li style="white-space: nowrap;">1.8.6-GCC-4.4.7-system</li>
+ <li style="white-space: nowrap;">1.8.6-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">1.8.6-iccifort-2015.3.187-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">1.8.8-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">1.8.8-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>impi</b><br />
+ <a href="http://software.intel.com/en-us/intel-mpi-library/">http://software.intel.com/en-us/intel-mpi-library/</a>
+ </td>
+ <td>The Intel(R) MPI Library for Linux* OS is a multi-fabric message
+ passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for
+ Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2017-BETA.ENG</li>
+ <li style="white-space: nowrap;">4.1.1.036-iccifort-2013.5.192</li>
+ <li style="white-space: nowrap;">4.1.1.036-iccifort-2013.5.192-GCC-4.8.3</li>
+ <li style="white-space: nowrap;">5.0.3.048</li>
+ <li style="white-space: nowrap;">5.0.3.048-iccifort-2015.3.187</li>
+ <li style="white-space: nowrap;">5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">5.1.1.109-iccifort-2016.0.109-GCC-4.9.3</li>
+ <li style="white-space: nowrap;">5.1.2.150-iccifort-2016.1.150</li>
+ <li style="white-space: nowrap;">5.1.2.150-iccifort-2016.1.150-GCC-4.9.3</li>
+ <li style="white-space: nowrap;">5.1.2.150-iccifort-2016.1.150-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">5.1.3.181-iccifort-2016.3.210-GCC-5.3.0-2.26</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>mpt</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.12</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="numlib"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">numlib</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>FFTW</b><br />
+ <a href="http://www.fftw.org">http://www.fftw.org</a>
+ </td>
+ <td>FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
+ in one or more dimensions, of arbitrary input size, and of both real and complex data.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.1.5-gompi-2015b</li>
+ <li style="white-space: nowrap;">2.1.5-iimpi-7.3.5-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">3.3.4-gompi-2015b</li>
+ <li style="white-space: nowrap;">3.3.4-gompi-2015e</li>
+ <li style="white-space: nowrap;">3.3.4-gompi-2015g</li>
+ <li style="white-space: nowrap;">3.3.4-gompi-2016.04</li>
+ <li style="white-space: nowrap;">3.3.4-intel-2015b</li>
+ <li style="white-space: nowrap;">3.3.4-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>GSL</b><br />
+ <a href="http://www.gnu.org/software/gsl/">http://www.gnu.org/software/gsl/</a>
+ </td>
+ <td>The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
+ The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.16-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Hypre</b><br />
+ <a href="https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html">https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html</a>
+ </td>
+ <td>Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers.
+ The problems of interest arise in the simulation codes being developed at LLNL and elsewhere
+ to study physical phenomena in the defense, environmental, energy, and biological sciences.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.10.0b-intel-2015b</li>
+ <li style="white-space: nowrap;">2.10.0b-intel-2016.01</li>
+ <li style="white-space: nowrap;">2.10.1-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>LAPACKE</b><br />
+ <a href="http://www.netlib.org/lapack/lapacke.html">http://www.netlib.org/lapack/lapacke.html</a>
+ </td>
+ <td>LAPACKE C Interface to LAPACK header files and library</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.5.0-LAPACK-3.5.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>OpenBLAS</b><br />
+ <a href="http://xianyi.github.com/OpenBLAS/">http://xianyi.github.com/OpenBLAS/</a>
+ </td>
+ <td>OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0</li>
+ <li style="white-space: nowrap;">0.2.14-GNU-5.1.0-2.25-LAPACK-3.5.0</li>
+ <li style="white-space: nowrap;">0.2.14-LAPACK-3.5.0</li>
+ <li style="white-space: nowrap;">0.2.14-gompi-2015e-LAPACK-3.5.0</li>
+ <li style="white-space: nowrap;">0.2.18-GCC-5.3.0-2.26-LAPACK-3.6.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>PETSc</b><br />
+ <a href="http://www.mcs.anl.gov/petsc">http://www.mcs.anl.gov/petsc</a>
+ </td>
+ <td>PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the
+ scalable (parallel) solution of scientific applications modeled by partial differential equations.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.6.1-intel-2015b-Python-2.7.9</li>
+ <li style="white-space: nowrap;">3.6.1-intel-2016.01-Python-2.7.9</li>
+ <li style="white-space: nowrap;">3.6.3-intel-2015b-Python-2.7.11</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>ScaLAPACK</b><br />
+ <a href="http://www.netlib.org/scalapack/">http://www.netlib.org/scalapack/</a>
+ </td>
+ <td>The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
+ redesigned for distributed memory MIMD parallel computers.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.0.2-OpenBLAS-0.2.14-LAPACK-3.5.0</li>
+ <li style="white-space: nowrap;">2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0</li>
+ <li style="white-space: nowrap;">2.0.2-gompi-2015e-OpenBLAS-0.2.14-LAPACK-3.5.0</li>
+ <li style="white-space: nowrap;">2.0.2-gompi-2015g-OpenBLAS-0.2.14-LAPACK-3.5.0</li>
+ <li style="white-space: nowrap;">2.0.2-gompi-2016.04-OpenBLAS-0.2.18-LAPACK-3.6.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>SuiteSparse</b><br />
+ <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">http://www.cise.ufl.edu/research/sparse/SuiteSparse/</a>
+ </td>
+ <td>SuiteSparse is a collection of libraries manipulate sparse matrices.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.4.3-intel-2015b-ParMETIS-4.0.3</li>
+ <li style="white-space: nowrap;">4.4.3-intel-2016.01-ParMETIS-4.0.3</li>
+ <li style="white-space: nowrap;">4.4.6-intel-2015b-ParMETIS-4.0.3</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>arpack-ng</b><br />
+ <a href="http://forge.scilab.org/index.php/p/arpack-ng/">http://forge.scilab.org/index.php/p/arpack-ng/</a>
+ </td>
+ <td>ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.3.0-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>imkl</b><br />
+ <a href="http://software.intel.com/en-us/intel-mkl/">http://software.intel.com/en-us/intel-mkl/</a>
+ </td>
+ <td>Intel Math Kernel Library is a library of highly optimized,
+ extensively threaded math routines for science, engineering, and financial
+ applications that require maximum performance. Core math functions include
+ BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">11.0.5.192-iimpi-5.5.0</li>
+ <li style="white-space: nowrap;">11.0.5.192-iimpi-5.5.0-GCC-4.8.3</li>
+ <li style="white-space: nowrap;">11.2.3.187</li>
+ <li style="white-space: nowrap;">11.2.3.187-iimpi-7.3.5</li>
+ <li style="white-space: nowrap;">11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">11.2.3.187-iompi-2015.03</li>
+ <li style="white-space: nowrap;">11.3.0.109-iimpi-2016.00-GCC-4.9.3</li>
+ <li style="white-space: nowrap;">11.3.1.150-iimpi-2016.00-GCC-4.9.3</li>
+ <li style="white-space: nowrap;">11.3.1.150-iimpi-2016.01-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">11.3.1.150-iimpi-8.3.5</li>
+ <li style="white-space: nowrap;">11.3.3.210-iimpi-2016.03-GCC-5.3.0-2.26</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="perf"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">perf</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>Advisor</b><br />
+ <a href="https://software.intel.com/intel-advisor-xe">https://software.intel.com/intel-advisor-xe</a>
+ </td>
+ <td>Vectorization Optimization and Thread Prototyping
+ - Vectorize & thread code or performance “dies”
+ - Easy workflow + data + tips = faster code faster
+ - Prioritize, Prototype & Predict performance gain
+ </td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2016_update2</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>MAP</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.2</li>
+ <li style="white-space: nowrap;">5.0.1</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>OPARI2</b><br />
+ <a href="http://www.score-p.org">http://www.score-p.org</a>
+ </td>
+ <td>OPARI2, the successor of Forschungszentrum Juelich's OPARI,
+ is a source-to-source instrumentation tool for OpenMP and hybrid codes.
+ It surrounds OpenMP directives and runtime library calls with calls to
+ the POMP2 measurement interface.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.1.4-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>OTF2</b><br />
+ <a href="http://www.score-p.org">http://www.score-p.org</a>
+ </td>
+ <td>The Open Trace Format 2 is a highly scalable, memory efficient event
+ trace data format plus support library. It will become the new standard trace format
+ for Scalasca, Vampir, and Tau and is open for other tools.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.4-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>PAPI</b><br />
+ <a href="http://icl.cs.utk.edu/projects/papi/">http://icl.cs.utk.edu/projects/papi/</a>
+ </td>
+ <td>PAPI provides the tool designer and application engineer with a consistent interface and
+ methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables
+ software engineers to see, in near real time, the relation between software performance and processor events.
+ In addition Component PAPI provides access to a collection of components
+ that expose performance measurement opportunites across the hardware and software stack.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.4.0-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>PerfReports</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.0.1</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Vampir</b><br />
+ <a href="http://www.vampir.eu">http://www.vampir.eu</a>
+ </td>
+ <td>The Vampir software tool provides an easy-to-use framework that enables
+ developers to quickly display and analyze arbitrary program behavior at any level of detail.
+ The tool suite implements optimized event analysis algorithms and customizable displays that
+ enable fast and interactive rendering of very complex performance monitoring data.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">8.5.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>ipp</b><br />
+ <a href="http://software.intel.com/en-us/articles/intel-ipp/">http://software.intel.com/en-us/articles/intel-ipp/</a>
+ </td>
+ <td>Intel Integrated Performance Primitives (Intel IPP) is an extensive library
+ of multicore-ready, highly optimized software functions for multimedia, data processing,
+ and communications applications. Intel IPP offers thousands of optimized functions
+ covering frequently used fundamental algorithms.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">9.0.1.150</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>perfboost</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>perfcatcher</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>perfsuite</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1a5.3</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="phys"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">phys</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>Meep</b><br />
+ <a href="http://ab-initio.mit.edu/wiki/index.php/Meep">http://ab-initio.mit.edu/wiki/index.php/Meep</a>
+ </td>
+ <td>Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package
+ developed at MIT to model electromagnetic systems.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.3-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>phono3py</b><br />
+ <a href="http://phonopy.sourceforge.net/phono3py/index.html">http://phonopy.sourceforge.net/phono3py/index.html</a>
+ </td>
+ <td>This software calculates phonon-phonon interaction related properties</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.9.14-ictce-7.3.5-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="system"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">system</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>hwloc</b><br />
+ <a href="http://www.open-mpi.org/projects/hwloc/">http://www.open-mpi.org/projects/hwloc/</a>
+ </td>
+ <td>The Portable Hardware Locality (hwloc) software package provides a portable abstraction
+ (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including
+ NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various
+ system attributes such as cache and memory information as well as the locality of I/O devices such as
+ network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering
+ information about modern computing hardware so as to exploit it accordingly and efficiently.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.11.0-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">1.11.0-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">1.11.2-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">1.11.3-GCC-5.3.0-2.26</li>
+ <li style="white-space: nowrap;">1.5-GCC-4.4.7-system</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libpciaccess</b><br />
+ <a href="http://cgit.freedesktop.org/xorg/lib/libpciaccess/">http://cgit.freedesktop.org/xorg/lib/libpciaccess/</a>
+ </td>
+ <td>Generic PCI access library.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.13.1-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="toolchain"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">toolchain</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>GNU</b><br />
+ <a href="http://www.gnu.org/software/">http://www.gnu.org/software/</a>
+ </td>
+ <td>Compiler-only toolchain with GCC and binutils.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.9.3-2.25</li>
+ <li style="white-space: nowrap;">5.1.0-2.25</li>
+ <li style="white-space: nowrap;">5.1.0-2.25-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>PRACE</b><br />
+ <a href="http://www.prace-ri.eu/PRACE-Common-Production">http://www.prace-ri.eu/PRACE-Common-Production</a>
+ </td>
+ <td>The PRACE Common Production Environment (PCPE) is a set of software tools and libraries
+ that are planned to be available on all PRACE execution sites. The PCPE also defines a set of environment
+ variables that try to make compilation on all sites as homogeneous and simple as possible.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">20150630-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>foss</b><br />
+ <a href="https://docs.it4i.cz/salomon/(none)">(none)</a>
+ </td>
+ <td>GNU Compiler Collection (GCC) based compiler toolchain, including
+ OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2015b</li>
+ <li style="white-space: nowrap;">2015e</li>
+ <li style="white-space: nowrap;">2015g</li>
+ <li style="white-space: nowrap;">2016.04</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>gompi</b><br />
+ <a href="https://docs.it4i.cz/salomon/(none)">(none)</a>
+ </td>
+ <td>GNU Compiler Collection (GCC) based compiler toolchain,
+ including OpenMPI for MPI support.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2015b</li>
+ <li style="white-space: nowrap;">2015e</li>
+ <li style="white-space: nowrap;">2015g</li>
+ <li style="white-space: nowrap;">2016.04</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>iccifort</b><br />
+ <a href="http://software.intel.com/en-us/intel-cluster-toolkit-compiler/">http://software.intel.com/en-us/intel-cluster-toolkit-compiler/</a>
+ </td>
+ <td>Intel C, C++ and Fortran compilers</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2013.5.192</li>
+ <li style="white-space: nowrap;">2013.5.192-GCC-4.8.3</li>
+ <li style="white-space: nowrap;">2015.3.187</li>
+ <li style="white-space: nowrap;">2015.3.187-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2015.3.187-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">2016.0.109-GCC-4.9.3</li>
+ <li style="white-space: nowrap;">2016.1.150</li>
+ <li style="white-space: nowrap;">2016.1.150-GCC-4.9.3</li>
+ <li style="white-space: nowrap;">2016.1.150-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2016.3.210-GCC-5.3.0-2.26</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>ictce</b><br />
+ <a href="http://software.intel.com/en-us/intel-cluster-toolkit-compiler/">http://software.intel.com/en-us/intel-cluster-toolkit-compiler/</a>
+ </td>
+ <td>Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.5.0</li>
+ <li style="white-space: nowrap;">7.3.5</li>
+ <li style="white-space: nowrap;">8.3.5</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>iimpi</b><br />
+ <a href="http://software.intel.com/en-us/intel-cluster-toolkit-compiler/">http://software.intel.com/en-us/intel-cluster-toolkit-compiler/</a>
+ </td>
+ <td>Intel C/C++ and Fortran compilers, alongside Intel MPI.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2016.00-GCC-4.9.3</li>
+ <li style="white-space: nowrap;">2016.01-GCC-4.9.3</li>
+ <li style="white-space: nowrap;">2016.01-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2016.03-GCC-5.3.0-2.26</li>
+ <li style="white-space: nowrap;">5.5.0</li>
+ <li style="white-space: nowrap;">5.5.0-GCC-4.8.3</li>
+ <li style="white-space: nowrap;">7.3.5</li>
+ <li style="white-space: nowrap;">7.3.5-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">8.3.5</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>intel</b><br />
+ <a href="http://software.intel.com/en-us/intel-cluster-toolkit-compiler/">http://software.intel.com/en-us/intel-cluster-toolkit-compiler/</a>
+ </td>
+ <td>Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2014.06</li>
+ <li style="white-space: nowrap;">2015b</li>
+ <li style="white-space: nowrap;">2015b-intel-2015b</li>
+ <li style="white-space: nowrap;">2016.00</li>
+ <li style="white-space: nowrap;">2016.01</li>
+ <li style="white-space: nowrap;">2016.03-GCC-5.3</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>prace</b><br />
+ <a href="http://www.prace-ri.eu/PRACE-Common-Production">http://www.prace-ri.eu/PRACE-Common-Production</a>
+ </td>
+ <td>**** PRACE Common Production Environment (PCPE) ****
+
+Initialisation of the PRACE common production environment. This
+allows you to assume that the following tools/libraries are available
+by default in your PATH/environment.
+
+ * Fortran, C, C++ Compilers
+ * MPI
+ * BLAS, LAPACK, BLACS, ScaLAPACK
+ * FFTW
+ * HDF5, NetCDF
+
+The compiler commands on are:
+
+ * mpif90 - Fortran compiler
+ * mpicc - C compiler
+ * mpicxx - C++ compiler
+
+For more information on the PCPE please see the documentation at:
+
+http://www.prace-ri.eu/PRACE-Common-Production
+
+For help using this system, please see Local User Guide available at:
+
+http://prace-ri.eu/Best-Practice-Guide-Anselm-HTML
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">20160107-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="tools"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">tools</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>APR</b><br />
+ <a href="http://apr.apache.org/">http://apr.apache.org/</a>
+ </td>
+ <td>Apache Portable Runtime (APR) libraries.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.5.2-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>APR-util</b><br />
+ <a href="http://apr.apache.org/">http://apr.apache.org/</a>
+ </td>
+ <td>Apache Portable Runtime (APR) util libraries.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.5.4-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Bash</b><br />
+ <a href="http://www.gnu.org/software/bash">http://www.gnu.org/software/bash</a>
+ </td>
+ <td>Bash is an sh-compatible command language interpreter that executes commands
+ read from the standard input or from a file. Bash also incorporates useful features from the
+ Korn and C shells (ksh and csh).</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.2-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>EasyBuild</b><br />
+ <a href="http://hpcugent.github.com/easybuild/">http://hpcugent.github.com/easybuild/</a>
+ </td>
+ <td>EasyBuild is a software build and installation framework
+written in Python that allows you to install software in a structured,
+repeatable and robust way.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.4.0</li>
+ <li style="white-space: nowrap;">2.5.0</li>
+ <li style="white-space: nowrap;">2.7.0</li>
+ <li style="white-space: nowrap;">2.8.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>HPL</b><br />
+ <a href="http://www.netlib.org/benchmark/hpl/">http://www.netlib.org/benchmark/hpl/</a>
+ </td>
+ <td>HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic
+ on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the
+ High Performance Computing Linpack Benchmark.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.1-foss-2015b</li>
+ <li style="white-space: nowrap;">2.1-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Inspector</b><br />
+ <a href="http://software.intel.com/en-us/intel-inspector-xe">http://software.intel.com/en-us/intel-inspector-xe</a>
+ </td>
+ <td>Intel Inspector XE 2013 is an easy to use memory error checker and thread checker for serial and parallel applications</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2016_update1</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>JOE</b><br />
+ <a href="http://joe-editor.sourceforge.net">http://joe-editor.sourceforge.net</a>
+ </td>
+ <td>JOE is a full featured terminal-based screen editor which
+is distributed under the GNU General Public License (GPL)</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.2</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>MATLAB</b><br />
+ <a href="index.html"></a>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2015a-COM</li>
+ <li style="white-space: nowrap;">2015a-EDU</li>
+ <li style="white-space: nowrap;">2015b-COM</li>
+ <li style="white-space: nowrap;">2015b-EDU</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>MIKE</b><br />
+ <a href="http://www.mikepoweredbydhi.com">http://www.mikepoweredbydhi.com</a>
+ </td>
+ <td>
+MIKE Powered by DHI is a part of DHI, the global organisation dedicated to
+solving challenges in water environments worldwide.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2014</li>
+ <li style="white-space: nowrap;">2016</li>
+ <li style="white-space: nowrap;">2016-SP2</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Mercurial</b><br />
+ <a href="http://mercurial.selenic.com/">http://mercurial.selenic.com/</a>
+ </td>
+ <td>Mercurial is a free, distributed source control management tool. It efficiently handles projects
+of any size and offers an easy and intuitive interface.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">3.5-Python-2.7.9</li>
+ <li style="white-space: nowrap;">3.7.3-foss-2015g-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>QEMU</b><br />
+ <a href="http://wiki.qemu.org/Main_Page">http://wiki.qemu.org/Main_Page</a>
+ </td>
+ <td>QEMU is a generic and open source machine emulator and
+virtualizer.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.1.2-GCC-4.4.7-system</li>
+ <li style="white-space: nowrap;">2.1.2-GCC-4.4.7-system-VDE2</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>SDE</b><br />
+ <a href="https://software.intel.com/en-us/articles/intel-software-development-emulator">https://software.intel.com/en-us/articles/intel-software-development-emulator</a>
+ </td>
+ <td>
+ Intel Software Development Emulator is a pintool that enables the development of applications using instruction set extensions that are not currently implemented in hardware.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">7.41.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Serf</b><br />
+ <a href="http://serf.apache.org/">http://serf.apache.org/</a>
+ </td>
+ <td>The serf library is a high performance C-based HTTP client library
+ built upon the Apache Portable Runtime (APR) library</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.3.8-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Subversion</b><br />
+ <a href="http://subversion.apache.org/">http://subversion.apache.org/</a>
+ </td>
+ <td> Subversion is an open source version control system.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.8.16-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Szip</b><br />
+ <a href="http://www.hdfgroup.org/doc_resource/SZIP/">http://www.hdfgroup.org/doc_resource/SZIP/</a>
+ </td>
+ <td>Szip compression software, providing lossless compression of scientific data</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.1</li>
+ <li style="white-space: nowrap;">2.1-foss-2015b</li>
+ <li style="white-space: nowrap;">2.1-foss-2015g</li>
+ <li style="white-space: nowrap;">2.1-ictce-7.3.5</li>
+ <li style="white-space: nowrap;">2.1-intel-2015b</li>
+ <li style="white-space: nowrap;">2.1-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>VDE2</b><br />
+ <a href="http://vde.sourceforge.net">http://vde.sourceforge.net</a>
+ </td>
+ <td>VDE is an ethernet compliant virtual network that
+can be spawned over a set of physical computer over the Internet.
+VDE is part of virtualsquare project.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.3.2-GCC-4.4.7-system</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>VTune</b><br />
+ <a href="http://software.intel.com/en-us/intel-vtune-amplifier-xe">http://software.intel.com/en-us/intel-vtune-amplifier-xe</a>
+ </td>
+ <td>Intel VTune Amplifier XE 2016 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2016_update1</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>VirtualGL</b><br />
+ <a href="http://www.virtualgl.org">http://www.virtualgl.org</a>
+ </td>
+ <td>VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the
+ability to run OpenGL applications with full 3D hardware acceleration.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.4.1</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Wine</b><br />
+ <a href="https://www.winehq.org">https://www.winehq.org</a>
+ </td>
+ <td>Wine (originally an acronym for "Wine Is Not an Emulator")
+is a compatibility layer capable of running Windows applications on several
+POSIX-compliant operating systems, such as Linux, Mac OSX, & BSD.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.7.29-GCC-4.4.7-system</li>
+ <li style="white-space: nowrap;">1.7.29-GNU-5.1.0-2.25</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>XZ</b><br />
+ <a href="http://tukaani.org/xz/">http://tukaani.org/xz/</a>
+ </td>
+ <td>xz: XZ utilities</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.2.2-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>binutils</b><br />
+ <a href="http://directory.fsf.org/project/binutils/">http://directory.fsf.org/project/binutils/</a>
+ </td>
+ <td>binutils: GNU binary utilities</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.25</li>
+ <li style="white-space: nowrap;">2.25-GCC-4.9.3-binutils-2.25</li>
+ <li style="white-space: nowrap;">2.25-GCC-5.1.0-binutils-2.25</li>
+ <li style="white-space: nowrap;">2.25-GCCcore-4.9.3</li>
+ <li style="white-space: nowrap;">2.25-GCCcore-5.3.0</li>
+ <li style="white-space: nowrap;">2.25-GCCcore-5.3.1-snapshot-20160419</li>
+ <li style="white-space: nowrap;">2.25-foss-2015b</li>
+ <li style="white-space: nowrap;">2.26</li>
+ <li style="white-space: nowrap;">2.26-GCCcore-5.3.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>bzip2</b><br />
+ <a href="http://www.bzip.org/">http://www.bzip.org/</a>
+ </td>
+ <td>bzip2 is a freely available, patent free, high-quality data compressor. It typically
+compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical
+compressors), whilst being around twice as fast at compression and six times faster at decompression.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.0.6</li>
+ <li style="white-space: nowrap;">1.0.6-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">1.0.6-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">1.0.6-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">1.0.6-foss-2015b</li>
+ <li style="white-space: nowrap;">1.0.6-foss-2015g</li>
+ <li style="white-space: nowrap;">1.0.6-gompi-2015e</li>
+ <li style="white-space: nowrap;">1.0.6-ictce-7.3.5</li>
+ <li style="white-space: nowrap;">1.0.6-intel-2015b</li>
+ <li style="white-space: nowrap;">1.0.6-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>cURL</b><br />
+ <a href="http://curl.haxx.se">http://curl.haxx.se</a>
+ </td>
+ <td>libcurl is a free and easy-to-use client-side URL transfer library,
+ supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS,
+ POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports
+ SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload,
+ proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate,
+ Kerberos), file transfer resume, http proxy tunneling and more.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">7.37.1</li>
+ <li style="white-space: nowrap;">7.37.1-foss-2015g</li>
+ <li style="white-space: nowrap;">7.37.1-intel-2015b</li>
+ <li style="white-space: nowrap;">7.37.1-intel-2016.01</li>
+ <li style="white-space: nowrap;">7.45.0-foss-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>expat</b><br />
+ <a href="http://expat.sourceforge.net/">http://expat.sourceforge.net/</a>
+ </td>
+ <td>Expat is an XML parser library written in C. It is a stream-oriented parser in which an application
+ registers handlers for things the parser might find in the XML document (like start tags)</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.1.0</li>
+ <li style="white-space: nowrap;">2.1.0-foss-2015b</li>
+ <li style="white-space: nowrap;">2.1.0-foss-2015g</li>
+ <li style="white-space: nowrap;">2.1.0-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>git</b><br />
+ <a href="http://git-scm.com/">http://git-scm.com/</a>
+ </td>
+ <td>Git is a free and open source distributed version control system designed
+to handle everything from small to very large projects with speed and efficiency.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.8.0</li>
+ <li style="white-space: nowrap;">2.8.0-GNU-4.9.3-2.25</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>gzip</b><br />
+ <a href="http://www.gnu.org/software/gzip/">http://www.gnu.org/software/gzip/</a>
+ </td>
+ <td>gzip (GNU zip) is a popular data compression program as a replacement for compress</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.6-foss-2015g</li>
+ <li style="white-space: nowrap;">1.6-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>itac</b><br />
+ <a href="http://software.intel.com/en-us/intel-trace-analyzer/">http://software.intel.com/en-us/intel-trace-analyzer/</a>
+ </td>
+ <td>The Intel Trace Collector is a low-overhead tracing library that performs
+ event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application
+ activities gathered by the Intel Trace Collector through graphical displays. </td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">9.1.2.024</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>numactl</b><br />
+ <a href="http://oss.sgi.com/projects/libnuma/">http://oss.sgi.com/projects/libnuma/</a>
+ </td>
+ <td>The numactl program allows you to run your application program on specific cpu's and memory nodes.
+ It does this by supplying a NUMA memory policy to the operating system before running your program.
+ The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.0.10-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2.0.10-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2.0.11</li>
+ <li style="white-space: nowrap;">2.0.11-GCC-4.9.3-2.25</li>
+ <li style="white-space: nowrap;">2.0.11-GCC-5.3.0-2.26</li>
+ <li style="white-space: nowrap;">2.0.9-GCC-4.4.7-system</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>parallel</b><br />
+ <a href="http://savannah.gnu.org/projects/parallel/">http://savannah.gnu.org/projects/parallel/</a>
+ </td>
+ <td>parallel: Build and execute shell commands in parallel</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">20150322-GNU-5.1.0-2.25</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>tcsh</b><br />
+ <a href="http://www.tcsh.org">http://www.tcsh.org</a>
+ </td>
+ <td>Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh).
+ It is a command language interpreter usable both as an interactive login shell and a shell script command
+ processor. It includes a command-line editor, programmable word completion, spelling correction, a history
+ mechanism, job control and a C-like syntax.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">6.18.01-intel-2015b</li>
+ <li style="white-space: nowrap;">6.19.00</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>turbovnc</b><br />
+ <a href="http://www.turbovnc.org">http://www.turbovnc.org</a>
+ </td>
+ <td>
+TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to
+provide peak performance for 3D and video workloads.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.2.3</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>util-linux</b><br />
+ <a href="http://www.kernel.org/pub/linux/utils/util-linux">http://www.kernel.org/pub/linux/utils/util-linux</a>
+ </td>
+ <td>Set of Linux utilities</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.26.1</li>
+ <li style="white-space: nowrap;">2.26.1-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ <div>
+ <h2 id="vis"><a class="tooltip" title="Go to list of categories..." href="list_of_modules.html#categories">vis</a></h2>
+ <table class="listing">
+ <thead>
+ <tr>
+ <th>Module</th>
+ <th>Description</th>
+ <th>Available versions</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>
+ <b>FLTK</b><br />
+ <a href="http://www.fltk.org">http://www.fltk.org</a>
+ </td>
+ <td>FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows,
+ and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL
+ and its built-in GLUT emulation.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.3.2-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>GLib</b><br />
+ <a href="http://www.gtk.org/">http://www.gtk.org/</a>
+ </td>
+ <td>GLib is one of the base libraries of the GTK+ project</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.40.0</li>
+ <li style="white-space: nowrap;">2.40.0-foss-2015g</li>
+ <li style="white-space: nowrap;">2.40.0-intel-2015b</li>
+ <li style="white-space: nowrap;">2.40.0-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>GPI-2</b><br />
+ <a href="http://www.gpi-site.com/gpi2/">http://www.gpi-site.com/gpi2/</a>
+ </td>
+ <td>GPI-2 is an API for the development of scalable,
+asynchronous and fault tolerant parallel applications.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.1.1-gompi-2015e</li>
+ <li style="white-space: nowrap;">1.1.1-gompi-2015e-MPI</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>JasPer</b><br />
+ <a href="http://www.ece.uvic.ca/~frodo/jasper/">http://www.ece.uvic.ca/~frodo/jasper/</a>
+ </td>
+ <td>The JasPer Project is an open-source initiative to provide a free
+ software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.900.1-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Mesa</b><br />
+ <a href="http://www.mesa3d.org/">http://www.mesa3d.org/</a>
+ </td>
+ <td>Mesa is an open-source implementation of the OpenGL specification -
+ a system for rendering interactive 3D graphics.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">11.0.8-foss-2015g-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>OSPRay</b><br />
+ <a href="http://www.ospray.org">http://www.ospray.org</a>
+ </td>
+ <td>
+ A Ray Tracing Based Rendering Engine for High-Fidelity Visualization</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.9.1</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>OpenCV</b><br />
+ <a href="http://opencv.org/">http://opencv.org/</a>
+ </td>
+ <td>OpenCV (Open Source Computer Vision Library) is an open source computer vision
+ and machine learning software library. OpenCV was built to provide
+ a common infrastructure for computer vision applications and to accelerate
+ the use of machine perception in the commercial products.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.4.9-intel-2015b</li>
+ <li style="white-space: nowrap;">3.0.0-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>OpenDX</b><br />
+ <a href="http://www.opendx.org">http://www.opendx.org</a>
+ </td>
+ <td>Open source visualization software package based on IBM's Visualization Data Explorer.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.4.4-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>ParaView</b><br />
+ <a href="http://www.paraview.org">http://www.paraview.org</a>
+ </td>
+ <td>ParaView is a scientific parallel visualizer.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.3-OSPRay</li>
+ <li style="white-space: nowrap;">5.0.0-binary</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>PyQt</b><br />
+ <a href="http://www.riverbankcomputing.co.uk/software/pyqt">http://www.riverbankcomputing.co.uk/software/pyqt</a>
+ </td>
+ <td>PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">4.11.3-foss-2015g-Python-2.7.9</li>
+ <li style="white-space: nowrap;">4.11.4-foss-2015g-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>SUMO</b><br />
+ <a href="http://www.sumo.dlr.de/wiki/Main_Page">http://www.sumo.dlr.de/wiki/Main_Page</a>
+ </td>
+ <td>Simulation of Urban MObility (SUMO) is an open source, highly portable,
+microscopic and continuous road traffic simulation package designed to handle large road networks.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.25.0-foss-2015g</li>
+ <li style="white-space: nowrap;">0.26.0-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>Tk</b><br />
+ <a href="http://www.tcl.tk/">http://www.tcl.tk/</a>
+ </td>
+ <td>Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building
+ a graphical user interface (GUI) in many different programming languages.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">8.5.12-intel-2015b</li>
+ <li style="white-space: nowrap;">8.6.4-GCC-4.9.3-2.25-no-X11</li>
+ <li style="white-space: nowrap;">8.6.4-GNU-4.9.3-2.25-no-X11</li>
+ <li style="white-space: nowrap;">8.6.4-foss-2015b-no-X11</li>
+ <li style="white-space: nowrap;">8.6.4-foss-2015g-no-X11</li>
+ <li style="white-space: nowrap;">8.6.4-intel-2015b-no-X11</li>
+ <li style="white-space: nowrap;">8.6.4-intel-2016.01-no-X11</li>
+ <li style="white-space: nowrap;">8.6.4-no-X11</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>VisIt</b><br />
+ <a href="https://wci.llnl.gov/simulation/computer-codes/visit">https://wci.llnl.gov/simulation/computer-codes/visit</a>
+ </td>
+ <td>VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.10.0</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>cairo</b><br />
+ <a href="http://cairographics.org">http://cairographics.org</a>
+ </td>
+ <td>Cairo is a 2D graphics library with support for multiple output devices.
+Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers,
+PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.12.18-foss-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>ffmpeg</b><br />
+ <a href="https://www.ffmpeg.org/">https://www.ffmpeg.org/</a>
+ </td>
+ <td>A complete, cross-platform solution to record, convert and stream audio and video.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.4-foss-2015g</li>
+ <li style="white-space: nowrap;">2.4-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>fixesproto</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X.org FixesProto protocol headers.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.0-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>fontconfig</b><br />
+ <a href="http://www.freedesktop.org/software/fontconfig">http://www.freedesktop.org/software/fontconfig</a>
+ </td>
+ <td>Fontconfig is a library designed to provide system-wide font configuration, customization and
+application access.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.11.1-foss-2015b</li>
+ <li style="white-space: nowrap;">2.11.1-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>freetype</b><br />
+ <a href="http://freetype.org">http://freetype.org</a>
+ </td>
+ <td>FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and
+ portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display
+ servers, font conversion tools, text image generation tools, and many other products as well.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.5.3</li>
+ <li style="white-space: nowrap;">2.5.3-foss-2015b</li>
+ <li style="white-space: nowrap;">2.5.3-foss-2015g</li>
+ <li style="white-space: nowrap;">2.5.3-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>gettext</b><br />
+ <a href="http://www.gnu.org/software/gettext/">http://www.gnu.org/software/gettext/</a>
+ </td>
+ <td>GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may
+build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools
+and documentation</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.19.2</li>
+ <li style="white-space: nowrap;">0.19.2-GNU-5.1.0-2.25</li>
+ <li style="white-space: nowrap;">0.19.2-foss-2015b</li>
+ <li style="white-space: nowrap;">0.19.2-foss-2015g</li>
+ <li style="white-space: nowrap;">0.19.2-intel-2015b</li>
+ <li style="white-space: nowrap;">0.19.2-intel-2016.01</li>
+ <li style="white-space: nowrap;">0.19.6-foss-2015g</li>
+ <li style="white-space: nowrap;">0.19.6-intel-2016.01</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>grace</b><br />
+ <a href="http://freecode.com/projects/grace">http://freecode.com/projects/grace</a>
+ </td>
+ <td>Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.1.25-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>inputproto</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X.org InputProto protocol headers.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.3</li>
+ <li style="white-space: nowrap;">2.3-foss-2015g</li>
+ <li style="white-space: nowrap;">2.3-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>kbproto</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X.org KBProto protocol headers.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.0.6</li>
+ <li style="white-space: nowrap;">1.0.6-foss-2015g</li>
+ <li style="white-space: nowrap;">1.0.6-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libGLU</b><br />
+ <a href="ftp://ftp.freedesktop.org/pub/mesa/glu/">ftp://ftp.freedesktop.org/pub/mesa/glu/</a>
+ </td>
+ <td>The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. </td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">9.0.0-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libICE</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X Inter-Client Exchange library for freedesktop.org</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.0.9</li>
+ <li style="white-space: nowrap;">1.0.9-foss-2015g</li>
+ <li style="white-space: nowrap;">1.0.9-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libX11</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X11 client-side library</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.6.2-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.6.2-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.6.2-foss-2015g-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.6.2-intel-2015b-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libXau</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>The libXau package contains a library implementing the X11 Authorization Protocol.
+This is useful for restricting client access to the display.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.0.8</li>
+ <li style="white-space: nowrap;">1.0.8-foss-2015g</li>
+ <li style="white-space: nowrap;">1.0.8-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libXdamage</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X Damage extension library</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.1.4-foss-2015g-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libXdmcp</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is
+useful for allowing clients to interact with the X Display Manager.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.1.2</li>
+ <li style="white-space: nowrap;">1.1.2-foss-2015g</li>
+ <li style="white-space: nowrap;">1.1.2-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libXext</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>Common X Extensions library</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.3.2-Python-2.7.8</li>
+ <li style="white-space: nowrap;">1.3.3</li>
+ <li style="white-space: nowrap;">1.3.3-foss-2015g</li>
+ <li style="white-space: nowrap;">1.3.3-foss-2015g-Python-2.7.9</li>
+ <li style="white-space: nowrap;">1.3.3-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libXfixes</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X Fixes extension library</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">5.0.1-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libXfont</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X font libary</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.5.1-foss-2015g-Python-2.7.9</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libXft</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X11 client-side library</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.3.2-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libXinerama</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>Xinerama multiple monitor library</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.1.3-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libXrender</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>X11 client-side library</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.9.8-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>libXt</b><br />
+ <a href="http://www.freedesktop.org/wiki/Software/xlibs">http://www.freedesktop.org/wiki/Software/xlibs</a>
+ </td>
+ <td>libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are
+ based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">1.1.4-foss-2015g-libX11-1.6.2</li>
+ <li style="white-space: nowrap;">1.1.4-intel-2015b-libX11-1.6.2</li>
+ <li style="white-space: nowrap;">1.1.4-libX11-1.6.2</li>
+ <li style="white-space: nowrap;">1.1.5-foss-2015g</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>motif</b><br />
+ <a href="http://motif.ics.com/">http://motif.ics.com/</a>
+ </td>
+ <td>Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building
+ applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems.
+ It was the standard toolkit for the Common Desktop Environment and thus for Unix.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">2.3.4-foss-2015g-libX11-1.6.2</li>
+ <li style="white-space: nowrap;">2.3.4-intel-2015b-libX11-1.6.2</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>p4vasp</b><br />
+ <a href="http://www.p4vasp.at">http://www.p4vasp.at</a>
+ </td>
+ <td>p4vasp is a visualization suite for the Vienna Ab-initio Simulation Package
+ (VASP). It contains an extensible GUI framework, that can be used to view
+ material structure, density of states, band-structure and more.
+</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.3.29-GNU-4.9.3-2.25</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <b>pixman</b><br />
+ <a href="http://www.pixman.org/">http://www.pixman.org/</a>
+ </td>
+ <td>Pixman is a low-level software library for pixel manipulation, providing features such as image
+compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.</td>
+ <td>
+ <ul>
+ <li style="white-space: nowrap;">0.32.6-foss-2015b</li>
+ <li style="white-space: nowrap;">0.32.6-intel-2015b</li>
+ </ul>
+ </td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+
+</div>
+
+ </div>
+
+
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+<li class="navTreeItem visualNoMarker navTreeCurrentNode section-list_of_modules">
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+<li class="navTreeItem visualNoMarker section-compute-nodes">
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+<li class="navTreeItem visualNoMarker navTreeFolderish section-software">
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+ <a href="software.html" title="In this section we provide overview of installed software and its usage.
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+ </a>
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+ </a>
+
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+</li>
+
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+<li class="navTreeItem visualNoMarker navTreeFolderish section-pbspro-documentation">
+
+
+
+
+ <a href="../pbspro-documentation.html" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder">
+
+ <span>PBSPro Documentation</span>
+ </a>
+
+
+
+
+</li>
+
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+
+ </ul>
+ <span class="portletBottomLeft"></span>
+ <span class="portletBottomRight"></span>
+ </dd>
+</dl>
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diff --git a/docs.it4i.cz/salomon/list_of_modules.md b/docs.it4i.cz/salomon/list_of_modules.md
index f031e2a0a..af6570b6b 100644
--- a/docs.it4i.cz/salomon/list_of_modules.md
+++ b/docs.it4i.cz/salomon/list_of_modules.md
@@ -363,7 +363,7 @@ Categories
<tr class="odd">
<td align="left"><strong>NWChem</strong><br />
<a href="http://www.nwchem-sw.org" class="uri">http://www.nwchem-sw.org</a></td>
-<td align="left">NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handlebiomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity.</td>
+<td align="left">NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity.</td>
<td align="left"><ul>
<li>6.3.revision2-2013-10-17-Python-2.7.8</li>
<li>6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8</li>
@@ -653,7 +653,7 @@ Categories
<tr class="odd">
<td align="left"><strong>Valgrind</strong><br />
<a href="http://valgrind.org/downloads/" class="uri">http://valgrind.org/downloads/</a></td>
-<td align="left">ValgrindDebugging and profiling tools</td>
+<td align="left">Valgrind: Debugging and profiling tools</td>
<td align="left"><ul>
<li>3.11.0-foss-2015b</li>
<li>3.11.0-intel-2015b</li>
@@ -703,7 +703,7 @@ Categories
<tr class="even">
<td align="left"><strong>Automake</strong><br />
<a href="http://www.gnu.org/software/automake/automake.html" class="uri">http://www.gnu.org/software/automake/automake.html</a></td>
-<td align="left">AutomakeGNU Standards-compliant Makefile generator</td>
+<td align="left">Automake: GNU Standards-compliant Makefile generator</td>
<td align="left"><ul>
<li>1.15</li>
<li>1.15-GCC-4.9.3-2.25</li>
@@ -717,7 +717,7 @@ Categories
<tr class="odd">
<td align="left"><strong>Autotools</strong><br />
<a href="http://autotools.io" class="uri">http://autotools.io</a></td>
-<td align="left">This bundle collect the standard GNU build toolsAutoconf, Automake and libtool</td>
+<td align="left">This bundle collect the standard GNU build tools: Autoconf, Automake and libtool</td>
<td align="left"><ul>
<li>20150215</li>
<li>20150215-GCC-4.9.3-2.25</li>
@@ -849,7 +849,7 @@ Categories
<tr class="odd">
<td align="left"><strong>SQLite</strong><br />
<a href="http://www.sqlite.org/" class="uri">http://www.sqlite.org/</a></td>
-<td align="left">SQLiteSQL Database Engine in a C Library</td>
+<td align="left">SQLite: SQL Database Engine in a C Library</td>
<td align="left"><ul>
<li>3.10.1-foss-2015g</li>
<li>3.8.10.2-GCC-4.9.3-2.25</li>
@@ -941,7 +941,7 @@ Categories
<tr class="even">
<td align="left"><strong>make</strong><br />
<a href="http://www.gnu.org/software/make/make.html" class="uri">http://www.gnu.org/software/make/make.html</a></td>
-<td align="left">make-3.82GNU version of make utility</td>
+<td align="left">make-3.82: GNU version of make utility</td>
<td align="left"><ul>
<li>3.82</li>
<li>3.82-intel-2015b</li>
@@ -1188,7 +1188,7 @@ Categories
<tr class="even">
<td align="left"><strong>NASM</strong><br />
<a href="http://www.nasm.us/" class="uri">http://www.nasm.us/</a></td>
-<td align="left">NASMGeneral-purpose x86 assembler</td>
+<td align="left">NASM: General-purpose x86 assembler</td>
<td align="left"><ul>
<li>2.11.05</li>
<li>2.11.05-foss-2015b</li>
@@ -1385,7 +1385,7 @@ Categories
<tr class="even">
<td align="left"><strong>LibTIFF</strong><br />
<a href="http://www.remotesensing.org/libtiff/" class="uri">http://www.remotesensing.org/libtiff/</a></td>
-<td align="left">tiffLibrary and tools for reading and writing TIFF data files</td>
+<td align="left">tiff: Library and tools for reading and writing TIFF data files</td>
<td align="left"><ul>
<li>4.0.3-intel-2015b</li>
</ul></td>
@@ -1606,7 +1606,7 @@ Categories
<tr class="even">
<td align="left"><strong>spatialindex</strong><br />
<a href="https://libspatialindex.github.io/index.html" class="uri">https://libspatialindex.github.io/index.html</a></td>
-<td align="left">The purpose of this library is to provide* An extensible framework that will support robust spatial indexing methods. * Support for sophisticated spatial queries. Range, point location, nearest neighbor and k-nearest neighbor as well as parametric queries (defined by spatial constraints) should be easy to deploy and run. * Easy to use interfaces for inserting, deleting and updating information.</td>
+<td align="left">The purpose of this library is to provide: * An extensible framework that will support robust spatial indexing methods. * Support for sophisticated spatial queries. Range, point location, nearest neighbor and k-nearest neighbor as well as parametric queries (defined by spatial constraints) should be easy to deploy and run. * Easy to use interfaces for inserting, deleting and updating information.</td>
<td align="left"><ul>
<li>1.8.5-foss-2015g</li>
</ul></td>
@@ -1773,7 +1773,7 @@ Categories
<tr class="odd">
<td align="left"><strong>numpy</strong><br />
<a href="http://www.numpy.org" class="uri">http://www.numpy.org</a></td>
-<td align="left">NumPy is the fundamental package for scientific computing with Python. It contains among other thingsa powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.</td>
+<td align="left">NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.</td>
<td align="left"><ul>
<li>1.8.2-intel-2015b-Python-2.7.11</li>
<li>1.8.2-intel-2015b-Python-2.7.9</li>
@@ -2310,7 +2310,7 @@ Categories
<tr class="odd">
<td align="left"><strong>prace</strong><br />
<a href="http://www.prace-ri.eu/PRACE-Common-Production" class="uri">http://www.prace-ri.eu/PRACE-Common-Production</a></td>
-<td align="left">**** PRACE Common Production Environment (PCPE) **** Initialisation of the PRACE common production environment. This allows you to assume that the following tools/libraries are available by default in your PATH/environment. * Fortran, C, C++ Compilers * MPI * BLAS, LAPACK, BLACS, ScaLAPACK * FFTW * HDF5, NetCDF The compiler commands on are* mpif90 - Fortran compiler * mpicc - C compiler * mpicxx - C++ compiler For more information on the PCPE please see the documentation athttp://www.prace-ri.eu/PRACE-Common-Production For help using this system, please see Local User Guide available athttp://prace-ri.eu/Best-Practice-Guide-Anselm-HTML</td>
+<td align="left">**** PRACE Common Production Environment (PCPE) **** Initialisation of the PRACE common production environment. This allows you to assume that the following tools/libraries are available by default in your PATH/environment. * Fortran, C, C++ Compilers * MPI * BLAS, LAPACK, BLACS, ScaLAPACK * FFTW * HDF5, NetCDF The compiler commands on are: * mpif90 - Fortran compiler * mpicc - C compiler * mpicxx - C++ compiler For more information on the PCPE please see the documentation at: http://www.prace-ri.eu/PRACE-Common-Production For help using this system, please see Local User Guide available at: http://prace-ri.eu/Best-Practice-Guide-Anselm-HTML</td>
<td align="left"><ul>
<li>20160107-intel-2016.01</li>
</ul></td>
@@ -2506,7 +2506,7 @@ Categories
<tr class="even">
<td align="left"><strong>XZ</strong><br />
<a href="http://tukaani.org/xz/" class="uri">http://tukaani.org/xz/</a></td>
-<td align="left">xzXZ utilities</td>
+<td align="left">xz: XZ utilities</td>
<td align="left"><ul>
<li>5.2.2-intel-2016.01</li>
</ul></td>
@@ -2514,7 +2514,7 @@ Categories
<tr class="odd">
<td align="left"><strong>binutils</strong><br />
<a href="http://directory.fsf.org/project/binutils/" class="uri">http://directory.fsf.org/project/binutils/</a></td>
-<td align="left">binutilsGNU binary utilities</td>
+<td align="left">binutils: GNU binary utilities</td>
<td align="left"><ul>
<li>2.25</li>
<li>2.25-GCC-4.9.3-binutils-2.25</li>
@@ -2610,7 +2610,7 @@ Categories
<tr class="odd">
<td align="left"><strong>parallel</strong><br />
<a href="http://savannah.gnu.org/projects/parallel/" class="uri">http://savannah.gnu.org/projects/parallel/</a></td>
-<td align="left">parallelBuild and execute shell commands in parallel</td>
+<td align="left">parallel: Build and execute shell commands in parallel</td>
<td align="left"><ul>
<li>20150322-GNU-5.1.0-2.25</li>
</ul></td>
diff --git a/docs.it4i.cz/salomon/network-1.html b/docs.it4i.cz/salomon/network-1.html
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+ <div id="parent-fieldname-text-40fbce9e3def4e3882ed5a3627aeb8a1" class="">
+ <p>All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube <a class="external-link" href="http://en.wikipedia.org/wiki/InfiniBand" target="_self" title="">Infiniband</a> network and by Gigabit <a class="external-link" href="http://en.wikipedia.org/wiki/Ethernet" target="_self" title="">Ethernet</a> network. Only <a class="external-link" href="http://en.wikipedia.org/wiki/InfiniBand" target="_self" title="">Infiniband</a> network may be used to transfer user data.</p>
+<h2 class=" ">Infiniband Network</h2>
+<p>All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube <a class="external-link" href="http://en.wikipedia.org/wiki/InfiniBand" target="_self" title="">Infiniband</a> network (56 Gbps). The network topology is a <a href="network-1/7d-enhanced-hypercube.html" title="" target="_self" class="internal-link">7D Enhanced hypercube</a>.</p>
+<p>Read more about schematic representation of the Salomon cluster <a href="network-1/ib-single-plane-topology.html" title="" target="_self" class="internal-link">IB single-plain topology</a> (<a href="network-1/7d-enhanced-hypercube.html" title="" target="_self" class="internal-link">hypercube dimension</a> 0).<a href="network-1/IB single-plane topology - Accelerated nodes.pdf/view.html" title="" class="state-missing-value contenttype-file"><span></span></a> </p>
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+<li class="navTreeItem visualNoMarker section-ib-single-plane-topology-icex-mcell-pdf"></li>
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+<p>The compute nodes may be accessed via the Infiniband network using ib0 network interface, in address range 10.17.0.0 (mask 255.255.224.0). The MPI may be used to establish native Infiniband connection among the nodes.</p>
+<p class="hiddenForView">The network provides <strong>2170MB/s</strong> transfer rates via the TCP connection (single stream) and up to <strong>3600MB/s</strong> via native Infiniband protocol.</p>
+<p>Â </p>
+<h2 class=" ">Example</h2>
+<pre class="prettyprint lang-sh">$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob<br />$ qstat -n -u username<br /> Req'd Req'd Elap<br />Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time<br />--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----<br />15209.isrv5 username qexp Name0 5530 4 96 -- 01:00 R 00:00<br /> r4i1n0/0*24+r4i1n1/0*24+r4i1n2/0*24+r4i1n3/0*24</pre>
+<p class=" ">In this example, we access the node r4i1n0 by Infiniband network via the ib0 interface.</p>
+<pre class="prettyprint lang-sh">$ ssh 10.17.35.19</pre>
+<p class=" ">In this example, we <span style="text-align: start; float: none; ">get information of the Infiniband network.</span></p>
+<pre class="prettyprint lang-sh">$ ifconfig<br />....<br />inet addr:10.17.35.19....<br />....<br /><br />$ ip addr show ib0<br /><br />....<br />inet 10.17.35.19....<br />....</pre>
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diff --git a/docs.it4i.cz/salomon/network-1.md b/docs.it4i.cz/salomon/network-1.md
index 22fc9e1c8..9f33cbadf 100644
--- a/docs.it4i.cz/salomon/network-1.md
+++ b/docs.it4i.cz/salomon/network-1.md
@@ -63,7 +63,7 @@ ib0 interface.
$ ssh 10.17.35.19
```
-In this example, we <span style="text-alignstart; floatnone; ">get
+In this example, we <span style="text-align: start; float: none; ">get
information of the Infiniband network.</span>
```
@@ -81,4 +81,3 @@ inet 10.17.35.19....
-
diff --git a/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.html b/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.html
new file mode 100644
index 000000000..7c47fb1b7
--- /dev/null
+++ b/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.html
@@ -0,0 +1,786 @@
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+ 7D Enhanced Hypercube
+ </h1>
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+
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+</div>
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+ <p class=" "><a href="../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_self" class="internal-link">More about Job submission - Placement by IB switch / Hypercube dimension.</a></p>
+<p>Nodes may be selected via the PBS resource attribute ehc_[1-7]d .</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>Hypercube dimension</th><th><span class="pun">node_group_key</span></th></tr>
+<tr class="even">
+<td>1D</td>
+<td>ehc_1d</td>
+</tr>
+<tr class="odd">
+<td>2D</td>
+<td>ehc_2d</td>
+</tr>
+<tr class="even">
+<td>3D</td>
+<td>ehc_3d</td>
+</tr>
+<tr class="odd">
+<td>4D</td>
+<td>ehc_4d</td>
+</tr>
+<tr class="even">
+<td>5D</td>
+<td>ehc_5d</td>
+</tr>
+<tr class="odd">
+<td>6D</td>
+<td>ehc_6d</td>
+</tr>
+<tr class="even">
+<td>7D</td>
+<td>ehc_7d</td>
+</tr>
+</tbody>
+</table>
+<p><a href="ib-single-plane-topology.html" title="" target="_self" class="internal-link">Schematic representation of the Salomon cluster IB single-plain topology represents <span class="internal-link">hypercube dimension</span> 0</a>.</p>
+<h3 class=" ">7D Enhanced Hypercube</h3>
+<p><a href="7D_Enhanced_hypercube.png" title="" target="_blank" class="internal-link"><img alt="7D_Enhanced_hypercube.png" src="https://docs.it4i.cz/salomon/network-1/7D_Enhanced_hypercube.png/@@images/03693a91-beec-4d04-bf11-7d89c20420a6.png" title="7D_Enhanced_hypercube.png" class="image-inline" /></a></p>
+<p>Â </p>
+<table class="plain">
+<tbody>
+<tr><th>Node type</th><th>Count</th><th>Short name</th><th>Long name</th><th>Rack</th></tr>
+<tr>
+<td>M-Cell compute nodes w/o accelerator</td>
+<td>576</td>
+<td>cns1 -cns576</td>
+<td>r1i0n0 - r4i7n17</td>
+<td>1-4</td>
+</tr>
+<tr>
+<td>compute nodes MIC accelerated</td>
+<td>432</td>
+<td>cns577 - cns1008</td>
+<td>r21u01n577 - r37u31n1008</td>
+<td>21-38</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" ">Â IB Topology</h3>
+<p>Â <a href="Salomon_IB_topology.png" title="" target="_blank" class="internal-link"><img alt=" Salomon IB topology" src="https://docs.it4i.cz/salomon/network-1/Salomon_IB_topology.png/@@images/93b8536b-60de-438d-ac4d-a33a843c4eb2.png" title=" Salomon IB topology" class="image-inline" /></a></p>
+
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index 95b9fd4ce..e35b1fd45 100644
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+ <p>A complete M-Cell assembly consists of four compute racks. Each rack contains 4x physical IRUs - Independent rack units. Using one dual socket node per one blade slot leads to 8 logical IRUs. Each rack contains 4x2 SGI ICE X IB Premium Blades.</p>
+<p>The SGI ICE X IB Premium Blade provides the first level of interconnection via dual 36-port Mellanox FDR InfiniBand ASIC switch with connections as follows:</p>
+<ul>
+<li>9 ports from each switch chip connect to the unified backplane, to connect the 18 compute node slots</li>
+<li>3 ports on each chip provide connectivity between the chips</li>
+<li>24 ports from each switch chip connect to the external bulkhead, for a total of 48</li>
+</ul>
+<h3><strong>IB single-plane topology - ICEX Mcell</strong></h3>
+<p>Each colour in each physical IRU represents one dual-switch ASIC switch.</p>
+<p><a href="ib-single-plane-topology/IB single-plane topology - ICEX Mcell.pdf" title="" target="_self" class="internal-link"><img alt="Mcell" src="ib-single-plane-topology/IBsingleplanetopologyICEXMcellsmall.png" title="Mcell" class="image-inline" /></a></p>
+<p>Â </p>
+<h3>IB single-plane topology - Accelerated nodes</h3>
+<p>Each of the 3 inter-connected D racks are equivalent to one half of Mcell rack. 18x D rack with MIC accelerated nodes [r21-r38] are equivalent to 3 Mcell racks as shown in a diagram <a href="7d-enhanced-hypercube.html" title="" target="_self" class="internal-link">7D Enhanced Hypercube</a>.</p>
+<p>As shown in a diagram <a href="Salomon_IB_topology.png" title="" target="_self" class="internal-link">IB Topology</a>:</p>
+<ul>
+<li>Racks 21, 22, 23, 24, 25, 26 are equivalent to one Mcell rack.</li>
+<li>Racks 27, 28, 29, 30, 31, 32 are equivalent to one Mcell rack.</li>
+<li>Racks 33, 34, 35, 36, 37, 38 are equivalent to one Mcell rack.</li>
+</ul>
+<p><a href="ib-single-plane-topology/IB single-plane topology - Accelerated nodes.pdf" title="" target="_self" class="internal-link"><img alt="Accelerated nodes" src="ib-single-plane-topology/IBsingleplanetopologyAcceleratednodessmall.png" title="Accelerated nodes" class="image-inline" /></a></p>
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diff --git a/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md b/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
index 0c0ccb47f..c803b9ae8 100644
--- a/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
+++ b/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
@@ -49,4 +49,3 @@ nodes](ib-single-plane-topology/IBsingleplanetopologyAcceleratednodessmall.png "
-
diff --git a/docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB single-plane topology - ICEX Mcell.pdf/view.html b/docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB single-plane topology - ICEX Mcell.pdf/view.html
new file mode 100644
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+ <p>A complete M-Cell assembly consists of four compute racks. Each rack contains 4x physical IRUs - Independent rack units. Using one dual socket node per one blade slot leads to 8 logical IRUs. Each rack contains 4x2 SGI ICE X IB Premium Blades.</p>
+<p>The SGI ICE X IB Premium Blade provides the first level of interconnection via dual 36-port Mellanox FDR InfiniBand ASIC switch with connections as follows:</p>
+<ul>
+<li>9 ports from each switch chip connect to the unified backplane, to connect the 18 compute node slots</li>
+<li>3 ports on each chip provide connectivity between the chips</li>
+<li>24 ports from each switch chip connect to the external bulkhead, for a total of 48</li>
+</ul>
+<h3><strong>IB single-plane topology - ICEX Mcell</strong></h3>
+<p>Each colour in each physical IRU represents one dual-switch ASIC switch.</p>
+<p><a href="IB single-plane topology - ICEX Mcell.pdf" title="" target="_self" class="internal-link"><img alt="Mcell" src="IBsingleplanetopologyICEXMcellsmall.png" title="Mcell" class="image-inline" /></a></p>
+<p>Â </p>
+<h3>IB single-plane topology - Accelerated nodes</h3>
+<p>Each of the 3 inter-connected D racks are equivalent to one half of Mcell rack. 18x D rack with MIC accelerated nodes [r21-r38] are equivalent to 3 Mcell racks as shown in a diagram <a href="../7d-enhanced-hypercube.html" title="" target="_self" class="internal-link">7D Enhanced Hypercube</a>.</p>
+<p>As shown in a diagram <a href="../Salomon_IB_topology.png" title="" target="_self" class="internal-link">IB Topology</a>:</p>
+<ul>
+<li>Racks 21, 22, 23, 24, 25, 26 are equivalent to one Mcell rack.</li>
+<li>Racks 27, 28, 29, 30, 31, 32 are equivalent to one Mcell rack.</li>
+<li>Racks 33, 34, 35, 36, 37, 38 are equivalent to one Mcell rack.</li>
+</ul>
+<p><a href="IB single-plane topology - Accelerated nodes.pdf" title="" target="_self" class="internal-link"><img alt="Accelerated nodes" src="IBsingleplanetopologyAcceleratednodessmall.png" title="Accelerated nodes" class="image-inline" /></a></p>
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diff --git a/docs.it4i.cz/salomon/network-1/ib-single-plane-topology/schematic-representation-of-the-salomon-cluster-ib-single-plain-topology-hypercube-dimension-0.md b/docs.it4i.cz/salomon/network-1/ib-single-plane-topology/schematic-representation-of-the-salomon-cluster-ib-single-plain-topology-hypercube-dimension-0.md
index b562b641e..438318c84 100644
--- a/docs.it4i.cz/salomon/network-1/ib-single-plane-topology/schematic-representation-of-the-salomon-cluster-ib-single-plain-topology-hypercube-dimension-0.md
+++ b/docs.it4i.cz/salomon/network-1/ib-single-plane-topology/schematic-representation-of-the-salomon-cluster-ib-single-plain-topology-hypercube-dimension-0.md
@@ -49,4 +49,3 @@ nodes](IBsingleplanetopologyAcceleratednodessmall.png "Accelerated nodes")](IB%2
-
diff --git a/docs.it4i.cz/salomon/network-1/network.html b/docs.it4i.cz/salomon/network-1/network.html
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+<h2 class=" ">Infiniband Network</h2>
+<p>All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube <a class="external-link" href="http://en.wikipedia.org/wiki/InfiniBand" target="_self" title="">Infiniband</a> network (56 Gbps). The network topology is a <a href="7d-enhanced-hypercube.html" title="" target="_self" class="internal-link">7D Enhanced hypercube</a>.</p>
+<p>Read more about schematic representation of the Salomon cluster <a href="ib-single-plane-topology.html" title="" target="_self" class="internal-link">IB single-plain topology</a> (<a href="7d-enhanced-hypercube.html" title="" target="_self" class="internal-link">hypercube dimension</a> 0).<a href="IB single-plane topology - Accelerated nodes.pdf/view.html" title="" class="state-missing-value contenttype-file"><span></span></a> </p>
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+<p>The compute nodes may be accessed via the Infiniband network using ib0 network interface, in address range 10.17.0.0 (mask 255.255.224.0). The MPI may be used to establish native Infiniband connection among the nodes.</p>
+<p class="hiddenForView">The network provides <strong>2170MB/s</strong> transfer rates via the TCP connection (single stream) and up to <strong>3600MB/s</strong> via native Infiniband protocol.</p>
+<p>Â </p>
+<h2 class=" ">Example</h2>
+<pre class="prettyprint lang-sh">$ qsub -q qexp -l select=4:ncpus=16 -N Name0 ./myjob<br />$ qstat -n -u username<br /> Req'd Req'd Elap<br />Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time<br />--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----<br />15209.isrv5 username qexp Name0 5530 4 96 -- 01:00 R 00:00<br /> r4i1n0/0*24+r4i1n1/0*24+r4i1n2/0*24+r4i1n3/0*24</pre>
+<p class=" ">In this example, we access the node r4i1n0 by Infiniband network via the ib0 interface.</p>
+<pre class="prettyprint lang-sh">$ ssh 10.17.35.19</pre>
+<p class=" ">In this example, we <span style="text-align: start; float: none; ">get information of the Infiniband network.</span></p>
+<pre class="prettyprint lang-sh">$ ifconfig<br />....<br />inet addr:10.17.35.19....<br />....<br /><br />$ ip addr show ib0<br /><br />....<br />inet 10.17.35.19....<br />....</pre>
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diff --git a/docs.it4i.cz/salomon/network-1/network.md b/docs.it4i.cz/salomon/network-1/network.md
index fc39403d4..33912ca68 100644
--- a/docs.it4i.cz/salomon/network-1/network.md
+++ b/docs.it4i.cz/salomon/network-1/network.md
@@ -61,7 +61,7 @@ ib0 interface.
$ ssh 10.17.35.19
```
-In this example, we <span style="text-alignstart; floatnone; ">get
+In this example, we <span style="text-align: start; float: none; ">get
information of the Infiniband network.</span>
```
@@ -79,4 +79,3 @@ inet 10.17.35.19....
-
diff --git a/docs.it4i.cz/salomon/prace.html b/docs.it4i.cz/salomon/prace.html
new file mode 100644
index 000000000..34cb6ef24
--- /dev/null
+++ b/docs.it4i.cz/salomon/prace.html
@@ -0,0 +1,962 @@
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+ <dl class="portalMessage info" id="kssPortalMessage" style="display:none">
+ <dt>Info</dt>
+ <dd></dd>
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+ <h1 id="parent-fieldname-title" class="documentFirstHeading">
+ PRACE User Support
+ </h1>
+
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+ <div id="viewlet-below-content-title">
+</div>
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+<dl id="document-toc" class="portlet toc" style="display: none">
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+ <div id="content-core">
+
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+ <div id="parent-fieldname-text-d1fb69d45afe43cea052f14182ce60a6" class="">
+ <h2 class=" ">Intro</h2>
+<p>PRACE users coming to Salomon as to TIER-1 system offered through the DECI calls are in general treated as standard users and so most of the general documentation applies to them as well. This section shows the main differences for quicker orientation, but often uses references to the original documentation. PRACE users who don't undergo the full procedure (including signing the IT4I AuP on top of the PRACE AuP) will not have a password and thus access to some services intended for regular users. This can lower their comfort, but otherwise they should be able to use the TIER-1 system as intended. Please see the <a href="../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html" title="" target="_self" class="internal-link">Obtaining Login Credentials section</a>, if the same level of access is required.</p>
+<p>All general <a class="external-link" href="http://www.prace-ri.eu/user-documentation/" target="_self" title="">PRACE User Documentation</a> should be read before continuing reading the local documentation here.</p>
+<h2 class=" "><a name="help-and-support"></a><a name="PRACE_support"></a>Help and Support</h2>
+<p>If you have any troubles, need information, request support or want to install additional software, please use <a class="external-link" href="http://www.prace-ri.eu/helpdesk-guide264/" target="_self" title="">PRACE Helpdesk</a>.</p>
+<p>Information about the local services are provided in the <a href="introduction.html" title="" target="_self" class="internal-link">introduction of general user documentation</a>. Please keep in mind, that standard PRACE accounts don't have a password to access the web interface of the local (IT4Innovations) request tracker and thus a new ticket should be created by sending an e-mail to support[at]it4i.cz.</p>
+<h2 class=" ">Obtaining Login Credentials</h2>
+<p>In general PRACE users already have a PRACE account setup through their HOMESITE (institution from their country) as a result of rewarded PRACE project proposal. This includes signed PRACE AuP, generated and registered certificates, etc.</p>
+<p>If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on the Salomon cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so please see the corresponding <a href="../get-started-with-it4innovations/obtaining-login-credentials.html" title="" target="_self" class="internal-link">section of the general documentation here</a>.</p>
+<h2 class=" ">Accessing the cluster</h2>
+<h3 class=" ">Access with GSI-SSH</h3>
+<p>For all PRACE users the method for interactive access (login) and data transfer based on grid services from Globus Toolkit (GSI SSH and GridFTP) is supported.</p>
+<p>The user will need a valid certificate and to be present in the PRACE LDAP (please contact your HOME SITE or the primary investigator of your project for LDAP account creation).</p>
+<p>Most of the information needed by PRACE users accessing the Salomon TIER-1 system can be found here:</p>
+<ul>
+<li><a class="external-link" href="http://www.prace-ri.eu/Users-General-FAQs" target="_self" title="">General user's FAQ</a></li>
+<li><a class="external-link" href="http://www.prace-ri.eu/Certificates-FAQ" target="_self" title="">Certificates FAQ</a></li>
+<li><a class="external-link" href="http://www.prace-ri.eu/Interactive-Access-Using-gsissh" target="_self" title="">Interactive access using GSISSH</a></li>
+<li><a class="external-link" href="http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details" target="_self" title="">Data transfer with GridFTP</a></li>
+<li><a class="external-link" href="http://www.prace-ri.eu/Data-Transfer-with-gtransfer" target="_self" title="">Data transfer with gtransfer</a></li>
+</ul>
+<p class=" ">Â </p>
+<p class=" ">Before you start to use any of the services don't forget to create a proxy certificate from your certificate:</p>
+<pre class=" ">$ grid-proxy-init</pre>
+<p>To check whether your proxy certificate is still valid (by default it's valid 12 hours), use:</p>
+<pre class=" ">$ grid-proxy-info</pre>
+<p>Â </p>
+<p>To access Salomon cluster, two login nodes running GSI SSH service are available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).</p>
+<p><strong>Access from PRACE network:</strong></p>
+<p>It is recommended to use the single DNS name <span class="monospace">salomon-prace.it4i.cz</span> which is distributed between the two login nodes. If needed, user can login directly to one of the login nodes. The addresses are:</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>Login address</th><th>Port</th><th>Protocol</th><th>Login node</th></tr>
+<tr class="even">
+<td>salomon-prace.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login1, login2, login3 or login4</td>
+</tr>
+<tr class="odd">
+<td>login1-prace.salomon.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login1</td>
+</tr>
+<tr class="even">
+<td>login2-prace.salomon.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login2</td>
+</tr>
+<tr class="odd">
+<td>login3-prace.salomon.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login3</td>
+</tr>
+<tr class="even">
+<td>login4-prace.salomon.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login4</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<pre class=" ">$ gsissh -p 2222 salomon-prace.it4i.cz</pre>
+<p>When logging from other PRACE system, the prace_service script can be used:</p>
+<pre class=" ">$ gsissh `prace_service -i -s salomon`</pre>
+<p>Â </p>
+<p><strong>Access from public Internet:</strong></p>
+<p>It is recommended to use the single DNS name <span class="monospace">salomon.it4i.cz</span> which is distributed between the two login nodes. If needed, user can login directly to one of the login nodes. The addresses are:</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>Login address</th><th>Port</th><th>Protocol</th><th>Login node</th></tr>
+<tr class="even">
+<td>salomon.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login1, login2, login3 or login4</td>
+</tr>
+<tr class="odd">
+<td>login1.salomon.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login1</td>
+</tr>
+<tr class="even">
+<td>login2.salomon.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login2</td>
+</tr>
+<tr class="odd">
+<td>login3.salomon.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login3</td>
+</tr>
+<tr class="even">
+<td>login4.salomon.it4i.cz</td>
+<td>2222</td>
+<td>gsissh</td>
+<td>login4</td>
+</tr>
+</tbody>
+</table>
+<pre class=" ">$ gsissh -p 2222 salomon.it4i.cz</pre>
+<p>When logging from other PRACE system, the <span class="monospace">prace_service</span> script can be used:</p>
+<pre class=" ">$ gsissh `prace_service -e -s salomon`</pre>
+<p>Â </p>
+<p>Although the preferred and recommended file transfer mechanism is <a class="anchor-link" href="prace.html#file-transfers" target="_self" title="">using GridFTP</a>, the GSI SSH implementation on Salomon supports also SCP, so for small files transfer gsiscp can be used:</p>
+<pre>$ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ salomon.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_</pre>
+<pre>$ gsiscp -P 2222 salomon.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_ </pre>
+<pre>$ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ salomon-prace.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_</pre>
+<pre>$ gsiscp -P 2222 salomon-prace.it4i.cz:_SALOMON_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_ </pre>
+<h3 class=" ">Access to X11 applications (VNC)</h3>
+<p>If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, please see the <a href="../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">section in general documentation</a>.</p>
+<p>If the user uses GSI SSH based access, then the procedure is similar to the SSH based access (<a href="../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">look here</a>), only the port forwarding must be done using GSI SSH:</p>
+<pre class=" ">$ gsissh -p 2222 salomon.it4i.cz -L 5961:localhost:5961</pre>
+<h3 class=" ">Access with SSH</h3>
+<p class=" ">After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information please see the <a href="accessing-the-cluster/shell-and-data-access/shell-and-data-access.html" title="" target="_self" class="internal-link">section in general documentation</a>.</p>
+<h2 class=" "><a name="file-transfers"></a>File transfers</h2>
+<p>PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see <a href="accessing-the-cluster/shell-and-data-access/shell-and-data-access.html" title="" target="_self" class="internal-link">the section in the general documentation</a>.</p>
+<p>Apart from the standard mechanisms, for PRACE users to transfer data to/from Salomon cluster, a GridFTP server running Globus Toolkit GridFTP service is available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).</p>
+<p>There's one control server and three backend servers for striping and/or backup in case one of them would fail.</p>
+<p><strong>Access from PRACE network:</strong></p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>Login address</th><th>Port</th><th>Node role</th></tr>
+<tr class="even">
+<td>gridftp-prace.salomon.it4i.cz</td>
+<td>2812</td>
+<td>Front end /control server</td>
+</tr>
+<tr class="odd">
+<td>lgw1-prace.salomon.it4i.cz</td>
+<td>2813</td>
+<td>Backend / data mover server</td>
+</tr>
+<tr class="even">
+<td>lgw2-prace.salomon.it4i.cz</td>
+<td>2813</td>
+<td>Backend / data mover server</td>
+</tr>
+<tr class="odd">
+<td>lgw3-prace.salomon.it4i.cz</td>
+<td>2813</td>
+<td>Backend / data mover server</td>
+</tr>
+</tbody>
+</table>
+<p>Copy files <strong>to</strong> Salomon by running the following commands on your local machine:</p>
+<pre>$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp-prace.salomon.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_</pre>
+<p>Or by using <span class="monospace">prace_service</span> script:</p>
+<pre>$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -i -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_</pre>
+<p>Copy files <strong>from</strong> Salomon:</p>
+<pre>$ globus-url-copy gsiftp://gridftp-prace.salomon.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_</pre>
+<p>Or by using <span class="monospace">prace_service</span> script:</p>
+<pre>$ globus-url-copy gsiftp://`prace_service -i -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_</pre>
+<p>Â </p>
+<p><strong>Access from public Internet:</strong></p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>Login address</th><th>Port</th><th>Node role</th></tr>
+<tr class="even">
+<td>gridftp.salomon.it4i.cz</td>
+<td>2812</td>
+<td>Front end /control server</td>
+</tr>
+<tr class="odd">
+<td>lgw1.salomon.it4i.cz</td>
+<td>2813</td>
+<td>Backend / data mover server</td>
+</tr>
+<tr class="even">
+<td>lgw2.salomon.it4i.cz</td>
+<td>2813</td>
+<td>Backend / data mover server</td>
+</tr>
+<tr class="odd">
+<td>lgw3.salomon.it4i.cz</td>
+<td>2813</td>
+<td>Backend / data mover server</td>
+</tr>
+</tbody>
+</table>
+<p>Copy files <strong>to</strong> Salomon by running the following commands on your local machine:</p>
+<pre>$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp.salomon.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_</pre>
+<p>Or by using <span class="monospace">prace_service</span> script:</p>
+<pre>$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -e -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_</pre>
+<p>Copy files <strong>from</strong> Salomon:</p>
+<pre>$ globus-url-copy gsiftp://gridftp.salomon.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_</pre>
+<p>Or by using <span class="monospace">prace_service</span> script:</p>
+<pre>$ globus-url-copy gsiftp://`prace_service -e -f salomon`/home/prace/_YOUR_ACCOUNT_ON_SALOMON_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_</pre>
+<p>Â </p>
+<p>Generally both shared file systems are available through GridFTP:</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>File system mount point</th><th>Filesystem</th><th>Comment</th></tr>
+<tr class="even">
+<td>/home</td>
+<td>Lustre</td>
+<td>Default HOME directories of users in format /home/prace/login/</td>
+</tr>
+<tr class="odd">
+<td>/scratch</td>
+<td>Lustre</td>
+<td>Shared SCRATCH mounted on the whole cluster</td>
+</tr>
+</tbody>
+</table>
+<p class=" ">More information about the shared file systems is available <a href="storage.html" title="" target="_self" class="internal-link">here</a>.</p>
+<p class=" ">Please note, that for PRACE users a "prace" directory is used also on the SCRATCH file system.</p>
+<table class="listing" summary="PRACE SCRATCH space">
+<tbody>
+<tr><th>Data type</th><th>Default path</th></tr>
+<tr class="even">
+<td>large project files</td>
+<td>/scratch/work/user/prace/login/</td>
+</tr>
+<tr class="odd">
+<td>large scratch/temporary data</td>
+<td>/scratch/temp/</td>
+</tr>
+</tbody>
+</table>
+<h2 class=" ">Usage of the cluster</h2>
+<p>There are some limitations for PRACE user when using the cluster. By default PRACE users aren't allowed to access special queues in the PBS Pro to have high priority or exclusive access to some special equipment like accelerated nodes and high memory (fat) nodes. There may be also restrictions obtaining a working license for the commercial software installed on the cluster, mostly because of the license agreement or because of insufficient amount of licenses.</p>
+<p>For production runs always use scratch file systems. The available file systems are described <a href="storage/storage.html" title="" target="_self" class="internal-link">here</a>.</p>
+<h3 class=" ">Software, Modules and PRACE Common Production Environment</h3>
+<p>All system wide installed software on the cluster is made available to the users via the modules. The information about the environment and modules usage is in this <a href="environment-and-modules.html" title="" target="_self" class="internal-link">section of general documentation</a>.</p>
+<p>PRACE users can use the "prace" module to use the <a class="external-link" href="http://www.prace-ri.eu/PRACE-common-production" target="_self" title="">PRACE Common Production Environment</a>.</p>
+<pre class=" ">$ module load prace</pre>
+<p>Â </p>
+<h3 class=" ">Resource Allocation and Job Execution</h3>
+<p>General information about the resource allocation, job queuing and job execution is in this <a href="resource-allocation-and-job-execution/introduction.html" title="" target="_self" class="internal-link">section of general documentation</a>.</p>
+<p>For PRACE users, the default production run queue is "qprace". PRACE users can also use two other queues "qexp" and "qfree".</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>queue</th><th>Active project</th><th>Project resources</th><th>Nodes</th><th>priority</th><th>authorization</th><th>walltime<br />default/max</th></tr>
+<tr class="even">
+<td><strong>qexp</strong><br />Express queue</td>
+<td>no</td>
+<td>none required</td>
+<td>32 nodes, max 8 per user</td>
+<td>150</td>
+<td>no</td>
+<td>1 / 1h</td>
+</tr>
+<tr class="odd">
+<td><strong>qprace</strong><br />Production queue</td>
+<td>yes<br /><br /></td>
+<td>> 0</td>
+<td><span>1006 nodes, max 86 per job</span></td>
+<td>0</td>
+<td>no</td>
+<td>24 / 48h</td>
+</tr>
+<tr class="even">
+<td><strong>qfree</strong><br />Free resource queue</td>
+<td>yes</td>
+<td>none required</td>
+<td>752 nodes, max 86 per job</td>
+<td>-1024</td>
+<td>no</td>
+<td>12 / 12h</td>
+</tr>
+</tbody>
+</table>
+<p class=" "><strong>qprace</strong>, the PRACE Production queue<strong></strong>: This queue is intended for normal production runs. It is required that active project with nonzero remaining resources is specified to enter the qprace. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprace is 48 hours. If the job needs longer time, it must use checkpoint/restart functionality.</p>
+<h3 class=" ">Accounting & Quota</h3>
+<p>The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. See <a href="resource-allocation-and-job-execution/resources-allocation-policy.html" title="" target="_self" class="internal-link">example in the general documentation</a>.</p>
+<p>PRACE users should check their project accounting using the <a class="external-link" href="http://www.prace-ri.eu/accounting-report-tool/" target="_self" title="">PRACE Accounting Tool (DART)</a>.</p>
+<p>Users who have undergone the full local registration procedure (including signing the IT4Innovations Acceptable Use Policy) and who have received local password may check at any time, how many core-hours have been consumed by themselves and their projects using the command "it4ifree". Please note that you need to know your user password to use the command and that the displayed core hours are "system core hours" which differ from PRACE "standardized core hours".</p>
+<p class="callout">The <strong>it4ifree</strong> command is a part of it4i.portal.clients package, located here:<br /><a class="external-link" href="https://pypi.python.org/pypi/it4i.portal.clients" target="_self" title="">https://pypi.python.org/pypi/it4i.portal.clients</a></p>
+<pre class=" ">$ it4ifree<br />Password:<br />    PID  Total Used ...by me Free<br />  -------- ------- ------ -------- -------<br />  OPEN-0-0 1500000 400644  225265 1099356<br />  DD-13-1   10000 2606 2606 7394</pre>
+<p class=" ">Â </p>
+<p class=" ">By default file system quota is applied. To check the current status of the quota (separate for HOME and SCRATCH) use</p>
+<pre>$ quota<br />$ lfs quota -u USER_LOGIN /scratch</pre>
+<p class=" ">If the quota is insufficient, please contact the <a class="anchor-link" href="prace.html#help-and-support" target="_self" title="">support</a> and request an increase.</p>
+<p>Â </p>
+<p>Â </p>
+
+ </div>
+
+
+ <!-- <div tal:content="structure here/@@rate-if-you-dare"/> -->
+
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+<li class="navTreeItem visualNoMarker section-list_of_modules">
+
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+<li class="navTreeItem visualNoMarker navTreeFolderish section-resource-allocation-and-job-execution">
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+<li class="navTreeItem visualNoMarker navTreeFolderish section-software">
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+ <a href="software.html" title="In this section we provide overview of installed software and its usage.
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+ </a>
+
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+</li>
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+<li class="navTreeItem visualNoMarker navTreeFolderish section-pbspro-documentation">
+
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+ <a href="../pbspro-documentation.html" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published navTreeFolderish contenttype-folder">
+
+ <span>PBSPro Documentation</span>
+ </a>
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+ <span class="portletBottomLeft"></span>
+ <span class="portletBottomRight"></span>
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diff --git a/docs.it4i.cz/salomon/prace.md b/docs.it4i.cz/salomon/prace.md
index 1caaec157..1270e9a12 100644
--- a/docs.it4i.cz/salomon/prace.md
+++ b/docs.it4i.cz/salomon/prace.md
@@ -329,7 +329,7 @@ users can also use two other queues "qexp" and "qfree".
Free resource queue
---------------------------------------------------------------------------------------------------------------------------------------------
-**qprace**, the PRACE Production queue****This queue is intended for
+**qprace**, the PRACE Production queue****: This queue is intended for
normal production runs. It is required that active project with nonzero
remaining resources is specified to enter the qprace. The queue runs
with medium priority and no special authorization is required to use it.
@@ -387,4 +387,3 @@ increase.
-
diff --git a/docs.it4i.cz/salomon/resource-allocation-and-job-execution.html b/docs.it4i.cz/salomon/resource-allocation-and-job-execution.html
new file mode 100644
index 000000000..4f5667874
--- /dev/null
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution.html
@@ -0,0 +1,771 @@
+
+<!DOCTYPE html>
+
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+ Resource Allocation and Job Execution
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+ <p>To run a <a href="resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_self" class="internal-link">job</a>, <a href="resource-allocation-and-job-execution/resources-allocation-policy.html" title="" target="_self" class="internal-link">computational resources</a> for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive informations about PBS Pro can be found in the <a href="../pbspro-documentation.html" title="" target="_self" class="internal-link">official documentation here</a>, especially in the <a href="../pbspro-documentation/pbspro-users-guide.1" title="" target="_self" class="internal-link">PBS Pro User's Guide</a>.</p>
+<h2 class=" ">Resources Allocation Policy</h2>
+<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. <a href="resource-allocation-and-job-execution/job-priority.html" title="" target="_self" class="internal-link">The Fairshare</a> at Salomon ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:</p>
+<ul>
+<li><strong>qexp</strong>, the Express queue</li>
+<li><strong>qprod</strong>, the Production queue<strong></strong></li>
+<li><strong>qlong</strong>, the Long queue</li>
+<li><strong>qmpp</strong>, the Massively parallel queue</li>
+<li><strong>qfat</strong>, the queue to access SMP UV2000 machine</li>
+<li><strong>qfree, </strong>the Free resource utilization queue</li>
+</ul>
+<p class="callout">Check the queue status at <a class="external-link" href="https://extranet.it4i.cz/rsweb/salomon/" target="_self" title="">https://extranet.it4i.cz/rsweb/salomon/</a></p>
+<p>Read more on the <a href="resource-allocation-and-job-execution/resources-allocation-policy.html" title="" target="_self" class="internal-link">Resource Allocation Policy</a> page.</p>
+<h2 class=" ">Job submission and execution</h2>
+<p class="callout">Use the <strong>qsub</strong> command to submit your jobs.</p>
+<p class=" ">The qsub submits the job into the queue. The qsub command creates a request to the PBS Job manager for allocation of specified resources. The <strong>smallest allocation unit is entire node, 24 cores</strong>, with exception of the qexp queue. The resources will be allocated when available, subject to allocation policies and constraints. <strong>After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.</strong></p>
+<p class=" ">Read more on the <a href="resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_self" class="internal-link">Job submission and execution</a> page.</p>
+<p class="hiddenForView">HTML commented section #1 (removed Capacity computing section, this will be optimized for Salomon)</p>
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diff --git a/docs.it4i.cz/salomon/resource-allocation-and-job-execution.md b/docs.it4i.cz/salomon/resource-allocation-and-job-execution.md
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--- a/docs.it4i.cz/salomon/resource-allocation-and-job-execution.md
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution.md
@@ -65,4 +65,3 @@ will be optimized for Salomon)
-
diff --git a/docs.it4i.cz/whats-new/news-feed/capacity-computing-updated-for-salomon b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing-example
similarity index 100%
rename from docs.it4i.cz/whats-new/news-feed/capacity-computing-updated-for-salomon
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diff --git a/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.html b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.html
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+ <h2 class=" ">Introduction</h2>
+<p>In many cases, it is useful to submit huge (<span>100+</span>) number of computational jobs into the PBS queue system. Huge number of (small) jobs is one of the most effective ways to execute embarrassingly parallel calculations, achieving best runtime, throughput and computer utilization.</p>
+<p>However, executing huge number of jobs via the PBS queue may strain the system. This strain may result in slow response to commands, inefficient scheduling and overall degradation of performance and user experience, for all users. For this reason, the number of jobs is <strong>limited to 100 per user, 1500 per job array</strong></p>
+<p class="callout">Please follow one of the procedures below, in case you wish to schedule more than <span>100</span> jobs at a time.</p>
+<ul>
+<li class="anchor-link" title="">Use <a class="anchor-link" href="capacity-computing.html#job-arrays" target="_self" title="">Job arrays</a> when running huge number of <a class="anchor-link" href="capacity-computing.html#shared-jobscript-on-one-node" target="_self" title="">multithread</a> (bound to one node only) or multinode (multithread across several nodes) jobs</li>
+<li>Use <a class="anchor-link" href="capacity-computing.html#gnu-parallel" target="_self" title="">GNU parallel</a> when running single core jobs</li>
+<li>Combine<a class="anchor-link" href="capacity-computing.html#combining-job-arrays-and-gnu-parallel" target="_self" title=""> GNU parallel with Job arrays</a>Â when running huge number of single core jobs</li>
+</ul>
+<h2 class=" ">Policy</h2>
+<ol>
+<li>A user is allowed to submit at most 100 jobs. Each job may be <a class="anchor-link" href="capacity-computing.html#job-arrays" target="_self" title="">a job array</a>.</li>
+<li>The array size is at most 1000 subjobs.</li>
+</ol>
+<h2 class=" "><a name="job-arrays"></a>Job arrays</h2>
+<p class="callout">Huge number of jobs may be easily submitted and managed as a job array.</p>
+<p>A job array is a compact representation of many jobs, called subjobs. The subjobs share the same job script, and have the same values for all attributes and resources, with the following exceptions:</p>
+<ul>
+<li>each subjob has a unique index, $PBS_ARRAY_INDEX</li>
+<li>job Identifiers of subjobs only differ by their indices</li>
+<li>the state of subjobs can differ (R,Q,...etc.)</li>
+</ul>
+<p>All subjobs within a job array have the same scheduling priority and schedule as independent jobs.<br />Entire job array is submitted through a single qsub command and may be managed by qdel, qalter, qhold, qrls and qsig commands as a single job.</p>
+<h3 class=" "><a name="shared-jobscript-on-one-node"></a>Shared jobscript</h3>
+<p>All subjobs in job array use the very same, single jobscript. Each subjob runs its own instance of the jobscript. The instances execute different work controlled by $PBS_ARRAY_INDEX variable.</p>
+<p><a name="array_example"></a>Example:</p>
+<p>Assume we have 900 input files with name beginning with "file" (e. g. file001, ..., file900). Assume we would like to use each of these input files with program executable myprog.x, each as a separate job.</p>
+<p>First, we create a tasklist file (or subjobs list), listing all tasks (subjobs) - all input files in our example:</p>
+<pre class="prettyprint lang-sh">$ find . -name 'file*' > tasklist</pre>
+<p>Then we create jobscript:</p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -A PROJECT_ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=24,walltime=02:00:00<br /><br /># change to local scratch directory<br />SCR=/scratch/work/user/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># get individual tasks from tasklist with index from PBS JOB ARRAY<br />TASK=$(sed -n "${PBS_ARRAY_INDEX}p" $PBS_O_WORKDIR/tasklist) <br /><br class=" " /># copy input file and executable to scratch <br />cp $PBS_O_WORKDIR/$TASK input ; cp $PBS_O_WORKDIR/myprog.x .<br /><br /># execute the calculation<br />./myprog.x < input > output<br /><br /># copy output file to submit directory<br />cp output $PBS_O_WORKDIR/$TASK.out</pre>
+<p class=" ">In this example, the submit directory holds the 900 input files, executable myprog.x and the jobscript file. As input for each run, we take the filename of input file from created tasklist file. We copy the input file to scratch /scratch/work/user/$USER/$PBS_JOBID, execute the myprog.x and copy the output file back to <span>the submit directory</span>, under the $TASK.out name. The myprog.x runs on one node only and must use threads to run in parallel. Be aware, that if the myprog.x <strong>is not multithreaded</strong>, then all the <strong>jobs are run as single thread programs in sequential</strong> manner. Due to allocation of the whole node, the <strong>accounted time is equal to the usage of whole node</strong>, while using only 1/24 of the node!</p>
+<p class=" ">If huge number of parallel multicore (in means of multinode multithread, e. g. MPI enabled) jobs is needed to run, then a job array approach should also be used. The main difference compared to previous example using one node is that the local scratch should not be used (as it's not shared between nodes) and MPI or other technique for parallel multinode run has to be used properly.</p>
+<h3 class=" ">Submit the job array</h3>
+<p>To submit the job array, use the qsub -J command. The 900 jobs of the <a class="anchor-link" href="capacity-computing.html#array_example" target="_self" title="">example above</a> may be submitted like this:</p>
+<pre class="prettyprint lang-sh">$ qsub -N JOBNAME -J 1-900 jobscript<br />506493[].isrv5</pre>
+<p>In this example, we submit a job array of 900 subjobs. Each subjob will run on full node and is assumed to take less than 2 hours (please note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue).</p>
+<p>Sometimes for testing purposes, you may need to submit only one-element array. This is not allowed by PBSPro, but there's a workaround:</p>
+<pre class="prettyprint lang-sh">$ qsub -N JOBNAME -J 9-10:2 jobscript</pre>
+<p>This will only choose the lower index (9 in this example) for submitting/running your job.</p>
+<h3 class=" ">Manage the job array</h3>
+<p>Check status of the job array by the qstat command.</p>
+<pre class="prettyprint lang-sh">$ qstat -a 506493[].isrv5<br /><br />isrv5:<br /> Req'd Req'd Elap<br />Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time<br />--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----<br />12345[].dm2 user2 qprod xx 13516 1 24 -- 00:50 B 00:02</pre>
+<p>The status B means that some subjobs are already running.</p>
+<p>Check status of the first 100 subjobs by the qstat command.</p>
+<pre class="prettyprint lang-sh">$ qstat -a 12345[1-100].isrv5<br /><br />isrv5:<br /> Req'd Req'd Elap<br />Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time<br />--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----<br />12345[1].isrv5 user2 qprod xx 13516 1 24 -- 00:50 R 00:02<br />12345[2].isrv5 user2 qprod xx 13516 1 24 -- 00:50 R 00:02<br />12345[3].isrv5 user2 qprod xx 13516 1 24 -- 00:50 R 00:01<br />12345[4].isrv5 user2 qprod xx 13516 1 24 -- 00:50 Q --<br /> . . . . . . . . . . .<br /> , . . . . . . . . . . <br />12345[100].isrv5 user2 qprod xx 13516 1 24 -- 00:50 Q --</pre>
+<p>Delete the entire job array. Running subjobs will be killed, queueing subjobs will be deleted.</p>
+<pre class="prettyprint lang-sh">$ qdel 12345[].isrv5</pre>
+<p>Deleting large job arrays may take a while.</p>
+<p>Display status information for all user's jobs, job arrays, and subjobs.</p>
+<pre class="prettyprint lang-sh">$ qstat -u $USER -t</pre>
+<p>Display status information for all user's subjobs.</p>
+<pre class="prettyprint lang-sh">$ qstat -u $USER -tJ</pre>
+<p>Read more on job arrays in the <a href="../../pbspro-documentation.html" title="" target="_self" class="internal-link">PBSPro Users guide</a>.</p>
+<h2 class=" "><a name="gnu-parallel"></a>GNU parallel</h2>
+<p class="callout">Use GNU parallel to run many single core tasks on one node.</p>
+<p class=" ">GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. GNU parallel is most useful in running single core jobs via the queue system on Anselm.</p>
+<p class=" ">For more information and examples see the parallel man page:</p>
+<pre class="prettyprint lang-sh">$ module add parallel<br />$ man parallel</pre>
+<h3 class=" ">GNU parallel jobscript</h3>
+<p class=" ">The GNU parallel shell executes multiple instances of the jobscript using all cores on the node. The instances execute different work, controlled by the $PARALLEL_SEQ variable.</p>
+<p><a name="gp_example"></a>Example:</p>
+<p>Assume we have 101 input files with name beginning with "file" (e. g. file001, ..., file101). Assume we would like to use each of these input files with program executable myprog.x, each as a separate single core job. We call these single core jobs tasks.</p>
+<p>First, we create a tasklist file, listing all tasks - all input files in our example:</p>
+<pre class="prettyprint lang-sh">$ find . -name 'file*' > tasklist</pre>
+<p>Then we create jobscript:</p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -A PROJECT_ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=24,walltime=02:00:00<br /><br class="prettyprint lang-sh" />[ -z "$PARALLEL_SEQ" ] && \<br />{ module add parallel ; exec parallel -a $PBS_O_WORKDIR/tasklist $0 ; }<br /><br /># change to local scratch directory<br />SCR=/scratch/work/user/$USER/$PBS_JOBID/$PARALLEL_SEQ<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># get individual task from tasklist<br />TASK=$1  <br /><br /># copy input file and executable to scratch <br />cp $PBS_O_WORKDIR/$TASK input <br /><br /># execute the calculation<br />cat input > output<br /><br /># copy output file to submit directory<br />cp output $PBS_O_WORKDIR/$TASK.out</pre>
+<p>In this example, tasks from tasklist are executed via the GNU parallel. The jobscript executes multiple instances of itself in parallel, on all cores of the node. Once an instace of jobscript is finished, new instance starts until all entries in tasklist are processed. Currently processed entry of the joblist may be retrieved via $1 variable. Variable $TASK expands to one of the input filenames from tasklist. We copy the input file to local scratch, execute the myprog.x and copy the output file back to the submit directory, under the $TASK.out name. </p>
+<h3 class=" ">Submit the job</h3>
+<p>To submit the job, use the qsub command. The 101 tasks' job of the <a class="anchor-link" href="capacity-computing.html#gp_example" target="_self" title="">example above</a> may be submitted like this:</p>
+<pre class="prettyprint lang-sh">$ qsub -N JOBNAME jobscript<br />12345.dm2</pre>
+<p>In this example, we submit a job of 101 tasks. 24 input files will be processed in parallel. The 101 tasks on 24 cores are assumed to complete in less than 2 hours.</p>
+<p>Please note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue.</p>
+<h2 class=" "><a name="combining-job-arrays-and-gnu-parallel"></a>Job arrays and GNU parallel</h2>
+<p class="callout">Combine the Job arrays and GNU parallel for best throughput of single core jobs</p>
+<p>While job arrays are able to utilize all available computational nodes, the GNU parallel can be used to efficiently run multiple single-core jobs on single node. The two approaches may be combined to utilize all available (current and future) resources to execute single core jobs.</p>
+<p class="callout">Every subjob in an array runs GNU parallel to utilize all cores on the node</p>
+<h3 class=" ">GNU parallel, shared jobscript</h3>
+<p class=" ">Combined approach, very similar to job arrays, can be taken. Job array is submitted to the queuing system. The subjobs run GNU parallel. The GNU parallel shell executes multiple instances of the jobscript using all cores on the node. The instances execute different work, controlled by the $PBS_JOB_ARRAY and $PARALLEL_SEQ variables.</p>
+<p><a name="combined_example"></a>Example:</p>
+<p>Assume we have 992 input files with name beginning with "file" (e. g. file001, ..., file992). Assume we would like to use each of these input files with program executable myprog.x, each as a separate single core job. We call these single core jobs tasks.</p>
+<p>First, we create a tasklist file, listing all tasks - all input files in our example:</p>
+<pre class="prettyprint lang-sh">$ find . -name 'file*' > tasklist</pre>
+<p>Next we create a file, controlling how many tasks will be executed in one subjob</p>
+<pre class="prettyprint lang-sh">$ seq 32 > numtasks</pre>
+<p>Then we create jobscript:</p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -A PROJECT_ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=24,walltime=02:00:00<br /><br />[ -z "$PARALLEL_SEQ" ] && \<br />{ module add parallel ; exec parallel -a $PBS_O_WORKDIR/numtasks $0 ; }<br /><br /># change to local scratch directory<br />SCR=/scratch/work/user/$USER/$PBS_JOBID/$PARALLEL_SEQ<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># get individual task from tasklist with index from PBS JOB ARRAY and index form Parallel<br />IDX=$(($PBS_ARRAY_INDEX + $PARALLEL_SEQ - 1))<br />TASK=$(sed -n "${IDX}p" $PBS_O_WORKDIR/tasklist)<br />[ -z "$TASK" ] && exit<br /><br /># copy input file and executable to scratch <br />cp $PBS_O_WORKDIR/$TASK input <br /><br /># execute the calculation<br />cat input > output<br /><br /># copy output file to submit directory<br />cp output $PBS_O_WORKDIR/$TASK.out</pre>
+<p>In this example, the jobscript executes in multiple instances in parallel, on all cores of a computing node. Variable $TASK expands to one of the input filenames from tasklist. We copy the input file to local scratch, execute the myprog.x and copy the output file back to the submit directory, under the $TASK.out name. The numtasks file controls how many tasks will be run per subjob. Once an task is finished, new task starts, until the number of tasks in numtasks file is reached.</p>
+<p class="callout">Select subjob walltime and number of tasks per subjob carefully</p>
+<p>Â When deciding this values, think about following guiding rules :</p>
+<ol>
+<li>Let n=N/24. Inequality (n+1) * T < W should hold. The N is number of tasks per subjob, T is expected single task walltime and W is subjob walltime. Short subjob walltime improves scheduling and job throughput.</li>
+<li>Number of tasks should be modulo 24.</li>
+<li>These rules are valid only when all tasks have similar task walltimes T.</li>
+</ol>
+<h3 class=" ">Submit the job array</h3>
+<p>To submit the job array, use the qsub -J command. The 992 tasks' job of the <a class="anchor-link" href="capacity-computing.html#combined_example" target="_self" title="">example above</a> may be submitted like this:</p>
+<pre class="prettyprint lang-sh">$ qsub -N JOBNAME -J 1-992:32 jobscript<br />12345[].dm2</pre>
+<p>In this example, we submit a job array of 31 subjobs. Note the -J 1-992:<strong>48</strong>, this must be the same as the number sent to numtasks file. Each subjob will run on full node and process 24 input files in parallel, 48 in total per subjob. Every subjob is assumed to complete in less than 2 hours.</p>
+<p>Please note the #PBS directives in the beginning of the jobscript file, dont' forget to set your valid PROJECT_ID and desired queue.</p>
+<h2 class=" ">Examples</h2>
+<p>Download the examples in <a href="capacity-computing-example" title="" target="_self" class="internal-link">capacity.zip</a>, illustrating the above listed ways to run huge number of jobs. We recommend to try out the examples, before using this for running production jobs.</p>
+<p>Unzip the archive in an empty directory on Anselm and follow the instructions in the README file</p>
+<pre class="prettyprint lang-sh">$ unzip capacity.zip<br />$ cd capacity<br />$ cat README</pre>
+<p>Â </p>
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diff --git a/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
index 0e950ac16..b6a6b3b89 100644
--- a/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
@@ -418,7 +418,7 @@ Examples
--------
Download the examples in
-[capacity.zip](../../whats-new/news-feed/capacity-computing-updated-for-salomon),Â
+[capacity.zip](capacity-computing-example),Â
illustrating the above listed ways to run huge number of jobs. We
recommend to try out the examples, before using this for running
production jobs.
@@ -433,3 +433,7 @@ $ cat README
```
Â
+
+
+
+
diff --git a/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.html b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.html
new file mode 100644
index 000000000..f1388ca3e
--- /dev/null
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.html
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+ <p>To run a <a href="job-submission-and-execution.html" title="" target="_self" class="internal-link">job</a>, <a href="resources-allocation-policy.html" title="" target="_self" class="internal-link">computational resources</a> for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which efficiently distributes workloads across the supercomputer. Extensive informations about PBS Pro can be found in the <a href="../../pbspro-documentation.html" title="" target="_self" class="internal-link">official documentation here</a>, especially in the <a href="../../pbspro-documentation/pbspro-users-guide.1" title="" target="_self" class="internal-link">PBS Pro User's Guide</a>.</p>
+<h2 class=" ">Resources Allocation Policy</h2>
+<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. <a href="job-priority.html" title="" target="_self" class="internal-link">The Fairshare</a> at Salomon ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are available to Anselm users:</p>
+<ul>
+<li><strong>qexp</strong>, the Express queue</li>
+<li><strong>qprod</strong>, the Production queue<strong></strong></li>
+<li><strong>qlong</strong>, the Long queue</li>
+<li><strong>qmpp</strong>, the Massively parallel queue</li>
+<li><strong>qfat</strong>, the queue to access SMP UV2000 machine</li>
+<li><strong>qfree, </strong>the Free resource utilization queue</li>
+</ul>
+<p class="callout">Check the queue status at <a class="external-link" href="https://extranet.it4i.cz/rsweb/salomon/" target="_self" title="">https://extranet.it4i.cz/rsweb/salomon/</a></p>
+<p>Read more on the <a href="resources-allocation-policy.html" title="" target="_self" class="internal-link">Resource Allocation Policy</a> page.</p>
+<h2 class=" ">Job submission and execution</h2>
+<p class="callout">Use the <strong>qsub</strong> command to submit your jobs.</p>
+<p class=" ">The qsub submits the job into the queue. The qsub command creates a request to the PBS Job manager for allocation of specified resources. The <strong>smallest allocation unit is entire node, 24 cores</strong>, with exception of the qexp queue. The resources will be allocated when available, subject to allocation policies and constraints. <strong>After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.</strong></p>
+<p class=" ">Read more on the <a href="job-submission-and-execution.html" title="" target="_self" class="internal-link">Job submission and execution</a> page.</p>
+<p class="hiddenForView">HTML commented section #1 (removed Capacity computing section, this will be optimized for Salomon)</p>
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+ <h2 class=" ">Job execution priority</h2>
+<p>Scheduler gives each job an execution priority and then uses this job execution priority to select which job(s) to run.</p>
+<p>Job execution priority is determined by these job properties (in order of importance):</p>
+<ol>
+<li>queue priority</li>
+<li>fairshare priority</li>
+<li>eligible time</li>
+</ol>
+<h3 class=" ">Queue priority</h3>
+<p>Queue priority is priority of queue where job is queued before execution.</p>
+<p>Queue priority has the biggest impact on job execution priority. Execution priority of jobs in higher priority queues is always greater than execution priority of jobs in lower priority queues. Other properties of job used for determining job execution priority (fairshare priority, eligible time) cannot compete with queue priority.</p>
+<p>Queue priorities can be seen at <a class="external-link" href="https://extranet.it4i.cz/rsweb/salomon/queues" target="_blank" title="">https://extranet.it4i.cz/rsweb/salomon/queues</a></p>
+<h3 class=" ">Fairshare priority</h3>
+<p>Fairshare priority is priority calculated on recent usage of resources. Fairshare priority is calculated per project, all members of project share same fairshare priority. Projects with higher recent usage have lower fairshare priority than projects with lower or none recent usage.</p>
+<p>Fairshare priority is used for ranking jobs with equal queue priority.</p>
+<p>Fairshare priority is calculated as</p>
+<p class=" "><img alt="" src="../../anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png" title="" class="image-inline" /></p>
+<p class=" ">where MAX_FAIRSHARE has value 1E6,<br />usage<sub>Project</sub> is cumulated usage by all members of selected project,<br /> usage<sub>Total</sub> is total usage by all users, by all projects.</p>
+<p class=" ">Usage counts allocated corehours (ncpus*walltime). Usage is decayed, or cut in half periodically, at the interval 168 hours (one week).<br />Jobs queued in queue qexp are not calculated to project's usage.</p>
+<p class="callout"><span>Calculated usage and fairshare priority can be seen at <a class="external-link" href="https://extranet.it4i.cz/rsweb/salomon/projects" target="_self" title="">https://extranet.it4i.cz/rsweb/salomon/projects</a>.</span></p>
+<p class=" "><span><br /><span>Calculated fairshare priority can be also seen as Resource_List.fairshare attribute of a job.</span><br /></span></p>
+<h3 class=" "><span>Eligible time</span></h3>
+<p>Eligible time is amount (in seconds) of eligible time job accrued while waiting to run. Jobs with higher eligible time gains higher pri<span><span></span></span>ority.</p>
+<p>Eligible time has the least impact on execution priority. Eligible time is used for sorting jobs with equal queue priority and fairshare priority. It is very, very difficult for <span>eligible time</span> to compete with fairshare priority.</p>
+<p><span><span>Eligible time can be seen as eligible_time attribute of job.</span></span></p>
+<h3 class=" ">Formula</h3>
+<p class=" ">Job execution priority (job sort formula) is calculated as:</p>
+<p class=" "><img alt="" src="../../anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png" title="" class="image-inline" /></p>
+<h3 class=" ">Job backfilling</h3>
+<p><span>The scheduler uses job backfilling.</span></p>
+<p>Backfilling means fitting smaller jobs around the higher-priority jobs that the scheduler is going to run next, in such a way that the higher-priority jobs are not delayed. Backfilling allows us to keep resources from becoming idle when the top job (job with the highest execution priority) cannot run.</p>
+<p>The scheduler makes a list of jobs to run in order of execution priority. Scheduler looks for smaller jobs that can fit into the usage gaps<br />around the highest-priority jobs in the list. The scheduler looks in the prioritized list of jobs and chooses the highest-priority smaller jobs that fit. Filler jobs are run only if they will not delay the start time of top jobs.</p>
+<p>It means, that jobs with lower execution priority can be run before jobs with higher execution priority.</p>
+<p class="exclamation">It is <strong>very beneficial to specify the walltime</strong> when submitting jobs.</p>
+<p class=" ">Specifying more accurate walltime enables better schedulling, better execution times and better resource usage. Jobs with suitable (small) walltime could be backfilled - and overtake job(s) with higher priority.</p>
+<h3 class=" ">Job placement</h3>
+<p>Job <a href="job-submission-and-execution.html#job_placement" title="" target="_self" class="internal-link">placement can be controlled by flags during submission</a>.</p>
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diff --git a/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
index 24d831ed4..31f9f1b5a 100644
--- a/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
@@ -16,16 +16,16 @@ of importance):
### Queue priority
-ueue priority is priority of queue where job is queued before
+Queue priority is priority of queue where job is queued before
execution.
-ueue priority has the biggest impact on job execution priority.
+Queue priority has the biggest impact on job execution priority.
Execution priority of jobs in higher priority queues is always greater
than execution priority of jobs in lower priority queues. Other
properties of job used for determining job execution priority (fairshare
priority, eligible time) cannot compete with queue priority.
-ueue priorities can be seen at
+Queue priorities can be seen at
<https://extranet.it4i.cz/rsweb/salomon/queues>
### Fairshare priority
@@ -109,4 +109,3 @@ walltime could be backfilled - and overtake job(s) with higher priority.
Job [placement can be controlled by flags during
submission](job-submission-and-execution.html#job_placement).
-
diff --git a/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.html b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.html
new file mode 100644
index 000000000..282e6a039
--- /dev/null
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.html
@@ -0,0 +1,931 @@
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+ <h2 class=" ">Job Submission</h2>
+<p>When allocating computational resources for the job, please specify</p>
+<ol>
+<li>suitable queue for your job (default is qprod)</li>
+<li>number of computational nodes required</li>
+<li>number of cores per node required</li>
+<li>maximum wall time allocated to your calculation, note that jobs exceeding maximum wall time will be killed</li>
+<li>Project ID</li>
+<li>Jobscript or interactive switch</li>
+</ol>
+<p class="callout">Use the <strong>qsub</strong> command to submit your job to a queue for allocation of the computational resources.</p>
+<p>Submit the job using the qsub command:</p>
+<pre class="prettyprint lang-sh">$ qsub -A Project_ID -q queue -l select=x:ncpus=y,walltime=[[hh:]mm:]ss[.ms] jobscript</pre>
+<p>The qsub submits the job into the queue, in another words the qsub command creates a request to the PBS Job manager for allocation of specified resources. The resources will be allocated when available, subject to above described policies and constraints. <strong>After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.</strong></p>
+<p class="callout">PBS statement nodes (qsub -l nodes=nodespec) is not supported on Salomon cluster.<strong><br /></strong></p>
+<h3 class=" ">Job Submission Examples</h3>
+<pre class="prettyprint lang-sh">$ qsub -A OPEN-0-0 -q qprod -l select=64:ncpus=24,walltime=03:00:00 ./myjob</pre>
+<p>In this example, we allocate 64 nodes, 24 cores per node, for 3 hours. We allocate these resources via the qprod queue, consumed resources will be accounted to the Project identified by Project ID OPEN-0-0. Jobscript myjob will be executed on the first node in the allocation.</p>
+<p>Â </p>
+<pre class="prettyprint lang-sh">$ qsub -q qexp -l select=4:ncpus=24 -I</pre>
+<p class=" ">In this example, we allocate 4 nodes, 24 cores per node, for 1 hour. We allocate these resources via the qexp queue. The resources will be available interactively</p>
+<p class=" ">Â </p>
+<pre class="prettyprint lang-sh">$ qsub -A OPEN-0-0 -q qlong -l select=10:ncpus=24 ./myjob</pre>
+<p class=" ">In this example, we allocate 10 nodes, 24 cores per node, for 72 hours. We allocate these resources via the qlong queue. Jobscript myjob will be executed on the first node in the allocation.</p>
+<p class=" ">Â </p>
+<pre class="prettyprint lang-sh">$ qsub -A OPEN-0-0 -q qfree -l select=10:ncpus=24 ./myjob</pre>
+<p class=" ">In this example, we allocate 10Â nodes, 24 cores per node, for 12 hours. We allocate these resources via the qfree queue. It is not required that the project OPEN-0-0 has any available resources left. Consumed resources are still accounted for. Jobscript myjob will be executed on the first node in the allocation.</p>
+<h3 class=" ">Intel Xeon Phi co-processors</h3>
+<p class=" ">To allocate a node with Xeon Phi co-processor, user needs to specify that in select statement. Currently only allocation of whole nodes with both Phi cards as the smallest chunk is supported. Standard PBSPro approach through attributes "accelerator", "naccelerators" and "accelerator_model" is used. The "accelerator_model" can be omitted, since on Salomon only one type of accelerator type/model is available.</p>
+<p class=" ">The absence of specialized queue for accessing the nodes with cards means, that the Phi cards can be utilized in any queue, including qexp for testing/experiments, qlong for longer jobs, qfree after the project resources have been spent, etc. The Phi cards are thus also available to PRACE users. There's no need to ask for permission to utilize the Phi cards in project proposals.</p>
+<pre class="prettyprint lang-sh">$ qsub -A OPEN-0-0 -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 ./myjob</pre>
+<p class=" ">In this example, we allocate 1 node, with 24 cores, with 2 Xeon Phi 7120p cards, running batch job ./myjob. The default time for qprod is used, e. g. 24 hours.</p>
+<pre class="prettyprint lang-sh">$ qsub -A OPEN-0-0 -I -q qlong -l select=4:ncpus=24:accelerator=True:naccelerators=2 -l walltime=56:00:00 -I</pre>
+<p class=" ">In this example, we allocate 4 nodes, with 24 cores per node (totalling 96 cores), with 2 Xeon Phi 7120p cards per node (totalling 8 Phi cards), running interactive job for 56 hours. The accelerator model name was omitted.</p>
+<h3 class=" ">UV2000 SMP</h3>
+<p class="callout">14 NUMA nodes available on UV2000<br /> Per NUMA node allocation.<br />Jobs are isolated by cpusets.</p>
+<p class=" ">The UV2000 (node uv1) offers 3328GB of RAM and 112 cores, distributed in 14 NUMA nodes. A NUMA node packs 8 cores and approx. 236GB RAM. In the PBS the UV2000 provides 14 chunks, a chunk per NUMA node (see <a href="resources-allocation-policy.html" title="" target="_self" class="internal-link">Resource allocation policy</a>). The jobs on UV2000 are isolated from each other by cpusets, so that a job by one user may not utilize CPU or memory allocated to a job by other user. Always, full chunks are allocated, a job may only use resources of the NUMA nodes allocated to itself.</p>
+<pre class="prettyprint lang-sh">Â $ qsub -A OPEN-0-0 -q qfat -l select=14 ./myjob</pre>
+<p class=" ">In this example, we allocate all 14 NUMA nodes (corresponds to 14 chunks), 112 cores of the SGI UV2000 node for 72 hours. Jobscript myjob will be executed on the node uv1.</p>
+<pre class="prettyprint lang-sh">$ qsub -A OPEN-0-0 -q qfat -l select=1:mem=2000GB ./myjob</pre>
+<p class=" ">In this example, we allocate 2000GB of memory on the UV2000 for 72 hours. By requesting 2000GB of memory, 10 chunks are allocated. Jobscript myjob will be executed on the node uv1.</p>
+<h3 class=" ">Useful tricks</h3>
+<p class=" ">All qsub options may be <a class="anchor-link" href="job-submission-and-execution.html#PBSsaved" target="_self" title="">saved directly into the jobscript</a>. In such a case, no options to qsub are needed.</p>
+<pre class="prettyprint lang-sh">$ qsub ./myjob</pre>
+<p>Â </p>
+<p>By default, the PBS batch system sends an e-mail only when the job is aborted. Disabling mail events completely can be done like this:</p>
+<pre class="prettyprint lang-sh">$ qsub -m n</pre>
+<h2 class=" "><a name="job_placement"></a>Advanced job placement</h2>
+<h3 class=" ">Placement by name</h3>
+<p>Specific nodes may be allocated via the PBS</p>
+<pre class="prettyprint lang-sh">qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=24:host=r24u35n680+1:ncpus=24:host=r24u36n681 -I</pre>
+<p>Or using short names</p>
+<pre class="prettyprint lang-sh">qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=24:host=cns680+1:ncpus=24:host=cns681 -I</pre>
+<p>In this example, we allocate nodes r24u35n680 and r24u36n681, all 24 cores per node, for 24 hours. Consumed resources will be accounted to the Project identified by Project ID OPEN-0-0. The resources will be available interactively.</p>
+<h3 class=" ">Placement by Hypercube dimension</h3>
+<p>Nodes may be selected via the PBS resource attribute ehc_[1-7]d .</p>
+<table class="listing">
+<tbody>
+<tr class="odd"><th>Hypercube dimension</th><th><span class="pun">node_group_key</span></th></tr>
+<tr class="even">
+<td>1D</td>
+<td>ehc_1d</td>
+</tr>
+<tr class="odd">
+<td>2D</td>
+<td>ehc_2d</td>
+</tr>
+<tr class="even">
+<td>3D</td>
+<td>ehc_3d</td>
+</tr>
+<tr class="odd">
+<td>4D</td>
+<td>ehc_4d</td>
+</tr>
+<tr class="even">
+<td>5D</td>
+<td>ehc_5d</td>
+</tr>
+<tr class="odd">
+<td>6D</td>
+<td>ehc_6d</td>
+</tr>
+<tr class="even">
+<td>7D</td>
+<td>ehc_7d</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<pre class="prettyprint lang-sh prettyprinted"><span class="pln">$ qsub </span><span class="pun">-</span><span class="pln">A OPEN</span><span class="pun">-</span><span class="lit">0</span><span class="pun">-</span><span class="lit">0</span><span class="pln"> </span><span class="pun">-</span><span class="pln">q qprod </span><span class="pun">-</span><span class="pln">l select</span><span class="pun">=</span><span class="lit">4</span><span class="pun">:</span><span class="pln">ncpus</span><span class="pun">=24 </span><span class="pln">-l place=group=ehc_1d <span class="pln"></span><span class="pun">-</span><span class="pln">I</span></span></pre>
+<div>In this example, we allocate 4 nodes, 24 cores, selecting only the nodes with <a href="../network-1/7d-enhanced-hypercube.html" title="" target="_self" class="internal-link">hypercube dimension</a> 1.</div>
+<h3 class=" ">Placement by IB switch</h3>
+<div class="internal-link">Groups of computational nodes are connected to chassis integrated Infiniband switches. These switches form the leaf switch layer of the <a href="../network-1.html" title="" target="_self" class="internal-link">Infiniband network</a> . Nodes sharing the leaf switch can communicate most efficiently. Sharing the same switch prevents hops in the network and provides for unbiased, most efficient network communication.</div>
+<div class="internal-link"></div>
+<div class="internal-link">There are at most 9 nodes sharing the same Infiniband switch.<br /><br /></div>
+<div class="internal-link">Infiniband switch list:</div>
+<pre class="prettyprint lang-sh">$ qmgr -c "print node @a" | grep switch<br />set node r4i1n11 resources_available.switch = r4i1s0sw1<br />set node r2i0n0 resources_available.switch = r2i0s0sw1<br />set node r2i0n1 resources_available.switch = r2i0s0sw1<br />...</pre>
+<div class="internal-link">List of all nodes per Infiniband switch:</div>
+<pre class="prettyprint lang-sh">$ qmgr -c "print node @a" | grep r36sw3<br />set node r36u31n964 resources_available.switch = r36sw3<br />set node r36u32n965 resources_available.switch = r36sw3<br />set node r36u33n966 resources_available.switch = r36sw3<br />set node r36u34n967 resources_available.switch = r36sw3<br />set node r36u35n968 resources_available.switch = r36sw3<br />set node r36u36n969 resources_available.switch = r36sw3<br />set node r37u32n970 resources_available.switch = r36sw3<br />set node r37u33n971 resources_available.switch = r36sw3<br />set node r37u34n972 resources_available.switch = r36sw3</pre>
+<div class="internal-link"></div>
+<p class=" ">Nodes sharing the same switch may be selected via the PBS resource attribute switch.</p>
+<div>We recommend allocating compute nodes of a single switch when best possible computational network performance is required to run the job efficiently:</div>
+<pre class="prettyprint lang-sh">$ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24:switch=r4i1s0sw1 ./myjob</pre>
+<div>In this example, we request all the 9 nodes sharing the r4i1s0sw1 switch for 24 hours.</div>
+<div>
+<pre class="prettyprint lang-sh">$ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24 -l place=group=switch ./myjob</pre>
+</div>
+<div>In this example, we request 9 nodes placed on the same switch using node grouping placement for 24 hours.</div>
+<div></div>
+<p class="hiddenForView">HTML commented section #1 (turbo boost is to be implemented)</p>
+
+<h2 class=" ">Job Management</h2>
+<p class="callout">Check status of your jobs using the <strong>qstat</strong> and <strong>check-pbs-jobs</strong> commands</p>
+<pre class="prettyprint lang-sh">$ qstat -a<br />$ qstat -a -u username<br />$ qstat -an -u username<br />$ qstat -f 12345.isrv5</pre>
+<p class=" "><a name="Acc_example"></a>Example:</p>
+<pre class="prettyprint lang-sh">$ qstat -a<br /><br />srv11:<br /> Req'd Req'd Elap<br />Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time<br />--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----<br />16287.isrv5 user1 qlong job1 6183 4 64 -- 144:0 R 38:25<br />16468.isrv5 user1 qlong job2 8060 4 64 -- 144:0 R 17:44<br />16547.isrv5 user2 qprod job3x 13516 2 32 -- 48:00 R 00:58</pre>
+<p class=" ">In this example user1 and user2 are running jobs named job1, job2 and job3x. The jobs job1 and job2 are using 4 nodes, 16 cores per node each. The job1 already runs for 38 hours and 25 minutes, job2 for 17 hours 44 minutes. The job1 already consumed 64*38.41 = 2458.6 core hours. The job3x already consumed 0.96*32 = 30.93 core hours. These consumed core hours will be accounted on the respective project accounts, regardless of whether the allocated cores were actually used for computations.</p>
+<p class=" ">Check status of your jobs using check-pbs-jobs command. Check presence of user's PBS jobs' processes on execution hosts. Display load, processes. Display job standard and error output. Continuously display (tail -f) job standard or error output.</p>
+<pre class="prettyprint lang-sh">$ check-pbs-jobs --check-all<br />$ check-pbs-jobs --print-load --print-processes<br />$ check-pbs-jobs --print-job-out --print-job-err<br />$ check-pbs-jobs --jobid JOBID --check-all --print-all<br />$ check-pbs-jobs --jobid JOBID --tailf-job-out</pre>
+<p class=" ">Examples:</p>
+<pre class="prettyprint lang-sh">$ check-pbs-jobs --check-all<br />JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3<br />Check session id: OK<br />Check processes<br />r3i6n2: OK<br />r3i6n3: No process</pre>
+<p class=" ">In this example we see that job 35141.dm2 currently runs no process on allocated node r3i6n2, which may indicate an execution error.</p>
+<pre class="prettyprint lang-sh">$ check-pbs-jobs --print-load --print-processes<br />JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3<br />Print load<br />r3i6n2: LOAD: 16.01, 16.01, 16.00<br />r3i6n3: LOAD: 0.01, 0.00, 0.01<br />Print processes<br /> %CPU CMD<br />r3i6n2: 0.0 -bash<br />r3i6n2: 0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC<br />r3i6n2: 99.7 run-task<br />...</pre>
+<p class=" ">In this example we see that job 35141.dm2 currently runs process run-task on node r3i6n2, using one thread only, while node r3i6n3 is empty, which may indicate an execution error.</p>
+<pre class="prettyprint lang-sh">$ check-pbs-jobs --jobid 35141.dm2 --print-job-out<br />JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3<br />Print job standard output:<br />======================== Job start ==========================<br />Started at   : Fri Aug 30 02:47:53 CEST 2013<br />Script name  : script<br />Run loop 1<br />Run loop 2<br />Run loop 3</pre>
+<p class=" ">In this example, we see actual output (some iteration loops) of the job 35141.dm2</p>
+<p class="callout">Manage your queued or running jobs, using the <strong>qhold</strong>, <strong>qrls</strong>, <strong>qdel</strong><strong>,</strong> <strong>qsig</strong> or <strong>qalter</strong> commands</p>
+<p class=" ">You may release your allocation at any time, using qdel command</p>
+<pre class="prettyprint lang-sh">$ qdel 12345.isrv5</pre>
+<p class=" ">You may kill a running job by force, using qsig command</p>
+<pre class="prettyprint lang-sh">$ qsig -s 9 12345.isrv5</pre>
+<p class=" ">Learn more by reading the pbs man page</p>
+<pre class="prettyprint lang-sh">$ man pbs_professional</pre>
+<h2 class=" ">Job Execution</h2>
+<h3 class=" ">Jobscript</h3>
+<p class="callout">Prepare the jobscript to run batch jobs in the PBS queue system</p>
+<p>The Jobscript is a user made script, controlling sequence of commands for executing the calculation. It is often written in bash, other scripts may be used as well. The jobscript is supplied to PBS <strong>qsub</strong> command as an argument and executed by the PBS Professional workload manager.</p>
+<p class="callout">The jobscript or interactive shell is executed on first of the allocated nodes.</p>
+<pre class="prettyprint lang-sh">$ qsub -q qexp -l select=4:ncpus=24 -N Name0 ./myjob<br />$ qstat -n -u username<br /><br />isrv5:<br /> Req'd Req'd Elap<br />Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time<br />--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----<br />15209.isrv5 username qexp Name0 5530 4 96 -- 01:00 R 00:00<br /> r21u01n577/0*24+r21u02n578/0*24+r21u03n579/0*24+r21u04n580/0*24</pre>
+<p> In this example, the nodes r21u01n577, r21u02n578, r21u03n579, r21u04n580 were allocated for 1 hour via the qexp queue. The jobscript myjob will be executed on the node r21u01n577, while the nodes r21u02n578, r21u03n579, r21u04n580 are available for use as well.</p>
+<p class="callout">The jobscript or interactive shell is by default executed in home directory</p>
+<pre class="prettyprint lang-sh">$ qsub -q qexp -l select=4:ncpus=24 -I<br />qsub: waiting for job 15210.isrv5 to start<br />qsub: job 15210.isrv5 ready<br /><br />$ pwd<br />/home/username</pre>
+<p class=" ">In this example, 4 nodes were allocated interactively for 1 hour via the qexp queue. The interactive shell is executed in the home directory.</p>
+<p class="callout">All nodes within the allocation may be accessed via ssh. Unallocated nodes are not accessible to user.</p>
+<p>The allocated nodes are accessible via ssh from login nodes. The nodes may access each other via ssh as well.</p>
+<p>Calculations on allocated nodes may be executed remotely via the MPI, ssh, pdsh or clush. You may find out which nodes belong to the allocation by reading the $PBS_NODEFILE file</p>
+<pre class="prettyprint lang-sh">qsub -q qexp -l select=2:ncpus=24 -I<br />qsub: waiting for job 15210.isrv5 to start<br />qsub: job 15210.isrv5 ready<br /><br />$ pwd<br />/home/username<br /><br />$ sort -u $PBS_NODEFILE<br />r2i5n6.ib0.smc.salomon.it4i.cz<br />r4i6n13.ib0.smc.salomon.it4i.cz<br />r4i7n0.ib0.smc.salomon.it4i.cz<br />r4i7n2.ib0.smc.salomon.it4i.cz<br /><br /> <br />$ pdsh -w r2i5n6,r4i6n13,r4i7n[0,2] hostname<br />r4i6n13: r4i6n13<br />r2i5n6: r2i5n6<br />r4i7n2: r4i7n2<br />r4i7n0: r4i7n0</pre>
+<p class=" ">In this example, the hostname program is executed via pdsh from the interactive shell. The execution runs on all four allocated nodes. The same result would be achieved if the pdsh is called from any of the allocated nodes or from the login nodes.</p>
+<h3 class=" ">Example Jobscript for MPI Calculation</h3>
+<p class="callout">Production jobs must use the /scratch directory for I/O</p>
+<p>The recommended way to run production jobs is to change to /scratch directory early in the jobscript, copy all inputs to /scratch, execute the calculations and copy outputs to home directory.</p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br /><br /># change to scratch directory, exit on failure<br />SCRDIR=/scratch/<span class="pln">work</span><span class="pun">/</span><span class="pln"></span>user/$USER/myjob<br />mkdir -p $SCRDIR<br />cd $SCRDIR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/input .<br />cp $PBS_O_WORKDIR/mympiprog.x .<br /><br /># load the mpi module<br />module load OpenMPI<br /><br /># execute the calculation<br />mpiexec -pernode ./mympiprog.x<br /><br /># copy output file to home<br />cp output $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
+<p class=" ">In this example, some directory on the /home holds the input file input and executable mympiprog.x . We create a directory myjob on the /scratch filesystem, copy input and executable files from the /home directory where the qsub was invoked ($PBS_O_WORKDIR) to /scratch, execute the MPI programm mympiprog.x and copy the output file back to the /home directory. The mympiprog.x is executed as one process per node, on all allocated nodes.</p>
+<p class="callout">Consider preloading inputs and executables onto <a href="../storage.html" title="" target="_self" class="internal-link">shared scratch</a> before the calculation starts.</p>
+<p>In some cases, it may be impractical to copy the inputs to scratch and outputs to home. This is especially true when very large input and output files are expected, or when the files should be reused by a subsequent calculation. In such a case, it is users responsibility to preload the input files on shared /scratch before the job submission and retrieve the outputs manually, after all calculations are finished.</p>
+<p class="callout"><a name="PBSsaved"></a>Store the qsub options within the jobscript. <br />Use <strong>mpiprocs</strong> and <strong>ompthreads</strong> qsub options to control the MPI job execution.</p>
+<p>Example jobscript for an MPI job with preloaded inputs and executables, options for qsub are stored within the script :</p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -q qprod<br />#PBS -N MYJOB<br />#PBS -l select=100:ncpus=24:mpiprocs=1:ompthreads=24<br />#PBS -A OPEN-0-0<br /><br /># change to scratch directory, exit on failure<br />SCRDIR=/scratch/<span class="pln">work</span><span class="pun">/</span><span class="pln"></span>user/$USER/myjob<br />cd $SCRDIR || exit<br /><br /><br /># load the mpi module<br />module load OpenMPI<br /><br /># execute the calculation<br />mpiexec ./mympiprog.x<br /><br /><br />#exit<br />exit</pre>
+<p class=" ">In this example, input and executable files are assumed preloaded manually in /scratch/$USER/myjob directory. Note the <strong>mpiprocs</strong> and <strong>ompthreads</strong> qsub options, controlling behavior of the MPI execution. The mympiprog.x is executed as one process per node, on all 100 allocated nodes. If mympiprog.x implements OpenMP threads, it will run 24 threads per node.</p>
+<p class="hiddenForView">HTML commented section #2 (examples need to be reworked)</p>
+
+<h3 class=" ">Example Jobscript for Single Node Calculation<a name="JobscriptLocal"></a></h3>
+<p class="callout">Local scratch directory is often useful for single node jobs. Local scratch will be deleted immediately after the job ends.<br />Be very careful, use of RAM disk filesystem is at the expense of operational memory.</p>
+<p>Example jobscript for single node calculation, using <a href="../storage.html" title="" target="_self" class="internal-link">local scratch</a> on the node:</p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br /><br /># change to local scratch directory<br />cd /lscratch/$PBS_JOBID || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/input .<br />cp $PBS_O_WORKDIR/myprog.x .<br /><br /># execute the calculation<br />./myprog.x<br /><br /># copy output file to home<br />cp output $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
+<p class=" ">In this example, some directory on the home holds the input file input and executable myprog.x . We copy input and executable files from the home directory where the qsub was invoked ($PBS_O_WORKDIR) to local scratch /lscratch/$PBS_JOBID, execute the myprog.x and copy the output file back to the /home directory. The myprog.x runs on one node only and may use threads.</p>
+<p class="hiddenForView">HTML commented section #3 (Capacity computing need to be reworked)</p>
+
+
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diff --git a/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
index 017c0a58e..792c2c27f 100644
--- a/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
@@ -336,10 +336,10 @@ Examples:
```
$ check-pbs-jobs --check-all
JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3
-Check session idOK
+Check session id: OK
Check processes
-r3i6n2OK
-r3i6n3No process
+r3i6n2: OK
+r3i6n3: No process
```
In this example we see that job 35141.dm2 currently runs no process on
@@ -349,13 +349,13 @@ allocated node r3i6n2, which may indicate an execution error.
$ check-pbs-jobs --print-load --print-processes
JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3
Print load
-r3i6n2LOAD16.01, 16.01, 16.00
-r3i6n3LOAD 0.01, 0.00, 0.01
+r3i6n2: LOAD: 16.01, 16.01, 16.00
+r3i6n3: LOAD: 0.01, 0.00, 0.01
Print processes
%CPU CMD
-r3i6n2 0.0 -bash
-r3i6n2 0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC
-r3i6n299.7 run-task
+r3i6n2: 0.0 -bash
+r3i6n2: 0.0 /bin/bash /var/spool/PBS/mom_priv/jobs/35141.dm2.SC
+r3i6n2: 99.7 run-task
...
```
@@ -368,8 +368,8 @@ $ check-pbs-jobs --jobid 35141.dm2 --print-job-out
JOB 35141.dm2, session_id 71995, user user2, nodes r3i6n2,r3i6n3
Print job standard output:
======================== Job start ==========================
-Started at   Fri Aug 30 02:47:53 CEST 2013
-Script name  script
+Started at   : Fri Aug 30 02:47:53 CEST 2013
+Script name  : script
Run loop 1
Run loop 2
Run loop 3
@@ -437,8 +437,8 @@ directory
```
$ qsub -q qexp -l select=4:ncpus=24 -I
-qsubwaiting for job 15210.isrv5 to start
-qsubjob 15210.isrv5 ready
+qsub: waiting for job 15210.isrv5 to start
+qsub: job 15210.isrv5 ready
$ pwd
/home/username
@@ -459,8 +459,8 @@ allocation by reading the $PBS_NODEFILE file
```
qsub -q qexp -l select=2:ncpus=24 -I
-qsubwaiting for job 15210.isrv5 to start
-qsubjob 15210.isrv5 ready
+qsub: waiting for job 15210.isrv5 to start
+qsub: job 15210.isrv5 ready
$ pwd
/home/username
@@ -473,10 +473,10 @@ r4i7n2.ib0.smc.salomon.it4i.cz
$ pdsh -w r2i5n6,r4i6n13,r4i7n[0,2] hostname
-r4i6n13r4i6n13
-r2i5n6r2i5n6
-r4i7n2r4i7n2
-r4i7n0r4i7n0
+r4i6n13: r4i6n13
+r2i5n6: r2i5n6
+r4i7n2: r4i7n2
+r4i7n0: r4i7n0
```
In this example, the hostname program is executed via pdsh from the
@@ -614,4 +614,3 @@ may use threads.
HTML commented section #3 (Capacity computing need to be reworked)
-
diff --git a/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.html b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.html
new file mode 100644
index 000000000..1c7d37fb7
--- /dev/null
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.html
@@ -0,0 +1,881 @@
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+ <h2 class=" ">Resources Allocation Policy</h2>
+<p>The resources are allocated to the job in a fairshare fashion, subject to constraints set by the queue and resources available to the Project. The Fairshare at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the <a href="job-priority.html" title="" target="_self" class="internal-link">Job scheduling</a> section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:</p>
+<p>Â </p>
+<table class="listing">
+<tbody>
+<tr><th>queue</th><th>active project</th><th>project resources</th><th>nodes</th><th>min ncpus*</th><th>priority</th><th>authorization</th><th>walltime<br />default/max</th></tr>
+<tr class="even">
+<td><strong>qexp</strong><br />Express queue</td>
+<td>no</td>
+<td>none required</td>
+<td>32 nodes, max 8 per user</td>
+<td>24</td>
+<td><span>150</span></td>
+<td>no</td>
+<td>1 / 1h</td>
+</tr>
+<tr class="odd">
+<td><strong>qprod</strong><br />Production queue</td>
+<td>yes<br /><br /></td>
+<td>> 0</td>
+<td>
+<p><span>1006 nodes, max 86 per job</span></p>
+</td>
+<td>24</td>
+<td>0</td>
+<td>no</td>
+<td>24 / 48h</td>
+</tr>
+<tr class="even">
+<td><strong>qlong</strong><br />Long queue</td>
+<td>yes</td>
+<td>> 0</td>
+<td>256 nodes, max 40 per job</td>
+<td>24</td>
+<td>0</td>
+<td>no</td>
+<td>72 / 144h</td>
+</tr>
+<tr class="odd">
+<td><strong>qmpp<br /></strong>Massive parallel queue</td>
+<td>yes</td>
+<td>> 0</td>
+<td>1006 nodes</td>
+<td>24</td>
+<td>0</td>
+<td>yes</td>
+<td>2 / 4h</td>
+</tr>
+<tr class="even">
+<td><strong>qfat<br /></strong>UV2000 queue</td>
+<td>yes</td>
+<td>
+<p>> 0</p>
+</td>
+<td>1 (uv1)</td>
+<td>8</td>
+<td>0</td>
+<td>yes</td>
+<td>24 / 48h</td>
+</tr>
+<tr class="odd">
+<td><strong>qfree</strong><br />Free resource queue</td>
+<td>yes</td>
+<td>none required</td>
+<td>752 nodes, max 86 per job</td>
+<td>24</td>
+<td>-1024</td>
+<td>no</td>
+<td>12 / 12h</td>
+</tr>
+
+<tr class="odd">
+<td><strong><strong>qviz</strong><br /></strong>Visualization queue</td>
+<td>yes</td>
+<td>none required</td>
+<td>2 (with NVIDIA Quadro K5000)</td>
+<td>4</td>
+<td>150</td>
+<td>no</td>
+<td>1 / 2h</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<p class="callout"><strong>The qfree queue is not free of charge</strong>. <a class="anchor-link" href="resources-allocation-policy.html#resources-accounting-policy" target="_self" title="">Normal accounting</a> applies. However, it allows for utilization of free resources, once a Project exhausted all its allocated computational resources. This does not apply for Directors Discreation's projects (DD projects) by default. Usage of qfree after exhaustion of DD projects computational resources is allowed after request for this queue.</p>
+<p>Â </p>
+<ul>
+<li><strong>qexp</strong>, the Express queue: This queue is dedicated for testing and running very small jobs. It is not required to specify a project to enter the qexp. <span><em><span>There are 2 nodes always reserved for this queue (w/o accelerator), maximum 8 nodes are available via the qexp for a particular user. </span></em></span>The nodes may be allocated on per core basis. No special authorization is required to use it. The maximum runtime in qexp is 1 hour.</li>
+<li><strong>qprod</strong>, the Production queue<strong></strong>: This queue is intended for normal production runs. It is required that active project with nonzero remaining resources is specified to enter the qprod. All nodes may be accessed via the qprod queue, however only 86 per job.<em> </em>Full nodes, 24 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprod is 48 hours.</li>
+<li><strong>qlong</strong>, the Long queue<strong></strong>: This queue is intended for long production runs. It is required that active project with nonzero remaining resources is specified to enter the qlong. Only 336 nodes without acceleration may be accessed via the qlong queue. Full nodes, 24 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it.<span><em> The maximum runtime in qlong is 144 hours (three times of the standard qprod time - 3 * 48 h)</em></span></li>
+<li><span><em></em><strong>qmpp</strong>, the massively parallel queue. This queue is intended for massively parallel runs. It is required that active project with nonzero remaining resources is specified to enter the qmpp. All nodes may be accessed via the qmpp queue.<em> </em>Full nodes, 24 cores per node are allocated. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qmpp is 4 hours. An PI<span> <em>needs explicitly</em> </span>ask <a class="external-link" href="https://support.it4i.cz/rt/" target="_self" title="">support</a> for authorization to enter the queue for all users associated to her/his Project.<br /></span></li>
+<li><span><em></em></span><strong>qfat</strong>, the UV2000 queue. This queue is dedicated to access the fat SGI UV2000 SMP machine. The machine (uv1) has 112 Intel IvyBridge cores at 3.3GHz and 3.25TB RAM. An PI<span> <em>needs explicitly</em> </span>ask <a class="external-link" href="https://support.it4i.cz/rt/" target="_self" title="">support</a> for authorization to enter the queue for all users associated to her/his Project.<strong></strong></li>
+<li><strong>qfree</strong>, the Free resource queue<strong></strong>: The queue qfree is intended for utilization of free resources, after a Project exhausted all its allocated computational resources (Does not apply to DD projects by default. DD projects have to request for persmission on qfree after exhaustion of computational resources.). It is required that active project is specified to enter the queue, however no remaining resources are required. Consumed resources will be accounted to the Project. Only 178 nodes without accelerator may be accessed from this queue. Full nodes, 24 cores per node are allocated. The queue runs with very low priority and no special authorization is required to use it. The maximum runtime in qfree is 12 hours.</li>
+
+<li><strong>qviz</strong>, the Visualization queue<strong></strong>: Intended for pre-/post-processing using OpenGL accelerated graphics. Currently when accessing the node, each user gets 4 cores of a CPU allocated, thus approximately 73 GB of RAM and 1/7 of the GPU capacity (default "chunk"). <em>If more GPU power or RAM is required, it is recommended to allocate more chunks (with 4 cores each) up to one whole node per user, so that all 28 cores, 512 GB RAM and whole GPU is exclusive. This is currently also the maximum allowed allocation per one user. One hour of work is allocated by default, the user may ask for 2 hours maximum.</em></li>
+</ul>
+<p>Â </p>
+<p class="callout">To access node with Xeon Phi co-processor user needs to specify that in <a href="job-submission-and-execution.html" title="" target="_self" class="internal-link">job submission select statement</a>.</p>
+<h3 class=" ">Notes<strong><br /></strong></h3>
+<p>The job wall clock time defaults to<strong> half the maximum time</strong>, see table above. Longer wall time limits can be <a href="job-submission-and-execution.html" title="" target="_self" class="internal-link">set manually, see examples</a>. <br /><br />Jobs that exceed the reserved wall clock time (Req'd Time) get killed automatically. Wall clock time limit can be changed for queuing jobs (state Q) using the qalter command, however can not be changed for a running job (state R).</p>
+<p>Salomon users may check current queue configuration at <a class="external-link" href="https://extranet.it4i.cz/rsweb/salomon/queues" target="_self" title="">https://extranet.it4i.cz/rsweb/salomon/queues</a>.</p>
+<h3 class=" ">Queue status</h3>
+<p class="callout">Check the status of jobs, queues and compute nodes at <a class="external-link" href="https://extranet.it4i.cz/rsweb/salomon" target="_self" title="">https://extranet.it4i.cz/rsweb/salomon/</a></p>
+<p>Â </p>
+<p><img alt="RSWEB Salomon" src="rswebsalomon.png" title="RSWEB Salomon" class="image-inline" /></p>
+<p>Â </p>
+<p>Display the queue status on Salomon:</p>
+<pre class="prettyprint lang-sh">$ qstat -q</pre>
+
+<p class=" ">The PBS allocation overview may be obtained also using the rspbs command.</p>
+<pre class="prettyprint lang-sh">$ rspbs<br />Usage: rspbs [options]<br /><br />Options:<br /> --version            show program's version number and exit<br /> -h, --help           show this help message and exit<br /> --get-server-details Print server<br /> --get-queues         Print queues<br /> --get-queues-details Print queues details<br /> --get-reservations   Print reservations<br /> --get-reservations-details<br />                       Print reservations details<br /> --get-nodes          Print nodes of PBS complex<br /> --get-nodeset        Print nodeset of PBS complex<br /> --get-nodes-details  Print nodes details<br /> --get-jobs           Print jobs<br /> --get-jobs-details   Print jobs details<br /> --get-jobs-check-params<br />                       Print jobid, job state, session_id, user, nodes<br /> --get-users          Print users of jobs<br /> --get-allocated-nodes<br />                       Print allocated nodes of jobs<br /> --get-allocated-nodeset<br />                       Print allocated nodeset of jobs<br /> --get-node-users     Print node users<br /> --get-node-jobs      Print node jobs<br /> --get-node-ncpus     Print number of ncpus per node<br /> --get-node-allocated-ncpus<br />                       Print number of allocated ncpus per node<br /> --get-node-qlist     Print node qlist<br /> --get-node-ibswitch  Print node ibswitch<br /> --get-user-nodes     Print user nodes<br /> --get-user-nodeset   Print user nodeset<br /> --get-user-jobs      Print user jobs<br /> --get-user-jobc      Print number of jobs per user<br /> --get-user-nodec     Print number of allocated nodes per user<br /> --get-user-ncpus     Print number of allocated ncpus per user<br /> --get-qlist-nodes    Print qlist nodes<br /> --get-qlist-nodeset  Print qlist nodeset<br /> --get-ibswitch-nodes Print ibswitch nodes<br /> --get-ibswitch-nodeset<br />                       Print ibswitch nodeset<br /> --summary            Print summary<br /> --get-node-ncpu-chart<br />                       Obsolete. Print chart of allocated ncpus per node<br /> --server=SERVER      Use given PBS server<br /> --state=STATE        Only for given job state<br /> --jobid=JOBID        Only for given job ID<br /> --user=USER          Only for given user<br /> --node=NODE          Only for given node<br /> --nodestate=NODESTATE<br />                       Only for given node state (affects only --get-node*<br />                       --get-qlist-* --get-ibswitch-* actions)<br /> --incl-finished      Include finished jobs<br /><br /></pre>
+<h2 class=" "><a name="resources-accounting-policy"></a>Resources Accounting Policy</h2>
+<h3 class=" ">The Core-Hour</h3>
+<p>The resources that are currently subject to accounting are the core-hours. The core-hours are accounted on the wall clock basis. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. 1 core-hour is defined as 1 processor core allocated for 1 hour of wall clock time. Allocating a full node (24 cores) for 1 hour accounts to 24 core-hours. See example in the <a href="job-submission-and-execution.html" title="" target="_self" class="internal-link">Job submission and execution</a> section.</p>
+<h3 class=" ">Check consumed resources</h3>
+<p class="callout">The <strong>it4ifree</strong> command is a part of it4i.portal.clients package, located here:<br /><a class="external-link" href="https://pypi.python.org/pypi/it4i.portal.clients" target="_self" title="">https://pypi.python.org/pypi/it4i.portal.clients</a></p>
+<p>User may check at any time, how many core-hours have been consumed by himself/herself and his/her projects. The command is available on clusters' login nodes.</p>
+<pre class="prettyprint lang-sh">$ it4ifree<br />Password:<br />    PID  Total Used ...by me Free<br />  -------- ------- ------ -------- -------<br />  OPEN-0-0 1500000 400644  225265 1099356<br />  DD-13-1   10000 2606 2606 7394</pre>
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+ <a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
+ <a href="mailto:support [at] it4i.cz">support [at] it4i.cz</a>
+ </p>
+ <!-- nagios_check_http_expect_string -->
+</div>
+
+ </div>
+ </div>
+
+ <!-- TODO -->
+ <!-- nagios_check_http_expect_string -->
+ <!-- TODO -->
+
+</div>
+</body>
+</html>
+
diff --git a/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
index 2fc78feb9..36ff83d28 100644
--- a/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -138,21 +138,21 @@ is allowed after request for this queue.
Â
-- **qexp**, the Express queueThis queue is dedicated for testing and
+- **qexp**, the Express queue: This queue is dedicated for testing and
running very small jobs. It is not required to specify a project to
enter the qexp. <span>*<span>There are 2 nodes always reserved for
this queue (w/o accelerator), maximum 8 nodes are available via the
qexp for a particular user. </span>*</span>The nodes may be
allocated on per core basis. No special authorization is required to
use it. The maximum runtime in qexp is 1 hour.
-- **qprod**, the Production queue****This queue is intended for
+- **qprod**, the Production queue****: This queue is intended for
normal production runs. It is required that active project with
nonzero remaining resources is specified to enter the qprod. All
nodes may be accessed via the qprod queue, however only 86 per job.
** Full nodes, 24 cores per node are allocated. The queue runs with
medium priority and no special authorization is required to use it.
The maximum runtime in qprod is 48 hours.
-- **qlong**, the Long queue****This queue is intended for long
+- **qlong**, the Long queue****: This queue is intended for long
production runs. It is required that active project with nonzero
remaining resources is specified to enter the qlong. Only 336 nodes
without acceleration may be accessed via the qlong queue. Full
@@ -178,7 +178,7 @@ is allowed after request for this queue.
[support](https://support.it4i.cz/rt/) for
authorization to enter the queue for all users associated to her/his
Project.****
-- **qfree**, the Free resource queue****The queue qfree is intended
+- **qfree**, the Free resource queue****: The queue qfree is intended
for utilization of free resources, after a Project exhausted all its
allocated computational resources (Does not apply to DD projects
by default. DD projects have to request for persmission on qfree
@@ -189,7 +189,7 @@ is allowed after request for this queue.
this queue. Full nodes, 24 cores per node are allocated. The queue
runs with very low priority and no special authorization is required
to use it. The maximum runtime in qfree is 12 hours.
-- **qviz**, the Visualization queue****Intended for
+- **qviz**, the Visualization queue****: Intended for
pre-/post-processing using OpenGL accelerated graphics. Currently
when accessing the node, each user gets 4 cores of a CPU allocated,
thus approximately 73 GB of RAM and 1/7 of the GPU capacity
@@ -243,7 +243,7 @@ command.
```
$ rspbs
-Usagerspbs [options]
+Usage: rspbs [options]
Options:
 --version            show program's version number and exit
@@ -335,4 +335,3 @@ Password:
Â
-
diff --git a/docs.it4i.cz/salomon/software.html b/docs.it4i.cz/salomon/software.html
new file mode 100644
index 000000000..de1da1c48
--- /dev/null
+++ b/docs.it4i.cz/salomon/software.html
@@ -0,0 +1,1150 @@
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+ <input id="searchbox_currentfolder_only" class="noborder" type="checkbox" name="path" value="/docs/salomon/software" />
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+
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+
+ <span class="documentByLine">
+
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+
+ </dt>
+
+ <dd>
+ <span class="description">An engineering simulation software </span>
+ </dd>
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+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+
+ <a href="software/comsol.html" class="contenttype-folder state-published url">COMSOL</a>
+ </span>
+
+ <span class="documentByLine">
+
+
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+
+
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+
+ </dt>
+
+ <dd>
+ <span class="description"> A finite element analysis, solver and Simulation software</span>
+ </dd>
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+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+
+ <a href="software/debuggers.1.html" class="contenttype-folder state-published url">Debuggers and profilers</a>
+ </span>
+
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+
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+
+ <dd>
+ <span class="description">A collection of development tools</span>
+ </dd>
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+
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+
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+
+ <span class="summary">
+
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+
+ <dt class="">
+
+ <span class="summary">
+
+ <a href="software/intel-suite.html" class="contenttype-folder state-published url">Intel Parallel studio</a>
+ </span>
+
+ <span class="documentByLine">
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+
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+
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+
+ <dd>
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+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+
+ <a href="software/mpi-1.html" class="contenttype-folder state-published url">MPI</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">Message Passing Interface libraries on ANSELM</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+
+ <a href="software/numerical-languages.1.html" class="contenttype-folder state-published url">Numerical languages</a>
+ </span>
+
+ <span class="documentByLine">
+
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+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">Interpreted languages for numerical computations</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+
+ <a href="software/compilers.html" class="contenttype-document state-published url">Compilers</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">Available compilers, including GNU, INTEL and UPC compilers</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+
+ <a href="software/intel-xeon-phi.html" class="contenttype-document state-published url">Intel Xeon Phi</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">A guide to Intel Xeon Phi usage</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+
+ <a href="software/java.html" class="contenttype-document state-published url">Java</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">Java on the cluster</span>
+ </dd>
+
+
+
+
+
+
+ <dt class="">
+
+ <span class="summary">
+
+ <a href="software/operating-system.html" class="contenttype-document state-published url">Operating System</a>
+ </span>
+
+ <span class="documentByLine">
+
+
+
+
+
+ </span>
+
+ </dt>
+
+ <dd>
+ <span class="description">The operating system, deployed on Salomon cluster</span>
+ </dd>
+
+
+
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+
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+
+
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+
+
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+
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+
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+
+
+
+
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+
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+
+
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+
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+<p>The clusters provides as commercial as academic variants. Academic variants are distinguished by "<strong>Academic...</strong>" word in the name of  license or by two letter preposition "<strong>aa_</strong>" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). <a href="ansys/licensing.html" title="" target="_self" class="internal-link">More about licensing here</a></p>
+<p>To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module:</p>
+<pre class=" ">$ module load ANSYS</pre>
+<p>ANSYS supports interactive regime, but due to assumed solution of extremely difficult tasks it is not recommended.</p>
+<p>If user needs to work in interactive regime we recommend to configure the RSM service on the client machine which allows to forward the solution to the clusters directly from the client's Workbench project (see ANSYS RSM service).</p>
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+ <p><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX" target="_blank" title="">ANSYS CFX</a> software is a high-performance, general purpose fluid dynamics program that has been applied to solve wide-ranging fluid flow problems for over 20 years. At the heart of ANSYS CFX is its advanced solver technology, the key to achieving reliable and accurate solutions quickly and robustly. The modern, highly parallelized solver is the foundation for an abundant choice of physical models to capture virtually any type of phenomena related to fluid flow. The solver and its many physical models are wrapped in a modern, intuitive, and flexible GUI and user environment, with extensive capabilities for customization and automation using session files, scripting and a powerful expression language.</p>
+<p><span>To run ANSYS CFX in batch mode you can utilize/modify the default cfx.pbs script and execute it via the qsub command.</span></p>
+<pre class=" ">#!/bin/bash<br />#PBS -l nodes=2:ppn=24<br />#PBS -q qprod<br />#PBS -N $USER-CFX-Project<br />#PBS -A OPEN-0-0<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/work/user<strong>/</strong>$USER"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />module load ANSYS<br /><br />#### Set number of processors per host listing<br />procs_per_host=24<br />#### Create host list<br />hl=""<br />for host in `cat $PBS_NODEFILE`<br />do<br /> if [ "$hl" = "" ]<br /> then hl="$host:$procs_per_host"<br /> else hl="${hl}:$host:$procs_per_host"<br /> fi<br />done<br /><br />echo Machines: $hl<br /><br /># prevent ANSYS from attempting to use scif0 interface<br />export MPI_IC_ORDER="UDAPL"<br /><br />#-dev input.def includes the input of CFX analysis in DEF format<br />#-P the name of prefered license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial))<br />cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r</pre>
+<p>Header of the pbs file (above) is common and description can be find <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_blank" class="internal-link">this site</a>. SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. <span>Input file has to be defined by common CFX def file which is attached to the cfx solver via parameter -def</span></p>
+<p><strong>License</strong>Â should be selected by parameter -P (Big letter <strong>P</strong>). Licensed products are the following: aa_r (ANSYSÂ <strong>Academic</strong>Â Research), ane3fl (ANSYS Multiphysics)-<strong>Commercial.</strong> <br /><span><a href="licensing.html" title="" target="_self" class="internal-link">More about licensing here</a></span></p>
+<p class="exclamation">Â We have observed that the -P settings does not always work. Please set your <a href="setting-license-preferences.html" title="" target="_self" class="internal-link">license preferences</a> instead.</p>
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+ <!-- nagios_check_http_expect_string -->
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diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md b/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
index 8e5c4b40c..908277472 100644
--- a/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
@@ -52,7 +52,7 @@ cfx.pbs script and execute it via the qsub command.</span>
fi
done
- echo Machines$hl
+ echo Machines: $hl
# prevent ANSYS from attempting to use scif0 interface
export MPI_IC_ORDER="UDAPL"
@@ -64,7 +64,7 @@ cfx.pbs script and execute it via the qsub command.</span>
Header of the pbs file (above) is common and description can be findÂ
[this
site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
-SVS FEM recommends to utilize sources by keywordsnodes, ppn. These
+SVS FEM recommends to utilize sources by keywords: nodes, ppn. These
keywords allows to address directly the number of nodes (computers) and
cores (ppn) which will be utilized in the job. Also the rest of code
assumes such structure of allocated resources.
@@ -76,7 +76,7 @@ CFX def file which is attached to the cfx solver via parameter
-def</span>
**License**Â should be selected by parameter -P (Big letter **P**).
-Licensed products are the followingaa_r
+Licensed products are the following: aa_r
(ANSYSÂ **Academic**Â Research), ane3fl (ANSYS
Multiphysics)-**Commercial.**
<span>[More about licensing here](licensing.html)</span>
diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view.html b/docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view.html
new file mode 100644
index 000000000..fa348d823
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-fluent-pbs-file/view.html
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+ <p><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent" target="_blank" title="">ANSYS Fluent</a> software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. Special models that give the software the ability to model in-cylinder combustion, aeroacoustics, turbomachinery, and multiphase systems have served to broaden its reach.</p>
+<h2 class=" "><span>1. Common way to run Fluent over pbs file</span></h2>
+<p><span>To run ANSYS Fluent in batch mode you can utilize/modify the default fluent.pbs script and execute it via the qsub command.</span></p>
+<pre class=" ">#!/bin/bash<br />#PBS -S /bin/bash<br />#PBS -l nodes=2:ppn=24<br />#PBS -q qprod<br />#PBS -N Fluent-Project<br />#PBS -A OPEN-0-0<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/work/user<strong>/</strong>$USER"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />#### Load ansys module so that we find the cfx5solve command<br />module load ANSYS<br /><br /># Use following line to specify MPI for message-passing instead<br />NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`<br /><br />/apps/cae/ANSYS/16.1/v161/fluent/bin/fluent 3d -t$NCORES -cnf=$PBS_NODEFILE -g -i fluent.jou</pre>
+<p>Header of the pbs file (above) is common and description can be find on <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_blank" class="internal-link">this site</a>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common Fluent journal file which is attached to the Fluent solver via parameter -i fluent.jou</p>
+<p>Journal file with definition of the input geometry and boundary conditions and defined process of solution has e.g. the following structure:</p>
+<pre class=" ">/file/read-case aircraft_2m.cas.gz<br />/solve/init<br />init<br />/solve/iterate<br />10<br />/file/write-case-dat aircraft_2m-solution<br />/exit yes</pre>
+<p><span>The appropriate dimension of the problem has to be set by parameter (2d/3d). </span></p>
+<h2 class=" "><span>2. Fast way to run Fluent from command line</span></h2>
+<div class="section" title="3.1.2. Usage">
+<pre class=" "><code class="systemitem">fluent</code> <span class="emphasis"><em>solver_version</em></span> <code class="systemitem">[</code><span class="emphasis"><em>FLUENT_options</em></span><code class="systemitem">] -i</code> <span class="emphasis"><em>journal_file</em></span> <code class="systemitem">-pbs</code></pre>
+<div class="section" title="3.1.2. Usage">
+<p>This syntax will start the ANSYS FLUENT job under PBS Professional using the <span class="monospace">qsub</span>Â command in a batch manner. When resources are available, PBS Professional will start the job and return a job ID, usually in the form of <span class="emphasis"><em>job_ID.hostname</em></span>. This job ID can then be used to query, control, or stop the job using standard PBS Professional commands, such as <span class="monospace">qstat</span>Â or <span class="monospace">qdel</span>. The job will be run out of the current working directory, and all output will be written to the file <span class="monospace">fluent.o</span><span>Â </span><span class="emphasis"><em>job_ID</em></span>. Â Â Â Â </p>
+<h2 class=" ">3. Running Fluent via user's config file</h2>
+<div class="section" title="3.3.1. Configuration File Example">
+<p>The sample script uses a configuration file called <span class="monospace">pbs_fluent.conf</span> Â if no command line arguments are present. This configuration file should be present in the directory from which the jobs are submitted (which is also the directory in which the jobs are executed). The following is an example of what the content of <span class="monospace">pbs_fluent.conf</span>Â can be:</p>
+<pre class="screen"> input="example_small.flin"
+ case="Small-1.65m.cas"
+ fluent_args="3d -pmyrinet"
+ outfile="fluent_test.out"
+ mpp="true"</pre>
+<p>The following is an explanation of the parameters:</p>
+<div>
+<div class="variablelist">
+<p class=" " style="padding-left: 30px; "><span><span class="monospace">input</span> is the name of the input file.</span></p>
+<p class=" " style="padding-left: 30px; "><span class="monospace">case</span> is the name of the <span class="monospace">.cas</span>Â file that the input file will utilize.</p>
+<p class=" " style="padding-left: 30px; "><span class="monospace">fluent_args</span> are extra ANSYS FLUENT arguments. As shown in the previous example, you can specify the interconnect by using the <span class="monospace">-p</span>Â interconnect command. The available interconnects include <span class="monospace">ethernet</span>Â (the default), <span class="monospace">myrinet</span>,<span class="monospace"> infiniband</span>, <span class="monospace">vendor</span>, <span class="monospace">altix</span><span>,</span> and <span class="monospace">crayx</span>. The MPI is selected automatically, based on the specified interconnect.</p>
+<p class=" " style="padding-left: 30px; "><span class="monospace">outfile</span> is the name of the file to which the standard output will be sent.</p>
+<p class=" " style="padding-left: 30px; "><span class="monospace">mpp="true"</span> will tell the job script to execute the job across multiple processors. Â Â Â Â Â Â Â Â </p>
+</div>
+</div>
+</div>
+</div>
+</div>
+<p><span>To run ANSYS Fluent in batch mode with user's config file you can utilize/modify the following script and execute it via the qsub command.</span></p>
+<div class="section" title="3.3.2. Altair’s Sample Script">
+<pre class="screen">#!/bin/sh<br />#PBS -l nodes=2:ppn=24<br />#PBS -1 qprod<br />#PBS -N Fluent-Project<br />#PBS -A OPEN-0-0<br />
+ cd $PBS_O_WORKDIR
+
+ #We assume that if they didn’t specify arguments then they should use the
+ #config file if [ "xx${input}${case}${mpp}${fluent_args}zz" = "xxzz" ]; then
+ if [ -f pbs_fluent.conf ]; then
+ . pbs_fluent.conf
+ else
+ printf "No command line arguments specified, "
+ printf "and no configuration file found. Exiting \n"
+ fi
+ fi
+
+
+ #Augment the ANSYS FLUENT command line arguments case "$mpp" in
+ true)
+ #MPI job execution scenario
+ num_nodes=â€cat $PBS_NODEFILE | sort -u | wc -lâ€
+ cpus=â€expr $num_nodes \* $NCPUSâ€
+ #Default arguments for mpp jobs, these should be changed to suit your
+ #needs.
+ fluent_args="-t${cpus} $fluent_args -cnf=$PBS_NODEFILE"
+ ;;
+ *)
+ #SMP case
+ #Default arguments for smp jobs, should be adjusted to suit your
+ #needs.
+ fluent_args="-t$NCPUS $fluent_args"
+ ;;
+ esac
+ #Default arguments for all jobs
+ fluent_args="-ssh -g -i $input $fluent_args"
+
+ echo "---------- Going to start a fluent job with the following settings:
+ Input: $input
+ Case: $case
+ Output: $outfile
+ Fluent arguments: $fluent_args"
+
+ #run the solver
+ /apps/cae/ANSYS/16.1/v161/fluent/bin/fluent $fluent_args > $outfile</pre>
+</div>
+<p><span>It runs the jobs out of the directory from which they are submitted (PBS_O_WORKDIR).</span></p>
+<h2 class=" ">4. Running Fluent in parralel</h2>
+<p><a name="license_preferences"></a>Fluent could be run in parallel only under Academic Research license. To do so this ANSYS Academic Research license must be placed before ANSYS CFD license in user preferences. To make this change <a href="setting-license-preferences.html" title="" target="_self" class="internal-link">anslic_admin utility should be run</a>.</p>
+<p>Â </p>
+
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+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
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diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md b/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
index dd17d7b50..cfb017293 100644
--- a/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
@@ -51,7 +51,7 @@ Header of the pbs file (above) is common and description can be find on
[this
site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
[SVS FEM](http://www.svsfem.cz) recommends to utilize
-sources by keywordsnodes, ppn. These keywords allows to address
+sources by keywords: nodes, ppn. These keywords allows to address
directly the number of nodes (computers) and cores (ppn) which will be
utilized in the job. Also the rest of code assumes such structure of
allocated resources.
@@ -189,10 +189,10 @@ command.</span>
fluent_args="-ssh -g -i $input $fluent_args"
echo "---------- Going to start a fluent job with the following settings:
- Input$input
- Case$case
- Output$outfile
- Fluent arguments$fluent_args"
+ Input: $input
+ Case: $case
+ Output: $outfile
+ Fluent arguments: $fluent_args"
#run the solver
/apps/cae/ANSYS/16.1/v161/fluent/bin/fluent $fluent_args > $outfile
diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view.html b/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view.html
new file mode 100644
index 000000000..2a9e88f36
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna-pbs-file/view.html
@@ -0,0 +1,1074 @@
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diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.html b/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.html
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--- /dev/null
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+ <p><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA" target="_blank" title="">ANSYS LS-DYNA</a> software provides convenient and easy-to-use access to the technology-rich, time-tested explicit solver without the need to contend with the complex input requirements of this sophisticated program. Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in numerous industries to resolve highly intricate design issues. <span>ANSYS Mechanical users have been able take advantage of complex explicit solutions for a long time utilizing the traditional ANSYS Parametric Design Language (APDL) environment. <span>These explicit capabilities are available to ANSYS Workbench users as well. The Workbench platform is a powerful, comprehensive, easy-to-use environment for engineering simulation. CAD import from all sources, geometry cleanup, automatic meshing, solution, parametric optimization, result visualization and comprehensive report generation are all available within a single fully interactive modern graphical user environment.</span></span></p>
+<p><span>To run ANSYS LS-DYNA in batch mode you can utilize/modify the default ansysdyna.pbs script and execute it via the qsub command.</span></p>
+<pre class=" ">#!/bin/bash<br />#PBS -l nodes=2:ppn=24<br />#PBS -q qprod<br />#PBS -N DYNA-Project<br />#PBS -A OPEN-0-0<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory><br />WORK_DIR="/scratch/work/user<strong>/</strong>$USER"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />module load ANSYS<br /><br />#### Set number of processors per node<br />procs_per_host=24<br />#### Create host list<br />hl=""<br />for host in `cat $PBS_NODEFILE`<br />do<br /> if [ "$hl" = "" ]<br /> then hl="$host:$procs_per_host"<br /> else hl="${hl}:$host:$procs_per_host"<br /> fi<br />done<br /><br />echo Machines: $hl<br /><br /># prevent ANSYS from attempting to use scif0 interface<br />export MPI_IC_ORDER="UDAPL"<br /><br />lsdyna161 -dis -usessh -machines "$hl" i=input.k</pre>
+<p><span>Header of the pbs file (above) is common and description can be find </span><span> on <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_blank" class="internal-link">this site</a>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</span></p>
+<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA .<strong>k</strong> file which is attached to the ansys solver via parameter i=</p>
+<p class="exclamation">Without setting environment variable MPI_IC_ORDER="UDAPL", ANSYS will fail to run on nodes with Xeon Phi accelerator (it will use the virtual interface of Phi cards instead of the real InfiniBand interface and MPI will fail.</p>
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diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md b/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
index 53f97aee3..e1e59d32e 100644
--- a/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
@@ -56,7 +56,7 @@ default ansysdyna.pbs script and execute it via the qsub command.</span>
fi
done
- echo Machines$hl
+ echo Machines: $hl
# prevent ANSYS from attempting to use scif0 interface
export MPI_IC_ORDER="UDAPL"
@@ -67,7 +67,7 @@ default ansysdyna.pbs script and execute it via the qsub command.</span>
find </span><span> on [this
site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
[SVS FEM](http://www.svsfem.cz) recommends to utilize
-sources by keywordsnodes, ppn. These keywords allows to address
+sources by keywords: nodes, ppn. These keywords allows to address
directly the number of nodes (computers) and cores (ppn) which will be
utilized in the job. Also the rest of code assumes such structure of
allocated resources.</span>
diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view.html b/docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view.html
new file mode 100644
index 000000000..3002b649e
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-mapdl-pbs-file/view.html
@@ -0,0 +1,1074 @@
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+ <p><span><strong><a class="external-link" href="http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics" target="_blank" title="">ANSYS Multiphysics</a></strong> software offers a comprehensive product solution for both multiphysics and single-physics analysis. The product includes structural, thermal, fluid and both high- and low-frequency electromagnetic analysis. The product also contains solutions for both direct and sequentially coupled physics problems including direct coupled-field elements and the ANSYS multi-field solver.</span></p>
+<p><span>To run ANSYS MAPDL in batch mode you can utilize/modify the default mapdl.pbs script and execute it via the qsub command.</span></p>
+<pre class=" ">#!/bin/bash<br />#PBS -l nodes=2:ppn=24<br />#PBS -q qprod<br />#PBS -N ANSYS-Project<br />#PBS -A OPEN-0-0<br /><br />#! Mail to user when job terminate or abort<br />#PBS -m ae<br /><br />#!change the working directory (default is home directory)<br />#cd <working directory> (working directory must exists)<br />WORK_DIR="/scratch/work/user/$USER"<br />cd $WORK_DIR<br /><br />echo Running on host `hostname`<br />echo Time is `date`<br />echo Directory is `pwd`<br />echo This jobs runs on the following processors:<br />echo `cat $PBS_NODEFILE`<br /><br />module load ANSYS/16.1<br /><br />#### Set number of processors per host listing<br />procs_per_host=24<br />#### Create host list<br />hl=""<br />for host in `cat $PBS_NODEFILE`<br />do<br /> if [ "$hl" = "" ]<br /> then hl="$host:$procs_per_host"<br /> else hl="${hl}:$host:$procs_per_host"<br /> fi<br />done<br /><br />echo Machines: $hl<br /><br /># prevent ANSYS from attempting to use scif0 interface<br />export MPI_IC_ORDER="UDAPL"<br /><br />#-i input.dat includes the input of analysis in APDL format<br />#-o file.out is output file from ansys where all text outputs will be redirected <br />#-p the name of license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial), aa_r_dy=Academic AUTODYN)<br />ansys161 -b -dis -usessh -p aa_r -i input.dat -o file.out -machines "$hl" -dir $WORK_DIR</pre>
+<p>Header of the PBS file (above) is common and description can be find on <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_blank" class="internal-link">this site</a>. <a class="external-link" href="http://www.svsfem.cz" target="_blank" title="">SVS FEM</a> recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.</p>
+<p>Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common APDL file which is attached to the ansys solver via parameter -i</p>
+<p><strong>License</strong> should be selected by parameter -p. Licensed products are the following: aa_r (ANSYS <strong>Academic</strong> Research), ane3fl (ANSYS Multiphysics)-<strong>Commercial</strong>, aa_r_dy (ANSYS <strong>Academic</strong> AUTODYN)<span> <br /><a href="licensing.html" title="" target="_self" class="internal-link">More about licensing here</a><br /></span></p>
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diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md b/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
index 48afd236f..691b8e710 100644
--- a/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
@@ -47,7 +47,7 @@ default mapdl.pbs script and execute it via the qsub command.</span>
fi
done
- echo Machines$hl
+ echo Machines: $hl
# prevent ANSYS from attempting to use scif0 interface
export MPI_IC_ORDER="UDAPL"
@@ -61,7 +61,7 @@ Header of the PBS file (above) is common and description can be find on
[this
site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
[SVS FEM](http://www.svsfem.cz) recommends to utilize
-sources by keywordsnodes, ppn. These keywords allows to address
+sources by keywords: nodes, ppn. These keywords allows to address
directly the number of nodes (computers) and cores (ppn) which will be
utilized in the job. Also the rest of code assumes such structure of
allocated resources.
@@ -72,7 +72,7 @@ file has to be specified. Input file has to be defined by common APDL
file which is attached to the ansys solver via parameter -i
**License** should be selected by parameter -p. Licensed products are
-the followingaa_r (ANSYS **Academic** Research), ane3fl (ANSYS
+the following: aa_r (ANSYS **Academic** Research), ane3fl (ANSYS
Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic**
AUTODYN)<span>
[More about licensing here](licensing.html)
diff --git a/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.html b/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.html
new file mode 100644
index 000000000..0686513ee
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.html
@@ -0,0 +1,1077 @@
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+ <p><strong><a class="external-link" href="http://www.svsfem.cz/" target="_blank" title="">SVS FEM</a></strong> as <em><strong><a class="external-link" href="http://www.ansys.com/" target="_self" title="">ANSYS Channel partner</a></strong></em> for Czech Republic provided all ANSYS licenses for all clusters and supports of all ANSYS Products (Multiphysics, Mechanical, MAPDL, CFX, Fluent, Maxwell, LS-DYNA...) to IT staff and ANSYS users. If you are challenging to problem of ANSYS functionality contact please <a class="email-link" href="mailto:hotline@svsfem.cz?subject=Ostrava%20-%20ANSELM" target="_self" title="">hotline@svsfem.cz</a></p>
+<p>The clusters provides as commercial as academic variants. Academic variants are distinguished by "<strong>Academic...</strong>" word in the name of  license or by two letter preposition "<strong>aa_</strong>" in the license feature name. Change of license is realized on command line respectively directly in user's pbs file (see individual products). <a href="licensing.html" title="" target="_self" class="internal-link">More about licensing here</a></p>
+<p>To load the latest version of any ANSYS product (Mechanical, Fluent, CFX, MAPDL,...) load the module:</p>
+<pre class=" ">$ module load ANSYS</pre>
+<p>ANSYS supports interactive regime, but due to assumed solution of extremely difficult tasks it is not recommended.</p>
+<p>If user needs to work in interactive regime we recommend to configure the RSM service on the client machine which allows to forward the solution to the clusters directly from the client's Workbench project (see ANSYS RSM service).</p>
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diff --git a/docs.it4i.cz/salomon/software/ansys/licensing.html b/docs.it4i.cz/salomon/software/ansys/licensing.html
new file mode 100644
index 000000000..4f0455a8c
--- /dev/null
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+
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+ <span id="breadcrumbs-current">Licensing and Available Versions</span>
+
+ </span>
+
+</div>
+</div>
+
+
+ <div class="">
+
+
+
+
+
+ <dl class="portalMessage info" id="kssPortalMessage" style="display:none">
+ <dt>Info</dt>
+ <dd></dd>
+ </dl>
+
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+
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+ <div id="content">
+
+
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+
+
+ <div id="viewlet-above-content-title"></div>
+
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+ Licensing and Available Versions
+ </h1>
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+
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+ <h2 class=" ">ANSYS licence can be used by:</h2>
+<ul>
+<li>all persons in the carrying out of the CE IT4Innovations Project (In addition to the primary licensee, which is VSB - Technical University of Ostrava, users are CE IT4Innovations third parties - CE IT4Innovations project partners, particularly the University of Ostrava, the Brno University of Technology - Faculty of Informatics, the Silesian University in Opava, Institute of Geonics AS CR.)</li>
+<li><span class="short_text" id="result_box"><span class="hps">all persons</span> <span class="hps">who have a valid</span> <span class="hps">license</span></span></li>
+<li><span class="short_text" id="result_box"><span class="hps">students of</span> <span class="hps">the Technical University</span></span></li>
+</ul>
+<h2 class=" ">ANSYS Academic Research</h2>
+<p>The licence intended to be used for science and research, publications, students’ projects (academic licence).</p>
+<h2 class=" ">ANSYS COM</h2>
+<p>The licence intended to be used for science and research, publications, students’ projects, commercial research with no commercial use restrictions.</p>
+<h2 class=" ">Available Versions</h2>
+<ul>
+<li>16.1</li>
+<li>17.0</li>
+</ul>
+<h2>License Preferences</h2>
+<p>Please <a href="setting-license-preferences.html" title="" target="_self" class="internal-link">see this page to set license preferences</a>.</p>
+<p>Â </p>
+
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+
+
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+ <b><a id="contact-form-href" href="#contact-form" i18n:translate="">Contact form</a></b>
+ <tal:contactform tal:content="structure python:getattr(context, 'contact-info')()"></tal:contactform>
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+ <span>Accessing the Cluster</span>
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+ </a>
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+</li>
+
+
+<li class="navTreeItem visualNoMarker section-list_of_modules">
+
+
+
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+ <a href="../../list_of_modules.html" title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document">
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+ <span>List of Available Modules</span>
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+
+
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+<li class="navTreeItem visualNoMarker navTreeFolderish section-resource-allocation-and-job-execution">
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+ <span>Resource Allocation and Job Execution</span>
+ </a>
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+<li class="navTreeItem visualNoMarker section-compute-nodes">
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+ </a>
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+<li class="navTreeItem visualNoMarker navTreeFolderish section-network-1">
+
+
+
+
+ <a href="../../network-1.html" title="" class="state-published navTreeFolderish contenttype-folder">
+
+ <span>Network</span>
+ </a>
+
+
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+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeItemInPath navTreeFolderish section-software">
+
+
+
+
+ <a href="../../software.html" title="In this section we provide overview of installed software and its usage.
+
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+" class="state-published navTreeItemInPath navTreeFolderish contenttype-folder">
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+<li class="navTreeItem visualNoMarker navTreeItemInPath navTreeFolderish section-ansys">
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+
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+
+ <a href="../ansys.html" title="An engineering simulation software " class="state-published navTreeItemInPath navTreeFolderish contenttype-folder">
+
+ <span>ANSYS</span>
+ </a>
+
+
+ <ul class="navTree navTreeLevel3">
+
+
+
+
+<li class="navTreeItem visualNoMarker section-ansys-mechanical-apdl">
+
+
+
+
+ <a href="ansys-mechanical-apdl.html" title="" class="state-published contenttype-document">
+
+ <span>ANSYS MAPDL</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-cfx">
+
+
+
+
+ <a href="ansys-cfx.html" title="" class="state-published contenttype-document">
+
+ <span>ANSYS CFX</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-fluent">
+
+
+
+
+ <a href="ansys-fluent.html" title="" class="state-published contenttype-document">
+
+ <span>ANSYS Fluent</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-ls-dyna">
+
+
+
+
+ <a href="ansys-ls-dyna.html" title="" class="state-published contenttype-document">
+
+ <span>ANSYS LS-DYNA</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker navTreeCurrentNode section-licensing">
+
+
+
+
+ <a href="licensing.html" title="" class="state-published navTreeCurrentItem navTreeCurrentNode contenttype-document">
+
+ <span>Licensing and Available Versions</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-mapdl-pbs-file">
+
+
+
+
+ <a href="ansys-mapdl-pbs-file/view.html" title="" class="state-missing-value contenttype-file">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>ANSYS MAPDL PBS file</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-cfx-pbs-file">
+
+
+
+
+ <a href="ansys-cfx-pbs-file/view.html" title="" class="state-missing-value contenttype-file">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>ANSYS CFX PBS file</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-fluent-pbs-file">
+
+
+
+
+ <a href="ansys-fluent-pbs-file/view.html" title="" class="state-missing-value contenttype-file">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>ANSYS Fluent PBS file</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ansys-ls-dyna-pbs-file">
+
+
+
+
+ <a href="ansys-ls-dyna-pbs-file/view.html" title="" class="state-missing-value contenttype-file">
+ <img width="16" height="16" src="https://docs.it4i.cz/sh.png" alt="Soubor" />
+ <span>ANSYS LS-DYNA PBS file</span>
+ </a>
+
+
+
+
+</li>
+
+
+<li class="navTreeItem visualNoMarker section-ls-dyna-pbs-file">
+
+
+
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+ <p>Some ANSYS tools allow you to explicitly specify usage of academic or commercial licenses in the command line (eg. <span class="monospace">ansys161 -p aa_r</span> to select Academic Research license). However, we have observed that not all tools obey this option and choose commercial license.</p>
+<p>Thus you need to configure preferred license order with ANSLIC_ADMIN. Please follow these steps and move Academic Research license to the  top or bottom of the list accordingly.</p>
+<p>Launch the ANSLIC_ADMIN utility in a graphical environment:</p>
+<pre class=" "> $ANSYSLIC_DIR/lic_admin/anslic_admin</pre>
+<p>ANSLIC_ADMIN Utility will be run</p>
+<p><a href="Fluent_Licence_1.jpg" title="" target="_blank" class="internal-link"><img alt="Fluent_Licence_1.jpg" src="https://docs.it4i.cz/salomon/software/ansys/Fluent_Licence_1.jpg/@@images/0203aca4-d4f8-4372-ab71-432fcf15df43.jpeg" title="Fluent_Licence_1.jpg" class="image-inline" /></a></p>
+<p><a href="Fluent_Licence_2.jpg" title="" target="_blank" class="internal-link"><img alt="Fluent_Licence_2.jpg" src="https://docs.it4i.cz/salomon/software/ansys/Fluent_Licence_2.jpg/@@images/5a50330d-afcf-4266-ba1b-1ab70c9ed1b1.jpeg" title="Fluent_Licence_2.jpg" class="image-inline" /></a></p>
+<p><a href="Fluent_Licence_3.jpg" title="" target="_blank" class="internal-link"><img alt="Fluent_Licence_3.jpg" src="https://docs.it4i.cz/salomon/software/ansys/Fluent_Licence_3.jpg/@@images/5f65d83b-44e3-419c-96d2-8a4419227b1e.jpeg" title="Fluent_Licence_3.jpg" class="image-inline" /></a></p>
+<p>Â </p>
+<p>ANSYS Academic Research license should be moved up to the top or down to the bottom of the list.</p>
+<p>Â </p>
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+ <h2 class=" ">Workbench Batch Mode</h2>
+<p>It is possible to run Workbench scripts in batch mode. You need to configure solvers of individual components to run in parallel mode. Open your project in Workbench. Then, for example, in Mechanical, go to Tools - Solve Process Settings ..., click Advanced button as shown on the screenshot.</p>
+<p><img alt="" src="AMsetPar1.png/@@images/a34a45cc-9385-4f05-b12e-efadf1bd93bb.png" title="" class="image-inline" /></p>
+<p>Enable Distribute Solution checkbox and enter number of cores (eg. 48 to run on two Salomon nodes). If you want the job to run on more then 1 node, you must also provide a so called MPI appfile. In the Additional Command Line Arguments input field, enter :</p>
+<pre class=" ">-mpifile /path/to/my/job/mpifile.txt</pre>
+<p>Where /path/to/my/job is the directory where your project is saved. We will create the file mpifile.txt programatically later in the batch script. For more information, refer to <em>ANSYS Mechanical APDL Parallel Processing</em> <em>Guide</em>.</p>
+<p>Now, save the project and close Workbench. We will use this script to launch the job:</p>
+<pre class=" ">#!/bin/bash
+#PBS -l select=2:ncpus=24
+#PBS -q qprod
+#PBS -N test9_mpi_2
+#PBS -A OPEN-0-0
+
+# Mail to user when job terminate or abort
+#PBS -m a
+
+# change the working directory
+WORK_DIR="$PBS_O_WORKDIR"
+cd $WORK_DIR
+
+echo Running on host `hostname`
+echo Time is `date`
+echo Directory is `pwd`
+echo This jobs runs on the following nodes:
+echo `cat $PBS_NODEFILE`
+
+module load ANSYS
+
+#### Set number of processors per host listing
+procs_per_host=24
+#### Create MPI appfile
+echo -n "" > mpifile.txt
+for host in `cat $PBS_NODEFILE`
+do
+ echo "-h $host -np $procs_per_host $ANSYS160_DIR/bin/ansysdis161 -dis" >> mpifile.txt
+done
+
+#-i input.dat includes the input of analysis in APDL format
+#-o file.out is output file from ansys where all text outputs will be redirected
+#-p the name of license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial), aa_r_dy=Academic AUTODYN)
+<br /># prevent using scsif0 interface on accelerated nodes
+export MPI_IC_ORDER="UDAPL"<br /># spawn remote process using SSH (default is RSH)
+export MPI_REMSH="/usr/bin/ssh"
+
+runwb2 -R jou6.wbjn -B -F test9.wbpj
+</pre>
+<p class="exclamation">The solver settings are saved in file solvehandlers.xml, which is not located in the project directory. Verify your solved settings when uploading a project from your local computer.</p>
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+ <h2 class=" ">About Molpro</h2>
+<p>Molpro is a software package used for accurate ab-initio quantum chemistry calculations. More information can be found at the <a class="external-link" href="http://www.molpro.net/" target="_self" title="">official webpage</a>.</p>
+<h2 class=" ">License</h2>
+<p>Molpro software package is available only to users that have a valid license. Please contact support to enable access to Molpro if you have a valid license appropriate for running on our cluster (eg. <span>academic research group licence, parallel execution).</span></p>
+<p class=" "><span>To run Molpro, you need to have a valid license token present in "<span class="monospace">$HOME/.molpro/token"</span></span>. You can download the token from <a class="external-link" href="https://www.molpro.net/licensee/?portal=licensee" target="_self" title="">Molpro website</a>.</p>
+<h2 class=" ">Installed version</h2>
+<p>Currently on Salomon is installed version 2010.1, patch level 57, parallel version compiled with Intel compilers and Intel MPI.</p>
+<p>Compilation parameters are default :</p>
+<table class="plain">
+<tbody>
+<tr><th>Parameter</th><th>Value</th></tr>
+<tr>
+<td><span>max number of atoms</span></td>
+<td>200</td>
+</tr>
+<tr>
+<td><span>max number of valence orbitals</span></td>
+<td>300</td>
+</tr>
+<tr>
+<td><span>max number of basis functions</span></td>
+<td>4095</td>
+</tr>
+<tr>
+<td><span>max number of states per symmmetry</span></td>
+<td>20</td>
+</tr>
+<tr>
+<td><span>max number of state symmetries</span></td>
+<td>16</td>
+</tr>
+<tr>
+<td><span>max number of records</span></td>
+<td>200</td>
+</tr>
+<tr>
+<td><span>max number of primitives</span></td>
+<td><span>maxbfn x [2]</span></td>
+</tr>
+</tbody>
+</table>
+<p class="p1">Â </p>
+<h2 class=" ">Running</h2>
+<p>Molpro is compiled for parallel execution using MPI and OpenMP. By default, Molpro reads the number of allocated nodes from PBS and launches a data server on one node. On the remaining allocated nodes, compute processes are launched, one process per node, each with 16 threads. You can modify this behavior by using -n, -t and helper-server options. Please refer to the <a class="external-link" href="http://www.molpro.net/info/2010.1/doc/manual/node9.html" target="_self" title="">Molpro documentation</a> for more details. </p>
+<p class="exclamation">The OpenMP parallelization in Molpro is limited and has been observed to produce limited scaling. We therefore recommend to use MPI parallelization only. This can be achieved by passing option <span class="monospace">mpiprocs=24:ompthreads=1</span> to PBS.</p>
+<p>You are advised to use the -d option to point to a directory in <a href="../../storage.html" title="" target="_self" class="internal-link">SCRATCH filesystem</a>. Molpro can produce a large amount of temporary data during its run, and it is important that these are placed in the fast scratch filesystem.</p>
+<h3 class=" ">Example jobscript</h3>
+<pre class=" ">#PBS -A IT4I-0-0<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=24:mpiprocs=24:ompthreads=1<br /><br />cd $PBS_O_WORKDIR<br /><br /># load Molpro module<br />module add Molpro/2010.1-patch-57-intel2015b<br /><br /># create a directory in the SCRATCH filesystem<br />mkdir -p /scratch/work/user/$USER/$PBS_JOBID<br /><br /># copy an example input<br />cp /apps/all/Molpro/2010.1-patch57/molprop_2010_1_Linux_x86_64_i8/examples/caffeine_opt_diis.com .<br /><br /># run Molpro with default options<br /><span>molpro -d /scratch/work/user/$USER/$PBS_JOBID caffeine_opt_diis.com<br /><br /># delete scratch directory<br />rm -rf /scratch/work/user/$USER/$PBS_JOBIDÂ </span></pre>
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+ <div id="parent-fieldname-text-ae075e224c9a45b2a8322380f9d8dc0f" class="">
+ <h2 class=" "><span>Introduction</span></h2>
+<p><span>NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.</span></p>
+<p><a class="external-link" href="http://www.nwchem-sw.org/index.php/Main_Page" target="_blank" title="">Homepage</a></p>
+<h2 class=" ">Installed versions</h2>
+<p>The following versions are currently installed :Â </p>
+<ul>
+<li><span>NWChem/6.3.revision2-2013-10-17-Python-2.7.8, current release. Compiled with Intel compilers, MKL and Intel MPI</span>
+<p class="p1">Â </p>
+</li>
+<li><span>NWChem/6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8</span></li>
+</ul>
+<p>For a current list of installed versions, execute :Â </p>
+<pre class=" ">module avail NWChem</pre>
+<p class="exclamation">The recommend to use version 6.5. Version 6.3 fails on Salomon nodes with accelerator, because it attempts to communicate over scif0 interface. In 6.5 this is avoided by setting ARMCI_OPENIB_DEVICE=mlx4_0, this setting is included in the module.</p>
+<h2 class=" ">Running</h2>
+<p>NWChem is compiled for parallel MPI execution. Normal procedure for MPI jobs applies. Sample jobscript :</p>
+<pre class=" ">#PBS -A IT4I-0-0<br />#PBS -q qprod<br /><span>#PBS -l select=1:ncpus=24:mpiprocs=24<br /></span><span><br />cd $PBS_O_WORKDIR<br />module add NWChem/6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8<br /></span><span>mpirun nwchem h2o.nw</span></pre>
+<h2 class=" "><span>Options</span></h2>
+<p>Please refer to <a class="external-link" href="http://www.nwchem-sw.org/index.php/Release62:Top-level" target="_self" title="">the documentation</a>Â and in the input file set the following directives :</p>
+<ul>
+<li><span>MEMORY : controls the amount of memory NWChem will use</span></li>
+<li><span>SCRATCH_DIR : set this to a directory in <a href="../../storage.html" title="" target="_self" class="internal-link">SCRATCH filesystem</a> (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"</span></li>
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diff --git a/docs.it4i.cz/salomon/software/chemistry/nwchem.md b/docs.it4i.cz/salomon/software/chemistry/nwchem.md
index 3d9d9a329..c37310924 100644
--- a/docs.it4i.cz/salomon/software/chemistry/nwchem.md
+++ b/docs.it4i.cz/salomon/software/chemistry/nwchem.md
@@ -56,8 +56,8 @@ Please refer to [the
documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level)Â and
in the input file set the following directives :
-- <span>MEMORY controls the amount of memory NWChem will use</span>
-- <span>SCRATCH_DIR set this to a directory in [SCRATCH
+- <span>MEMORY : controls the amount of memory NWChem will use</span>
+- <span>SCRATCH_DIR : set this to a directory in [SCRATCH
filesystem](../../storage.html)Â (or run the
calculation completely in a scratch directory). For certain
calculations, it might be advisable to reduce I/O by forcing
diff --git a/docs.it4i.cz/salomon/software/chemistry/phono3py-input.html b/docs.it4i.cz/salomon/software/chemistry/phono3py-input.html
new file mode 100644
index 000000000..b75bb4dfe
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/chemistry/phono3py-input.html
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+ <h2>Â Introduction</h2>
+<p class=" ">This GPL software calculates phonon-phonon interactions via the third order force constants. It allows to obtain lattice thermal conductivity, phonon lifetime/linewidth, imaginary part of self energy at the lowest order, joint density of states (JDOS) and weighted-JDOS. For details see Phys. Rev. B 91, 094306 (2015) and http://atztogo.github.io/phono3py/index.html<br /><br /></p>
+<p class="callout">Load the phono3py/0.9.14-ictce-7.3.5-Python-2.7.9 module</p>
+<pre class="prettyprint lang-sh">$ module load phono3py/0.9.14-ictce-7.3.5-Python-2.7.9</pre>
+<h2>Example of calculating thermal conductivity of Si using VASP code.</h2>
+<h3>Calculating force constants</h3>
+<p>One needs to calculate second order and third order force constants using the diamond structure of silicon stored in <a href="phono3py-input/poscar-si" title="" target="_self" class="internal-link">POSCAR</a>Â (the same form as in VASP) using single displacement calculations within supercell.</p>
+<pre class="prettyprint lang-sh">$ cat POSCAR<br />Â Si<br />Â Â 1.0<br />Â Â Â Â 5.4335600309153529Â Â Â 0.0000000000000000Â Â Â 0.0000000000000000<br />Â Â Â Â 0.0000000000000000Â Â Â 5.4335600309153529Â Â Â 0.0000000000000000<br />Â Â Â Â 0.0000000000000000Â Â Â 0.0000000000000000Â Â Â 5.4335600309153529<br />Â Si<br />Â Â 8<br />Direct<br />Â Â 0.8750000000000000Â 0.8750000000000000Â 0.8750000000000000<br />Â Â 0.8750000000000000Â 0.3750000000000000Â 0.3750000000000000<br />Â Â 0.3750000000000000Â 0.8750000000000000Â 0.3750000000000000<br />Â Â 0.3750000000000000Â 0.3750000000000000Â 0.8750000000000000<br />Â Â 0.1250000000000000Â 0.1250000000000000Â 0.1250000000000000<br />Â Â 0.1250000000000000Â 0.6250000000000000Â 0.6250000000000000<br />Â Â 0.6250000000000000Â 0.1250000000000000Â 0.6250000000000000<br />Â Â 0.6250000000000000Â 0.6250000000000000Â 0.1250000000000000<br /><br /></pre>
+<h3>Generating displacement using 2x2x2 supercell for both second and third order force constants</h3>
+<pre class="prettyprint lang-sh">$ <span class="n">phono3py</span> <span class="o">-</span><span class="n">d</span> <span class="o">--</span><span class="n">dim</span><span class="o">=</span><span class="s2">"2 2 2"</span> <span class="o">-</span><span class="n">c</span> <span class="n">POSCAR</span><span class="o"></span><span class="n"></span></pre>
+<p class=" "><span class="n">111 displacements is created stored in <span class="n">disp_fc3.yaml</span>, and the structure input files with this displacements are POSCAR-00XXX, where the XXX=111.<br /></span></p>
+<pre class="prettyprint lang-sh"><span class="n">disp_fc3.yaml POSCAR-00008 POSCAR-00017 POSCAR-00026 POSCAR-00035 POSCAR-00044 POSCAR-00053 POSCAR-00062 POSCAR-00071 POSCAR-00080 POSCAR-00089 POSCAR-00098 POSCAR-00107<br />POSCAR        POSCAR-00009 POSCAR-00018 POSCAR-00027 POSCAR-00036 POSCAR-00045 POSCAR-00054 POSCAR-00063 POSCAR-00072 POSCAR-00081 POSCAR-00090 POSCAR-00099 POSCAR-00108<br />POSCAR-00001  POSCAR-00010 POSCAR-00019 POSCAR-00028 POSCAR-00037 POSCAR-00046 POSCAR-00055 POSCAR-00064 POSCAR-00073 POSCAR-00082 POSCAR-00091 POSCAR-00100 POSCAR-00109<br />POSCAR-00002  POSCAR-00011 POSCAR-00020 POSCAR-00029 POSCAR-00038 POSCAR-00047 POSCAR-00056 POSCAR-00065 POSCAR-00074 POSCAR-00083 POSCAR-00092 POSCAR-00101 POSCAR-00110<br />POSCAR-00003  POSCAR-00012 POSCAR-00021 POSCAR-00030 POSCAR-00039 POSCAR-00048 POSCAR-00057 POSCAR-00066 POSCAR-00075 POSCAR-00084 POSCAR-00093 POSCAR-00102 POSCAR-00111<br />POSCAR-00004  POSCAR-00013 POSCAR-00022 POSCAR-00031 POSCAR-00040 POSCAR-00049 POSCAR-00058 POSCAR-00067 POSCAR-00076 POSCAR-00085 POSCAR-00094 POSCAR-00103<br />POSCAR-00005  POSCAR-00014 POSCAR-00023 POSCAR-00032 POSCAR-00041 POSCAR-00050 POSCAR-00059 POSCAR-00068 POSCAR-00077 POSCAR-00086 POSCAR-00095 POSCAR-00104<br />POSCAR-00006  POSCAR-00015 POSCAR-00024 POSCAR-00033 POSCAR-00042 POSCAR-00051 POSCAR-00060 POSCAR-00069 POSCAR-00078 POSCAR-00087 POSCAR-00096 POSCAR-00105<br />POSCAR-00007  POSCAR-00016 POSCAR-00025 POSCAR-00034 POSCAR-00043 POSCAR-00052 POSCAR-00061 POSCAR-00070 POSCAR-00079 POSCAR-00088 POSCAR-00097 POSCAR-00106</span></pre>
+<p class=" "><span class="n"> For each displacement the forces needs to be calculated, i.e. in form of the output file of VASP (vasprun.xml). For a single VASP calculations one needs <a href="phono3py-input/KPOINTS" title="" target="_self" class="internal-link">KPOINTS</a>, <a href="phono3py-input/POTCAR" title="" target="_self" class="internal-link">POTCAR</a>, <a href="phono3py-input/INCAR" title="" target="_self" class="internal-link">INCAR</a> in your case directory (where you have POSCARS) and those 111 displacements calculations can be generated by <a href="phono3py-input/prepare.sh" title="" target="_self" class="internal-link">prepare.sh</a> script. Then each of the single 111 calculations is submitted <a href="phono3py-input/run.sh" title="" target="_self" class="internal-link">run.sh</a> by <a href="phono3py-input/submit.sh" title="" target="_self" class="internal-link">submit.sh</a>.</span></p>
+<pre class="prettyprint lang-sh"><span class="n">$./prepare.sh<br />$ls<br />disp-00001Â disp-00009Â disp-00017Â disp-00025Â disp-00033Â disp-00041Â disp-00049Â disp-00057Â disp-00065Â disp-00073Â disp-00081Â disp-00089Â disp-00097Â disp-00105Â Â Â Â INCAR<br />disp-00002Â disp-00010Â disp-00018Â disp-00026Â disp-00034Â disp-00042Â disp-00050Â disp-00058Â disp-00066Â disp-00074Â disp-00082Â disp-00090Â disp-00098Â disp-00106Â Â Â Â KPOINTS<br />disp-00003Â disp-00011Â disp-00019Â disp-00027Â disp-00035Â disp-00043Â disp-00051Â disp-00059Â disp-00067Â disp-00075Â disp-00083Â disp-00091Â disp-00099Â disp-00107Â Â Â Â POSCAR<br />disp-00004Â disp-00012Â disp-00020Â disp-00028Â disp-00036Â disp-00044Â disp-00052Â disp-00060Â disp-00068Â disp-00076Â disp-00084Â disp-00092Â disp-00100Â disp-00108Â Â Â Â POTCAR<br />disp-00005Â disp-00013Â disp-00021Â disp-00029Â disp-00037Â disp-00045Â disp-00053Â disp-00061Â disp-00069Â disp-00077Â disp-00085Â disp-00093Â disp-00101Â disp-00109Â Â Â Â prepare.sh<br />disp-00006Â disp-00014Â disp-00022Â disp-00030Â disp-00038Â disp-00046Â disp-00054Â disp-00062Â disp-00070Â disp-00078Â disp-00086Â disp-00094Â disp-00102Â disp-00110Â Â Â Â run.sh<br />disp-00007Â disp-00015Â disp-00023Â disp-00031Â disp-00039Â disp-00047Â disp-00055Â disp-00063Â disp-00071Â disp-00079Â disp-00087Â disp-00095Â disp-00103Â disp-00111Â Â Â Â submit.sh<br />disp-00008Â disp-00016Â disp-00024Â disp-00032Â disp-00040Â disp-00048Â disp-00056Â disp-00064Â disp-00072Â disp-00080Â disp-00088Â disp-00096Â disp-00104Â disp_fc3.yaml<br /></span></pre>
+<p class=" "><span class="n">Taylor your run.sh script to fit into your project and other needs and submit all 111 calculations using submit.sh script</span></p>
+<pre class="prettyprint lang-sh"><span class="n">$ ./submit.sh</span></pre>
+<h2><span class="n">Collecting results and post-processing with phono3py</span></h2>
+<p><span class="n">Once all jobs are finished and vasprun.xml is created in each disp-XXXXX directory the collection is done by </span></p>
+<pre class="prettyprint lang-sh"><span class="n">$ <span class="n">phono3py</span> <span class="o">--</span><span class="n">cf3</span> <span class="n">disp</span><span class="o">-</span><span class="p">{</span><span class="mf">00001.</span><span class="o">.</span><span class="mi">00111</span><span class="p">}</span><span class="o">/</span><span class="n">vasprun</span><span class="o">.</span><span class="n">xml</span></span></pre>
+<p><span class="n"><span class="n">and <code class="docutils literal"><span class="pre">disp_fc2.yaml, <code class="docutils literal"><span class="pre">FORCES_FC2</span></code>, <code class="docutils literal"><span class="pre">FORCES_FC3</span></code></span></code> and disp_fc3.yaml should appear and put into the hdf format by </span></span></p>
+<pre class="prettyprint lang-sh"><span class="n">$ phono3py</span> <span class="o">--</span><span class="n">dim</span><span class="o">=</span><span class="s2">"2 2 2"</span> -c POSCAR</pre>
+<p class=" ">resulting in <code class="docutils literal"><span class="pre">fc2.hdf5</span></code> and <code class="docutils literal"><span class="pre">fc3.hdf5</span></code></p>
+<h3 class=" ">Thermal conductivity</h3>
+<p class=" "><span class="pre">The phonon lifetime calculations takes some time, however is independent on grid points, so could be splitted: <br /></span></p>
+<pre class="prettyprint lang-sh"><span class="pre">$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" --sigma 0.1 --wgp</span></pre>
+<h3><span class="n">Inspecting ir_grid_points.yaml</span></h3>
+<pre class="prettyprint lang-sh">$ grep grid_point ir_grid_points.yaml<br />num_reduced_ir_grid_points: 35<br />ir_grid_points:Â # [address, weight]<br />- grid_point: 0<br />- grid_point: 1<br />- grid_point: 2<br />- grid_point: 3<br />- grid_point: 4<br />- grid_point: 10<br />- grid_point: 11<br />- grid_point: 12<br />- grid_point: 13<br />- grid_point: 20<br />- grid_point: 21<br />- grid_point: 22<br />- grid_point: 30<br />- grid_point: 31<br />- grid_point: 40<br />- grid_point: 91<br />- grid_point: 92<br />- grid_point: 93<br />- grid_point: 94<br />- grid_point: 101<br />- grid_point: 102<br />- grid_point: 103<br />- grid_point: 111<br />- grid_point: 112<br />- grid_point: 121<br />- grid_point: 182<br />- grid_point: 183<br />- grid_point: 184<br />- grid_point: 192<br />- grid_point: 193<br />- grid_point: 202<br />- grid_point: 273<br />- grid_point: 274<br />- grid_point: 283<br />- grid_point: 364</pre>
+<p>one finds which grid points needed to be calculated, for instance using following</p>
+<pre class="prettyprint lang-sh"><span class="n">$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCARÂ --sigma 0.1 --br --write-gamma --gp="0 1 2</span></pre>
+<p><span class="n">one calculates grid points 0, 1, 2. To automize one can use for instance scripts to submit 5 points in series, see <a href="phono3py-input/gofree-cond1.sh" title="" target="_self" class="internal-link">gofree-cond1.sh </a></span></p>
+<pre class="prettyprint lang-sh"><span class="n">$ qsub gofree-cond1.sh</span></pre>
+<p><span class="n">Finally the thermal conductivity result is produced by grouping single conductivity per grid calculations using </span></p>
+<pre class="prettyprint lang-sh"><span class="n">$ <span class="n">phono3py</span> <span class="o">--</span><span class="n">fc3</span> <span class="o">--</span><span class="n">fc2</span> <span class="o">--</span><span class="n">dim</span><span class="o">=</span><span class="s2">"2 2 2"</span> <span class="o">--</span><span class="n">mesh</span><span class="o">=</span><span class="s2">"</span>9 9 9" <span class="o">--</span><span class="n">br</span> <span class="o">--</span><span class="n">read_gamma</span></span></pre>
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diff --git a/docs.it4i.cz/salomon/software/chemistry/phono3py.md b/docs.it4i.cz/salomon/software/chemistry/phono3py.md
index b1b6982d1..bf08e5256 100644
--- a/docs.it4i.cz/salomon/software/chemistry/phono3py.md
+++ b/docs.it4i.cz/salomon/software/chemistry/phono3py.md
@@ -143,43 +143,43 @@ $ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" --sigma 0.1 --wgp
```
$ grep grid_point ir_grid_points.yaml
-num_reduced_ir_grid_points35
+num_reduced_ir_grid_points: 35
ir_grid_points:Â # [address, weight]
-- grid_point0
-- grid_point1
-- grid_point2
-- grid_point3
-- grid_point4
-- grid_point10
-- grid_point11
-- grid_point12
-- grid_point13
-- grid_point20
-- grid_point21
-- grid_point22
-- grid_point30
-- grid_point31
-- grid_point40
-- grid_point91
-- grid_point92
-- grid_point93
-- grid_point94
-- grid_point101
-- grid_point102
-- grid_point103
-- grid_point111
-- grid_point112
-- grid_point121
-- grid_point182
-- grid_point183
-- grid_point184
-- grid_point192
-- grid_point193
-- grid_point202
-- grid_point273
-- grid_point274
-- grid_point283
-- grid_point364
+- grid_point: 0
+- grid_point: 1
+- grid_point: 2
+- grid_point: 3
+- grid_point: 4
+- grid_point: 10
+- grid_point: 11
+- grid_point: 12
+- grid_point: 13
+- grid_point: 20
+- grid_point: 21
+- grid_point: 22
+- grid_point: 30
+- grid_point: 31
+- grid_point: 40
+- grid_point: 91
+- grid_point: 92
+- grid_point: 93
+- grid_point: 94
+- grid_point: 101
+- grid_point: 102
+- grid_point: 103
+- grid_point: 111
+- grid_point: 112
+- grid_point: 121
+- grid_point: 182
+- grid_point: 183
+- grid_point: 184
+- grid_point: 192
+- grid_point: 193
+- grid_point: 202
+- grid_point: 273
+- grid_point: 274
+- grid_point: 283
+- grid_point: 364
```
one finds which grid points needed to be calculated, for instance using
diff --git a/docs.it4i.cz/salomon/software/compilers.html b/docs.it4i.cz/salomon/software/compilers.html
new file mode 100644
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+ Compilers
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+ Available compilers, including GNU, INTEL and UPC compilers
+ </div>
+
+
+
+
+
+ <div id="viewlet-above-content-body">
+<dl id="document-toc" class="portlet toc" style="display: none">
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+ <div id="content-core">
+
+
+
+ <div id="parent-fieldname-text-a15db844be22422b94229952cdd6ac93" class="">
+ <p>There are several compilers for different programming languages available on the cluster:</p>
+<ul>
+<li>C/C++</li>
+<li>Fortran 77/90/95/HPF</li>
+<li>Unified Parallel C</li>
+<li>Java</li>
+</ul>
+<p class=" ">The C/C++ and Fortran compilers are provided by:</p>
+<p class=" ">Opensource:</p>
+<ul>
+<li>GNU GCC</li>
+<li>Clang/LLVM</li>
+</ul>
+<p>Commercial licenses:</p>
+<ul>
+<li>Intel</li>
+<li>PGI</li>
+</ul>
+<h2 class=" ">Intel Compilers</h2>
+<p class=" ">For information about the usage of Intel Compilers and other Intel products, please read the <a href="intel-suite.html" title="" target="_self" class="internal-link">Intel Parallel studio</a> page.</p>
+<h2 class=" ">PGI Compilers</h2>
+<p>The Portland Group Cluster Development Kit (PGI CDK) is available.</p>
+<pre>$ module load PGI<br />$ pgcc -v<br />$ pgc++ -v<br />$ pgf77 -v<br />$ pgf90 -v<br />$ pgf95 -v<br />$ pghpf -v</pre>
+<p class=" ">The PGI CDK also incudes tools for debugging and profiling.</p>
+<p class=" ">PGDBG OpenMP/MPI debugger and PGPROF OpenMP/MPI profiler are available</p>
+<pre class=" ">$ module load PGI<br />$ module load Java<br />$ pgdbg &<br />$ pgprof &</pre>
+<p class=" ">For more information, see the <a class="external-link" href="http://www.pgroup.com/products/pgicdk.htm" target="_self" title="">PGI page</a>.</p>
+<h2 class=" ">GNU</h2>
+<p>For compatibility reasons there are still available the original (old 4.4.7-11) versions of GNU compilers as part of the OS. These are accessible in the search path by default.</p>
+<p>It is strongly recommended to use the up to date version which comes with the module GCC:</p>
+<pre class=" ">$ module load GCC<br />$ gcc -v<br />$ g++ -v<br />$ gfortran -v</pre>
+<p class=" ">With the module loaded two environment variables are predefined. One for maximum optimizations on the cluster's architecture, and the other for debugging purposes:</p>
+<pre class=" ">$ echo $OPTFLAGS<br />-O3 -march=native</pre>
+<pre class=" ">$ echo $DEBUGFLAGS<br />-O0 -g</pre>
+<p class=" ">For more information about the possibilities of the compilers, please see the man pages.</p>
+<h2 class=" ">Unified Parallel C</h2>
+<p class=" ">UPC is supported by two compiler/runtime implementations:</p>
+<ul>
+<li>GNU - SMP/multi-threading support only</li>
+<li>Berkley - multi-node support as well as SMP/multi-threading support</li>
+</ul>
+<h3 class=" ">GNU UPC Compiler</h3>
+<p>To use the GNU UPC compiler and run the compiled binaries use the module gupc</p>
+<pre class=" ">$ module add gupc<br />$ gupc -v<br />$ g++ -v</pre>
+<p>Simple program to test the compiler</p>
+<pre class=" ">$ cat count.upc <br /><br />/* hello.upc - a simple UPC example */<br />#include <upc.h><br />#include <stdio.h><br /><br />int main() {<br />Â if (MYTHREAD == 0) {<br />Â Â Â printf("Welcome to GNU UPC!!!\n");<br />Â }<br />Â upc_barrier;<br />Â printf(" - Hello from thread %i\n", MYTHREAD);<br />Â return 0;<br />} </pre>
+<p>To compile the example use</p>
+<pre class=" ">$ gupc -o count.upc.x count.upc</pre>
+<p>To run the example with 5 threads issue</p>
+<pre class=" ">$ ./count.upc.x -fupc-threads-5</pre>
+<p class=" ">For more informations see the man pages.</p>
+<h3 class=" ">Berkley UPC Compiler</h3>
+<p>To use the Berkley UPC compiler and runtime environment to run the binaries use the module bupc</p>
+<pre class=" ">$ module add bupc<br />$ upcc -version</pre>
+<p>As default UPC network the "smp" is used. This is very quick and easy way for testing/debugging, but limited to one node only.</p>
+<p>For production runs, it is recommended to use the native Infiband implementation of UPC network "ibv". For testing/debugging using multiple nodes, the "mpi" UPC network is recommended. Please note, that <strong>the selection of the network is done at the compile time</strong> and not at runtime (as expected)!</p>
+<p>Example UPC code:</p>
+<pre class=" ">$ cat hello.upc <br /><br />/* hello.upc - a simple UPC example */<br />#include <upc.h><br />#include <stdio.h><br /><br />int main() {<br />Â if (MYTHREAD == 0) {<br />Â Â Â printf("Welcome to Berkeley UPC!!!\n");<br />Â }<br />Â upc_barrier;<br />Â printf(" - Hello from thread %i\n", MYTHREAD);<br />Â return 0;<br />} </pre>
+<p class=" ">To compile the example with the "ibv" UPC network use</p>
+<pre class=" ">$ upcc -network=ibv -o hello.upc.x hello.upc </pre>
+<p class=" ">To run the example with 5 threads issue</p>
+<pre class=" ">$ upcrun -n 5 ./hello.upc.x</pre>
+<p class=" ">To run the example on two compute nodes using all 48 cores, with 48 threads, issue</p>
+<pre class=" ">$ qsub -I -q qprod -A PROJECT_ID -l select=2:ncpus=24 <br />$ module add bupc<br />$ upcrun -n 48 ./hello.upc.x</pre>
+<p class=" ">Â For more informations see the man pages.</p>
+<h2 class=" ">Java</h2>
+<p>For information how to use Java (runtime and/or compiler), please read the <a href="java.html" title="" target="_self" class="internal-link">Java page</a>.</p>
+<p class="hiddenForView">nVidia CUDA</p>
+<p class="hiddenForView">For information how to work with nVidia CUDA, please read the <a href="../../anselm-cluster-documentation/software/nvidia-cuda.html" title="" target="_self" class="internal-link">nVidia CUDA page</a>.</p>
+
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+ <h2 class=" "><span><span>Introduction<br /></span></span></h2>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com" target="_self" title="">COMSOL</a></span></span><span><span> is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.</span></span></p>
+<ul>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/structural-mechanics-module" target="_self" title="">Structural Mechanics Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/heat-transfer-module" target="_self" title="">Heat Transfer Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/cfd-module" target="_self" title="">CFD Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/acoustics-module" target="_self" title="">Acoustics Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span>and <a class="external-link" href="http://www.comsol.com/products" target="_self" title="">many others</a></span></span></p>
+</li>
+</ul>
+<p align="JUSTIFY"><span><span>COMSOL also allows an </span></span><span><span><span><span>interface support for equation-based modelling of </span></span></span></span><span><span>partial differential equations.</span></span></p>
+<h2 class=" "><span><span>Execution<br /></span></span></h2>
+<p align="JUSTIFY"><span><span>On the clusters COMSOL is available in the latest stable version. There are two variants of the release:</span></span></p>
+<ul>
+<li>
+<p align="JUSTIFY"><span><span><b>Non commercial</b></span></span><span><span> or so called </span></span><span><span><b>EDU variant</b></span></span><span><span>, which can be used for research and educational purposes.</span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><b>Commercial</b></span></span><span><span> or so called </span></span><span><span><b>COM variant</b></span></span><span><span>, which can used also for commercial activities. </span></span><span><span><b>COM variant</b></span></span><span><span> has only subset of features compared to the </span></span><span><span><b>EDU variant</b></span></span><span><span> available. <span class="internal-link"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> will be posted <span class="hps">here soon</span>.</span></span><br /></span></span></p>
+</li>
+</ul>
+<p align="JUSTIFY"><span><span>To load the of COMSOL load the module</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>$ module load COMSOL/51-EDU</span></span></pre>
+<p align="JUSTIFY"><span><span>By default the </span></span><span><span><b>EDU variant</b></span></span><span><span> will be loaded. If user needs other version or variant, load the particular version. To obtain the list of available versions use</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>$ module avail <span><span>COMSOL</span></span></span></span></pre>
+<p align="JUSTIFY"><span><span>If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the <a href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">Virtual Network Computing (VNC)</a>.</span></span></p>
+<pre class="prettyprint lang-sh"><span><span><span>$ xhost +<br />$ qsub -I -X</span></span></span><span><span><span><span> </span></span></span></span><span><span><span>-A</span></span></span><span><span> </span></span><span><span><span><span>PROJECT_ID </span></span></span></span><span><span><span>-q </span></span></span><span><span><span><span>qprod</span></span></span></span><span><span><span> -l </span></span></span><span><span><span><span>select=1:ppn=24</span><br />$ module load </span></span></span><span><span>COMSOL<span><br />$ </span></span></span><span><span>comsol<br /></span></span></pre>
+<p align="JUSTIFY"><span><span>To run COMSOL in batch mode, without the COMSOL Desktop GUI environment, user can utilized the default (comsol.pbs) job script and execute it via the qsub command.</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>#!/bin/bash<br />#PBS -l select=3:ppn=24<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -A PROJECT_ID<br /><br />cd /scratch/work/user<strong>/</strong>$USER/ || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load COMSOL<br /># module load COMSOL/51-EDU<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log<br /><br /></span></span></pre>
+<p align="JUSTIFY"><span><span>Working directory has to be created before sending the (comsol.pbs) job script into the queue. Input file (name_input_f.mph) has to be in working directory or full path to input file has to be specified. The appropriate path to the temp directory of the job has to be set by command option (-tmpdir).</span></span></p>
+<h2 class=" ">LiveLink™<i> </i>for MATLAB<sup>®</sup></h2>
+<p align="JUSTIFY"><span><span>COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL</span></span><span><span><sup><span><span><span><span><span><span><span><b>®</b></span></span></span></span></span></span></span></sup></span></span><span><span> API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB. </span></span></p>
+<p align="JUSTIFY"><span><span>LiveLink for MATLAB is available in both </span></span><span><span><b>EDU</b></span></span><span><span> and </span></span><span><span><b>COM</b></span></span><span><span> </span></span><span><span><b>variant</b></span></span><span><span> of the COMSOL release. On the clusters 1 commercial (</span></span><span><span><b>COM</b></span></span><span><span>) license and the 5 educational (</span></span><span><span><b>EDU</b></span></span><span><span>) licenses of LiveLink for MATLAB (please see the <a href="isv_licenses.html" title="" target="_self" class="internal-link">ISV Licenses</a>) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.</span></span></p>
+<pre class="prettyprint lang-sh">$ xhost +<br />$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ppn=24<br />$ module load MATLAB<br />$ module load COMSOL<br />$ comsol server MATLAB</pre>
+<p align="JUSTIFY"><span><span>At the first time to launch the LiveLink for MATLAB (client-MATLAB/server-COMSOL connection) the login and password is requested and this information is not requested again.</span></span></p>
+<p align="JUSTIFY"><span><span>To run LiveLink for MATLAB in batch mode with (comsol_matlab.pbs) job script you can utilize/modify the following script and execute it via the qsub command.</span></span></p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l select=3:ppn=24<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -AÂ PROJECT_ID<br /><br />cd /scratch/work/user/$USER || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load MATLAB<br />module load COMSOL/51-EDU<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/<strong>work/user/</strong>$USER/work &<br />cd /apps/cae/COMSOL/51/mli<br />matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/<strong>work/user/</strong>$USER/work; test_job"</pre>
+<p>This example shows how to run Livelink for MATLAB with following configuration: 3 nodes and 16 cores per node. Working directory has to be created before submitting (comsol_matlab.pbs) job script into the queue. Input file (test_job.m) has to be in working directory or full path to input file has to be specified. The Matlab command option (-r ”mphstart”) created a connection with a COMSOL server using the default port number.<br /><br /></p>
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diff --git a/docs.it4i.cz/salomon/software/comsol.md b/docs.it4i.cz/salomon/software/comsol.md
index e72ccbc9d..072943b44 100644
--- a/docs.it4i.cz/salomon/software/comsol.md
+++ b/docs.it4i.cz/salomon/software/comsol.md
@@ -198,7 +198,7 @@ matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/work/user/$USER/work;
```
This example shows how to run Livelink for MATLAB with following
-configuration3 nodes and 16 cores per node. Working directory has to
+configuration: 3 nodes and 16 cores per node. Working directory has to
be created before submitting (comsol_matlab.pbs) job script into the
queue. Input file (test_job.m) has to be in working directory or full
path to input file has to be specified. The Matlab command option (-r
diff --git a/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.html b/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.html
new file mode 100644
index 000000000..788127d78
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.html
@@ -0,0 +1,946 @@
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+ <h2 class=" "><span><span>Introduction<br /></span></span></h2>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com" target="_self" title="">COMSOL</a></span></span><span><span> is a powerful environment for modelling and solving various engineering and scientific problems based on partial differential equations. COMSOL is designed to solve coupled or multiphysics phenomena. For many standard engineering problems COMSOL provides add-on products such as electrical, mechanical, fluid flow, and chemical applications.</span></span></p>
+<ul>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/structural-mechanics-module" target="_self" title="">Structural Mechanics Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/heat-transfer-module" target="_self" title="">Heat Transfer Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/cfd-module" target="_self" title="">CFD Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><a class="external-link" href="http://www.comsol.com/acoustics-module" target="_self" title="">Acoustics Module</a>, </span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span>and <a class="external-link" href="http://www.comsol.com/products" target="_self" title="">many others</a></span></span></p>
+</li>
+</ul>
+<p align="JUSTIFY"><span><span>COMSOL also allows an </span></span><span><span><span><span>interface support for equation-based modelling of </span></span></span></span><span><span>partial differential equations.</span></span></p>
+<h2 class=" "><span><span>Execution<br /></span></span></h2>
+<p align="JUSTIFY"><span><span>On the clusters COMSOL is available in the latest stable version. There are two variants of the release:</span></span></p>
+<ul>
+<li>
+<p align="JUSTIFY"><span><span><b>Non commercial</b></span></span><span><span> or so called </span></span><span><span><b>EDU variant</b></span></span><span><span>, which can be used for research and educational purposes.</span></span></p>
+</li>
+<li>
+<p align="JUSTIFY"><span><span><b>Commercial</b></span></span><span><span> or so called </span></span><span><span><b>COM variant</b></span></span><span><span>, which can used also for commercial activities. </span></span><span><span><b>COM variant</b></span></span><span><span> has only subset of features compared to the </span></span><span><span><b>EDU variant</b></span></span><span><span> available. <span class="internal-link"><span class="short_text" id="result_box"><span class="hps">More</span> <span class="hps">about licensing</span> will be posted <span class="hps">here soon</span>.</span></span><br /></span></span></p>
+</li>
+</ul>
+<p align="JUSTIFY"><span><span>To load the of COMSOL load the module</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>$ module load COMSOL/51-EDU</span></span></pre>
+<p align="JUSTIFY"><span><span>By default the </span></span><span><span><b>EDU variant</b></span></span><span><span> will be loaded. If user needs other version or variant, load the particular version. To obtain the list of available versions use</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>$ module avail <span><span>COMSOL</span></span></span></span></pre>
+<p align="JUSTIFY"><span><span>If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">Virtual Network Computing (VNC)</a>.</span></span></p>
+<pre class="prettyprint lang-sh"><span><span><span>$ xhost +<br />$ qsub -I -X</span></span></span><span><span><span><span> </span></span></span></span><span><span><span>-A</span></span></span><span><span> </span></span><span><span><span><span>PROJECT_ID </span></span></span></span><span><span><span>-q </span></span></span><span><span><span><span>qprod</span></span></span></span><span><span><span> -l </span></span></span><span><span><span><span>select=1:ppn=24</span><br />$ module load </span></span></span><span><span>COMSOL<span><br />$ </span></span></span><span><span>comsol<br /></span></span></pre>
+<p align="JUSTIFY"><span><span>To run COMSOL in batch mode, without the COMSOL Desktop GUI environment, user can utilized the default (comsol.pbs) job script and execute it via the qsub command.</span></span></p>
+<pre class="prettyprint lang-sh"><span><span>#!/bin/bash<br />#PBS -l select=3:ppn=24<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -A PROJECT_ID<br /><br />cd /scratch/work/user<strong>/</strong>$USER/ || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load COMSOL<br /># module load COMSOL/51-EDU<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} batch -configuration /tmp –mpiarg –rmk –mpiarg pbs -tmpdir /scratch/$USER/ -inputfile name_input_f.mph -outputfile name_output_f.mph -batchlog name_log_f.log<br /><br /></span></span></pre>
+<p align="JUSTIFY"><span><span>Working directory has to be created before sending the (comsol.pbs) job script into the queue. Input file (name_input_f.mph) has to be in working directory or full path to input file has to be specified. The appropriate path to the temp directory of the job has to be set by command option (-tmpdir).</span></span></p>
+<h2 class=" ">LiveLink™<i> </i>for MATLAB<sup>®</sup></h2>
+<p align="JUSTIFY"><span><span>COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL</span></span><span><span><sup><span><span><span><span><span><span><span><b>®</b></span></span></span></span></span></span></span></sup></span></span><span><span> API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB. </span></span></p>
+<p align="JUSTIFY"><span><span>LiveLink for MATLAB is available in both </span></span><span><span><b>EDU</b></span></span><span><span> and </span></span><span><span><b>COM</b></span></span><span><span> </span></span><span><span><b>variant</b></span></span><span><span> of the COMSOL release. On the clusters 1 commercial (</span></span><span><span><b>COM</b></span></span><span><span>) license and the 5 educational (</span></span><span><span><b>EDU</b></span></span><span><span>) licenses of LiveLink for MATLAB (please see the <a href="../isv_licenses.html" title="" target="_self" class="internal-link">ISV Licenses</a>) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode.</span></span></p>
+<pre class="prettyprint lang-sh">$ xhost +<br />$ qsub -I -X -A PROJECT_ID -q qexp -l select=1:ppn=24<br />$ module load MATLAB<br />$ module load COMSOL<br />$ comsol server MATLAB</pre>
+<p align="JUSTIFY"><span><span>At the first time to launch the LiveLink for MATLAB (client-MATLAB/server-COMSOL connection) the login and password is requested and this information is not requested again.</span></span></p>
+<p align="JUSTIFY"><span><span>To run LiveLink for MATLAB in batch mode with (comsol_matlab.pbs) job script you can utilize/modify the following script and execute it via the qsub command.</span></span></p>
+<pre class="prettyprint lang-sh">#!/bin/bash<br />#PBS -l select=3:ppn=24<br />#PBS -q qprod<br />#PBS -N JOB_NAME<br />#PBS -AÂ PROJECT_ID<br /><br />cd /scratch/work/user/$USER || exit<br /><br />echo Time is `date`<br />echo Directory is `pwd`<br />echo '***PBS_NODEFILE***START*******'<br />cat $PBS_NODEFILE<br />echo '***PBS_NODEFILE***END*********'<br /><br />text_nodes < cat $PBS_NODEFILE<br /><br />module load MATLAB<br />module load COMSOL/51-EDU<br /><br />ntask=$(wc -l $PBS_NODEFILE)<br /><br />comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/<strong>work/user/</strong>$USER/work &<br />cd /apps/cae/COMSOL/51/mli<br />matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/<strong>work/user/</strong>$USER/work; test_job"</pre>
+<p>This example shows how to run Livelink for MATLAB with following configuration: 3 nodes and 16 cores per node. Working directory has to be created before submitting (comsol_matlab.pbs) job script into the queue. Input file (test_job.m) has to be in working directory or full path to input file has to be specified. The Matlab command option (-r ”mphstart”) created a connection with a COMSOL server using the default port number.<br /><br /></p>
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diff --git a/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md b/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
index 6f1a85e47..692b59043 100644
--- a/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
+++ b/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
@@ -198,7 +198,7 @@ matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/work/user/$USER/work;
```
This example shows how to run Livelink for MATLAB with following
-configuration3 nodes and 16 cores per node. Working directory has to
+configuration: 3 nodes and 16 cores per node. Working directory has to
be created before submitting (comsol_matlab.pbs) job script into the
queue. Input file (test_job.m) has to be in working directory or full
path to input file has to be specified. The Matlab command option (-r
diff --git a/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.html b/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.html
new file mode 100644
index 000000000..eb49cfe41
--- /dev/null
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+ <h2 class=" ">Comsol licence can be used by:</h2>
+<ul>
+<li>all persons in the carrying out of the CE IT4Innovations Project (In addition to the primary licensee, which is VSB - Technical University of Ostrava, users are CE IT4Innovations third parties - CE IT4Innovations project partners, particularly the University of Ostrava, the Brno University of Technology - Faculty of Informatics, the Silesian University in Opava, Institute of Geonics AS CR.)</li>
+<li><span class="short_text" id="result_box"><span class="hps">all persons</span> <span class="hps">who have a valid</span> <span class="hps">license</span></span></li>
+<li><span class="short_text" id="result_box"><span class="hps">students of</span> <span class="hps">the Technical University</span></span></li>
+</ul>
+<h2 class=" ">Comsol EDU Network Licence</h2>
+<p>The licence intended to be used for science and research, publications, students’ projects, teaching (academic licence).</p>
+<h2 class=" ">Comsol COM Network Licence</h2>
+<p>The licence intended to be used for science and research, publications, students’ projects, commercial research with no commercial use restrictions. <span id="result_box"><span class="hps">E</span><span class="hps">nables</span> <span class="hps">the solution</span> <span class="hps">of at least</span> <span class="hps">one job</span> <span class="hps">by one user</span> <span class="hps">in one</span> <span class="hps">program start.</span></span></p>
+<h2 class=" ">Available Versions</h2>
+<ul>
+<li>ver. 51</li>
+</ul>
+
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+
+
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+ <h2 class=" ">Introduction</h2>
+<p>We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations.<br />On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.</p>
+<h2 class=" ">Intel debugger</h2>
+<p class="exclamation">Intel debugger is no longer available since Parallel Studio version 2015</p>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">X display</a> for running the GUI.</p>
+<pre class=" ">$ module load intel<br />$ idb</pre>
+<p>Read more at the <a href="intel-suite/intel-debugger.html" title="" target="_self" class="internal-link">Intel Debugger</a> page.</p>
+<h2 class=" ">Allinea Forge (DDT/MAP)</h2>
+<p>Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
+<pre class=" ">$ module load Forge<br />$ forge</pre>
+<p>Read more at the <a href="debuggers/allinea-ddt.html" title="" target="_self" class="internal-link">Allinea DDT</a> page.</p>
+<h2 class=" ">Allinea Performance Reports</h2>
+<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.</p>
+<pre class=" ">$ module load PerformanceReports/6.0 <br />$ perf-report mpirun -n 64 ./my_application argument01 argument02</pre>
+<p class=" ">Read more at the <a href="debuggers/allinea-performance-reports.html" title="" target="_self" class="internal-link">Allinea Performance Reports</a> page.</p>
+<h2 class=" ">RougeWave Totalview</h2>
+<p>TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.</p>
+<pre class=" ">$ module load TotalView/8.15.4-6-linux-x86-64<br />$ totalview</pre>
+<p>Read more at the <a href="debuggers/total-view.html" title="" target="_self" class="internal-link">Totalview</a> page.</p>
+<h2 class=" ">Vampir trace analyzer</h2>
+<p>Vampir is a GUI trace analyzer for traces in OTF format.</p>
+<pre>$ module load Vampir/8.5.0<br />$ vampir</pre>
+<p>Read more at the <a href="debuggers/vampir.html" title="" target="_self" class="internal-link">Vampir</a> page.</p>
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diff --git a/docs.it4i.cz/salomon/software/debuggers.1.md b/docs.it4i.cz/salomon/software/debuggers.1.md
index 4b0714580..7ad373d5c 100644
--- a/docs.it4i.cz/salomon/software/debuggers.1.md
+++ b/docs.it4i.cz/salomon/software/debuggers.1.md
@@ -46,8 +46,7 @@ implementation.
$ forge
Read more at the [Allinea
-DDT](../../whats-new/news-feed/allinea-forge-documentation-updated.html)
-page.
+DDT](debuggers/allinea-ddt.html) page.
Allinea Performance Reports
---------------------------
diff --git a/docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/image_view_fullscreen.html b/docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/image_view_fullscreen.html
new file mode 100644
index 000000000..fa1a38bc1
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/image_view_fullscreen.html
@@ -0,0 +1,50 @@
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+
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+ <title>Vampir screenshot</title>
+
+ <style type="text/css" media="screen">
+ body {
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+ line-height:1.5em;
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+ padding: 5px;
+ max-width: 100%; height: auto;
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+
+ #content-core {
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+
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+
+<body>
+
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+ <a href="view.html"><span>Zpět na portál</span><br /><img src="image" alt="Vampir screenshot" title="Vampir screenshot" height="647" width="1071" /></a>
+
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+
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+
diff --git a/docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/view.html b/docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png/view.html
new file mode 100644
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+</div>
+
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+ <div class="">
+
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+ <dl class="portalMessage info" id="kssPortalMessage" style="display:none">
+ <dt>Info</dt>
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+ Aislinn
+ </h1>
+
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+</div>
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+ <div id="parent-fieldname-text-3b9cf6f12d234ce7bec766f581840816" class="">
+ <ul class="simple">
+<li>Aislinn is a dynamic verifier for MPI programs. For a fixed input it covers all possible runs with respect to nondeterminism introduced by MPI.
+It allows to detect bugs (for sure) that occurs very rare in normal runs.</li>
+<li>Aislinn detects problems like invalid memory accesses, deadlocks, misuse of MPI, and resource leaks.</li>
+<li>Aislinn is open-source software; you can use it without any licensing limitations.</li>
+<li>Web page of the project: <a class="reference external" href="http://verif.cs.vsb.cz/aislinn/">http://verif.cs.vsb.cz/aislinn/</a></li>
+</ul>
+<div class="note">
+<p class="first admonition-title">Note</p>
+<p class="last">Aislinn is software developed at IT4Innovations and some parts are still considered experimental. If you have any questions or experienced any problems, please contact the author: <a class="reference external" href="mailto:stanislav.bohm@vsb.cz">stanislav.bohm@vsb.cz</a>.</p>
+</div>
+<div class="section" id="usage">
+<h3>Usage</h3>
+<p>Let us have the following program that contains a bug that is not manifested in all runs:</p>
+<pre class="literal-block">
+#include <mpi.h>
+#include <stdlib.h>
+
+int main(int argc, char **argv) {
+ int rank;
+
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+
+ if (rank == 0) {
+ int *mem1 = (int*) malloc(sizeof(int) * 2);
+ int *mem2 = (int*) malloc(sizeof(int) * 3);
+ int data;
+ MPI_Recv(&data, 1, MPI_INT, MPI_ANY_SOURCE, 1,
+ MPI_COMM_WORLD, MPI_STATUS_IGNORE);
+ mem1[data] = 10; // <---------- Possible invalid memory write
+ MPI_Recv(&data, 1, MPI_INT, MPI_ANY_SOURCE, 1,
+ MPI_COMM_WORLD, MPI_STATUS_IGNORE);
+ mem2[data] = 10;
+ free(mem1);
+ free(mem2);
+ }
+
+ if (rank == 1 || rank == 2) {
+ MPI_Send(&rank, 1, MPI_INT, 0, 1, MPI_COMM_WORLD);
+ }
+
+ MPI_Finalize();
+ return 0;
+}
+</pre>
+<p>The program does the following: process 0 receives two messages from anyone and
+processes 1 and 2 send a message to process 0. If a message from process 1 is
+received first, then the run does not expose the error.
+If a message from process 2 is received
+first, then invalid memory write occurs at line 16.</p>
+<p>To verify this program by Aislinn, we first load Aislinn itself:</p>
+<pre class="literal-block">
+$ module load aislinn
+</pre>
+<p>Now we compile the program by Aislinn implementation of MPI.
+There are <tt class="docutils literal">mpicc</tt> for C programs and <tt class="docutils literal">mpicxx</tt> for C++ programs.
+Only MPI parts of the verified application has to be recompiled; non-MPI parts may remain untouched.
+Let us assume that our program is in <tt class="docutils literal">test.cpp</tt>.</p>
+<pre class="literal-block">
+$ mpicc -g test.cpp -o test
+</pre>
+<p>The <tt class="docutils literal"><span class="pre">-g</span></tt> flag is not necessary, but it puts more debugging information into the program, hence Aislinn
+may provide more detailed report. The command produces executable file <tt class="docutils literal">test</tt>.</p>
+<p>Now we run the Aislinn itself. The argument <tt class="docutils literal"><span class="pre">-p</span> 3</tt> specifies that we want to verify our program for the case of three MPI processes</p>
+<pre class="literal-block">
+$ aislinn -p 3 ./test
+==AN== INFO: Aislinn v0.3.0
+==AN== INFO: Found error 'Invalid write'
+==AN== INFO: 1 error(s) found
+==AN== INFO: Report written into 'report.html'
+</pre>
+<p>Aislinn found an error and produced HTML report. To view it, we can use any browser, e.g.:</p>
+<blockquote>
+$ firefox report.html</blockquote>
+<p>At the beginning of the report there are some basic summaries of the verification.
+In the second part (depicted in the following picture), the error is described.</p>
+<img alt="Part of report.html" src="http://verif.cs.vsb.cz/aislinn/doc/report.png" />
+<p>It shows us:</p>
+<blockquote>
+<ul class="simple">
+<li>Error occurs in process 0 in test.cpp on line 16.</li>
+<li>Stdout and stderr streams are empty. (The program does not write anything).</li>
+<li>The last part shows MPI calls for each process that occurs in the invalid run. The more detailed information about each call can be obtained by mouse cursor.</li>
+</ul>
+</blockquote>
+</div>
+<div class="section" id="limitations">
+<h3>Limitations</h3>
+<p>Since the verification is a non-trivial process there are some of limitations.</p>
+<ul class="simple">
+<li>The verified process has to terminate in all runs, i.e. we cannot answer the halting problem.</li>
+<li>The verification is a computationally and memory demanding process. We put an effort to make it efficient and it is an important point for further research. However covering all runs will be
+always more demanding than techniques that examines only a single run. The good practise is to start with small instances and when it is feasible, make them bigger.
+The Aislinn is good to find bugs that are hard to find because they occur very rarely (only in a rare scheduling). Such bugs often do not need big instances.</li>
+<li>Aislinn expects that your program is a "standard MPI" program, i.e. processes communicate only through MPI, the verified program does not interacts with the system in some unusual ways (e.g. opening sockets).</li>
+</ul>
+<p>There are also some limitations bounded to the current version and they will be removed in the future:</p>
+<ul class="simple">
+<li>All files containing MPI calls have to be recompiled by MPI implementation provided by Aislinn.
+The files that does not contain MPI calls, they do not have to recompiled.
+Aislinn MPI implementation supports many commonly used calls from MPI-2 and MPI-3
+related to point-to-point communication, collective communication, and
+communicator management. Unfortunately, MPI-IO and one-side communication is not implemented yet.</li>
+<li>Each MPI can use only one thread (if you use OpenMP, set <tt class="docutils literal">OMP_NUM_THREADS</tt> to 1).</li>
+<li>There are some limitations for using files, but if the program just reads inputs and writes results, it is ok.</li>
+</ul>
+</div>
+
+
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diff --git a/docs.it4i.cz/salomon/software/debuggers/aislinn.md b/docs.it4i.cz/salomon/software/debuggers/aislinn.md
index 04eee31b4..9f4f0e634 100644
--- a/docs.it4i.cz/salomon/software/debuggers/aislinn.md
+++ b/docs.it4i.cz/salomon/software/debuggers/aislinn.md
@@ -9,14 +9,14 @@ Aislinn
misuse of MPI, and resource leaks.
- Aislinn is open-source software; you can use it without any
licensing limitations.
-- Web page of the project<http://verif.cs.vsb.cz/aislinn/>
+- Web page of the project: <http://verif.cs.vsb.cz/aislinn/>
Note
Aislinn is software developed at IT4Innovations and some parts are still
considered experimental. If you have any questions or experienced any
-problems, please contact the author<stanislav.bohm@vsb.cz>.
+problems, please contact the author: <stanislav.bohm@vsb.cz>.
### Usage
Let us have the following program that contains a bug that is not
@@ -55,7 +55,7 @@ int main(int argc, char **argv) {
}
```
-The program does the followingprocess 0 receives two messages from
+The program does the following: process 0 receives two messages from
anyone and processes 1 and 2 send a message to process 0. If a message
from process 1 is received first, then the run does not expose the
error. If a message from process 2 is received first, then invalid
@@ -88,10 +88,10 @@ processes
```
$ aislinn -p 3 ./test
-==AN== INFOAislinn v0.3.0
-==AN== INFOFound error 'Invalid write'
-==AN== INFO1 error(s) found
-==AN== INFOReport written into 'report.html'
+==AN== INFO: Aislinn v0.3.0
+==AN== INFO: Found error 'Invalid write'
+==AN== INFO: 1 error(s) found
+==AN== INFO: Report written into 'report.html'
```
Aislinn found an error and produced HTML report. To view it, we can use
diff --git a/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.html b/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.html
new file mode 100644
index 000000000..8800e2238
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+ <span id="breadcrumbs-current">Allinea Forge (DDT,MAP)</span>
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+
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+ </h1>
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+ <div id="content-core">
+
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+ <div id="parent-fieldname-text-511a06f5754c4639aadc2137f2b2322f" class="">
+ <p class=" ">Allinea Forge consist of two tools - debugger DDT and profiler MAP.</p>
+<p class=" ">Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
+<p class=" ">Allinea MAP is a profiler for C/C++/Fortran HPC codes. It is designed for profiling parallel code, which uses pthreads, OpenMP or MPI.</p>
+<h2 class=" ">License and Limitations for the clusters Users</h2>
+<p class=" ">On the clusters users can debug OpenMP or MPI code that runs up to 64 parallel processes. In case of debugging GPU or Xeon Phi accelerated codes the limit is 8 accelerators. These limitation means that:</p>
+<ul>
+<li>1 user can debug up 64 processes, or</li>
+<li>32 users can debug 2 processes, etc.</li>
+</ul>
+<p class=" ">In case of debugging on accelerators:</p>
+<ul>
+<li>1 user can debug on up to 8 accelerators, or </li>
+<li>8 users can debug on single accelerator. </li>
+</ul>
+<h2 class=" ">Compiling Code to run with Forge</h2>
+<h3 class=" ">Modules</h3>
+<p>Load all necessary modules to compile the code. For example:Â </p>
+<pre class=" ">$ module load intel<br />$ module load impi ... or ... module load OpenMPI </pre>
+<p class=" ">Load the Allinea DDT module:</p>
+<pre class=" ">$ module load Forge</pre>
+<p>Compile the code:</p>
+<pre class="code-basic" style="text-align: start; ">$ mpicc -g -O0 -o test_debug test.c<br /><br />$ mpif90 -g -O0 -o test_debug test.f</pre>
+<h3 class=" ">Compiler flags</h3>
+<p>Before debugging, you need to compile your code with theses flags:</p>
+<p class="callout"><strong>-g</strong> : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.<br /><br /><strong>-O0</strong> : Suppress all optimizations.</p>
+<p>Â </p>
+<h2 class=" ">Direct starting a Job with Forge</h2>
+<p class=" ">Be sure to log in with an <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link"><span class="internal-link">X window forwarding</span> enabled</a>. This could mean using the -X in the ssh: Â </p>
+<pre class=" ">$ ssh -X username@clustername.it4i.cz </pre>
+<p class=" ">Other options is to access login node using VNC. Please see the detailed information on <span class="internal-link"><a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">how to <span class="internal-link">use graphic user interface on the clusters</span></a></span><span class="internal-link"></span>.</p>
+<p class=" ">From the login node an interactive session <strong>with X windows forwarding</strong> (-X option) can be started by following command:Â </p>
+<pre class=" ">$ qsub -I -X -A NONE-0-0 -q qexp -lselect=1:ncpus=24:mpiprocs=24,walltime=01:00:00Â </pre>
+<p class=" ">Then launch the debugger with the ddt command followed by the name of the executable to debug:</p>
+<pre class=" ">$ ddt test_debug</pre>
+<p class="exclamation">Forge now has common GUI for both DDT and MAP. In interactive mode, you can launch Forge using <span class="monospace">forge, ddt or map, </span>the latter two will just launch forge and swith to the respective tab in the common GUI.</p>
+<p class=" ">A<span style="text-align: start; "> submission window that appears have a prefilled path to the executable to debug. You can select the number of MPI processors and/or OpenMP threads on which to run and press run. Command line arguments to a program can be entered to the</span> "Arguments<span class="Apple-converted-space">" </span><span style="text-align: start; ">box.</span></p>
+<p class=" "><a href="ddt1.png" title="" target="_blank" class="internal-link"><img src="ddt1.png" width="451" title="" class="image-inline" alt="" height="513" /></a>Â </p>
+<p class=" ">To start the debugging directly without the submission window, user can specify the debugging and execution parameters from the command line. For example the number of MPI processes is set by option "-np 4". Skipping the dialog is done by "-start" option. To see the list of the "ddt" command line parameters, run "ddt --help". Â </p>
+<pre class=" ">ddt -start -np 4 ./hello_debug_impi</pre>
+<p class=" ">All of the above text also applies for MAP, just replace ddt command with map.</p>
+<h2 class=" ">Reverse connect</h2>
+<p>Forge now provides a new convenient mode of operation, called Reverse connect. Instead of launching a job from the GUI, the process is reserved - DDT/MAP is launched as a server in the job which then connects to a running instance of your GUI.</p>
+<p>To use Reverse connect, use a jobscript that you would normally use to launch your application, just prepend ddt/map --connect to your application:</p>
+<pre>map --connect mpirun -np 24 ./mpi-test<br />ddt --connect mpirun -np 24 ./mpi-test</pre>
+<p>Launch Forge GUI on login node and submit the job using qsub. When the job starts running, Forge will ask you to accept the connection:</p>
+<p><img alt="Allinea Reverse Connect" src="Snmekobrazovky20160211v14.27.45.png/@@images/3550e4ae-2eab-4571-8387-11a112dd6ca8.png" title="Allinea Reverse Connect" class="image-inline" /></p>
+<p>After accepting the request, you can start remote profiling/debugging.</p>
+<h2 class=" ">Xeon Phi</h2>
+<p>Forge allows debugging and profiling of both offload and native mode Xeon Phi programs.</p>
+<h3>Offload mode</h3>
+<p class=" ">It is recommended to set the following environment values on the offload host:</p>
+<pre class=" ">export MYO_WATCHDOG_MONITOR=-1 # To make sure the host process isn't killed when we enter a debugging session<br />export AMPLXE_COI_DEBUG_SUPPORT=true # To make sure that debugging symbols are accessible on the host and the card<br />unset OFFLOAD_MAIN # To make sure allinea DDT can attach to offloaded codes</pre>
+<p>Then use one of the above mentioned methods to launch Forge. (Reverse connect also works.)</p>
+<h3>Native mode</h3>
+<p>Native mode programs can be profiled/debugged using the remote launch feature. First, you need to create a script that will setup the environment on the Phi card. An example:</p>
+<pre>#!/bin/bash<br /># adjust PATH and LD_LIBRARY_PATH according to the toolchain/libraries your app is using.<br />export PATH=/apps/all/impi/5.0.3.048-iccifort-2015.3.187/mic/bin:$PATH<br />export LD_LIBRARY_PATH=/apps/all/impi/5.0.3.048-iccifort-2015.3.187/mic/lib:/apps/all/ifort/2015.3.187/lib/mic:/apps/all/icc/2015.3.187/lib/mic:$LD_LIBRARY_PATH<br />export MIC_OMP_NUM_THREADS=60<br />export MYO_WATCHDOG_MONITOR=-1<br />export AMPLXE_COI_DEBUG_SUPPORT=true<br />unset OFFLOAD_MAIN<br />export I_MPI_MIC=1</pre>
+<p class=" ">Save the script in eg.<span class="monospace"> ~/remote-mic.sh. </span>Now, start an interactive graphical session on a node with accelerator:</p>
+<pre class=" ">$ qsub â€IX â€q qexp â€l select=1:ncpus=24:accelerator=True</pre>
+<p class=" ">Launch Forge :</p>
+<pre class=" ">$ module load Forge<br />$ forge&</pre>
+<p>Now click on the remote launch drop-down list, select "Configure..." and Add a new remote connection with the following parameters:<br /><br /></p>
+<p>Connection name: mic0</p>
+<p>Hostname: mic0</p>
+<p>Remote Installation Directory:Â /apps/all/Forge/5.1-43967/</p>
+<p>Remote script: ~/remote-mic.sh</p>
+<p>You can click Test Remote Launch to verify the configuration. After you save the remote launch configuration and select it in the dropdown list, you can use the Run button in the main windows to remotely launch your program on mic0.</p>
+<h2 class=" ">Documentation</h2>
+<p>Users can find original User Guide after loading the Forge module:Â </p>
+<pre class=" ">$EBROOTFORGE/doc/userguide-forge.pdf</pre>
+<p class=" ">Â </p>
+<p class=" ">Â </p>
+<p class=" ">Â [1] Discipline, Magic, Inspiration and Science: Best Practice Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May 10, 2013, <a class="external-link" href="https://computing.llnl.gov/tutorials/allineaDDT/index.html" target="_self" title="">link </a></p>
+<p class=" ">Â </p>
+
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diff --git a/docs.it4i.cz/whats-new/news-feed/allinea-forge-documentation-updated.md b/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md
similarity index 87%
rename from docs.it4i.cz/whats-new/news-feed/allinea-forge-documentation-updated.md
rename to docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md
index 99d97cc97..e34630d9f 100644
--- a/docs.it4i.cz/whats-new/news-feed/allinea-forge-documentation-updated.md
+++ b/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md
@@ -59,11 +59,11 @@ $ mpif90 -g -O0 -o test_debug test.f
Before debugging, you need to compile your code with theses flags:
-**-g** Generates extra debugging information usable by GDB. -g3
+**-g** : Generates extra debugging information usable by GDB. -g3
includes even more debugging information. This option is available for
GNU and INTEL C/C++ and Fortran compilers.
-**-O0** Suppress all optimizations.
+**-O0** : Suppress all optimizations.
Â
@@ -72,15 +72,15 @@ Direct starting a Job with Forge
Be sure to log in with an [<span class="internal-link">X window
forwarding</span>
-enabled](../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
-This could mean using the -X in the sshÂ
+enabled](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+This could mean using the -X in the ssh: Â
$ ssh -X username@clustername.it4i.cz
Other options is to access login node using VNC. Please see the detailed
information on <span class="internal-link">[how to <span
class="internal-link">use graphic user interface on the
-clusters</span>](../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)</span><span
+clusters</span>](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)</span><span
class="internal-link"></span>.
From the login node an interactive session **with X windows forwarding**
@@ -98,16 +98,15 @@ can launch Forge using <span class="monospace">forge, ddt or map,
</span>the latter two will just launch forge and swith to the respective
tab in the common GUI.
-A<span style="text-alignstart; "> submission window that appears have
+A<span style="text-align: start; "> submission window that appears have
a prefilled path to the executable to debug. You can select the number
of MPI processors and/or OpenMP threads on which to run and press run.
Command line arguments to a program can be entered to the</span>
"Arguments<span class="Apple-converted-space">" </span><span
-style="text-alignstart; ">box.</span>
+style="text-align: start; ">box.</span>
-[{.image-inline
-width="451"
-height="513"}](../../salomon/software/debuggers/ddt1.png)Â
+[{.image-inline width="451"
+height="513"}](ddt1.png)Â
To start the debugging directly without the submission window, user can
specify the debugging and execution parameters from the command line.
@@ -139,7 +138,7 @@ Launch Forge GUI on login node and submit the job using qsub. When the
job starts running, Forge will ask you to accept the connection:
+Connect](Snmekobrazovky20160211v14.27.45.png/@@images/3550e4ae-2eab-4571-8387-11a112dd6ca8.png "Allinea Reverse Connect")
After accepting the request, you can start remote profiling/debugging.
@@ -192,13 +191,13 @@ Now click on the remote launch drop-down list, select "Configure..." and
Add a new remote connection with the following parameters:
-Connection namemic0
+Connection name: mic0
-Hostnamemic0
+Hostname: mic0
Remote Installation Directory:Â /apps/all/Forge/5.1-43967/
-Remote script~/remote-mic.sh
+Remote script: ~/remote-mic.sh
You can click Test Remote Launch to verify the configuration. After you
save the remote launch configuration and select it in the dropdown list,
@@ -216,7 +215,7 @@ Users can find original User Guide after loading the Forge module:Â
Â
-Â [1] Discipline, Magic, Inspiration and ScienceBest Practice
+Â [1] Discipline, Magic, Inspiration and Science: Best Practice
Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May
10, 2013,
[link](https://computing.llnl.gov/tutorials/allineaDDT/index.html)
@@ -224,5 +223,3 @@ Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May
Â
-
-
diff --git a/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.html b/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.html
new file mode 100644
index 000000000..4436833f0
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.html
@@ -0,0 +1,1029 @@
+
+<!DOCTYPE html>
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+ Allinea Performance Reports
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+ <h2 class=" ">Introduction</h2>
+<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs.</p>
+<p>The Allinea Performance Reports is most useful in profiling MPI programs.</p>
+<p>Our license is limited to 64 MPI processes.</p>
+<h2 class=" ">Modules</h2>
+<p>Allinea Performance Reports version 6.0 is available</p>
+<pre class=" ">$ module load PerformanceReports/6.0</pre>
+<p class=" ">The module sets up environment variables, required for using the Allinea Performance Reports. </p>
+<h2 class=" ">Usage</h2>
+<p class="callout">Use the the perf-report wrapper on your (MPI) program.</p>
+<p>Instead of <a href="../mpi-1.html" title="" target="_self" class="internal-link">running your MPI program the usual way</a>, use the the perf report wrapper:</p>
+<pre class=" ">$ perf-report mpirun ./mympiprog.x</pre>
+<p class=" ">The mpi program will run as usual. The perf-report creates two additional files, in *.txt and *.html format, containing the performance report. Note that <span class="internal-link">demanding MPI codes should be run within </span><a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_self" class="internal-link"><span class="internal-link">the queue system</span></a>.</p>
+<h2 class=" ">Example</h2>
+<p class=" ">In this example, we will be profiling the mympiprog.x MPI program, using Allinea performance reports. Assume that the code is compiled with intel compilers and linked against intel MPI library:</p>
+<p class=" ">First, we allocate some nodes via the express queue:</p>
+<pre class=" ">$ qsub -q qexp -l select=2:ppn=24:mpiprocs=24:ompthreads=1 -I<br />qsub: waiting for job 262197.dm2 to start<br />qsub: job 262197.dm2 ready</pre>
+<p class=" ">Then we load the modules and run the program the usual way:</p>
+<pre class=" ">$ module load intel impi PerfReports/6.0<br />$ mpirun ./mympiprog.x</pre>
+<p class=" ">Now lets profile the code:</p>
+<pre class=" ">$ perf-report mpirun ./mympiprog.x</pre>
+<p class=" ">Performance report files <a href="mympiprog_32p_2014-10-15_16-56.txt" title="" target="_self" class="internal-link">mympiprog_32p*.txt</a> and <a href="mympiprog_32p_2014-10-15_16-56.html" title="" target="_self" class="internal-link">mympiprog_32p*.html</a> were created. We can see that the code is very efficient on MPI and is CPU bounded.</p>
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diff --git a/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md b/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md
index 42b3a76bf..c4bee9336 100644
--- a/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md
+++ b/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md
@@ -56,8 +56,8 @@ compilers and linked against intel MPI library:
First, we allocate some nodes via the express queue:
$ qsub -q qexp -l select=2:ppn=24:mpiprocs=24:ompthreads=1 -I
- qsubwaiting for job 262197.dm2 to start
- qsubjob 262197.dm2 ready
+ qsub: waiting for job 262197.dm2 to start
+ qsub: job 262197.dm2 ready
Then we load the modules and run the program the usual way:
@@ -75,4 +75,3 @@ and
were created. We can see that the code is very efficient on MPI and is
CPU bounded.
-
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new file mode 100644
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+ Intel VTune Amplifier XE
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+ <h2 class=" ">Introduction</h2>
+<p>Intel<em>® </em>VTune™ <span>Amplifier, part of Intel Parallel studio, is a GUI profiling tool designed for Intel processors. It offers a graphical performance analysis of single core and multithreaded applications. A highlight of the features:</span></p>
+<ul>
+<li>Hotspot analysis</li>
+<li>Locks and waits analysis</li>
+<li>Low level specific counters, such as branch analysis and memory bandwidth</li>
+<li>Power usage analysis - frequency and sleep states.</li>
+</ul>
+<div></div>
+<div><a href="vtune-amplifier" title="" target="_blank" class="internal-link"><img alt="screenshot" src="https://docs.it4i.cz/salomon/software/debuggers/vtune-amplifier/@@images/7ca8748b-69ad-4b53-9667-29c2fdaa8913.png" title="VTune Amplifier" class="image-inline" /></a></div>
+<h2 class=" ">Usage</h2>
+<p><span>To profile an application with VTune Amplifier, special kernel modules need to be loaded. The modules are not loaded on the login nodes, thus direct profiling on login nodes is not possible. By default, the kernel modules ale not loaded on compute nodes neither. In order to have the modules loaded, you need to specify vtune=version PBS resource at job submit. The version is the same as for <em>environment module</em>. For example to use <span class="monospace">VTune/2016_update1</span>:</span></p>
+<pre><span>$ qsub -q qexp -A OPEN-0-0 -I -l select=1,vtune=2016_update1</span></pre>
+<p>After that, you can verify the modules sep*, pax and vtsspp are present in the kernel :</p>
+<pre>$ lsmod | grep -e sep -e pax -e vtsspp<br />vtsspp 362000 0<br />sep3_15 546657 0<br />pax 4312 0</pre>
+<p>To launch the GUI, first load the module:</p>
+<pre class=" "><span class="s1">$ module add VTune/2016_update1</span></pre>
+<p class=" "><span class="s1">and launch the GUI :</span></p>
+<pre class=" "><span class="s1">$Â </span><span>amplxe-gui</span></pre>
+<p class=" "><span>The GUI will open in new window. Click on "<em>New Project...</em>" to create a new project. After clicking <em>OK</em>, a new window with project properties will appear. Â At "<em>Application:</em>", select the bath to your binary you want to profile (the binary should be compiled with -g flag). Some additional options such as command line arguments can be selected. At "<em>Managed code profiling mode:</em>" select "<em>Native</em>" (unless you want to profile managed mode .NET/Mono applications). After clicking <em>OK</em>, your project is created.</span></p>
+<p class=" ">To run a new analysis, click "<em>New analysis...</em>". You will see a list of possible analysis. Some of them will not be possible on the current CPU (eg. Intel Atom analysis is not possible on Sandy bridge CPU), the GUI will show an error box if you select the wrong analysis. For example, select "<em>Advanced Hotspots</em>". Clicking on <em>Start </em>will start profiling of the application.</p>
+<h2 class=" ">Remote Analysis</h2>
+<p>VTune Amplifier also allows a form of remote analysis. In this mode, data for analysis is collected from the command line without GUI, and the results are then loaded to GUI on another machine. This allows profiling without interactive graphical jobs. To perform a remote analysis, launch a GUI somewhere, open the new analysis window and then click the button "<em>Command line</em>" in bottom right corner. It will show the command line needed to perform the selected analysis.</p>
+<p>The command line will look like this:</p>
+<pre class=" ">/apps/all/VTune/2016_update1/vtune_amplifier_xe_2016.1.1.434111/bin64/amplxe-cl -collect advanced-hotspots -app-working-dir /home/sta545/tmp -- /home/sta545/tmp/sgemm</pre>
+<p>Copy the line to clipboard and then you can paste it in your jobscript or in command line. After the collection is run, open the GUI once again, click the menu button in the upper right corner, and select "<em>Open > Result...</em>". The GUI will load the results from the run.</p>
+<h2 class=" ">Xeon Phi</h2>
+<p>It is possible to analyze both native and offloaded Xeon Phi applications. </p>
+<h3>Native mode</h3>
+<p>This mode is useful for native Xeon Phi applications launched directly on the card. In <em>Analysis Target</em> window, select <em>Intel Xeon Phi coprocessor (native), </em>choose path to the binary and MIC card to run on.</p>
+<h3>Offload mode</h3>
+<p>This mode is useful for applications that are launched from the host and use offload, OpenCL or mpirun. In <em>Analysis Target</em> window, select <em>Intel Xeon Phi coprocessor (native), </em>choose path to the binary and MIC card to run on.</p>
+<p>Â </p>
+<p class="exclamation">If the analysis is interrupted or aborted, further analysis on the card might be impossible and you will get errors like "ERROR connecting to MIC card". In this case please contact our support to reboot the MIC card.</p>
+<p class=" ">You may also use remote analysis to collect data from the MIC and then analyze it in the GUI later :</p>
+<p class=" ">Native launch:</p>
+<pre class=" ">$ /apps/all/VTune/2016_update1/vtune_amplifier_xe_2016.1.1.434111/bin64/amplxe-cl -target-system mic-native:0 -collect advanced-hotspots -- /home/sta545/tmp/vect-add-mic</pre>
+<p class=" ">Host launch:</p>
+<pre class=" ">$ /apps/all/VTune/2016_update1/vtune_amplifier_xe_2016.1.1.434111/bin64/amplxe-cl -target-system mic-host-launch:0 -collect advanced-hotspots -- /home/sta545/tmp/sgemm</pre>
+<p class=" ">You can obtain this command line by pressing the "Command line..." button on Analysis Type screen. </p>
+<h2 class=" ">References</h2>
+<ol>
+<li><span><a class="external-link" href="https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf" target="_self" title="">https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf</a> Performance Tuning for Intel® Xeon Phi™ Coprocessors</span></li>
+<li><span><a class="external-link" href="https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation" target="_self" title="">https://software.intel.com/en-us/intel-vtune-amplifier-xe-support/documentation</a> <span>Intel® VTune™ Amplifier Support</span></span></li>
+<li><span><span><a class="external-link" href="https://software.intel.com/en-us/amplifier_help_linux" target="_self" title="">https://software.intel.com/en-us/amplifier_help_linux</a>Â Linux user guide</span></span></li>
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diff --git a/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md b/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
index a386df679..deee29179 100644
--- a/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
+++ b/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
@@ -139,4 +139,3 @@ References
3. <span><span><https://software.intel.com/en-us/amplifier_help_linux>Â Linux
user guide</span></span>
-
diff --git a/docs.it4i.cz/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.html b/docs.it4i.cz/salomon/software/debuggers/mympiprog_32p_2014-10-15_16-56.html
new file mode 100644
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+ return getHorizontalPosition(i, cfg.w/2, (Math.max(j.value, 0)/cfg.maxValue)*cfg.factor);
+ })
+ .attr("cy", function(j, i){
+ return getVerticalPosition(i, cfg.h/2, (Math.max(j.value, 0)/cfg.maxValue)*cfg.factor);
+ })
+ .attr("data-id", function(j){return j.axis})
+ .style("fill", cfg.color(series)).style("fill-opacity", .9)
+ .on('mouseover', function (d){
+ newX = parseFloat(d3.select(this).attr('cx')) - 10;
+ newY = parseFloat(d3.select(this).attr('cy')) - 5;
+ tooltip.attr('x', newX).attr('y', newY).text(d.value).transition(200).style('opacity', 1);
+ z = "polygon."+d3.select(this).attr("class");
+ g.selectAll("polygon").transition(200).style("fill-opacity", 0.1);
+ g.selectAll(z).transition(200).style("fill-opacity", .7);
+ })
+ .on('mouseout', function(){
+ tooltip.transition(200).style('opacity', 0);
+ g.selectAll("polygon").transition(200).style("fill-opacity", cfg.opacityArea);
+ })
+ .append("svg:title")
+ .text(function(j){return Math.max(j.value, 0)});
+
+ series++;
+ });
+ //Tooltip
+ tooltip = g.append('text').style('opacity', 0).style('font-family', 'sans-serif').style('font-size', '13px');
+ }
+}
+
+</script>
+<script type="text/javascript">window.onload = function() {
+ var cpu = 88.6;
+ var mpi = 11.4;
+ var io = 0.0;
+
+ // Draw radar chart, choose its color based on application classification
+ var radar_data = [[ { axis: "CPU", value: cpu },
+ { axis: "MPI", value: mpi },
+ { axis: "I/O", value: io } ]];
+ var radar_options = { w: 200, h: 200, factor: 0.7, fontSize: 16, radius: 0,
+ opacityArea: 0.64, maxValue: 100,
+ color: function() {
+ if ("cpu" == "io") return "#ed8140";
+ if ("cpu" == "cpu") return "#4fd32e";
+ if ("cpu" == "mpi") return "#409ded";
+ else return "#bb58d6";
+ }
+ };
+ RadarChart.draw("#time_radar", radar_data, radar_options);
+
+ // Wrap the exe path on slashes if necessary
+ var exe_path = document.getElementById("exe_path");
+ exe_path.innerHTML = exe_path.innerHTML.replace(/\//g, '/​'); // insert a zero width space after slashes as a word wrap hint
+
+ // Format our byte value numbers to show at most 2 decimal places, but only if required to attain 3 digits of precision
+ // 1234.56 -> "1234"
+ // 12.3456 -> "12.3"
+ // 1.23456 -> "1.23"
+ // 0.00000 -> "0.00"
+ var formatNumber = function(num) {
+ if (num > 100) return new Number(num).toFixed(0); // 1234.56 -> 1234
+ if (num > 10) return new Number(num).toFixed(1); // 12.3456 -> 12.3
+ else return new Number(num).toFixed(2); // 1.23456 -> 1.23 and 0 -> 0.00
+ }
+
+ // Parse a number, but return 0 for invalid numbers, not NaN
+ var toNumber = function(num_str) {
+ var num = Number(num_str)
+ return isNaN(num) ? 0 : num;
+ }
+
+ // Scale byte values to bytes, kB, MB or GB as appropriate
+ var fillBytes = function(base_name, bytes_str, per_second) {
+ var units = "bytes";
+ var scale = 1.0;
+ var bytes = Number(bytes_str)
+ if (isNaN(bytes) ) { units = "" ; }
+ else if (bytes > 1000000000) { units = "GB"; scale = 1*1000*1000*1000; }
+ else if (bytes > 1000000 ) { units = "MB"; scale = 1*1000*1000 }
+ else if (bytes > 1000 ) { units = "kB"; scale = 1*1000 }
+ var num = isNaN(bytes) ? bytes_str : formatNumber(bytes / scale);
+ var elementNum = document.getElementById(base_name + "_num");
+ elementNum.innerHTML = num;
+ var elementUnits = document.getElementById(base_name + "_units");
+ elementUnits.innerHTML = units + (per_second && !isNaN(bytes) ? "/s" : "");
+ };
+
+ // Fill all the byte numbers and their units with the scaled values
+ fillBytes("mpi_colrate", "1.65e+02", true);
+ fillBytes("mpi_p2prate", "0.00e+00", true);
+ fillBytes("io_readrate", "0.00e+00", true);
+ fillBytes("io_writerate", "0.00e+00", true);
+ fillBytes("ram_mean", "2.33e+07", false);
+ fillBytes("ram_peak", "2.35e+07", false);
+
+ // Set widths for all graphs
+ var bar = function(name, width) {
+ var rounded = Math.round(width);
+ if (!isFinite(rounded) || rounded < 1)
+ document.getElementById(name).style.width = "1px"
+ else
+ document.getElementById(name).style.width = rounded + "px";
+ };
+ bar("cpu_bar", cpu * 2);
+ bar("mpi_bar", mpi * 2);
+ bar("io_bar", io * 2);
+
+ bar("cpu_num_bar", toNumber("50.0") / 2);
+ bar("cpu_vec_bar", toNumber("50.0") / 2);
+ bar("cpu_mem_bar", toNumber("0.0") / 2);
+ bar("cpu_other_bar", toNumber("0.0") / 2);
+
+ bar("mpi_col_bar", toNumber("100.0") / 2);
+ bar("mpi_p2p_bar", toNumber("0.0") / 2);
+ var mpi_scale = Math.max(toNumber("1.65e+02"), toNumber("0.00e+00"));
+ bar("mpi_colrate_bar", 50 * toNumber("1.65e+02") / mpi_scale);
+ bar("mpi_p2prate_bar", 50 * toNumber("0.00e+00") / mpi_scale);
+
+ bar("io_read_bar", toNumber("0.0") / 2);
+ bar("io_write_bar", toNumber("0.0") / 2);
+ var io_scale = Math.max(toNumber("0.00e+00"), toNumber("0.00e+00"));
+ bar("io_readrate_bar", 50 * toNumber("0.00e+00") / io_scale);
+ bar("io_writerate_bar", 50 * toNumber("0.00e+00") / io_scale);
+
+ bar("ram_mean_bar", 50 * toNumber("2.33e+07") / toNumber("2.35e+07"));
+ bar("ram_peak_bar", 50);
+ bar("ram_node_bar", toNumber("2.8") / 2);
+
+ // Formatting replacement helper function
+ var replaceIn = function(elementId, re, new_text) {
+ element = document.getElementById(elementId);
+ element.innerHTML = element.innerHTML.replace(re, new_text);
+ };
+
+ // Add formatting for the overview advice section
+ replaceIn('overview_advice', /CPU/g, '<span class="cpu_span">CPU</span>');
+ replaceIn('overview_advice', /MPI/g, '<span class="mpi_span">MPI</span>');
+ replaceIn('overview_advice', /I\/O/g, '<span class="io_span">I\/O</span>');
+
+ // Add formatting for the CPU advice section
+ if ( 88.6 < 0.05 )
+ replaceIn('cpu_explanation', /application code/g, '<span class="cpu_span">application code</span>');
+ replaceIn('cpu_explanation', /vectorized instructions/g, '<span class="cpu_vec_span">vectorized instructions</span>');
+ replaceIn('cpu_explanation', /memory accesses/g, '<span class="cpu_mem_span">memory accesses</span>');
+ replaceIn('cpu_explanation', /memory-bound/g, '<span class="cpu_mem_span">memory-bound</span>');
+ replaceIn('cpu_explanation', /arithmetic-bound/g, '<span class="cpu_num_span">arithmetic-bound</span>');
+ replaceIn('cpu_explanation', /numerical computation/g, '<span class="cpu_num_span">numerical computation</span>');
+
+ // Add formatting for the MPI advice section
+ if ( 11.4 < 0.05 )
+ replaceIn('mpi_explanation', /MPI/g, '<span class="mpi_span">MPI</span>');
+ replaceIn('mpi_explanation', /collective calls/g, '<span class="mpi_col_span">collective calls</span>');
+ replaceIn('mpi_explanation', /point-to-point calls/g, '<span class="mpi_p2p_span">point-to-point calls</span>');
+ replaceIn('mpi_explanation', / very low/g, ' <span class="mpi_colrate_span">very low</span>');
+ replaceIn('mpi_explanation', / low/g, ' <span class="mpi_colrate_span">low</span>');
+ replaceIn('mpi_explanation', / average/g, ' <span class="mpi_colrate_span">average</span>');
+ replaceIn('mpi_explanation', / very high/g, ' <span class="mpi_colrate_span">very high</span>');
+ replaceIn('mpi_explanation', / high/g, ' <span class="mpi_colrate_span">high</span>');
+
+ // Add formatting for the I/O advice section
+ if ( 0.0 < 0.05 )
+ replaceIn('io_explanation', /I\/O/g, '<span class="io_span">I/O</span>');
+ replaceIn('io_explanation', /read operations/g, '<span class="io_read_span">read operations</span>');
+ replaceIn('io_explanation', /write operations/g, '<span class="io_write_span">write operations</span>');
+ replaceIn('io_explanation', / very low/g, ' <span class="io_readrate_span">very low</span>');
+ replaceIn('io_explanation', / low/g, ' <span class="io_readrate_span">low</span>');
+ replaceIn('io_explanation', / average/g, ' <span class="io_readrate_span">average</span>');
+ replaceIn('io_explanation', / very high/g, ' <span class="io_readrate_span">very high</span>');
+ replaceIn('io_explanation', / high/g, ' <span class="io_readrate_span">high</span>');
+
+ // Add formatting for the RAM advice section
+ replaceIn('ram_explanation', /high/g, ' <span class="ram_node_span">high</span>');
+ replaceIn('ram_explanation', /well-balanced/g, '<span class="ram_peak_span">well-balanced</span>');
+ replaceIn('ram_explanation', /significant variation/g, '<span class="ram_peak_span">significant variation</span>');
+ replaceIn('ram_explanation', /peak node memory usage/g, '<span class="ram_node_span">peak node memory usage</span>');
+
+ // Hide the error warning if the script got this far
+ document.getElementById('error').style.display = 'none';
+};
+</script>
+</head>
+
+<body>
+<div id="content">
+
+<div class="header">
+ <div class="logo"><img src="http://content.allinea.com/downloads/performance-report-logo.png" alt="Allinea Performance Reports" /></div>
+ <div class="header_left">
+ <div class="application_details">
+ <table>
+ <tr><td class="details_key">Executable:</td><td id="exe_name">mympiprog.x</td></tr>
+ <tr><td class="details_key">Resources:</td><td id="num_procs">32 processes, 2 nodes</td></tr>
+ <tr><td class="details_key">Machine:</td><td id="machine_name">cn182</td></tr>
+ <tr><td class="details_key">Start time:</td><td id="start_date">Wed Oct 15 16:56:23 2014</td></tr>
+ <tr><td class="details_key">Total time:</td><td id="time_string">7 seconds (0 minutes)</td></tr>
+ <tr><td class="details_key">Full path:</td><td id="exe_path">/home/user</td></tr>
+ <tr><td class="details_key">Notes:</td><td id="notes"></td></tr>
+ </table>
+ </div>
+ </div>
+ <div id="time_radar"></div>
+ <div class="clear"></div>
+</div>
+<hr />
+<div id="error">
+<p><strong>Error: javascript is not running</strong></p>
+<p>The graphs in this Performance Report require <strong>javascript</strong>, which is disabled or not working.</p>
+<p>Check whether your javascript support is enabled or try another browser.<p>
+<p>Remember, you can always contact <a href="mailto:support@allinea.com">support@allinea.com</a>, we're very nice!</p>
+</div>
+<div class="summary">
+ <div class="heading">Summary: mympiprog.x is <span class="cpu_span">CPU-bound</span> in this configuration</div>
+ <div>The total wallclock time was spent as follows:</div>
+ <table class="summary_table">
+ <tr><td class="heading_cpu">CPU</td><td class="percent">88.6%</td><td class="bar_graph"><div id="cpu_bar" /></td>
+ <td class="details"><p>Time spent running application code. High values are usually good.</p><p>This is <span id="summary_cpu_class">high</span>; check the CPU performance section for optimization advice.</p></td></tr>
+ <tr><td class="heading_mpi">MPI</td><td class="percent">11.4%</td><td class="bar_graph"><div id="mpi_bar" /></td>
+ <td class="details"><p>Time spent in MPI calls. High values are usually bad.</p><p>This is <span id="summary_mpi_class">very low</span>; this code may benefit from increasing the process count.</p></td></tr>
+ <tr><td class="heading_io">I/O</td><td class="percent">0.0%</td><td class="bar_graph"><div id="io_bar" /></td>
+ <td class="details"><p>Time spent in filesystem I/O. High values are usually bad.</p><p>This is <span id="summary_io_class">negligible</span>; there's no need to investigate I/O performance.</p></td></tr>
+ </table>
+ <div class="overview_general_advice"><p>This application run was <span class="cpu_span">CPU-bound</span>. A breakdown of this time and advice for investigating further is in the <span class="cpu_span">CPU</span> section below.</p><p id="overview_advice">As very little time is spent in MPI calls, this code may also benefit from running at larger scales.</p></div>
+</div>
+<hr />
+<div class="subsections">
+ <div class="ltcol">
+ <div class="heading_cpu">CPU</div>
+ <div>A breakdown of how the <span class="cpu_span">88.6</span>% total CPU time was spent:</div>
+ <table id="cpu_chart">
+ <tr><td>Scalar numeric ops</td><td class="right_cell"><span class="cpu_num_span">50.0</span>%</td><td class="mini_bar_graph"><div id="cpu_num_bar" /></td></tr>
+ <tr><td>Vector numeric ops</td><td class="right_cell"><span class="cpu_vec_span">50.0</span>%</td><td class="mini_bar_graph"><div id="cpu_vec_bar" /></td></tr>
+ <tr><td>Memory accesses</td><td class="right_cell"><span class="cpu_mem_span">0.0</span>%</td><td class="mini_bar_graph"><div id="cpu_mem_bar" /></td></tr>
+ <tr><td>Other</td><td class="right_cell"><span class="cpu_other_span">0.0</span>%</td><td class="mini_bar_graph"><div id="cpu_other_bar" /></td></tr>
+ </table>
+ <div id="cpu_explanation">
+ <div class="explanation">The per-core performance is arithmetic-bound. Try to increase the amount of time spent in vectorized instructions by analyzing the compiler's vectorization reports.</div>
+ <div class="explanation"></div>
+ </div>
+ </div>
+ <div class="rtcol">
+ <div class="heading_mpi">MPI</div>
+ <div>Of the <span class="mpi_span">11.4</span>% total time spent in MPI calls:</div>
+ <table id="mpi_chart">
+ <tr><td>Time in collective calls</td><td class="right_cell"><span class="mpi_col_span">100.0</span>%</td><td class="mini_bar_graph"><div id="mpi_col_bar" /></td></tr>
+ <tr><td>Time in point-to-point calls</td><td class="right_cell"><span class="mpi_p2p_span">0.0</span>%</td><td class="mini_bar_graph"><div id="mpi_p2p_bar" /></td></tr>
+ <tr><td>Effective process collective rate</td><td class="right_cell"><span class="mpi_colrate_span"><span id="mpi_colrate_num">1.65e+02</span></span> <span id="mpi_colrate_units"></span></td><td class="mini_bar_graph"><div id="mpi_colrate_bar" /></td></tr>
+ <tr><td>Effective process point-to-point rate</td><td class="right_cell"><span class="mpi_p2prate_span"><span id="mpi_p2prate_num">0.00e+00</span></span> <span id="mpi_p2prate_units"></span></td><td class="mini_bar_graph"><div id="mpi_p2prate_bar" /></td></tr>
+ </table>
+ <div id="mpi_explanation">
+ <div class="explanation">Most of the time is spent in collective calls with a very low transfer rate. This suggests load imbalance is causing synchonization overhead; use an MPI profiler to investigate further.</div>
+ <div class="explanation"></div>
+ </div>
+ </div>
+ <div class="clear"></div>
+</div>
+<div class="subsections">
+ <div class="ltcol">
+ <div class="heading_io">I/O</div>
+ <div>A breakdown of how the <span class="io_span">0.0</span>% total I/O time was spent:</div>
+ <table id="io_chart">
+ <tr><td>Time in reads</td><td class="right_cell"><span class="io_read_span">0.0</span>%</td><td class="mini_bar_graph"><div id="io_read_bar" /></td></tr>
+ <tr><td>Time in writes</td><td class="right_cell"><span class="io_write_span">0.0</span>%</td><td class="mini_bar_graph"><div id="io_write_bar" /></td></tr>
+ <tr><td>Effective process read rate</td><td class="right_cell"><span class="io_readrate_span"><span id="io_readrate_num">0.00e+00</span></span> <span id="io_readrate_units"></span></td><td class="mini_bar_graph"><div id="io_readrate_bar" /></td></tr>
+ <tr><td>Effective process write rate</td><td class="right_cell"><span class="io_writerate_span"><span id="io_writerate_num">0.00e+00</span></span> <span id="io_writerate_units"></span></td><td class="mini_bar_graph"><div id="io_writerate_bar" /></td></tr>
+ </table>
+ <div id="io_explanation">
+ <div class="explanation">No time is spent in I/O operations. There's nothing to optimize here!</div>
+ <div class="explanation"></div>
+ </div>
+ </div>
+ <div class="rtcol">
+ <div class="heading_ram">Memory</div>
+ <div>Per-process memory usage may also affect scaling:</div>
+ <table id="ram_chart">
+ <tr><td>Mean process memory usage</td><td class="right_cell"><span class="ram_mean_span"><span id="ram_mean_num">2.33e+07</span></span> <span id="ram_mean_units"></span></td><td class="mini_bar_graph"><div id="ram_mean_bar" /></td></tr>
+ <tr><td>Peak process memory usage</td><td class="right_cell"><span class="ram_peak_span"><span id="ram_peak_num">2.35e+07</span></span> <span id="ram_peak_units"></span></td><td class="mini_bar_graph"><div id="ram_peak_bar" /></td></tr>
+ <tr><td>Peak node memory usage</td><td class="right_cell"><span class="ram_node_span">2.8</span>%</td><td class="mini_bar_graph"><div id="ram_node_bar" /></td></tr>
+ </table>
+ <div id="ram_explanation">
+ <div class="explanation">The peak node memory usage is very low. You may be able to reduce the amount of allocation time used by running with fewer MPI processes and more data on each process.</div>
+ <div class="explanation"></div>
+ </div>
+ </div>
+ <div class="clear"></div>
+</div>
+</div> <!-- content -->
+</body>
+</html>
diff --git a/docs.it4i.cz/salomon/software/debuggers/score-p.html b/docs.it4i.cz/salomon/software/debuggers/score-p.html
new file mode 100644
index 000000000..9db6a1fc0
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/debuggers/score-p.html
@@ -0,0 +1,351 @@
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+ <h2 class=" ">Introduction</h2>
+<p>We provide state of the art programms and tools to develop, profile and debug HPC codes at IT4Innovations.<br />On these pages, we provide an overview of the profiling and debugging tools available on Anslem at IT4I.</p>
+<h2 class=" ">Intel debugger</h2>
+<p class="exclamation">Intel debugger is no longer available since Parallel Studio version 2015</p>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">X display</a> for running the GUI.</p>
+<pre class=" ">$ module load intel<br />$ idb</pre>
+<p>Read more at the <a href="../intel-suite/intel-debugger.html" title="" target="_self" class="internal-link">Intel Debugger</a> page.</p>
+<h2 class=" ">Allinea Forge (DDT/MAP)</h2>
+<p>Allinea DDT, is a commercial debugger primarily for debugging parallel MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel Xeon Phi accelerators. DDT provides all the standard debugging features (stack trace, breakpoints, watches, view variables, threads etc.) for every thread running as part of your program, or for every process - even if these processes are distributed across a cluster using an MPI implementation.</p>
+<pre class=" ">$ module load Forge<br />$ forge</pre>
+<p>Read more at the <a href="allinea-ddt.html" title="" target="_self" class="internal-link">Allinea DDT</a> page.</p>
+<h2 class=" ">Allinea Performance Reports</h2>
+<p>Allinea Performance Reports characterize the performance of HPC application runs. After executing your application through the tool, a synthetic HTML report is generated automatically, containing information about several metrics along with clear behavior statements and hints to help you improve the efficiency of your runs. Our license is limited to 64 MPI processes.</p>
+<pre class=" ">$ module load PerformanceReports/6.0 <br />$ perf-report mpirun -n 64 ./my_application argument01 argument02</pre>
+<p class=" ">Read more at the <a href="allinea-performance-reports.html" title="" target="_self" class="internal-link">Allinea Performance Reports</a> page.</p>
+<h2 class=" ">RougeWave Totalview</h2>
+<p>TotalView is a source- and machine-level debugger for multi-process, multi-threaded programs. Its wide range of tools provides ways to analyze, organize, and test programs, making it easy to isolate and identify problems in individual threads and processes in programs of great complexity.</p>
+<pre class=" ">$ module load TotalView/8.15.4-6-linux-x86-64<br />$ totalview</pre>
+<p>Read more at the <a href="total-view.html" title="" target="_self" class="internal-link">Totalview</a> page.</p>
+<h2 class=" ">Vampir trace analyzer</h2>
+<p>Vampir is a GUI trace analyzer for traces in OTF format.</p>
+<pre>$ module load Vampir/8.5.0<br />$ vampir</pre>
+<p>Read more at the <a href="vampir.html" title="" target="_self" class="internal-link">Vampir</a> page.</p>
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diff --git a/docs.it4i.cz/salomon/software/debuggers/summary.md b/docs.it4i.cz/salomon/software/debuggers/summary.md
index 200487b7d..f367995a7 100644
--- a/docs.it4i.cz/salomon/software/debuggers/summary.md
+++ b/docs.it4i.cz/salomon/software/debuggers/summary.md
@@ -45,9 +45,7 @@ implementation.
$ module load Forge
$ forge
-Read more at the [Allinea
-DDT](../../../whats-new/news-feed/allinea-forge-documentation-updated.html)
-page.
+Read more at the [Allinea DDT](allinea-ddt.html) page.
Allinea Performance Reports
---------------------------
@@ -88,3 +86,7 @@ Vampir is a GUI trace analyzer for traces in OTF format.
$ vampir
Read more at the [Vampir](vampir.html) page.
+
+
+
+
diff --git a/docs.it4i.cz/salomon/software/debuggers/total-view.html b/docs.it4i.cz/salomon/software/debuggers/total-view.html
new file mode 100644
index 000000000..7441a0666
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/debuggers/total-view.html
@@ -0,0 +1,1049 @@
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+ <span dir="ltr" id="breadcrumbs-4">
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+ <div class="">
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+ <dl class="portalMessage info" id="kssPortalMessage" style="display:none">
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+ Total View
+ </h1>
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+</div>
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+ TotalView is a GUI-based source code multi-process, multi-thread debugger.
+ </div>
+
+
+
+
+
+ <div id="viewlet-above-content-body">
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+ <div id="content-core">
+
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+ <div id="parent-fieldname-text-1799a53b5ab741889e10f612a3dd8224" class="">
+ <h2 class=" ">License and Limitations for cluster Users</h2>
+<p>On the cluster users can debug OpenMP or MPI code that runs up to 64 parallel processes. These limitation means that:<br /><br />Â Â Â 1 user can debug up 64 processes, or<br />Â Â Â 32 users can debug 2 processes, etc.<br /><br />Debugging of GPU accelerated codes is also supported.</p>
+<p>You can check the status of the licenses <a class="external-link" href="https://extranet.it4i.cz/rsweb/anselm/license/totalview" target="_self" title="">here</a>.</p>
+<h2 class=" ">Compiling Code to run with TotalView</h2>
+<h3 class=" ">Modules</h3>
+<p>Load all necessary modules to compile the code. For example:</p>
+<pre class=" ">module load intel<br /><br />module load impi  ... or ... module load OpenMPI/X.X.X-icc</pre>
+<p>Load the TotalView module:</p>
+<pre class=" ">module load TotalView/8.15.4-6-linux-x86-64</pre>
+<p>Compile the code:</p>
+<pre class=" ">mpicc -g -O0 -o test_debug test.c<br /><br />mpif90 -g -O0 -o test_debug test.f</pre>
+<h3 class=" ">Compiler flags</h3>
+<p>Before debugging, you need to compile your code with theses flags:</p>
+<p class="exclamation"><strong>-g</strong> : Generates extra debugging information usable by GDB. -g3 includes even more debugging information. This option is available for GNU and INTEL C/C++ and Fortran compilers.<br /><br /><strong>-O0</strong> : Suppress all optimizations.</p>
+<h2 class=" ">Starting a Job with TotalView</h2>
+<p>Be sure to log in with an X window forwarding enabled. This could mean using the -X in the ssh:Â </p>
+<pre class=" ">ssh -X username@salomon.it4i.cz </pre>
+<p>Other options is to access login node using VNC. Please see the detailed information on how to use graphic user interface on Anselm <a href="https://docs.it4i.cz/salomon/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33#VNC" title="" target="_self" class="internal-link">here</a>.</p>
+<p>From the login node an interactive session with X windows forwarding (-X option) can be started by following command:</p>
+<pre class=" ">qsub -I -X -A NONE-0-0 -q qexp -lselect=1:ncpus=24:mpiprocs=24,walltime=01:00:00 </pre>
+<p>Then launch the debugger with the totalview command followed by the name of the executable to debug.</p>
+<h3 class=" ">Debugging a serial code</h3>
+<p>To debug a serial code use:</p>
+<pre class=" ">totalview test_debug</pre>
+<h3 class=" ">Debugging a parallel code - option 1</h3>
+<p>To debug a parallel code compiled with <span><strong>OpenMPI</strong></span> you need to setup your TotalView environment:Â </p>
+<p class="callout"><strong>Please note:</strong> To be able to run parallel debugging procedure from the command line without stopping the debugger in the mpiexec source code you have to add the following function to your <strong>~/.tvdrc</strong> file:</p>
+<pre class=" ">proc mpi_auto_run_starter {loaded_id} {<br />Â Â Â set starter_programs {mpirun mpiexec orterun}<br />Â Â Â set executable_name [TV::symbol get $loaded_id full_pathname]<br />Â Â Â set file_component [file tail $executable_name]<br /><br />Â Â Â if {[lsearch -exact $starter_programs $file_component] != -1} {<br />Â Â Â Â Â Â Â puts "**************************************"<br />Â Â Â Â Â Â Â puts "Automatically starting $file_component"<br />Â Â Â Â Â Â Â puts "**************************************"<br />Â Â Â Â Â Â Â dgo<br />Â Â Â }<br />}<br /><br /># Append this function to TotalView's image load callbacks so that<br /># TotalView run this program automatically.<br /><br />dlappend TV::image_load_callbacks mpi_auto_run_starter</pre>
+<p>The source code of this function can be also found in</p>
+<pre class=" ">/apps/all/OpenMPI/1.10.1-GNU-4.9.3-2.25/etc/openmpi-totalview.tcl</pre>
+<p class="callout">You can also add only following line to you ~/.tvdrc file instead of the entire function: <br /><br /><strong>source /apps/all/OpenMPI/1.10.1-GNU-4.9.3-2.25/etc/openmpi-totalview.tcl</strong></p>
+<p>You need to do this step only once. See also <a class="external-link" href="https://www.open-mpi.org/faq/?category=running#run-with-tv" target="_self" title="">OpenMPI FAQ entry</a></p>
+<p>Now you can run the parallel debugger using:</p>
+<pre class=" ">mpirun -tv -n 5 ./test_debug</pre>
+<p>When following dialog appears click on "Yes"</p>
+<p><a href="totalview1.png" title="" target="_blank" class="internal-link"><img alt="" src="https://docs.it4i.cz/salomon/software/debuggers/totalview1.png/@@images/45a91b6e-7f4d-4084-a5ba-d1ee703adaa1.png" title="" class="image-inline" /></a></p>
+<p>At this point the main TotalView GUI window will appear and you can insert the breakpoints and start debugging:</p>
+<p><a href="totalview2.png" title="" target="_blank" class="internal-link"><img alt="" src="totalview2.png" title="" class="image-inline" /></a></p>
+<h3 class=" ">Debugging a parallel code - option 2</h3>
+<p>Other option to start new parallel debugging session from a command line is to let TotalView to execute mpirun by itself. In this case user has to specify a MPI implementation used to compile the source code. </p>
+<p>The following example shows how to start debugging session with Intel MPI:</p>
+<pre class=" ">module load intel/2015b-intel-2015b impi/5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25 TotalView/8.15.4-6-linux-x86-64<br /><br />totalview -mpi "Intel MPI-Hydra" -np 8 ./hello_debug_impi</pre>
+<p>After running previous command you will see the same window as shown in the screenshot above.</p>
+<p>More information regarding the command line parameters of the TotalView can be found TotalView Reference Guide, Chapter 7: TotalView Command Syntax.  </p>
+<h2 class=" ">Documentation</h2>
+<p>[1] The <a class="external-link" href="http://www.roguewave.com/support/product-documentation/totalview-family.aspx#totalview" target="_self" title="">TotalView documentation</a> web page is a good resource for learning more about some of the advanced TotalView features.</p>
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diff --git a/docs.it4i.cz/salomon/software/debuggers/total-view.md b/docs.it4i.cz/salomon/software/debuggers/total-view.md
index 1ca6fda93..b39e006c7 100644
--- a/docs.it4i.cz/salomon/software/debuggers/total-view.md
+++ b/docs.it4i.cz/salomon/software/debuggers/total-view.md
@@ -42,11 +42,11 @@ Compile the code:
Before debugging, you need to compile your code with theses flags:
-**-g** Generates extra debugging information usable by GDB. -g3
+**-g** : Generates extra debugging information usable by GDB. -g3
includes even more debugging information. This option is available for
GNU and INTEL C/C++ and Fortran compilers.
-**-O0** Suppress all optimizations.
+**-O0** : Suppress all optimizations.
Starting a Job with TotalView
-----------------------------
@@ -143,7 +143,7 @@ After running previous command you will see the same window as shown in
the screenshot above.
More information regarding the command line parameters of the TotalView
-can be found TotalView Reference Guide, Chapter 7TotalView Command
+can be found TotalView Reference Guide, Chapter 7: TotalView Command
Syntax. Â
Documentation
@@ -154,4 +154,3 @@ documentation](http://www.roguewave.com/support/product-documentation/totalview-
web page is a good resource for learning more about some of the advanced
TotalView features.
-
diff --git a/docs.it4i.cz/salomon/software/debuggers/valgrind.html b/docs.it4i.cz/salomon/software/debuggers/valgrind.html
new file mode 100644
index 000000000..3ec9cb288
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/debuggers/valgrind.html
@@ -0,0 +1,1050 @@
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+ Valgrind is a tool for memory debugging and profiling.
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+ <h2 class=" ">About Valgrind</h2>
+<p class=" ">Valgrind is an open-source tool, used mainly for debuggig memory-related problems, such as memory leaks, use of uninitalized memory etc. in C/C++ applications. The toolchain was however extended over time with more functionality, such as debugging of threaded applications, cache profiling, not limited only to C/C++.</p>
+<p class=" ">Valgind is an extremely useful tool for debugging memory errors such as <a class="external-link" href="http://en.wikipedia.org/wiki/Off-by-one_error" target="_self" title="">off-by-one</a>. Valgrind uses a virtual machine and dynamic recompilation of binary code, because of that, you can expect that programs being debugged by Valgrind run 5-100 times slower.</p>
+<p class=" ">The main tools available in Valgrind are :</p>
+<ul>
+<li><strong>Memcheck</strong>, the original, must used and default tool. Verifies memory access in you program and can detect use of unitialized memory, out of bounds memory access, memory leaks, double free, etc.</li>
+<li><strong>Massif</strong>, a heap profiler.</li>
+<li><strong>Hellgrind</strong> and <strong>DRD</strong> can detect race conditions in multi-threaded applications.</li>
+<li><strong>Cachegrind</strong>, a cache profiler.</li>
+<li><strong>Callgrind</strong>, a callgraph analyzer.</li>
+<li>For a full list and detailed documentation, please refer to the <a class="external-link" href="http://valgrind.org/docs/" target="_self" title="">official Valgrind documentation</a>.</li>
+</ul>
+<h2 class=" ">Installed versions</h2>
+<p>There are two versions of Valgrind available on the cluster.</p>
+<ul>
+<li><span>Version 3.8.1, installed by operating system vendor in </span><span class="monospace">/usr/bin/valgrind. </span><span>This version is available by default, without the need to load any module. This version however does not provide additional MPI support. Also, it does not support AVX2 instructions, <strong>debugging of an AVX2-enabled executable with this version will fail</strong></span></li>
+<li><span><span>Version 3.11.0 built by ICC with support for Intel MPI, available in <a href="../../environment-and-modules.html" title="" target="_self" class="internal-link">module</a>Â </span></span><span class="monospace">Valgrind/3.11.0-intel-2015b. </span>After loading the module, this version replaces the default valgrind.</li>
+<li>Version 3.11.0 built by GCC with support for Open MPI, module <span class="monospace">Valgrind/3.11.0-foss-2015b</span></li>
+</ul>
+<h2 class=" ">Usage</h2>
+<p>Compile the application which you want to debug as usual. It is advisable to add compilation flags <span class="monospace">-g </span>(to add debugging information to the binary so that you will see original source code lines in the output) and <span class="monospace">-O0</span> (to disable compiler optimizations). </p>
+<p>For example, lets look at this C code, which has two problems :</p>
+<pre class=" ">#include <stdlib.h><br /><br />void f(void) <br />{<br /> int* x = malloc(10 * sizeof(int));<br /> x[10] = 0; // problem 1: heap block overrun<br />} // problem 2: memory leak -- x not freed<br /><br />int main(void)<br />{<br /> f();<br /> return 0;<br />}</pre>
+<p>Now, compile it with Intel compiler :</p>
+<pre class=" ">$ module add intel<br />$ icc -g valgrind-example.c -o valgrind-example </pre>
+<p>Now, lets run it with Valgrind. The syntax is :</p>
+<p><span class="monospace">valgrind [valgrind options] <your program binary> [your program options]</span></p>
+<p>If no Valgrind options are specified, Valgrind defaults to running Memcheck tool. Please refer to the Valgrind documentation for a full description of command line options.</p>
+<pre class=" ">$ valgrind ./valgrind-example<br />==12652== Memcheck, a memory error detector<br />==12652== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.<br />==12652== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info<br />==12652== Command: ./valgrind-example<br />==12652== <br /><span>==12652== Invalid write of size 4</span><br />==12652== at 0x40053E: f (valgrind-example.c:6)<br />==12652== by 0x40054E: main (valgrind-example.c:11)<br /><span>==12652== Address 0x5861068 is 0 bytes after a block of size 40 alloc'd</span><br />==12652== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)<br />==12652== by 0x400528: f (valgrind-example.c:5)<br />==12652== by 0x40054E: main (valgrind-example.c:11)<br />==12652== <br />==12652== <br />==12652== HEAP SUMMARY:<br />==12652== in use at exit: 40 bytes in 1 blocks<br />==12652== total heap usage: 1 allocs, 0 frees, 40 bytes allocated<br />==12652== <br />==12652== LEAK SUMMARY:<br /><span>==12652== definitely lost: 40 bytes in 1 blocks</span><br />==12652== indirectly lost: 0 bytes in 0 blocks<br />==12652== possibly lost: 0 bytes in 0 blocks<br />==12652== still reachable: 0 bytes in 0 blocks<br />==12652== suppressed: 0 bytes in 0 blocks<br />==12652== Rerun with --leak-check=full to see details of leaked memory<br />==12652== <br />==12652== For counts of detected and suppressed errors, rerun with: -v<br />==12652== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 6 from 6)</pre>
+<p>In the output we can see that Valgrind has detected both errors - the off-by-one memory access at line 5 and a memory leak of 40 bytes. If we want a detailed analysis of the memory leak, we need to run Valgrind with <span class="monospace">--leak-check=full</span> option :</p>
+<pre class=" ">$ valgrind --leak-check=full ./valgrind-example<br />==23856== Memcheck, a memory error detector<br />==23856== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.<br />==23856== Using Valgrind-3.6.0 and LibVEX; rerun with -h for copyright info<br />==23856== Command: ./valgrind-example<br />==23856== <br />==23856== Invalid write of size 4<br />==23856== at 0x40067E: f (valgrind-example.c:6)<br />==23856== by 0x40068E: main (valgrind-example.c:11)<br />==23856== Address 0x66e7068 is 0 bytes after a block of size 40 alloc'd<br />==23856== at 0x4C26FDE: malloc (vg_replace_malloc.c:236)<br />==23856== by 0x400668: f (valgrind-example.c:5)<br />==23856== by 0x40068E: main (valgrind-example.c:11)<br />==23856== <br />==23856== <br />==23856== HEAP SUMMARY:<br />==23856== in use at exit: 40 bytes in 1 blocks<br />==23856== total heap usage: 1 allocs, 0 frees, 40 bytes allocated<br />==23856== <br />==23856== 40 bytes in 1 blocks are definitely lost in loss record 1 of 1<br />==23856== at 0x4C26FDE: malloc (vg_replace_malloc.c:236)<br />==23856== by 0x400668: f (valgrind-example.c:5)<br />==23856== by 0x40068E: main (valgrind-example.c:11)<br />==23856== <br />==23856== LEAK SUMMARY:<br />==23856== definitely lost: 40 bytes in 1 blocks<br />==23856== indirectly lost: 0 bytes in 0 blocks<br />==23856== possibly lost: 0 bytes in 0 blocks<br />==23856== still reachable: 0 bytes in 0 blocks<br />==23856== suppressed: 0 bytes in 0 blocks<br />==23856== <br />==23856== For counts of detected and suppressed errors, rerun with: -v<br />==23856== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 6 from 6)</pre>
+<p>Now we can see that the memory leak is due to the <span class="monospace">malloc()</span> at line 6.</p>
+<h2 class=" "><span>Usage with MPI</span></h2>
+<p>Although Valgrind is not primarily a parallel debugger, it can be used to debug parallel applications as well. When launching your parallel applications, prepend the valgrind command. For example :</p>
+<pre class=" ">$ mpirun -np 4 valgrind myapplication</pre>
+<p class=" ">The default version without MPI support will however report a large number of false errors in the MPI library, such as :</p>
+<pre class=" ">==30166== Conditional jump or move depends on uninitialised value(s)<br />==30166== at 0x4C287E8: strlen (mc_replace_strmem.c:282)<br />==30166== by 0x55443BD: I_MPI_Processor_model_number (init_interface.c:427)<br />==30166== by 0x55439E0: I_MPI_Processor_arch_code (init_interface.c:171)<br />==30166== by 0x558D5AE: MPID_nem_impi_init_shm_configuration (mpid_nem_impi_extensions.c:1091)<br />==30166== by 0x5598F4C: MPID_nem_init_ckpt (mpid_nem_init.c:566)<br />==30166== by 0x5598B65: MPID_nem_init (mpid_nem_init.c:489)<br />==30166== by 0x539BD75: MPIDI_CH3_Init (ch3_init.c:64)<br />==30166== by 0x5578743: MPID_Init (mpid_init.c:193)<br />==30166== by 0x554650A: MPIR_Init_thread (initthread.c:539)<br />==30166== by 0x553369F: PMPI_Init (init.c:195)<br />==30166== by 0x4008BD: main (valgrind-example-mpi.c:18)</pre>
+<p class=" ">so it is better to use the MPI-enabled valgrind from module. The MPI versions requires library :Â </p>
+<p class=" "><span class="monospace">$EBROOTVALGRIND/lib/valgrind/libmpiwrap-amd64-linux.so</span></p>
+<p class=" ">which must be included in the<span class="monospace"> LD_PRELOAD </span>environment variable.</p>
+<p class=" ">Lets look at this MPI example :</p>
+<pre class=" "><span>#include <</span><span>stdlib.h</span><span>><br /></span><span>#include <</span><span>mpi.h</span><span>></span><span>Â <br /><br /></span><span>int</span><span> main(</span><span>int</span><span> </span><span>argc</span><span>, char *</span><span>argv</span><span>[])<br /></span><span>{<br /></span><span>Â Â Â Â Â </span><span>int</span><span> *data = </span><span>malloc</span><span>(</span><span>sizeof</span><span>(</span><span>int</span><span>)*99);<br /></span><span><br />Â </span><span>Â Â Â Â </span><span>MPI_Init</span><span>(&</span><span>argc</span><span>, &</span><span>argv</span><span>);<br /></span><span>Â Â Â Â MPI_Bcast</span><span>(data, 100, MPI_INT, 0, MPI_COMM_WORLD);<br /></span><span>Â Â Â Â Â </span><span>MPI_Finalize</span><span>();</span><span>Â <br /></span><span><br />Â Â Â Â Â Â Â return 0;<br /></span><span>}</span></pre>
+<p class=" ">There are two errors - use of uninitialized memory and invalid length of the buffer. Lets debug it with valgrind :</p>
+<pre class=" ">$ module add intel impi<br />$ mpiicc -g valgrind-example-mpi.c -o valgrind-example-mpi<br />$ module add Valgrind/3.11.0-intel-2015b<br />$ <span>mpirun -np 2 -env LD_PRELOAD $EBROOTVALGRIND/lib/valgrind/libmpiwrap-amd64-linux.so valgrind ./valgrind-example-mpi</span></pre>
+<p class=" ">Prints this output : (note that there is output printed for every launched MPI process)</p>
+<pre class=" ">==31318== Memcheck, a memory error detector<br />==31318== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.<br />==31318== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info<br />==31318== Command: ./valgrind-example-mpi<br />==31318== <br />==31319== Memcheck, a memory error detector<br />==31319== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.<br />==31319== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info<br />==31319== Command: ./valgrind-example-mpi<br />==31319== <br />valgrind MPI wrappers 31319: Active for pid 31319<br />valgrind MPI wrappers 31319: Try MPIWRAP_DEBUG=help for possible options<br />valgrind MPI wrappers 31318: Active for pid 31318<br />valgrind MPI wrappers 31318: Try MPIWRAP_DEBUG=help for possible options<br />==31319== Unaddressable byte(s) found during client check request<br />==31319== at 0x4E35974: check_mem_is_addressable_untyped (libmpiwrap.c:960)<br />==31319== by 0x4E5D0FE: PMPI_Bcast (libmpiwrap.c:908)<br />==31319== by 0x400911: main (valgrind-example-mpi.c:20)<br />==31319== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd<br />==31319== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)<br />==31319== by 0x4007BC: main (valgrind-example-mpi.c:8)<br />==31319== <br />==31318== Uninitialised byte(s) found during client check request<br />==31318== at 0x4E3591D: check_mem_is_defined_untyped (libmpiwrap.c:952)<br />==31318== by 0x4E5D06D: PMPI_Bcast (libmpiwrap.c:908)<br />==31318== by 0x400911: main (valgrind-example-mpi.c:20)<br />==31318== Address 0x6929040 is 0 bytes inside a block of size 396 alloc'd<br />==31318== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)<br />==31318== by 0x4007BC: main (valgrind-example-mpi.c:8)<br />==31318== <br />==31318== Unaddressable byte(s) found during client check request<br />==31318== at 0x4E3591D: check_mem_is_defined_untyped (libmpiwrap.c:952)<br />==31318== by 0x4E5D06D: PMPI_Bcast (libmpiwrap.c:908)<br />==31318== by 0x400911: main (valgrind-example-mpi.c:20)<br />==31318== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd<br />==31318== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)<br />==31318== by 0x4007BC: main (valgrind-example-mpi.c:8)<br />==31318== <br />==31318== <br />==31318== HEAP SUMMARY:<br />==31318== in use at exit: 3,172 bytes in 67 blocks<br />==31318== total heap usage: 191 allocs, 124 frees, 81,203 bytes allocated<br />==31318== <br />==31319== <br />==31319== HEAP SUMMARY:<br />==31319== in use at exit: 3,172 bytes in 67 blocks<br />==31319== total heap usage: 175 allocs, 108 frees, 48,435 bytes allocated<br />==31319== <br />==31318== LEAK SUMMARY:<br />==31318== definitely lost: 408 bytes in 3 blocks<br />==31318== indirectly lost: 256 bytes in 1 blocks<br />==31318== possibly lost: 0 bytes in 0 blocks<br />==31318== still reachable: 2,508 bytes in 63 blocks<br />==31318== suppressed: 0 bytes in 0 blocks<br />==31318== Rerun with --leak-check=full to see details of leaked memory<br />==31318== <br />==31318== For counts of detected and suppressed errors, rerun with: -v<br />==31318== Use --track-origins=yes to see where uninitialised values come from<br />==31318== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 4 from 4)<br />==31319== LEAK SUMMARY:<br />==31319== definitely lost: 408 bytes in 3 blocks<br />==31319== indirectly lost: 256 bytes in 1 blocks<br />==31319== possibly lost: 0 bytes in 0 blocks<br />==31319== still reachable: 2,508 bytes in 63 blocks<br />==31319== suppressed: 0 bytes in 0 blocks<br />==31319== Rerun with --leak-check=full to see details of leaked memory<br />==31319== <br />==31319== For counts of detected and suppressed errors, rerun with: -v<br />==31319== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 4 from 4)</pre>
+<p class=" ">We can see that Valgrind has reported use of unitialised memory on the master process (which reads the array to be broadcasted) and use of unaddresable memory on both processes.</p>
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diff --git a/docs.it4i.cz/salomon/software/debuggers/valgrind.md b/docs.it4i.cz/salomon/software/debuggers/valgrind.md
index 7ccab8998..8781ae49a 100644
--- a/docs.it4i.cz/salomon/software/debuggers/valgrind.md
+++ b/docs.it4i.cz/salomon/software/debuggers/valgrind.md
@@ -67,8 +67,8 @@ For example, lets look at this C code, which has two problems :
void f(void)
{
int* x = malloc(10 * sizeof(int));
- x[10] = 0; // problem 1heap block overrun
- } // problem 2memory leak -- x not freed
+ x[10] = 0; // problem 1: heap block overrun
+ } // problem 2: memory leak -- x not freed
int main(void)
{
@@ -94,31 +94,31 @@ description of command line options.
==12652== Memcheck, a memory error detector
==12652== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
==12652== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
- ==12652== Command./valgrind-example
+ ==12652== Command: ./valgrind-example
==12652==
==12652== Invalid write of size 4
- ==12652== at 0x40053Ef (valgrind-example.c:6)
- ==12652== by 0x40054Emain (valgrind-example.c:11)
+ ==12652== at 0x40053E: f (valgrind-example.c:6)
+ ==12652== by 0x40054E: main (valgrind-example.c:11)
==12652== Address 0x5861068 is 0 bytes after a block of size 40 alloc'd
- ==12652== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
- ==12652== by 0x400528f (valgrind-example.c:5)
- ==12652== by 0x40054Emain (valgrind-example.c:11)
+ ==12652== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)
+ ==12652== by 0x400528: f (valgrind-example.c:5)
+ ==12652== by 0x40054E: main (valgrind-example.c:11)
==12652==
==12652==
==12652== HEAP SUMMARY:
- ==12652== in use at exit40 bytes in 1 blocks
- ==12652== total heap usage1 allocs, 0 frees, 40 bytes allocated
+ ==12652== in use at exit: 40 bytes in 1 blocks
+ ==12652== total heap usage: 1 allocs, 0 frees, 40 bytes allocated
==12652==
==12652== LEAK SUMMARY:
- ==12652== definitely lost40 bytes in 1 blocks
- ==12652== indirectly lost0 bytes in 0 blocks
- ==12652== possibly lost0 bytes in 0 blocks
- ==12652== still reachable0 bytes in 0 blocks
- ==12652== suppressed0 bytes in 0 blocks
+ ==12652== definitely lost: 40 bytes in 1 blocks
+ ==12652== indirectly lost: 0 bytes in 0 blocks
+ ==12652== possibly lost: 0 bytes in 0 blocks
+ ==12652== still reachable: 0 bytes in 0 blocks
+ ==12652== suppressed: 0 bytes in 0 blocks
==12652== Rerun with --leak-check=full to see details of leaked memory
==12652==
- ==12652== For counts of detected and suppressed errors, rerun with-v
- ==12652== ERROR SUMMARY1 errors from 1 contexts (suppressed6 from 6)
+ ==12652== For counts of detected and suppressed errors, rerun with: -v
+ ==12652== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 6 from 6)
In the output we can see that Valgrind has detected both errors - the
off-by-one memory access at line 5 and a memory leak of 40 bytes. If we
@@ -129,35 +129,35 @@ with <span class="monospace">--leak-check=full</span> option :
==23856== Memcheck, a memory error detector
==23856== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al.
==23856== Using Valgrind-3.6.0 and LibVEX; rerun with -h for copyright info
- ==23856== Command./valgrind-example
+ ==23856== Command: ./valgrind-example
==23856==
==23856== Invalid write of size 4
- ==23856== at 0x40067Ef (valgrind-example.c:6)
- ==23856== by 0x40068Emain (valgrind-example.c:11)
+ ==23856== at 0x40067E: f (valgrind-example.c:6)
+ ==23856== by 0x40068E: main (valgrind-example.c:11)
==23856== Address 0x66e7068 is 0 bytes after a block of size 40 alloc'd
- ==23856== at 0x4C26FDEmalloc (vg_replace_malloc.c:236)
- ==23856== by 0x400668f (valgrind-example.c:5)
- ==23856== by 0x40068Emain (valgrind-example.c:11)
+ ==23856== at 0x4C26FDE: malloc (vg_replace_malloc.c:236)
+ ==23856== by 0x400668: f (valgrind-example.c:5)
+ ==23856== by 0x40068E: main (valgrind-example.c:11)
==23856==
==23856==
==23856== HEAP SUMMARY:
- ==23856== in use at exit40 bytes in 1 blocks
- ==23856== total heap usage1 allocs, 0 frees, 40 bytes allocated
+ ==23856== in use at exit: 40 bytes in 1 blocks
+ ==23856== total heap usage: 1 allocs, 0 frees, 40 bytes allocated
==23856==
==23856== 40 bytes in 1 blocks are definitely lost in loss record 1 of 1
- ==23856== at 0x4C26FDEmalloc (vg_replace_malloc.c:236)
- ==23856== by 0x400668f (valgrind-example.c:5)
- ==23856== by 0x40068Emain (valgrind-example.c:11)
+ ==23856== at 0x4C26FDE: malloc (vg_replace_malloc.c:236)
+ ==23856== by 0x400668: f (valgrind-example.c:5)
+ ==23856== by 0x40068E: main (valgrind-example.c:11)
==23856==
==23856== LEAK SUMMARY:
- ==23856== definitely lost40 bytes in 1 blocks
- ==23856== indirectly lost0 bytes in 0 blocks
- ==23856== possibly lost0 bytes in 0 blocks
- ==23856== still reachable0 bytes in 0 blocks
- ==23856== suppressed0 bytes in 0 blocks
+ ==23856== definitely lost: 40 bytes in 1 blocks
+ ==23856== indirectly lost: 0 bytes in 0 blocks
+ ==23856== possibly lost: 0 bytes in 0 blocks
+ ==23856== still reachable: 0 bytes in 0 blocks
+ ==23856== suppressed: 0 bytes in 0 blocks
==23856==
- ==23856== For counts of detected and suppressed errors, rerun with-v
- ==23856== ERROR SUMMARY2 errors from 2 contexts (suppressed6 from 6)
+ ==23856== For counts of detected and suppressed errors, rerun with: -v
+ ==23856== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 6 from 6)
Now we can see that the memory leak is due to the <span
class="monospace">malloc()</span> at line 6.
@@ -175,17 +175,17 @@ The default version without MPI support will however report a large
number of false errors in the MPI library, such as :
==30166== Conditional jump or move depends on uninitialised value(s)
- ==30166== at 0x4C287E8strlen (mc_replace_strmem.c:282)
- ==30166== by 0x55443BDI_MPI_Processor_model_number (init_interface.c:427)
- ==30166== by 0x55439E0I_MPI_Processor_arch_code (init_interface.c:171)
- ==30166== by 0x558D5AEMPID_nem_impi_init_shm_configuration (mpid_nem_impi_extensions.c:1091)
- ==30166== by 0x5598F4CMPID_nem_init_ckpt (mpid_nem_init.c:566)
- ==30166== by 0x5598B65MPID_nem_init (mpid_nem_init.c:489)
- ==30166== by 0x539BD75MPIDI_CH3_Init (ch3_init.c:64)
- ==30166== by 0x5578743MPID_Init (mpid_init.c:193)
- ==30166== by 0x554650AMPIR_Init_thread (initthread.c:539)
- ==30166== by 0x553369FPMPI_Init (init.c:195)
- ==30166== by 0x4008BDmain (valgrind-example-mpi.c:18)
+ ==30166== at 0x4C287E8: strlen (mc_replace_strmem.c:282)
+ ==30166== by 0x55443BD: I_MPI_Processor_model_number (init_interface.c:427)
+ ==30166== by 0x55439E0: I_MPI_Processor_arch_code (init_interface.c:171)
+ ==30166== by 0x558D5AE: MPID_nem_impi_init_shm_configuration (mpid_nem_impi_extensions.c:1091)
+ ==30166== by 0x5598F4C: MPID_nem_init_ckpt (mpid_nem_init.c:566)
+ ==30166== by 0x5598B65: MPID_nem_init (mpid_nem_init.c:489)
+ ==30166== by 0x539BD75: MPIDI_CH3_Init (ch3_init.c:64)
+ ==30166== by 0x5578743: MPID_Init (mpid_init.c:193)
+ ==30166== by 0x554650A: MPIR_Init_thread (initthread.c:539)
+ ==30166== by 0x553369F: PMPI_Init (init.c:195)
+ ==30166== by 0x4008BD: main (valgrind-example-mpi.c:18)
so it is better to use the MPI-enabled valgrind from module. The MPI
versions requires library :Â
@@ -220,79 +220,83 @@ the buffer. Lets debug it with valgrind :
$ module add Valgrind/3.11.0-intel-2015b
$ mpirun -np 2 -env LD_PRELOAD $EBROOTVALGRIND/lib/valgrind/libmpiwrap-amd64-linux.so valgrind ./valgrind-example-mpi
-Prints this output (note that there is output printed for every
+Prints this output : (note that there is output printed for every
launched MPI process)
==31318== Memcheck, a memory error detector
==31318== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
==31318== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
- ==31318== Command./valgrind-example-mpi
+ ==31318== Command: ./valgrind-example-mpi
==31318==
==31319== Memcheck, a memory error detector
==31319== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
==31319== Using Valgrind-3.9.0 and LibVEX; rerun with -h for copyright info
- ==31319== Command./valgrind-example-mpi
+ ==31319== Command: ./valgrind-example-mpi
==31319==
- valgrind MPI wrappers 31319Active for pid 31319
- valgrind MPI wrappers 31319Try MPIWRAP_DEBUG=help for possible options
- valgrind MPI wrappers 31318Active for pid 31318
- valgrind MPI wrappers 31318Try MPIWRAP_DEBUG=help for possible options
+ valgrind MPI wrappers 31319: Active for pid 31319
+ valgrind MPI wrappers 31319: Try MPIWRAP_DEBUG=help for possible options
+ valgrind MPI wrappers 31318: Active for pid 31318
+ valgrind MPI wrappers 31318: Try MPIWRAP_DEBUG=help for possible options
==31319== Unaddressable byte(s) found during client check request
- ==31319== at 0x4E35974check_mem_is_addressable_untyped (libmpiwrap.c:960)
- ==31319== by 0x4E5D0FEPMPI_Bcast (libmpiwrap.c:908)
- ==31319== by 0x400911main (valgrind-example-mpi.c:20)
+ ==31319== at 0x4E35974: check_mem_is_addressable_untyped (libmpiwrap.c:960)
+ ==31319== by 0x4E5D0FE: PMPI_Bcast (libmpiwrap.c:908)
+ ==31319== by 0x400911: main (valgrind-example-mpi.c:20)
==31319== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd
- ==31319== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
- ==31319== by 0x4007BCmain (valgrind-example-mpi.c:8)
+ ==31319== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)
+ ==31319== by 0x4007BC: main (valgrind-example-mpi.c:8)
==31319==
==31318== Uninitialised byte(s) found during client check request
- ==31318== at 0x4E3591Dcheck_mem_is_defined_untyped (libmpiwrap.c:952)
- ==31318== by 0x4E5D06DPMPI_Bcast (libmpiwrap.c:908)
- ==31318== by 0x400911main (valgrind-example-mpi.c:20)
+ ==31318== at 0x4E3591D: check_mem_is_defined_untyped (libmpiwrap.c:952)
+ ==31318== by 0x4E5D06D: PMPI_Bcast (libmpiwrap.c:908)
+ ==31318== by 0x400911: main (valgrind-example-mpi.c:20)
==31318== Address 0x6929040 is 0 bytes inside a block of size 396 alloc'd
- ==31318== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
- ==31318== by 0x4007BCmain (valgrind-example-mpi.c:8)
+ ==31318== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)
+ ==31318== by 0x4007BC: main (valgrind-example-mpi.c:8)
==31318==
==31318== Unaddressable byte(s) found during client check request
- ==31318== at 0x4E3591Dcheck_mem_is_defined_untyped (libmpiwrap.c:952)
- ==31318== by 0x4E5D06DPMPI_Bcast (libmpiwrap.c:908)
- ==31318== by 0x400911main (valgrind-example-mpi.c:20)
+ ==31318== at 0x4E3591D: check_mem_is_defined_untyped (libmpiwrap.c:952)
+ ==31318== by 0x4E5D06D: PMPI_Bcast (libmpiwrap.c:908)
+ ==31318== by 0x400911: main (valgrind-example-mpi.c:20)
==31318== Address 0x69291cc is 0 bytes after a block of size 396 alloc'd
- ==31318== at 0x4C27AAAmalloc (vg_replace_malloc.c:291)
- ==31318== by 0x4007BCmain (valgrind-example-mpi.c:8)
+ ==31318== at 0x4C27AAA: malloc (vg_replace_malloc.c:291)
+ ==31318== by 0x4007BC: main (valgrind-example-mpi.c:8)
==31318==
==31318==
==31318== HEAP SUMMARY:
- ==31318== in use at exit3,172 bytes in 67 blocks
- ==31318== total heap usage191 allocs, 124 frees, 81,203 bytes allocated
+ ==31318== in use at exit: 3,172 bytes in 67 blocks
+ ==31318== total heap usage: 191 allocs, 124 frees, 81,203 bytes allocated
==31318==
==31319==
==31319== HEAP SUMMARY:
- ==31319== in use at exit3,172 bytes in 67 blocks
- ==31319== total heap usage175 allocs, 108 frees, 48,435 bytes allocated
+ ==31319== in use at exit: 3,172 bytes in 67 blocks
+ ==31319== total heap usage: 175 allocs, 108 frees, 48,435 bytes allocated
==31319==
==31318== LEAK SUMMARY:
- ==31318== definitely lost408 bytes in 3 blocks
- ==31318== indirectly lost256 bytes in 1 blocks
- ==31318== possibly lost0 bytes in 0 blocks
- ==31318== still reachable2,508 bytes in 63 blocks
- ==31318== suppressed0 bytes in 0 blocks
+ ==31318== definitely lost: 408 bytes in 3 blocks
+ ==31318== indirectly lost: 256 bytes in 1 blocks
+ ==31318== possibly lost: 0 bytes in 0 blocks
+ ==31318== still reachable: 2,508 bytes in 63 blocks
+ ==31318== suppressed: 0 bytes in 0 blocks
==31318== Rerun with --leak-check=full to see details of leaked memory
==31318==
- ==31318== For counts of detected and suppressed errors, rerun with-v
+ ==31318== For counts of detected and suppressed errors, rerun with: -v
==31318== Use --track-origins=yes to see where uninitialised values come from
- ==31318== ERROR SUMMARY2 errors from 2 contexts (suppressed4 from 4)
+ ==31318== ERROR SUMMARY: 2 errors from 2 contexts (suppressed: 4 from 4)
==31319== LEAK SUMMARY:
- ==31319== definitely lost408 bytes in 3 blocks
- ==31319== indirectly lost256 bytes in 1 blocks
- ==31319== possibly lost0 bytes in 0 blocks
- ==31319== still reachable2,508 bytes in 63 blocks
- ==31319== suppressed0 bytes in 0 blocks
+ ==31319== definitely lost: 408 bytes in 3 blocks
+ ==31319== indirectly lost: 256 bytes in 1 blocks
+ ==31319== possibly lost: 0 bytes in 0 blocks
+ ==31319== still reachable: 2,508 bytes in 63 blocks
+ ==31319== suppressed: 0 bytes in 0 blocks
==31319== Rerun with --leak-check=full to see details of leaked memory
==31319==
- ==31319== For counts of detected and suppressed errors, rerun with-v
- ==31319== ERROR SUMMARY1 errors from 1 contexts (suppressed4 from 4)
+ ==31319== For counts of detected and suppressed errors, rerun with: -v
+ ==31319== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 4 from 4)
We can see that Valgrind has reported use of unitialised memory on the
master process (which reads the array to be broadcasted) and use of
unaddresable memory on both processes.
+
+
+
+
diff --git a/docs.it4i.cz/salomon/software/debuggers/vampir.html b/docs.it4i.cz/salomon/software/debuggers/vampir.html
new file mode 100644
index 000000000..09353c891
--- /dev/null
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+ <p>Vampir is a commercial trace analysis and visualisation tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as <a href="score-p.html" title="" target="_self" class="internal-link">Score-P</a>) first to collect the traces.</p>
+<h2 class=" "><img alt="Vampir screenshot" src="Snmekobrazovky20160708v12.33.35.png/@@images/42d90ce5-8468-4edb-94bb-4009853d9f65.png" title="Vampir screenshot" class="image-inline" /></h2>
+<h2 class=" ">Installed versions</h2>
+<p>Version 8.5.0 is currently installed as module <span class="monospace">Vampir/8.5.0</span> :</p>
+<pre>$ module load Vampir/8.5.0<br />$ vampir &</pre>
+<h2>User manual</h2>
+<p>You can find the detailed user manual in PDF format in <span class="monospace">$EBROOTVAMPIR/doc/vampir-manual.pdf</span></p>
+<h2>References</h2>
+<ol>
+<li><a class="external-link" href="https://www.vampir.eu" target="_self" title="">https://www.vampir.eu</a></li>
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+ Intel Parallel Studio
+ </h1>
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+
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+ <div id="parent-fieldname-text-20d9f0898b694621a77070007f3bf715" class="">
+ <p>The Salomon cluster provides following elements of the Intel Parallel Studio XE</p>
+<table class="listing">
+<tbody>
+<tr><th>Intel Parallel Studio XE</th></tr>
+<tr class="even">
+<td>Intel Compilers</td>
+</tr>
+<tr class="odd">
+<td>Intel Debugger</td>
+</tr>
+<tr class="even">
+<td>Intel MKL Library</td>
+</tr>
+<tr class="odd">
+<td>Intel Integrated Performance Primitives Library</td>
+</tr>
+<tr class="even">
+<td>Intel Threading Building Blocks Library</td>
+</tr>
+<tr class="even">
+<td>Intel Trace Analyzer and Collector</td>
+</tr>
+<tr class="even">
+<td>Intel Advisor</td>
+</tr>
+<tr class="even">
+<td>Intel Inspector</td>
+</tr>
+</tbody>
+</table>
+<h2 class=" ">Intel compilers</h2>
+<p>The Intel compilers version 131.3 are available, via module iccifort/2013.5.192-GCC-4.8.3. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.</p>
+<pre class=" ">$ module load intel<br />$ icc -v<br />$ ifort -v</pre>
+<p>Read more at the <a href="intel-suite/intel-compilers.html" title="" target="_self" class="internal-link">Intel Compilers</a> page.</p>
+<h2 class=" ">Intel debugger</h2>
+<p class="exclamation">IDB is no longer available since Parallel Studio 2015.</p>
+<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a href="../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">X display</a> for running the GUI.</p>
+<pre class=" ">$ module load intel<br />$ idb</pre>
+<p>Read more at the <a href="intel-suite/intel-debugger.html" title="" target="_self" class="internal-link">Intel Debugger</a> page.</p>
+<h2 class=" ">Intel Math Kernel Library</h2>
+<p>Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.</p>
+<pre class=" ">$ module load imkl</pre>
+<p>Read more at the <a href="intel-suite/intel-mkl.html" title="" target="_self" class="internal-link">Intel MKL</a> page.</p>
+<h2 class=" ">Intel Integrated Performance Primitives</h2>
+<p>Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.</p>
+<pre class=" ">$ module load ipp</pre>
+<p>Read more at the <a href="intel-suite/intel-integrated-performance-primitives.html" title="" target="_self" class="internal-link">Intel IPP</a> page.</p>
+<h2 class=" ">Intel Threading Building Blocks</h2>
+<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.</p>
+<pre class=" ">$ module load tbb</pre>
+<p>Read more at the <a href="intel-suite/intel-tbb.html" title="" target="_self" class="internal-link">Intel TBB</a> page.</p>
+
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diff --git a/docs.it4i.cz/salomon/software/intel-suite.md b/docs.it4i.cz/salomon/software/intel-suite.md
index 04b91fab8..a61af67ce 100644
--- a/docs.it4i.cz/salomon/software/intel-suite.md
+++ b/docs.it4i.cz/salomon/software/intel-suite.md
@@ -56,7 +56,7 @@ Intel Math Kernel Library
Intel Math Kernel Library (Intel MKL) is a library of math kernel
subroutines, extensively threaded and optimized for maximum performance.
-Intel MKL unites and provides these basic componentsBLAS, LAPACK,
+Intel MKL unites and provides these basic components: BLAS, LAPACK,
ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
many more.
diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.html b/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.html
new file mode 100644
index 000000000..41c08e702
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.html
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+ <p class=" ">is tool aiming to assist you in vectorization and threading of your code. You can use it to profile your application and identify loops, that could benefit from vectorization and/or threading parallelism.</p>
+<h2 class=" ">Installed versions</h2>
+<p>The following versions are currently available on Salomon as modules:</p>
+<table class="plain">
+<tbody>
+<tr>
+<td><strong>Version</strong></td>
+<td><strong>Module</strong></td>
+</tr>
+<tr>
+<td>2016 Update 2</td>
+<td>Advisor/2016_update2</td>
+</tr>
+</tbody>
+</table>
+<h2>Usage</h2>
+<p>Your program should be compiled with -g switch to include symbol names. You should compile with -O2 or higher to see code that is already vectorized by the compiler.</p>
+<p>Profiling is possible either directly from the GUI, or from command line.</p>
+<p>To profile from GUI, launch Advisor:</p>
+<pre>$ advixe-gui</pre>
+<p>Then select menu File -> New -> Project. Choose a directory to save project data to. After clicking OK, Project properties window will appear, where you can configure path to your binary, launch arguments, working directory etc. After clicking OK, the project is ready.</p>
+<p>In the left pane, you can switch between Vectorization and Threading workflows. Each has several possible steps which you can execute by clicking Collect button. Alternatively, you can click on Command Line, to see the command line required to run the analysis directly from command line.</p>
+<h2>References</h2>
+<ol>
+<li><a class="external-link" href="https://software.intel.com/en-us/advisorxe_2015_tut_lin_c" target="_self" title="">Intel® Advisor 2015 Tutorial: Find Where to Add Parallelism - C++ Sample</a></li>
+<li><a class="external-link" href="https://software.intel.com/en-us/intel-advisor-xe" target="_self" title="">Product page</a></li>
+<li><a class="external-link" href="https://software.intel.com/en-us/intel-advisor-2016-user-guide-linux" target="_self" title="">Documentation</a></li>
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diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md b/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
index 7e173873c..c0e3f55bd 100644
--- a/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
@@ -44,7 +44,7 @@ command line.
References
----------
-1. [Intel® Advisor 2015 TutorialFind Where to Add Parallelism - C++
+1. [Intel® Advisor 2015 Tutorial: Find Where to Add Parallelism - C++
Sample](https://software.intel.com/en-us/advisorxe_2015_tut_lin_c)
2. [Product
page](https://software.intel.com/en-us/intel-advisor-xe)
diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.html b/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.html
new file mode 100644
index 000000000..e54174b0e
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.html
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+ <p>The Intel compilers in multiple versions are available, via module intel. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.</p>
+<pre class=" ">$ module load intel<br />$ icc -v<br />$ ifort -v</pre>
+<p class=" ">The intel compilers provide for vectorization of the code, via the AVX2 instructions and support threading parallelization via OpenMP</p>
+<p class=" ">For maximum performance on the Salomon cluster compute nodes, compile your programs using the AVX2 instructions, with reporting where the vectorization was used. We recommend following compilation options for high performance</p>
+<pre class=" ">$ icc -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec myprog.c mysubroutines.c -o myprog.x<br />$ ifort -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec myprog.f mysubroutines.f -o myprog.x</pre>
+<p class=" ">In this example, we compile the program enabling interprocedural optimizations between source files (-ipo), aggresive loop optimizations (-O3) and vectorization (-xCORE-AVX2)</p>
+<p class=" ">The compiler recognizes the omp, simd, vector and ivdep pragmas for OpenMP parallelization and AVX2 vectorization. Enable the OpenMP parallelization by the <strong>-openmp</strong> compiler switch.</p>
+<pre class=" "><span>$ icc -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec </span>-openmp<span> myprog.c mysubroutines.c -o myprog.x</span><br /><span>$ ifort -ipo -O3 -xCORE-AVX2 -qopt-report1 -qopt-report-phase=vec </span>-openmp<span> myprog.f mysubroutines.f -o myprog.x</span></pre>
+<p>Read more at <a class="external-link" href="https://software.intel.com/en-us/intel-cplusplus-compiler-16.0-user-and-reference-guide" target="_self" title="">https://software.intel.com/en-us/intel-cplusplus-compiler-16.0-user-and-reference-guide</a></p>
+<h2 class=" ">Sandy Bridge/Ivy Bridge/Haswell binary compatibility</h2>
+<p>Anselm nodes are currently equipped with Sandy Bridge CPUs, while Salomon compute nodes are equipped with Haswell based architecture. The UV1 SMP compute server has Ivy Bridge CPUs, which are equivalent to Sandy Bridge (only smaller manufacturing technology). <span>The new processors are backward compatible with the Sandy Bridge nodes, so all programs that ran on the Sandy Bridge processors, should also run on the new Haswell nodes. </span><span>To get optimal performance out of the Haswell processors a program should make use of the special </span><span>AVX2 instructions for this processor. One can do this by recompiling codes with the compiler flags </span><span>designated to invoke these instructions. For the Intel compiler suite, there are two ways of doing </span><span>this:</span></p>
+<ul>
+<li><span>Using compiler flag (both for Fortran and C): <span class="monospace">-xCORE-AVX2</span>. This will create a binary </span><span class="s1">with AVX2 instructions, specifically for the Haswell processors. Note that the executable </span><span>will not run on Sandy Bridge/Ivy Bridge nodes.</span></li>
+<li><span>Using compiler flags (both for Fortran and C): <span class="monospace">-xAVX -axCORE-AVX2</span>. This will </span><span>generate multiple, feature specific auto-dispatch code paths for Intel® processors, if there is </span><span>a performance benefit. So this binary will run both on Sandy Bridge/Ivy Bridge and Haswell </span><span>processors. During runtime it will be decided which path to follow, dependent on which </span><span>processor you are running on. In general this will result in larger binaries.</span></li>
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diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md b/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md
index 5ffa75328..39bbbf195 100644
--- a/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md
@@ -55,13 +55,13 @@ flags </span><span>designated to invoke these instructions. For the
Intel compiler suite, there are two ways of
doing </span><span>this:</span>
-- <span>Using compiler flag (both for Fortran and C)<span
+- <span>Using compiler flag (both for Fortran and C): <span
class="monospace">-xCORE-AVX2</span>. This will create a
binary </span><span class="s1">with AVX2 instructions, specifically
for the Haswell processors. Note that the
executable </span><span>will not run on Sandy Bridge/Ivy
Bridge nodes.</span>
-- <span>Using compiler flags (both for Fortran and C)<span
+- <span>Using compiler flags (both for Fortran and C): <span
class="monospace">-xAVX -axCORE-AVX2</span>. This
will </span><span>generate multiple, feature specific auto-dispatch
code paths for Intel® processors, if there is </span><span>a
diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.html b/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.html
new file mode 100644
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+ <p class="exclamation">IDB is no longer available since Intel Parallel Studio 2015</p>
+<h2 class=" ">Debugging serial applications</h2>
+<p>The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">X display</a> for running the GUI.</p>
+<pre class=" ">$ module load intel/2014.06<br />$ module load Java<br />$ idb</pre>
+<p>The debugger may run in text mode. To debug in text mode, use</p>
+<pre class=" ">$ idbc</pre>
+<p>To debug on the compute nodes, module intel must be loaded. <br />The GUI on compute nodes may be accessed using the same way as in <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">the GUI section </a></p>
+<p>Example:</p>
+<pre class=" ">$ qsub -q qexp -l select=1:ncpus=24 -X -I<br />qsub: waiting for job 19654.srv11 to start<br />qsub: job 19654.srv11 ready<br /><br />$ module load intel<br />$ module load Java<br />$ icc -O0 -g myprog.c -o myprog.x<br />$ idb ./myprog.x</pre>
+<p>In this example, we allocate 1 full compute node, compile program myprog.c with debugging options -O0 -g and run the idb debugger interactively on the myprog.x executable. The GUI access is via X11 port forwarding provided by the PBS workload manager.</p>
+<h2 class=" ">Debugging parallel applications</h2>
+<p>Intel debugger is capable of debugging multithreaded and MPI parallel programs as well.</p>
+<h3 class=" ">Small number of MPI ranks</h3>
+<p>For debugging small number of MPI ranks, you may execute and debug each rank in separate xterm terminal (do not forget the <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">X display</a>). Using Intel MPI, this may be done in following way:</p>
+<pre class=" ">$ qsub -q qexp -l select=2:ncpus=24 -X -I<br />qsub: waiting for job 19654.srv11 to start<br />qsub: job 19655.srv11 ready<br /><br />$ module load intel impi<br />$ mpirun -ppn 1 -hostfile $PBS_NODEFILE --enable-x xterm -e idbc ./mympiprog.x</pre>
+<p>In this example, we allocate 2 full compute node, run xterm on each node and start idb debugger in command line mode, debugging two ranks of mympiprog.x application. The xterm will pop up for each rank, with idb prompt ready. The example is not limited to use of Intel MPI</p>
+<h3 class=" ">Large number of MPI ranks</h3>
+<p>Run the idb debugger from within the MPI debug option. This will cause the debugger to bind to all ranks and provide aggregated outputs across the ranks, pausing execution automatically just after startup. You may then set break points and step the execution manually. Using Intel MPI:</p>
+<pre class=" ">$ qsub -q qexp -l select=2:ncpus=24 -X -I<br />qsub: waiting for job 19654.srv11 to start<br />qsub: job 19655.srv11 ready<br /><br />$ module load intel impi<br />$ mpirun -n 48 -idb ./mympiprog.x</pre>
+<h3 class=" ">Debugging multithreaded application</h3>
+<p>Run the idb debugger in GUI mode. The menu Parallel contains number of tools for debugging multiple threads. One of the most useful tools is the <strong>Serialize Execution</strong> tool, which serializes execution of concurrent threads for easy orientation and identification of concurrency related bugs.</p>
+<h2 class=" ">Further information</h2>
+<p>Exhaustive manual on idb features and usage is published at Intel website, <a class="external-link" href="https://software.intel.com/sites/products/documentation/doclib/iss/2013/compiler/cpp-lin/" target="_self" title="">https://software.intel.com/sites/products/documentation/doclib/iss/2013/compiler/cpp-lin/</a></p>
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diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md b/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md
index 87c35df8a..273d0931a 100644
--- a/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md
@@ -33,8 +33,8 @@ section](../../../get-started-with-it4innovations/accessing-the-clusters/graphic
Example:
$ qsub -q qexp -l select=1:ncpus=24 -X -I
- qsubwaiting for job 19654.srv11 to start
- qsubjob 19654.srv11 ready
+ qsub: waiting for job 19654.srv11 to start
+ qsub: job 19654.srv11 ready
$ module load intel
$ module load Java
@@ -60,8 +60,8 @@ display](../../../get-started-with-it4innovations/accessing-the-clusters/graphic
Using Intel MPI, this may be done in following way:
$ qsub -q qexp -l select=2:ncpus=24 -X -I
- qsubwaiting for job 19654.srv11 to start
- qsubjob 19655.srv11 ready
+ qsub: waiting for job 19654.srv11 to start
+ qsub: job 19655.srv11 ready
$ module load intel impi
$ mpirun -ppn 1 -hostfile $PBS_NODEFILE --enable-x xterm -e idbc ./mympiprog.x
@@ -79,8 +79,8 @@ the ranks, pausing execution automatically just after startup. You may
then set break points and step the execution manually. Using Intel MPI:
$ qsub -q qexp -l select=2:ncpus=24 -X -I
- qsubwaiting for job 19654.srv11 to start
- qsubjob 19655.srv11 ready
+ qsub: waiting for job 19654.srv11 to start
+ qsub: job 19655.srv11 ready
$ module load intel impi
$ mpirun -n 48 -idb ./mympiprog.x
diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.html b/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.html
new file mode 100644
index 000000000..a0decb95a
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.html
@@ -0,0 +1,1049 @@
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+ <span id="breadcrumbs-current">Intel Inspector</span>
+
+ </span>
+
+</div>
+</div>
+
+
+ <div class="">
+
+
+
+
+
+ <dl class="portalMessage info" id="kssPortalMessage" style="display:none">
+ <dt>Info</dt>
+ <dd></dd>
+ </dl>
+
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+
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+ <div id="content">
+
+
+
+
+
+ <div id="viewlet-above-content-title"></div>
+
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+
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+ <h1 id="parent-fieldname-title" class="documentFirstHeading">
+ Intel Inspector
+ </h1>
+
+
+
+
+ <div id="viewlet-below-content-title">
+</div>
+
+
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+ <div id="content-core">
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+ <div id="parent-fieldname-text-6a80a8d0d1514d18b78df06d42288bcf" class="">
+ <p>Intel Inspector is a dynamic memory and threading error checking tool for C/C++/Fortran applications. It can detect issues such as memory leaks, invalid memory references, uninitalized variables, race conditions, deadlocks etc.</p>
+<h2 class=" ">Installed versions</h2>
+<p>The following versions are currently available on Salomon as modules:</p>
+<table class="plain">
+<tbody>
+<tr>
+<td><strong>Version</strong></td>
+<td><strong>Module</strong></td>
+</tr>
+<tr>
+<td>2016 Update 1</td>
+<td>Inspector/2016_update1</td>
+</tr>
+</tbody>
+</table>
+<h2>Usage</h2>
+<p>Your program should be compiled with -g switch to include symbol names. Optimizations can be turned on.</p>
+<p>Debugging is possible either directly from the GUI, or from command line.</p>
+<h3>GUI mode</h3>
+<p>To debug from GUI, launch Inspector:</p>
+<pre>$ inspxe-gui &</pre>
+<p>Then select menu File -> New -> Project. Choose a directory to save project data to. After clicking OK, Project properties window will appear, where you can configure path to your binary, launch arguments, working directory etc. After clicking OK, the project is ready.</p>
+<p>In the main pane, you can start a predefined analysis type or define your own. Click Start to start the analysis. Alternatively, you can click on Command Line, to see the command line required to run the analysis directly from command line.</p>
+<h3>Batch mode</h3>
+<p>Analysis can be also run from command line in batch mode. Batch mode analysis is run with command <span class="monospace">inspxe-cl</span>. To obtain the required parameters, either consult the documentation or you can configure the analysis in the GUI and then click "Command Line" button in the lower right corner to the respective command line.</p>
+<p>Results obtained from batch mode can be then viewed in the GUI by selecting File -> Open -> Result...</p>
+<h2>References</h2>
+<ol>
+<li><a class="external-link" href="https://software.intel.com/en-us/intel-inspector-xe" target="_self" title="">Product page</a></li>
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+ <h2 class=" ">Intel Integrated Performance Primitives</h2>
+<p>Intel Integrated Performance Primitives, version 9.0.1, compiled for AVX2 vector instructions is available, via module ipp. The IPP is a very rich library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax, as well as cryptographic functions, linear algebra functions and many more.</p>
+<p class="callout">Check out IPP before implementing own math functions for data processing, it is likely already there.</p>
+<pre class=" ">$ module load ipp</pre>
+<p>The module sets up environment variables, required for linking and running ipp enabled applications.</p>
+<h2 class=" ">IPP example</h2>
+<pre class=" ">#include "ipp.h"<br />#include <stdio.h><br />int main(int argc, char* argv[])<br />{<br /> const IppLibraryVersion *lib;<br /> Ipp64u fm;<br /> IppStatus status;<br /><br /> status= ippInit(); //IPP initialization with the best optimization layer<br /> if( status != ippStsNoErr ) {<br /> printf("IppInit() Error:\n");<br /> printf("%s\n", ippGetStatusString(status) );<br /> return -1;<br /> }<br /><br /> //Get version info<br /> lib = ippiGetLibVersion();<br /> printf("%s %s\n", lib->Name, lib->Version);<br /><br /> //Get CPU features enabled with selected library level<br /> fm=ippGetEnabledCpuFeatures();<br /> printf("SSE :%c\n",(fm>>1)&1?'Y':'N');<br /> printf("SSE2 :%c\n",(fm>>2)&1?'Y':'N');<br /> printf("SSE3 :%c\n",(fm>>3)&1?'Y':'N');<br /> printf("SSSE3 :%c\n",(fm>>4)&1?'Y':'N');<br /> printf("SSE41 :%c\n",(fm>>6)&1?'Y':'N');<br /> printf("SSE42 :%c\n",(fm>>7)&1?'Y':'N');<br /> printf("AVX :%c\n",(fm>>8)&1 ?'Y':'N');<br /> printf("AVX2 :%c\n", (fm>>15)&1 ?'Y':'N' );<br /> printf("----------\n");<br /> printf("OS Enabled AVX :%c\n", (fm>>9)&1 ?'Y':'N');<br /> printf("AES :%c\n", (fm>>10)&1?'Y':'N');<br /> printf("CLMUL :%c\n", (fm>>11)&1?'Y':'N');<br /> printf("RDRAND :%c\n", (fm>>13)&1?'Y':'N');<br /> printf("F16C :%c\n", (fm>>14)&1?'Y':'N');<br /><br /> return 0;<br />}</pre>
+<p>Â Compile above example, using any compiler and the ipp module.</p>
+<pre class=" ">$ module load intel<br />$ module load ipp<br /><br />$ icc testipp.c -o testipp.x -lippi -lipps -lippcore</pre>
+<p>You will need the ipp module loaded to run the ipp enabled executable. This may be avoided, by compiling library search paths into the executable</p>
+<pre class=" ">$ module load intel<br />$ module load ipp<br /><br />$ icc testipp.c -o testipp.x -Wl,-rpath=$LIBRARY_PATH -lippi -lipps -lippcore</pre>
+<h2 class=" ">Code samples and documentation</h2>
+<p>Intel provides number of <a class="external-link" href="https://software.intel.com/en-us/articles/code-samples-for-intel-integrated-performance-primitives-library" target="_self" title="">Code Samples for IPP</a>, illustrating use of IPP.</p>
+<p>Read full documentation on IPP <a class="external-link" href="http://software.intel.com/sites/products/search/search.php?q=&x=15&y=6&product=ipp&version=7.1&docos=lin" target="_self" title="">on Intel website,</a> in particular the <a class="external-link" href="http://software.intel.com/sites/products/documentation/doclib/ipp_sa/71/ipp_manual/index.htm" target="_self" title="">IPP Reference manual.</a></p>
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+ <div class="section" id="GUID-316F80A0-5B6B-4776-A343-D780A4F97798">
+<h2 class=" ">Intel Math Kernel Library</h2>
+<p>Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL provides these basic math kernels:</p>
+<a name="d4841e16"></a>
+<ul id="d4841e16">
+<li id="d4841e18"><a name="d4841e18"></a>BLAS (level 1, 2, and 3) and LAPACK linear algebra routines, offering vector, vector-matrix, and matrix-matrix operations.</li>
+<li id="d4841e21"><a name="d4841e21"></a>The PARDISO direct sparse solver, an iterative sparse solver, and supporting sparse BLAS (level 1, 2, and 3) routines for solving sparse systems of equations.</li>
+<li id="d4841e24"><a name="d4841e24"></a>ScaLAPACK distributed processing linear algebra routines for Linux* and Windows* operating systems, as well as the Basic Linear Algebra Communications Subprograms (BLACS) and the Parallel Basic Linear Algebra Subprograms (PBLAS).</li>
+<li id="d4841e27"><a name="d4841e27"></a>Fast Fourier transform (FFT) functions in one, two, or three dimensions with support for mixed radices (not limited to sizes that are powers of 2), as well as distributed versions of these functions.</li>
+<li id="d4841e30"><a name="d4841e30"></a>Vector Math Library (VML) routines for optimized mathematical operations on vectors.</li>
+<li id="d4841e34"><a name="d4841e34"></a>Vector Statistical Library (VSL) routines, which offer high-performance vectorized random number generators (RNG) for several probability distributions, convolution and correlation routines, and summary statistics functions.</li>
+<li id="d4841e37"><a name="d4841e37"></a>Data Fitting Library, which provides capabilities for spline-based approximation of functions, derivatives and integrals of functions, and search.</li>
+<li>Extended Eigensolver, a shared memory version of an eigensolver based on the Feast Eigenvalue Solver.</li>
+</ul>
+</div>
+<p id="GUID-9AE2AC5E-EE1B-4ADA-9686-88AC98114A99">For details see the <a class="external-link" href="http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mklman/index.htm" target="_self" title="">Intel MKL Reference Manual</a>.</p>
+<p>Intel MKL version 11.2.3.187 is available on the cluster</p>
+<pre class=" ">$ module load imkl</pre>
+<p>The module sets up environment variables, required for linking and running mkl enabled applications. The most important variables are the $MKLROOT, $CPATH, $LD_LIBRARY_PATH and $MKL_EXAMPLES</p>
+<p class="callout">Intel MKL library may be linked using any compiler. <br />With intel compiler use -mkl option to link default threaded MKL.</p>
+<h3 class=" ">Interfaces</h3>
+<p class=" ">Intel MKL library provides number of interfaces. The fundamental once are the LP64 and ILP64. The Intel MKL ILP64 libraries use the 64-bit integer type (necessary for indexing large arrays, with more than 2<sup id="GUID-009D71C5-A667-418A-B71B-0A4588D03BD2">31</sup>-1 elements), whereas the LP64 libraries index arrays with the 32-bit integer type.</p>
+<table class="listing">
+<tbody>
+<tr><th>Interface</th><th>Integer type</th></tr>
+<tr>
+<td>LP64</td>
+<td>32-bit, int, integer(kind=4), MPI_INT</td>
+</tr>
+<tr>
+<td>ILP64</td>
+<td>64-bit, long int, integer(kind=8), MPI_INT64</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" ">Linking</h3>
+<p>Linking Intel MKL libraries may be complex. Intel <a class="external-link" href="http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor" target="_self" title="">mkl link line advisor</a> helps. See also <a class="anchor-link" href="intel-mkl.html#examples" target="_self" title="">examples</a> below.</p>
+<p>You will need the mkl module loaded to run the mkl enabled executable. This may be avoided, by compiling library search paths into the executable. Include rpath on the compile line:</p>
+<pre class=" ">$ icc .... -Wl,-rpath=$LIBRARY_PATH ...</pre>
+<h3 class=" ">Threading</h3>
+<p class="callout">Advantage in using Intel MKL library is that it brings threaded parallelization to applications that are otherwise not parallel.</p>
+<p>For this to work, the application must link the threaded MKL library (default). Number and behaviour of MKL threads may be controlled via the OpenMP environment variables, such as OMP_NUM_THREADS and KMP_AFFINITY. MKL_NUM_THREADS takes precedence over OMP_NUM_THREADS</p>
+<pre class=" ">$ export OMP_NUM_THREADS=24<br />$ export KMP_AFFINITY=granularity=fine,compact,1,0</pre>
+<p>The application will run with 24 threads with affinity optimized for fine grain parallelization.</p>
+<h2 class=" "><a name="examples"></a>Examples</h2>
+<p>Number of examples, demonstrating use of the Intel MKL library and its linking is available on clusters, in the $MKL_EXAMPLES directory. In the examples below, we demonstrate linking Intel MKL to Intel and GNU compiled program for multi-threaded matrix multiplication.</p>
+<h3 class=" ">Working with examples</h3>
+<pre class=" ">$ module load intel<br />$ module load imkl<br />$ cp -a $MKL_EXAMPLES/cblas /tmp/<br />$ cd /tmp/cblas<br /><br />$ make sointel64 function=cblas_dgemm</pre>
+<p>In this example, we compile, link and run the cblas_dgemm example, demonstrating use of MKL example suite installed on clusters.</p>
+<h3 class=" ">Example: MKL and Intel compiler</h3>
+<pre class=" ">$ module load intel<br />$ module load imkl<br />$ cp -a $MKL_EXAMPLES/cblas /tmp/<br />$ cd /tmp/cblas<br />$ <br />$ icc -w source/cblas_dgemmx.c source/common_func.c -mkl -o cblas_dgemmx.x<br />$ ./cblas_dgemmx.x data/cblas_dgemmx.d<br /><br /></pre>
+<p>In this example, we compile, link and run the cblas_dgemm example, demonstrating use of MKL with icc -mkl option. Using the -mkl option is equivalent to:</p>
+<pre class=" ">$ icc -w source/cblas_dgemmx.c source/common_func.c -o cblas_dgemmx.x \<br />-I$MKL_INC_DIR -L$MKL_LIB_DIR -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5</pre>
+<p>In this example, we compile and link the cblas_dgemm example, using LP64 interface to threaded MKL and Intel OMP threads implementation.</p>
+<h3 class=" ">Example: Intel MKL and GNU compiler</h3>
+<pre class=" ">$ module load GCC<br />$ module load imkl<br />$ cp -a $MKL_EXAMPLES/cblas /tmp/<br />$ cd /tmp/cblas<br /> <br />$ gcc -w source/cblas_dgemmx.c source/common_func.c -o cblas_dgemmx.x \<br />-lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lm<br /><br />$ ./cblas_dgemmx.x data/cblas_dgemmx.d</pre>
+<p>In this example, we compile, link and run the cblas_dgemm example, using LP64 interface to threaded MKL and gnu OMP threads implementation.</p>
+<h2 class=" ">MKL and MIC accelerators</h2>
+<p>The Intel MKL is capable to automatically offload the computations o the MIC accelerator. See section <a href="../intel-xeon-phi.html" title="" target="_self" class="internal-link">Intel Xeon Phi</a> for details.</p>
+<h2 class=" ">LAPACKE C Interface</h2>
+<p>MKL includes LAPACKE C Interface to LAPACK. For some reason, although Intel is the author of LAPACKE, the LAPACKE header files are not present in MKL. For this reason, we have prepared <span class="monospace">LAPACKE</span> module, which includes Intel's LAPACKE headers from official LAPACK, which you can use to compile code using LAPACKE interface against MKL.</p>
+<h2 class=" ">Further reading</h2>
+<p>Read more on <a class="external-link" href="http://software.intel.com/en-us/intel-mkl" target="_self" title="">Intel website</a>, in particular the <a class="external-link" href="https://software.intel.com/en-us/intel-mkl/documentation/linux" target="_self" title="">MKL users guide</a>.</p>
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diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md b/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
index 545eda041..e196a69fc 100644
--- a/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
@@ -144,7 +144,7 @@ compiled program for multi-threaded matrix multiplication.
In this example, we compile, link and run the cblas_dgemm example,
demonstrating use of MKL example suite installed on clusters.
-### ExampleMKL and Intel compiler
+### Example: MKL and Intel compiler
$ module load intel
$ module load imkl
@@ -164,7 +164,7 @@ equivalent to:
In this example, we compile and link the cblas_dgemm example, using
LP64 interface to threaded MKL and Intel OMP threads implementation.
-### ExampleIntel MKL and GNU compiler
+### Example: Intel MKL and GNU compiler
$ module load GCC
$ module load imkl
diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.html b/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.html
new file mode 100644
index 000000000..01b22156e
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.html
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+ <div id="content-core">
+
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+
+ <div id="parent-fieldname-text-20d9f0898b694621a77070007f3bf715" class="">
+ <p>The Salomon cluster provides following elements of the Intel Parallel Studio XE</p>
+<table class="listing">
+<tbody>
+<tr><th>Intel Parallel Studio XE</th></tr>
+<tr class="even">
+<td>Intel Compilers</td>
+</tr>
+<tr class="odd">
+<td>Intel Debugger</td>
+</tr>
+<tr class="even">
+<td>Intel MKL Library</td>
+</tr>
+<tr class="odd">
+<td>Intel Integrated Performance Primitives Library</td>
+</tr>
+<tr class="even">
+<td>Intel Threading Building Blocks Library</td>
+</tr>
+<tr class="even">
+<td>Intel Trace Analyzer and Collector</td>
+</tr>
+<tr class="even">
+<td>Intel Advisor</td>
+</tr>
+<tr class="even">
+<td>Intel Inspector</td>
+</tr>
+</tbody>
+</table>
+<h2 class=" ">Intel compilers</h2>
+<p>The Intel compilers version 131.3 are available, via module iccifort/2013.5.192-GCC-4.8.3. The compilers include the icc C and C++ compiler and the ifort fortran 77/90/95 compiler.</p>
+<pre class=" ">$ module load intel<br />$ icc -v<br />$ ifort -v</pre>
+<p>Read more at the <a href="intel-compilers.html" title="" target="_self" class="internal-link">Intel Compilers</a> page.</p>
+<h2 class=" ">Intel debugger</h2>
+<p class="exclamation">IDB is no longer available since Parallel Studio 2015.</p>
+<p>Â The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">X display</a> for running the GUI.</p>
+<pre class=" ">$ module load intel<br />$ idb</pre>
+<p>Read more at the <a href="intel-debugger.html" title="" target="_self" class="internal-link">Intel Debugger</a> page.</p>
+<h2 class=" ">Intel Math Kernel Library</h2>
+<p>Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, extensively threaded and optimized for maximum performance. Intel MKL unites and provides these basic components: BLAS, LAPACK, ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and many more.</p>
+<pre class=" ">$ module load imkl</pre>
+<p>Read more at the <a href="intel-mkl.html" title="" target="_self" class="internal-link">Intel MKL</a> page.</p>
+<h2 class=" ">Intel Integrated Performance Primitives</h2>
+<p>Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is available, via module ipp. The IPP is a library of highly optimized algorithmic building blocks for media and data applications. This includes signal, image and frame processing algorithms, such as FFT, FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many more.</p>
+<pre class=" ">$ module load ipp</pre>
+<p>Read more at the <a href="intel-integrated-performance-primitives.html" title="" target="_self" class="internal-link">Intel IPP</a> page.</p>
+<h2 class=" ">Intel Threading Building Blocks</h2>
+<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. It is designed to promote scalable data parallel programming. Additionally, it fully supports nested parallelism, so you can build larger parallel components from smaller parallel components. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner.</p>
+<pre class=" ">$ module load tbb</pre>
+<p>Read more at the <a href="intel-tbb.html" title="" target="_self" class="internal-link">Intel TBB</a> page.</p>
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diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md b/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md
index e3d2898dc..91639197a 100644
--- a/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md
@@ -56,7 +56,7 @@ Intel Math Kernel Library
Intel Math Kernel Library (Intel MKL) is a library of math kernel
subroutines, extensively threaded and optimized for maximum performance.
-Intel MKL unites and provides these basic componentsBLAS, LAPACK,
+Intel MKL unites and provides these basic components: BLAS, LAPACK,
ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
many more.
diff --git a/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.html b/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.html
new file mode 100644
index 000000000..f08bbe7dd
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.html
@@ -0,0 +1,1035 @@
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+ <h2 class=" ">Intel Threading Building Blocks</h2>
+<p>Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner. The tasks are executed by a runtime scheduler and may be offloaded to <a href="../intel-xeon-phi.html" title="" target="_self" class="internal-link">MIC accelerator</a>.</p>
+<p>Intel TBB version 4.3.5.187 is available on the cluster.</p>
+<pre class=" ">$ module load tbb</pre>
+<p>The module sets up environment variables, required for linking and running tbb enabled applications.</p>
+<p class="callout">Link the tbb library, using -ltbb</p>
+<h2 class=" ">Examples</h2>
+<p>Number of examples, demonstrating use of TBB and its built-in scheduler is available on Anselm, in the $TBB_EXAMPLES directory.</p>
+<pre class=" ">$ module load intel<br />$ module load tbb<br />$ cp -a $TBB_EXAMPLES/common $TBB_EXAMPLES/parallel_reduce /tmp/<br />$ cd /tmp/parallel_reduce/primes<br />$ icc -O2 -DNDEBUG -o primes.x main.cpp primes.cpp -ltbb<br />$ ./primes.x</pre>
+<p>In this example, we compile, link and run the primes example, demonstrating use of parallel task-based reduce in computation of prime numbers.</p>
+<p>You will need the tbb module loaded to run the tbb enabled executable. This may be avoided, by compiling library search paths into the executable.</p>
+<pre class=" ">$ icc -O2 -o primes.x main.cpp primes.cpp -Wl,-rpath=$LIBRARY_PATH -ltbb</pre>
+<h2 class=" ">Further reading</h2>
+<p>Read more on Intel website, <a class="external-link" href="http://software.intel.com/sites/products/documentation/doclib/tbb_sa/help/index.htm" target="_self" title="">http://software.intel.com/sites/products/documentation/doclib/tbb_sa/help/index.htm</a></p>
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+ <p>Intel Trace Analyzer and Collector (ITAC) is a tool to collect and graphicaly analyze behaviour of MPI applications. It helps you to analyze communication patterns of your application, identify hotspots, perform correctnes checking (identify deadlocks, data corruption etc), simulate how your application would run on a different interconnect. </p>
+<p class=" ">ITAC is a offline analysis tool - first you run your application to collect a trace file, then you can open the trace in a GUI analyzer to view it.</p>
+<h2 class=" ">Installed version</h2>
+<p>Currently on Salomon is version 9.1.2.024 available as module <span class="monospace">itac/9.1.2.024</span></p>
+<h2 class=" ">Collecting traces</h2>
+<p>ITAC can collect traces from applications that are using Intel MPI. To generate a trace, simply add -trace option to your mpirun command :</p>
+<pre>$ module load itac/9.1.2.024<br />$ mpirun -trace myapp</pre>
+<p class=" ">The trace will be saved in file myapp.stf in the current directory.</p>
+<h2>Viewing traces</h2>
+<p>To view and analyze the trace, open ITAC GUI in a <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">graphical environment</a> :</p>
+<pre>$ module load itac/9.1.2.024<br />$ traceanalyzer</pre>
+<p class=" ">The GUI will launch and you can open the produced *.stf file.</p>
+<p class=" "><img alt="Intel Trace Analyzer" src="Snmekobrazovky20151204v15.35.12.png/@@images/fb3b3ac2-a88f-4e55-a25e-23f1da2200cb.png" title="Intel Trace Analyzer" class="image-inline" /></p>
+<p class=" ">Please refer to Intel documenation about usage of the GUI tool.</p>
+<h2>References</h2>
+<ol>
+<li><a class="external-link" href="https://software.intel.com/en-us/get-started-with-itac-for-linux" target="_self" title="">Getting Started with Intel® Trace Analyzer and Collector</a></li>
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+ Intel Xeon Phi
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+ A guide to Intel Xeon Phi usage
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+ <p>Intel Xeon Phi accelerator can be programmed in several modes. The default mode on the cluster is offload mode, but all modes described in this document are supported.</p>
+<h2 class=" ">Intel Utilities for Xeon Phi</h2>
+<p class=" ">To get access to a compute node with Intel Xeon Phi accelerator, use the PBS interactive session</p>
+<pre class=" ">$ <b><span>qsub -I -q qprod -l select=1:ncpus=24:<span class="pun"></span><span class="pln">accelerator</span><span class="pun">=</span><span class="typ">True</span><span class="pun">:</span><span class="pln">naccelerators</span><span class="pun">=</span><span class="lit">2</span><span class="pun">:</span><span class="pln">accelerator_model</span><span class="pun">=</span><span class="pln">phi7120</span> -A NONE-0-0</span><span><br /></span></b></pre>
+<p class=" ">To set up the environment module "intel" has to be loaded, without specifying the version, default version is loaded (at time of writing this, it's 2015b)</p>
+<pre class=" ">$ <b id="docs-internal-guid-682b5230-f75a-61fe-6896-fa351a3da434"><span>module load intel</span></b></pre>
+<p>Information about the hardware can be obtained by running the micinfo program on the host.</p>
+<pre><strong>$ /usr/bin/micinfo</strong></pre>
+<p>The output of the "micinfo" utility executed on one of the cluster node is as follows. (note: to get PCIe related details the command has to be run with root privileges)</p>
+<pre>MicInfo Utility Log
+Created Mon Aug 17 13:55:59 2015
+
+
+ System Info
+ HOST OS : Linux
+ OS Version : 2.6.32-504.16.2.el6.x86_64
+ Driver Version : 3.4.1-1
+ MPSS Version : 3.4.1
+ Host Physical Memory : 131930 MB
+
+Device No: 0, Device Name: mic0
+
+ Version
+ Flash Version : 2.1.02.0390
+ SMC Firmware Version : 1.16.5078
+ SMC Boot Loader Version : 1.8.4326
+ uOS Version : 2.6.38.8+mpss3.4.1
+ Device Serial Number : ADKC44601414
+
+ Board
+ Vendor ID : 0x8086
+ Device ID : 0x225c
+ Subsystem ID : 0x7d95
+ Coprocessor Stepping ID : 2
+ PCIe Width : x16
+ PCIe Speed : 5 GT/s
+ PCIe Max payload size : 256 bytes
+ PCIe Max read req size : 512 bytes
+ Coprocessor Model : 0x01
+ Coprocessor Model Ext : 0x00
+ Coprocessor Type : 0x00
+ Coprocessor Family : 0x0b
+ Coprocessor Family Ext : 0x00
+ Coprocessor Stepping : C0
+ Board SKU : C0PRQ-7120 P/A/X/D
+ ECC Mode : Enabled
+ SMC HW Revision : Product 300W Passive CS
+
+ Cores
+ Total No of Active Cores : 61
+ Voltage : 1007000 uV
+ Frequency : 1238095 kHz
+
+ Thermal
+ Fan Speed Control : N/A
+ Fan RPM : N/A
+ Fan PWM : N/A
+ Die Temp : 60 C
+
+ GDDR
+ GDDR Vendor : Samsung
+ GDDR Version : 0x6
+ GDDR Density : 4096 Mb
+ GDDR Size : 15872 MB
+ GDDR Technology : GDDR5
+ GDDR Speed : 5.500000 GT/s
+ GDDR Frequency : 2750000 kHz
+ GDDR Voltage : 1501000 uV
+
+Device No: 1, Device Name: mic1
+
+ Version
+ Flash Version : 2.1.02.0390
+ SMC Firmware Version : 1.16.5078
+ SMC Boot Loader Version : 1.8.4326
+ uOS Version : 2.6.38.8+mpss3.4.1
+ Device Serial Number : ADKC44500454
+
+ Board
+ Vendor ID : 0x8086
+ Device ID : 0x225c
+ Subsystem ID : 0x7d95
+ Coprocessor Stepping ID : 2
+ PCIe Width : x16
+ PCIe Speed : 5 GT/s
+ PCIe Max payload size : 256 bytes
+ PCIe Max read req size : 512 bytes
+ Coprocessor Model : 0x01
+ Coprocessor Model Ext : 0x00
+ Coprocessor Type : 0x00
+ Coprocessor Family : 0x0b
+ Coprocessor Family Ext : 0x00
+ Coprocessor Stepping : C0
+ Board SKU : C0PRQ-7120 P/A/X/D
+ ECC Mode : Enabled
+ SMC HW Revision : Product 300W Passive CS
+
+ Cores
+ Total No of Active Cores : 61
+ Voltage : 998000 uV
+ Frequency : 1238095 kHz
+
+ Thermal
+ Fan Speed Control : N/A
+ Fan RPM : N/A
+ Fan PWM : N/A
+ Die Temp : 59 C
+
+ GDDR
+ GDDR Vendor : Samsung
+ GDDR Version : 0x6
+ GDDR Density : 4096 Mb
+ GDDR Size : 15872 MB
+ GDDR Technology : GDDR5
+ GDDR Speed : 5.500000 GT/s
+ GDDR Frequency : 2750000 kHz
+ GDDR Voltage : 1501000 uV
+</pre>
+<h2 class=" ">Offload Mode</h2>
+<p>To compile a code for Intel Xeon Phi a MPSS stack has to be installed on the machine where compilation is executed. Currently the MPSS stack is only installed on compute nodes equipped with accelerators.</p>
+<pre class=" ">$ <b><b><span>qsub -I -q qprod -l select=1:ncpus=24:<span class="pun"></span><span class="pln">accelerator</span><span class="pun">=</span><span class="typ">True</span><span class="pun">:</span><span class="pln">naccelerators</span><span class="pun">=</span><span class="lit">2</span><span class="pun">:</span><span class="pln">accelerator_model</span><span class="pun">=</span><span class="pln">phi7120</span> -A </span><span>NONE-0-0</span></b><span></span></b><br />$ <b id="docs-internal-guid-682b5230-f75a-61fe-6896-fa351a3da434"><span>module load intel</span></b></pre>
+<p class=" ">For debugging purposes it is also recommended to set environment variable "OFFLOAD_REPORT". Value can be set from 0 to 3, where higher number means more debugging information.</p>
+<pre class=" "><strong>export OFFLOAD_REPORT=3</strong></pre>
+<p>A very basic example of code that employs offload programming technique is shown in the next listing. Please note that this code is sequential and utilizes only single core of the accelerator.</p>
+<pre class=" "><strong>$ vim source-offload.cpp</strong></pre>
+<pre class=" ">#include <iostream><br /><br />int main(int argc, char* argv[])<br />{<br />Â Â Â const int niter = 100000;<br />Â Â Â double result = 0;<br /><br />Â #pragma offload target(mic)<br />Â Â Â for (int i = 0; i < niter; ++i) {<br />Â Â Â Â Â Â Â const double t = (i + 0.5) / niter;<br />Â Â Â Â Â Â Â result += 4.0 / (t * t + 1.0);<br />Â Â Â }<br />Â Â Â result /= niter;<br />Â Â Â std::cout << "Pi ~ " << result << '\n';<br />}</pre>
+<p class=" ">To compile a code using Intel compiler run</p>
+<pre class=" ">$ <b id="docs-internal-guid-682b5230-f75c-afdc-a14d-16c9bb7c4b0b"><span>icc source-offload.cpp -o bin-offload</span></b></pre>
+<p class=" ">To execute the code, run the following command on the host</p>
+<pre class=" "><b><span>./bin-offload</span></b></pre>
+<h3 class=" ">Parallelization in Offload Mode Using OpenMP</h3>
+<p class=" ">One way of paralelization a code for Xeon Phi is using OpenMP directives. The following example shows code for parallel vector addition. </p>
+<pre class=" ">$ vim ./vect-add<strong> </strong></pre>
+<pre class=" ">#include <stdio.h><br /><br />typedef int T;<br /><br />#define SIZE 1000<br /><br />#pragma offload_attribute(push, target(mic))<br />T in1[SIZE];<br />T in2[SIZE];<br />T res[SIZE];<br />#pragma offload_attribute(pop)<br /><br />// MIC function to add two vectors<br />__attribute__((target(mic))) add_mic(T *a, T *b, T *c, int size) {<br />Â int i = 0;<br />Â #pragma omp parallel for<br />Â Â Â for (i = 0; i < size; i++)<br />Â Â Â Â Â c[i] = a[i] + b[i];<br />}<br /><br />// CPU function to add two vectors<br />void add_cpu (T *a, T *b, T *c, int size) {<br />Â int i;<br />Â for (i = 0; i < size; i++)<br />Â Â Â c[i] = a[i] + b[i];<br />}<br /><br />// CPU function to generate a vector of random numbers<br />void random_T (T *a, int size) {<br />Â int i;<br />Â for (i = 0; i < size; i++)<br />Â Â Â a[i] = rand() % 10000; // random number between 0 and 9999<br />}<br /><br />// CPU function to compare two vectors<br />int compare(T *a, T *b, T size ){<br />Â int pass = 0;<br />Â int i;<br />Â for (i = 0; i < size; i++){<br />Â Â Â if (a[i] != b[i]) {<br />Â Â Â Â Â printf("Value mismatch at location %d, values %d and %d\n",i, a[i], b[i]);<br />Â Â Â Â Â pass = 1;<br />Â Â Â }<br />Â }<br />Â if (pass == 0) printf ("Test passed\n"); else printf ("Test Failed\n");<br />Â return pass;<br />}<br /><br /><br />int main()<br />{<br />Â int i;<br />Â random_T(in1, SIZE);<br />Â random_T(in2, SIZE);<br /><br />Â #pragma offload target(mic) in(in1,in2)Â inout(res)<br />Â {<br /><br />Â Â Â // Parallel loop from main function<br />Â Â Â #pragma omp parallel for<br />Â Â Â for (i=0; i<SIZE; i++)<br />Â Â Â Â Â res[i] = in1[i] + in2[i];<br /><br />Â Â Â // or parallel loop is called inside the function<br />Â Â Â add_mic(in1, in2, res, SIZE);<br /><br />Â }<br /><br /><br />Â //Check the results with CPU implementation<br />Â T res_cpu[SIZE];<br />Â add_cpu(in1, in2, res_cpu, SIZE);<br />Â compare(res, res_cpu, SIZE);<br /><br />}</pre>
+<p>During the compilation Intel compiler shows which loops have been vectorized in both host and accelerator. This can be enabled with compiler option "-vec-report2". To compile and execute the code run</p>
+<pre class=" "><strong>$ icc vect-add.c -openmp_report2 -vec-report2 -o vect-add</strong><br /><br /><strong>$ ./vect-add </strong></pre>
+<p>Some interesting compiler flags useful not only for code debugging are:</p>
+<p class="callout">Debugging <br />Â openmp_report[0|1|2] - controls the compiler based vectorization diagnostic level <br />Â vec-report[0|1|2] - controls the OpenMP parallelizer diagnostic level<br /><br />Performance ooptimization<br />Â xhost - FOR HOST ONLY - to generate AVX (Advanced Vector Extensions) instructions.</p>
+<h2 class=" ">Automatic Offload using Intel MKL Library</h2>
+<p>Intel MKL includes an Automatic Offload (AO) feature that enables computationally intensive MKL functions called in user code to benefit from attached Intel Xeon Phi coprocessors automatically and transparently.</p>
+<p class="callout">Behavioural of automatic offload mode is controlled by functions called within the program or by environmental variables. Complete list of controls is listed <a class="external-link" href="http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm" target="_self" title=""><span class="external-link">here</span></a>.</p>
+<p>The Automatic Offload may be enabled by either an MKL function call within the code:</p>
+<pre class=" ">mkl_mic_enable();</pre>
+<p>or by setting environment variable</p>
+<pre class=" ">$ export MKL_MIC_ENABLE=1</pre>
+<p>To get more information about automatic offload please refer to "<a class="external-link" href="http://software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf" target="_self" title="">Using Intel® MKL Automatic Offload on Intel ® Xeon Phi™ Coprocessors</a>" white paper or <a class="external-link" href="https://software.intel.com/en-us/articles/intel-math-kernel-library-documentation" target="_self" title=""><span class="external-link">Intel MKL documentation</span></a>.</p>
+<h3 class=" ">Automatic offload example #1</h3>
+<p>Following example show how to automatically offload an SGEMM (single precision - g<span dir="auto">eneral matrix multiply</span>) function to MIC coprocessor.</p>
+<p>At first get an interactive PBS session on a node with MIC accelerator and load "intel" module that automatically loads "mkl" module as well.</p>
+<pre class=" ">$ <b><span>qsub -I -q qprod -l select=1:ncpus=24:<span class="pun"></span><span class="pln">accelerator</span><span class="pun">=</span><span class="typ">True</span><span class="pun">:</span><span class="pln">naccelerators</span><span class="pun">=</span><span class="lit">2</span><span class="pun">:</span><span class="pln">accelerator_model</span><span class="pun">=</span><span class="pln">phi7120</span> -A </span><span>NONE-0-0</span></b><br />$ module load intel</pre>
+<p> The code can be copied to a file and compiled without any necessary modification. </p>
+<pre class=" ">$ vim sgemm-ao-short.c</pre>
+<pre class="prettyprint lang-cpp">#include <stdio.h><br />#include <stdlib.h><br />#include <malloc.h><br />#include <stdint.h><br /><br />#include "mkl.h"<br /><br />int main(int argc, char **argv)<br />{<br />       float *A, *B, *C; /* Matrices */<br /><br />       MKL_INT N = 2560; /* Matrix dimensions */<br />       MKL_INT LD = N; /* Leading dimension */<br />       int matrix_bytes; /* Matrix size in bytes */<br />       int matrix_elements; /* Matrix size in elements */<br /><br />       float alpha = 1.0, beta = 1.0; /* Scaling factors */<br />       char transa = 'N', transb = 'N'; /* Transposition options */<br /><br />       int i, j; /* Counters */<br /><br />       matrix_elements = N * N;<br />       matrix_bytes = sizeof(float) * matrix_elements;<br /><br />       /* Allocate the matrices */<br />       A = malloc(matrix_bytes); B = malloc(matrix_bytes); C = malloc(matrix_bytes);<br /><br />       /* Initialize the matrices */<br />       for (i = 0; i < matrix_elements; i++) {<br />               A[i] = 1.0; B[i] = 2.0; C[i] = 0.0;<br />       }<br /><br />       printf("Computing SGEMM on the host\n");<br />       sgemm(&transa, &transb, &N, &N, &N, &alpha, A, &N, B, &N, &beta, C, &N);<br /><br />       printf("Enabling Automatic Offload\n");<br />       /* Alternatively, set environment variable MKL_MIC_ENABLE=1 */<br />       mkl_mic_enable();<br />       <br />       int ndevices = mkl_mic_get_device_count(); /* Number of MIC devices */<br />       printf("Automatic Offload enabled: %d MIC devices present\n",  ndevices);<br /><br />       printf("Computing SGEMM with automatic workdivision\n");<br />       sgemm(&transa, &transb, &N, &N, &N, &alpha, A, &N, B, &N, &beta, C, &N);<br /><br />       /* Free the matrix memory */<br />       free(A); free(B); free(C);<br /><br />       printf("Done\n");<br /><br />   return 0;<br />}</pre>
+<p class="callout">Please note: This example is simplified version of an example from MKL. The expanded version can be found here: <strong>$MKL_EXAMPLES/mic_ao/blasc/source/sgemm.c</strong></p>
+<p>To compile a code using Intel compiler use:</p>
+<pre class=" ">$ icc -mkl sgemm-ao-short.c -o sgemm</pre>
+<p>For debugging purposes enable the offload report to see more information about automatic offloading.</p>
+<pre class=" ">$ export OFFLOAD_REPORT=2</pre>
+<p>The output of a code should look similar to following listing, where lines starting with [MKL] are generated by offload reporting:</p>
+<pre class=" ">[user@r31u03n799 ~]$ ./sgemm <br />Computing SGEMM on the host<br />Enabling Automatic Offload<br />Automatic Offload enabled: 2 MIC devices present<br />Computing SGEMM with automatic workdivision<br />[MKL] [MIC --] [AO Function]Â Â Â SGEMM<br />[MKL] [MIC --] [AO SGEMM Workdivision]Â Â Â 0.44 0.28 0.28<br />[MKL] [MIC 00] [AO SGEMM CPU Time]Â Â Â 0.252427 seconds<br />[MKL] [MIC 00] [AO SGEMM MIC Time]Â Â Â 0.091001 seconds<br />[MKL] [MIC 00] [AO SGEMM CPU->MIC Data]Â Â Â 34078720 bytes<br />[MKL] [MIC 00] [AO SGEMM MIC->CPU Data]Â Â Â 7864320 bytes<br />[MKL] [MIC 01] [AO SGEMM CPU Time]Â Â Â 0.252427 seconds<br />[MKL] [MIC 01] [AO SGEMM MIC Time]Â Â Â 0.094758 seconds<br />[MKL] [MIC 01] [AO SGEMM CPU->MIC Data]Â Â Â 34078720 bytes<br />[MKL] [MIC 01] [AO SGEMM MIC->CPU Data]Â Â Â 7864320 bytes<br />Done</pre>
+<p class="callout">Behavioral of automatic offload mode is controlled by functions called within the program or by environmental variables. Complete list of controls is listed <a class="external-link" href="http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mkl_userguide_lnx/GUID-3DC4FC7D-A1E4-423D-9C0C-06AB265FFA86.htm" target="_self" title=""><span class="external-link">here</span></a>.</p>
+<p>To get more information about automatic offload please refer to "<a class="external-link" href="http://software.intel.com/sites/default/files/11MIC42_How_to_Use_MKL_Automatic_Offload_0.pdf" target="_self" title="">Using Intel® MKL Automatic Offload on Intel ® Xeon Phi™ Coprocessors</a>" white paper or <a class="external-link" href="https://software.intel.com/en-us/articles/intel-math-kernel-library-documentation" target="_self" title=""><span class="external-link">Intel MKL documentation</span></a>.</p>
+<h3 class=" ">Automatic offload example #2</h3>
+<p>In this example, we will demonstrate automatic offload control via an environment vatiable MKL_MIC_ENABLE. The function DGEMM will be offloaded.</p>
+<p>At first get an interactive PBS session on a node with MIC accelerator.</p>
+<pre class=" ">$ <b><span>qsub -I -q qprod -l select=1:ncpus=24:<span class="pun"></span><span class="pln">accelerator</span><span class="pun">=</span><span class="typ">True</span><span class="pun">:</span><span class="pln">naccelerators</span><span class="pun">=</span><span class="lit">2</span><span class="pun">:</span><span class="pln">accelerator_model</span><span class="pun">=</span><span class="pln">phi7120</span> -A </span><span>NONE-0-0<br /></span></b></pre>
+<p class=" ">Once in, we enable the offload and run the Octave software. In octave, we generate two large random matrices and let them multiply together.</p>
+<pre class=" ">$ export MKL_MIC_ENABLE=1<br />$ export OFFLOAD_REPORT=2<br />$ module load Octave/3.8.2-intel-2015b<br /><br />$ octave -q<br />octave:1> A=rand(10000);<br />octave:2> B=rand(10000);<br />octave:3> C=A*B;<br />[MKL] [MIC --] [AO Function]Â Â Â DGEMM<br />[MKL] [MIC --] [AO DGEMM Workdivision]Â Â Â 0.14 0.43 0.43<br />[MKL] [MIC 00] [AO DGEMM CPU Time]Â Â Â 3.814714 seconds<br />[MKL] [MIC 00] [AO DGEMM MIC Time]Â Â Â 2.781595 seconds<br />[MKL] [MIC 00] [AO DGEMM CPU->MIC Data]Â Â Â 1145600000 bytes<br />[MKL] [MIC 00] [AO DGEMM MIC->CPU Data]Â Â Â 1382400000 bytes<br />[MKL] [MIC 01] [AO DGEMM CPU Time]Â Â Â 3.814714 seconds<br />[MKL] [MIC 01] [AO DGEMM MIC Time]Â Â Â 2.843016 seconds<br />[MKL] [MIC 01] [AO DGEMM CPU->MIC Data]Â Â Â 1145600000 bytes<br />[MKL] [MIC 01] [AO DGEMM MIC->CPU Data]Â Â Â 1382400000 bytes<br />octave:4> exit</pre>
+<p class=" ">On the example above we observe, that the DGEMM function workload was split over CPU, MIC 0 and MIC 1, in the ratio 0.14 0.43 0.43. The matrix multiplication was done on the CPU, accelerated by two Xeon Phi accelerators.</p>
+<h2 class=" ">Native Mode</h2>
+<p>In the native mode a program is executed directly on Intel Xeon Phi without involvement of the host machine. Similarly to offload mode, the code is compiled on the host computer with Intel compilers.</p>
+<p>To compile a code user has to be connected to a compute with MIC and load Intel compilers module. To get an interactive session on a compute node with an Intel Xeon Phi and load the module use following commands:Â </p>
+<pre class=" ">$ <b><span>qsub -I -q qprod -l select=1:ncpus=24:<span class="pun"></span><span class="pln">accelerator</span><span class="pun">=</span><span class="typ">True</span><span class="pun">:</span><span class="pln">naccelerators</span><span class="pun">=</span><span class="lit">2</span><span class="pun">:</span><span class="pln">accelerator_model</span><span class="pun">=</span><span class="pln">phi7120</span> -A NONE-0-0</span><span><br /><br />$ module load intel<br /></span></b></pre>
+<p class="callout">Please note that particular version of the Intel module is specified. This information is used later to specify the correct library paths.</p>
+<p>To produce a binary compatible with Intel Xeon Phi architecture user has to specify "-mmic" compiler flag. Two compilation examples are shown below. The first example shows how to compile OpenMP parallel code "vect-add.c" for host only:</p>
+<pre class=" "><strong>$ icc -xhost -no-offload -fopenmp vect-add.c -o vect-add-host</strong></pre>
+<p>To run this code on host, use:</p>
+<pre class=" "><strong>$ ./vect-add-host</strong></pre>
+<p>The second example shows how to compile the same code for Intel Xeon Phi:</p>
+<pre class=" "><strong>$ icc -mmic -fopenmp vect-add.c -o vect-add-mic</strong></pre>
+<h3 class=" ">Execution of the Program in Native Mode on Intel Xeon Phi</h3>
+<p>The user access to the Intel Xeon Phi is through the SSH. Since user home directories are mounted using NFS on the accelerator, users do not have to copy binary files or libraries between the host and accelerator. Â </p>
+<p>Get the PATH of MIC enabled libraries for currently used Intel Compiler (here was icc/2015.3.187-GNU-5.1.0-2.25 used) :</p>
+<pre class=" "><strong>$ echo $MIC_LD_LIBRARY_PATH</strong><br />/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic</pre>
+<p class=" ">To connect to the accelerator run:</p>
+<pre class=" "><strong>$ ssh mic0</strong></pre>
+<p>If the code is sequential, it can be executed directly:</p>
+<pre class=" "><strong>mic0 $ ~/path_to_binary/vect-add-seq-mic</strong></pre>
+<p>If the code is parallelized using OpenMP a set of additional libraries is required for execution. To locate these libraries new path has to be added to the LD_LIBRARY_PATH environment variable prior to the execution:</p>
+<pre class=" "><strong>mic0 $ export LD_LIBRARY_PATH=/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic:$LD_LIBRARY_PATH</strong></pre>
+<p class="callout">Please note that the path exported in the previous example contains path to a specific compiler (here the version is 2015.3.187-GNU-5.1.0-2.25). This version number has to match with the version number of the Intel compiler module that was used to compile the code on the host computer.</p>
+<p class=" ">For your information the list of libraries and their location required for execution of an OpenMP parallel code on Intel Xeon Phi is:<span class="discreet visualHighlight"></span></p>
+<p class="callout"><span>/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic<br /><br />libiomp5.so <br />libimf.so <br />libsvml.so <br />libirng.so <br />libintlc.so.5 <br /></span></p>
+<p class=" "><span>Finally, to run the compiled code use: </span></p>
+<pre class=" "><strong>$ ~/path_to_binary/vect-add-mic</strong></pre>
+<h2 class=" "><span>OpenCL</span></h2>
+<p><span>OpenCL (Open Computing Language) is an open standard for general-purpose parallel programming for diverse mix of multi-core CPUs, GPU coprocessors, and other parallel processors. OpenCL provides a flexible execution model and uniform programming environment for software developers to write portable code for systems running on both the CPU and graphics processors or accelerators like the Intel® Xeon Phi.</span></p>
+<p><span>On Anselm OpenCL is installed only on compute nodes with MIC accelerator, therefore OpenCL code can be compiled only on these nodes. </span></p>
+<pre class=" "><span>module load opencl-sdk opencl-rt<br /></span></pre>
+<p><span>Always load "opencl-sdk" (providing devel files like headers) and "opencl-rt" (providing dynamic library libOpenCL.so) modules to compile and link OpenCL code. Load "opencl-rt" for running your compiled code.<br /></span></p>
+<p><span>There are two basic examples of OpenCL code in the following directory: </span></p>
+<pre class=" "><span><strong>/apps/intel/opencl-examples/</strong><br /></span></pre>
+<p><span>First example "CapsBasic" detects OpenCL compatible hardware, here CPU and MIC, and prints basic information about the capabilities of it. <br /></span></p>
+<pre class=" "><strong>/apps/intel/opencl-examples/CapsBasic/capsbasic</strong></pre>
+<p><span>To compile and run the example copy it to your home directory, get a PBS interactive session on of the nodes with MIC and run make for compilation. Make files are very basic and shows how the OpenCL code can be compiled on Anselm. </span></p>
+<pre class=" "><strong>$ cp /apps/intel/opencl-examples/CapsBasic/* .</strong><br /><strong>$ qsub -I -q qprod <b><span>-l select=1:ncpus=24:<span class="pun"></span><span class="pln">accelerator</span><span class="pun">=</span><span class="typ">True</span><span class="pun">:</span><span class="pln">naccelerators</span><span class="pun">=</span><span class="lit">2</span><span class="pun">:</span><span class="pln">accelerator_model</span><span class="pun">=</span><span class="pln">phi7120</span></span></b> -A NONE-0-0</strong><br /><strong>$ make</strong></pre>
+<p><span>The compilation command for this example is: </span></p>
+<pre class=" "><strong>$ g++ capsbasic.cpp -lOpenCL -o capsbasic -I/apps/intel/opencl/include/</strong></pre>
+<p><span>After executing the complied binary file, following output should be displayed. <br /></span></p>
+<pre class=" "><span><strong>./capsbasic</strong><br /><br /><strong>Number of available platforms: 1</strong><br /><strong>Platform names:</strong><br /><strong>Â Â Â [0] Intel(R) OpenCL [Selected]</strong><br /><strong>Number of devices available for each type:</strong><br /><strong>Â Â Â CL_DEVICE_TYPE_CPU: 1</strong><br /><strong>Â Â Â CL_DEVICE_TYPE_GPU: 0</strong><br /><strong>Â Â Â CL_DEVICE_TYPE_ACCELERATOR: 1</strong><br /><br /><strong>*** Detailed information for each device ***</strong><br /><br /><strong>CL_DEVICE_TYPE_CPU[0]</strong><br /><strong>Â Â Â CL_DEVICE_NAME:Â Â Â Â Â Â Â Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz</strong><br /><strong>Â Â Â CL_DEVICE_AVAILABLE: 1</strong><br /><br /><strong>...</strong><br /><br /><strong>CL_DEVICE_TYPE_ACCELERATOR[0]</strong><br /><strong>Â Â Â CL_DEVICE_NAME: Intel(R) Many Integrated Core Acceleration Card</strong><br /><strong>Â Â Â CL_DEVICE_AVAILABLE: 1</strong><br /><br /><strong>...</strong><br /></span></pre>
+<p class="callout"><span>More information about this example can be found on Intel website: <a href="http://software.intel.com/en-us/vcsource/samples/caps-basic/">http://software.intel.com/en-us/vcsource/samples/caps-basic/</a><br /></span></p>
+<p class=" "><span>The second example that can be found in "/apps/intel/opencl-examples" </span><span>directory is General Matrix Multiply. You can follow the the same procedure to download the example to your directory and compile it. <br /></span></p>
+<pre class=" "><strong>$ cp -r /apps/intel/opencl-examples/* .</strong><br /><strong>$ qsub -I -q qprod <b><span>-l select=1:ncpus=24:<span class="pun"></span><span class="pln">accelerator</span><span class="pun">=</span><span class="typ">True</span><span class="pun">:</span><span class="pln">naccelerators</span><span class="pun">=</span><span class="lit">2</span><span class="pun">:</span><span class="pln">accelerator_model</span><span class="pun">=</span><span class="pln">phi7120</span></span></b> -A NONE-0-0</strong><br /><strong>$ cd GEMM <br />$ make</strong></pre>
+<p class=" "><span>The compilation command for this example is: </span></p>
+<pre class=" "><span><strong>$ g++ cmdoptions.cpp gemm.cpp ../common/basic.cpp ../common/cmdparser.cpp ../common/oclobject.cpp -I../common -lOpenCL -o gemm -I/apps/intel/opencl/include/</strong><br /></span></pre>
+<p class=" "><span>To see the performance of Intel Xeon Phi performing the DGEMM run the example as follows: </span></p>
+<pre class=" "><span><strong>./gemm -d 1</strong><br /><strong>Platforms (1):</strong><br /><strong> [0] Intel(R) OpenCL [Selected]</strong><br /><strong>Devices (2):</strong><br /><strong> [0] Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz</strong><br /><strong> [1] Intel(R) Many Integrated Core Acceleration Card [Selected]</strong><br /><strong>Build program options: "-DT=float -DTILE_SIZE_M=1 -DTILE_GROUP_M=16 -DTILE_SIZE_N=128 -DTILE_GROUP_N=1 -DTILE_SIZE_K=8"</strong><br /><strong>Running gemm_nn kernel with matrix size: 3968x3968</strong><br /><strong>Memory row stride to ensure necessary alignment: 15872 bytes</strong><br /><strong>Size of memory region for one matrix: 62980096 bytes</strong><br /><strong>Using alpha = 0.57599 and beta = 0.872412</strong><br /><strong>...<br />Host time: 0.292953 sec.</strong><br /><strong>Host perf: 426.635 GFLOPS</strong><br /><strong>Host time: 0.293334 sec.</strong><br /><strong>Host perf: 426.081 GFLOPS</strong><br /><strong>...</strong><br /></span></pre>
+<p class="callout"><span>Please note: GNU compiler is used to compile the OpenCL codes for Intel MIC. You do not need to load Intel compiler module. <br /></span></p>
+<h2 class=" "><span>MPI</span></h2>
+<h3 class=" ">Environment setup and compilation</h3>
+<p>To achieve best MPI performance always use following setup for Intel MPI on Xeon Phi accelerated nodes:</p>
+<pre class=" "><strong>$ export I_MPI_FABRICS=shm:dapl</strong><br /><strong>$ export I_MPI_DAPL_PROVIDER_LIST=ofa-v2-mlx4_0-1u,ofa-v2-scif0,ofa-v2-mcm-1</strong></pre>
+<p>This ensures, that MPI inside node will use SHMEM communication, between HOST and Phi the IB SCIF will be used and between different nodes or Phi's on diferent nodes a CCL-Direct proxy will be used.</p>
+<p class="callout">Please note: Other FABRICS like tcp,ofa may be used (even combined with shm) but there's severe loss of performance (by order of magnitude). <br />Usage of single DAPL PROVIDER (e. g. I_MPI_DAPL_PROVIDER=ofa-v2-mlx4_0-1u) will cause failure of Host<->Phi and/or Phi<->Phi communication.<br />Usage of the I_MPI_DAPL_PROVIDER_LIST on non-accelerated node will cause failure of any MPI communication, since those nodes don't have SCIF device and there's no CCL-Direct proxy runnig.</p>
+<p class=" ">Again an MPI code for Intel Xeon Phi has to be compiled on a compute node with accelerator and MPSS software stack installed. To get to a compute node with accelerator use:</p>
+<pre class=" ">$ <b><span>qsub -I -q qprod <b><span>-l select=1:ncpus=24:<span class="pun"></span><span class="pln">accelerator</span><span class="pun">=</span><span class="typ">True</span><span class="pun">:</span><span class="pln">naccelerators</span><span class="pun">=</span><span class="lit">2</span><span class="pun">:</span><span class="pln">accelerator_model</span><span class="pun">=</span><span class="pln">phi7120</span></span></b> -A NONE-0-0</span><span></span></b></pre>
+<p class=" ">The only supported implementation of MPI standard for Intel Xeon Phi is Intel MPI. To setup a fully functional development environment a combination of Intel compiler and Intel MPI has to be used. On a host load following modules before compilation:</p>
+<pre class=" "><strong>$ module load intel impi</strong></pre>
+<p class=" ">To compile an MPI code for host use:</p>
+<pre class=" "><strong>$ mpiicc -xhost -o mpi-test mpi-test.c</strong></pre>
+<p class=" ">To compile the same code for Intel Xeon Phi architecture use:</p>
+<pre class=" "><strong>$ mpiicc -mmic -o mpi-test-mic mpi-test.c</strong></pre>
+<p class=" ">Or, if you are using Fortran :</p>
+<pre class=" "><strong>$ mpiifort -mmic -o mpi-test-mic mpi-test.f90</strong></pre>
+<p>An example of basic MPI version of "hello-world" example in C language, that can be executed on both host and Xeon Phi is (can be directly copy and pasted to a .c file)</p>
+<pre class="prettyprint lang-cpp">#include <stdio.h><br />#include <mpi.h><br /><br /><br />int main (argc, argv)<br />Â Â Â Â int argc;<br />Â Â Â Â char *argv[];<br />{<br />Â int rank, size;<br /><br />Â int len;<br />Â char node[MPI_MAX_PROCESSOR_NAME];<br /><br />Â MPI_Init (&argc, &argv);Â Â Â Â Â /* starts MPI */<br />Â MPI_Comm_rank (MPI_COMM_WORLD, &rank);Â Â Â Â Â Â Â /* get current process id */<br />Â MPI_Comm_size (MPI_COMM_WORLD, &size);Â Â Â Â Â Â Â /* get number of processes */<br /><br />Â MPI_Get_processor_name(node,&len);<br /><br />Â printf( "Hello world from process %d of %d on host %s \n", rank, size, node );<br />Â MPI_Finalize();<br />Â return 0; <br />}</pre>
+<h3 class=" ">MPI programming models</h3>
+<p><span>Intel MPI for the Xeon Phi coprocessors offers different MPI programming models:</span></p>
+<p class="callout"><strong>Host-only model</strong> - all MPI ranks reside on the host. The coprocessors can be used by using offload pragmas. (Using MPI calls inside offloaded code is not supported.)<strong><br /><br />Coprocessor-only model</strong> - all MPI ranks reside only on the coprocessors.<br /><br /><strong>Symmetric model</strong> - the MPI ranks reside on both the host and the coprocessor. Most general MPI case.</p>
+<h3 class=" "><span>Host-only model</span></h3>
+<p class=" "><span></span>In this case all environment variables are set by modules, so to execute the compiled MPI program on a single node, use:</p>
+<pre class=" "><strong>$ mpirun -np 4 ./mpi-test</strong></pre>
+<p>The output should be similar to:</p>
+<pre class=" ">Hello world from process 1 of 4 on host r38u31n1000<br />Hello world from process 3 of 4 on host r38u31n1000<br />Hello world from process 2 of 4 on host r38u31n1000<br />Hello world from process 0 of 4 on host r38u31n1000</pre>
+<h3 class=" ">Coprocessor-only model</h3>
+<p class=" "><span>There are two ways how to execute an MPI code on a single coprocessor: 1.) lunch the program using "<strong>mpirun</strong>" from the coprocessor; or 2.) lunch the task using "<strong>mpiexec.hydra</strong>" from a host. <br /></span></p>
+<p><strong>Execution on coprocessor</strong>Â </p>
+<p>Similarly to execution of OpenMP programs in native mode, since the environmental module are not supported on MIC, user has to setup paths to Intel MPI libraries and binaries manually. One time setup can be done by creating a "<strong>.profile</strong>" file in user's home directory. This file sets up the environment on the MIC automatically once user access to the accelerator through the SSH.</p>
+<p class=" ">At first get the LD_LIBRARY_PATH for currenty used Intel Compiler and Intel MPI:</p>
+<pre class=" ">$ echo $MIC_LD_LIBRARY_PATH<br />/apps/all/imkl/11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25/mkl/lib/mic:/apps/all/imkl/11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25/lib/mic:/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic/</pre>
+<p class=" ">Use it in your ~/.profile:</p>
+<pre class=" ">$ <b id="docs-internal-guid-739185ef-4ba1-96b6-ed2f-45da8a2b73f9"><span>vim ~/.profile </span></b></pre>
+<pre class=" ">PS1='[\u@\h \W]\$ '<br />export PATH=/usr/bin:/usr/sbin:/bin:/sbin<br /><br />#IMPI<br />export PATH=/apps/all/impi/5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25/mic/bin/:$PATH<br /><br />#OpenMP (ICC, IFORT), IMKL and IMPI<br />export LD_LIBRARY_PATH=/apps/all/imkl/11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25/mkl/lib/mic:/apps/all/imkl/11.2.3.187-iimpi-7.3.5-GNU-5.1.0-2.25/lib/mic:/apps/all/icc/2015.3.187-GNU-5.1.0-2.25/composer_xe_2015.3.187/compiler/lib/mic:$LD_LIBRARY_PATH<br /><br /></pre>
+<p class="callout">Please note: <br />Â - this file sets up both environmental variable for both MPI and OpenMP libraries.<br />Â - this file sets up the paths to a particular version of Intel MPI library and particular version of an Intel compiler. These versions have to match with loaded modules.</p>
+<p class=" ">To access a MIC accelerator located on a node that user is currently connected to, use:</p>
+<pre class=" ">$ ssh mic0</pre>
+<p class=" ">or in case you need specify a MIC accelerator on a particular node, use:</p>
+<pre class=" ">$ ssh r38u31n1000-mic0</pre>
+<p class=" ">To run the MPI code in parallel on multiple core of the accelerator, use:</p>
+<pre class=" ">$ mpirun -np 4 ./mpi-test-mic</pre>
+<p class=" ">The output should be similar to:</p>
+<pre class=" ">Hello world from process 1 of 4 on host r38u31n1000-mic0<br />Hello world from process 2 of 4 on host r38u31n1000-mic0<br />Hello world from process 3 of 4 on host r38u31n1000-mic0<br />Hello world from process 0 of 4 on host r38u31n1000-mic0</pre>
+<p><strong>Â </strong></p>
+<p><strong>Execution on host</strong></p>
+<p>If the MPI program is launched from host instead of the coprocessor, the environmental variables are not set using the ".profile" file. Therefore user has to specify library paths from the command line when calling "mpiexec".</p>
+<p>First step is to tell mpiexec that the MPI should be executed on a local accelerator by setting up the environmental variable "I_MPI_MIC"</p>
+<pre class=" "><strong>$ export I_MPI_MIC=1</strong></pre>
+<p>Now the MPI program can be executed as:</p>
+<pre class=" ">$ <b id="docs-internal-guid-739185ef-4bb6-852f-9000-e3083ee1e76c"><span>mpirun -genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH -host mic0 -n 4 ~/mpi-test-mic<br /></span></b></pre>
+<p class=" ">or using mpirun</p>
+<pre class=" ">$ <b id="docs-internal-guid-739185ef-4bb6-852f-9000-e3083ee1e76c"><span>mpirun -genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH -host mic0 -n 4 ~/mpi-test-mic<br /></span></b></pre>
+<p class="callout">Please note:<br />Â - the full path to the binary has to specified (here: "<b id="docs-internal-guid-739185ef-4bb6-852f-9000-e3083ee1e76c"><span>~/mpi-test-mic</span></b>") <br />Â - the LD_LIBRARY_PATH has to match with Intel MPI module used to compile the MPI code</p>
+<p class=" ">The output should be again similar to:</p>
+<pre class=" ">Hello world from process 1 of 4 on host r38u31n1000-mic0<br />Hello world from process 2 of 4 on host r38u31n1000-mic0<br />Hello world from process 3 of 4 on host r38u31n1000-mic0<br />Hello world from process 0 of 4 on host r38u31n1000-mic0</pre>
+<p class="callout">Please note that the "mpiexec.hydra" requires a file "<b id="docs-internal-guid-739185ef-4bc0-04bf-f978-e263bb4527e2"><span>pmi_proxy</span></b>" from Intel MPI library to be copied to the MIC filesystem. If the file is missing please contact the system administrators. A simple test to see if the file is present is to execute:</p>
+<pre class=" ">Â Â <span class="monospace">$ ssh mic0 ls /bin/pmi_proxy</span><br />Â <span class="monospace">/bin/pmi_proxy</span></pre>
+<p><strong>Â </strong></p>
+<p><strong>Execution on host - MPI processes distributed over multiple accelerators on multiple nodes</strong></p>
+<p class=" "><span>To get access to multiple nodes with MIC accelerator, user has to use PBS to allocate the resources. To start interactive session, that allocates 2 compute nodes = 2 MIC accelerators run qsub command with following parameters: </span></p>
+<pre class=" "><strong>$ qsub -I -q qprod <b><span>-l select=2:ncpus=24:<span class="pun"></span><span class="pln">accelerator</span><span class="pun">=</span><span class="typ">True</span><span class="pun">:</span><span class="pln">naccelerators</span><span class="pun">=</span><span class="lit">2</span><span class="pun">:</span><span class="pln">accelerator_model</span><span class="pun">=</span><span class="pln">phi7120</span></span></b> -A NONE-0-0<br /><br />$ module load intel <strong>impi</strong><br /></strong></pre>
+<p class=" "><span>This command connects user through ssh to one of the nodes immediately. To see the other nodes that have been allocated use: </span></p>
+<pre class=" "><span>$ cat $PBS_NODEFILE</span></pre>
+<p class=" "><span>For example: </span></p>
+<pre class=" "><span>r38u31n1000.bullx<br />r38u32n1001.bullx<br /></span></pre>
+<p class=" "><span>This output means that the PBS allocated nodes r38u31n1000 and r38u32n1001, which means that user has direct access to "<strong>r38u31n1000-mic0</strong>" and "<strong><span>r38u32n1001</span>-mic0</strong>" accelerators.</span></p>
+<p class="callout"><span>Please note: At this point user can connect to any of the allocated nodes or any of the allocated MIC accelerators using ssh: <br />- to connect to the second node : <strong><span class="monospace">$ ssh <span>r38u32n1001</span></span></strong> <br /><span>- to connect to the accelerator on the first node from the first node: <span class="monospace"><strong>$ ssh <span>r38u31n1000</span>-mic0</strong></span></span> or <strong><span class="monospace">$ ssh mic0</span> </strong><br /><strong>-</strong> to connect to the accelerator on the second node from the first node: <span class="monospace"><strong>$ ssh <span>r38u32n1001</span>-mic0</strong></span><br /></span></p>
+<p><span>At this point we expect that correct modules are loaded and binary is compiled. For parallel execution the mpiexec.hydra is used.</span> Again the first step is to tell mpiexec that the MPI can be executed on MIC accelerators by setting up the environmental variable "I_MPI_MIC", don't forget to have correct FABRIC and PROVIDER defined.</p>
+<pre class=" "><strong>$ export I_MPI_MIC=1<br />$ export I_MPI_FABRICS=shm:dapl</strong><br /><strong>$ export I_MPI_DAPL_PROVIDER_LIST=ofa-v2-mlx4_0-1u,ofa-v2-scif0,ofa-v2-mcm-1</strong></pre>
+<p class=" "><span>The launch the MPI program use:</span></p>
+<pre class=" "><strong>$ mpirun -genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH \<br /> -host <span>r38u31n1000</span>-mic0 -n 4 ~/mpi-test-mic \<br />: -host <span>r38u32n1001</span>-mic0 -n 6 ~/mpi-test-mic</strong></pre>
+<p class=" ">or using mpirun:</p>
+<pre class=" "><strong>$ mpirun -genv LD_LIBRARY_PATH \<br /> -host <span>r38u31n1000</span>-mic0 -n 4 ~/mpi-test-mic \<br />: -host <span>r38u32n1001</span>-mic0 -n 6 ~/mpi-test-mic</strong></pre>
+<p class=" ">In this case four MPI processes are executed on accelerator r38u31n1000-mic and six processes are executed on accelerator r38u32n1001-mic0. The sample output (sorted after execution) is:</p>
+<pre class=" ">Hello world from process 0 of 10 on host <span>r38u31n1000</span>-mic0<br />Hello world from process 1 of 10 on host <span>r38u31n1000</span>-mic0<br />Hello world from process 2 of 10 on host <span>r38u31n1000</span>-mic0<br />Hello world from process 3 of 10 on host <span>r38u31n1000</span>-mic0<br />Hello world from process 4 of 10 on host <span>r38u32n1001</span>-mic0<br />Hello world from process 5 of 10 on host <span>r38u32n1001</span>-mic0<br />Hello world from process 6 of 10 on host <span>r38u32n1001</span>-mic0<br />Hello world from process 7 of 10 on host <span>r38u32n1001</span>-mic0<br />Hello world from process 8 of 10 on host <span>r38u32n1001</span>-mic0<br />Hello world from process 9 of 10 on host <span>r38u32n1001</span>-mic0</pre>
+<p class=" ">The same way MPI program can be executed on multiple hosts:Â </p>
+<pre class=" "><strong>$ mpirun -genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH </strong>\<strong><br /> -host <span>r38u31n1000</span> -n 4 ~/mpi-test \</strong><br /><strong>: -host <span>r38u32n1001</span> -n 6 ~/mpi-test</strong></pre>
+<h3 class=" "><span>Symmetric model </span></h3>
+<p><span>In a symmetric mode MPI programs are executed on both host computer(s) and MIC accelerator(s). Since MIC has a different architecture and requires different binary file produced by the Intel compiler two different files has to be compiled before MPI program is executed. </span></p>
+<p><span>In the previous section we have compiled two binary files, one for hosts "<strong>mpi-test</strong>" and one for MIC accelerators "<strong>mpi-test-mic</strong>". These two binaries can be executed at once using mpiexec.hydra:<br /></span></p>
+<pre class=" "><span>$ <strong>mpirun</strong> \<span><br /> -genv $MIC_LD_LIBRARY_PATH \<br /> -host <strong><span>r38u32n1001</span></strong> -n 2 ~/mpi-test \<br />: -host <strong><span>r38u32n1001</span></strong>-mic0 -n 2 ~/mpi-test-mic<br /></span></span></pre>
+<p>In this example the first two parameters (line 2 and 3) sets up required environment variables for execution. The third line specifies binary that is executed on host (here r38u32n1001) and the last line specifies the binary that is execute on the accelerator (here r38u32n1001-mic0).</p>
+<p class=" "><span>The output of the program is: </span></p>
+<pre class=" "><span>Hello world from process 0 of 4 on host r38u32n1001<br />Hello world from process 1 of 4 on host r38u32n1001<br />Hello world from process 2 of 4 on host r38u32n1001-mic0<br />Hello world from process 3 of 4 on host r38u32n1001-mic0<br /></span></pre>
+<p class=" "><span>The execution procedure can be simplified by using the mpirun command with the machine file a a parameter. Machine file contains list of all nodes and accelerators that should used to execute MPI processes. </span></p>
+<p class=" "><span>An example of a machine file that uses 2 <span>hosts (r38u32n1001 and r38u33n1002) and 2 accelerators <strong>(r38u32n1001-mic0</strong> and <strong><span><span>r38u33n1002</span></span>-mic0</strong>) to run 2 MPI processes on each</span> of them:<br /></span></p>
+<pre class=" "><span>$ cat hosts_file_mix<br />r38u32n1001:2<br />r38u32n1001-mic0:2<br /><span>r38u33n1002</span>:2<br /><span><span>r38u33n1002</span></span>-mic0:2<br /></span></pre>
+<p class=" "><span>In addition if a naming convention is set in a way that the name of the binary for host is <strong>"bin_name"</strong> and the name of the binary for the accelerator is <strong>"bin_name-mic"</strong> then by setting up the environment variable <strong>I_MPI_MIC_POSTFIX</strong> to <strong>"-mic"</strong> user do not have to specify the names of booth binaries. In this case mpirun needs just the name of the host binary file (i.e. "mpi-test") and uses the suffix to get a name of the binary for accelerator (i..e. "mpi-test-mic"). <br /></span></p>
+<pre class=" "><span>$ export I_MPI_MIC_POSTFIX=-mic</span></pre>
+<p>Â <span>To run the MPI code using mpirun and the machine file "hosts_file_mix" use: <br /></span></p>
+<pre class=" "><span>$ mpirun \<br /> -genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH \<br /> -machinefile hosts_file_mix \<br /> ~/mpi-test<br /></span></pre>
+<p class=" "><span>A possible output of the MPI "hello-world" example executed on two hosts and two accelerators is:<br /></span></p>
+<pre class=" "><span>Hello world from process 0 of 8 on host <span><span>r38u31n1000</span></span><br />Hello world from process 1 of 8 on host r38u31n1000<br />Hello world from process 2 of 8 on host r38u31n1000-mic0<br />Hello world from process 3 of 8 on host r38u31n1000-mic0<br />Hello world from process 4 of 8 on host <span><span>r38u32n1001</span></span><br />Hello world from process 5 of 8 on host <span><span>r38u32n1001</span></span><br />Hello world from process 6 of 8 on host <span><span>r38u32n1001</span></span>-mic0<br />Hello world from process 7 of 8 on host <span><span>r38u32n1001</span></span>-mic0<br /></span></pre>
+<p><strong>Using the PBS automatically generated node-files <br /></strong></p>
+<p>PBS also generates a set of node-files that can be used instead of manually creating a new one every time. Three node-files are genereated:</p>
+<p class="callout"><strong>Host only node-file:</strong> <br />Â - /lscratch/${PBS_JOBID}/nodefile-cn<br /><strong>MIC only node-file</strong>: <br />Â - /lscratch/${PBS_JOBID}/nodefile-mic<br /><strong>Host and MIC node-file</strong>: <br />Â - /lscratch/${PBS_JOBID}/nodefile-mix</p>
+<p>Please note each host or accelerator is listed only per files. User has to specify how many jobs should be executed per node using "-n" parameter of the mpirun command.</p>
+<h2 class=" ">Optimization</h2>
+<p class=" ">For more details about optimization techniques please read Intel document <a class="external text" href="http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization" rel="nofollow" title="http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization">Optimization and Performance Tuning for Intel® Xeon Phi™ Coprocessors</a>.</p>
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diff --git a/docs.it4i.cz/salomon/software/intel-xeon-phi.md b/docs.it4i.cz/salomon/software/intel-xeon-phi.md
index a33edb224..57b85d4b6 100644
--- a/docs.it4i.cz/salomon/software/intel-xeon-phi.md
+++ b/docs.it4i.cz/salomon/software/intel-xeon-phi.md
@@ -30,7 +30,7 @@ the micinfo program on the host.
$ /usr/bin/micinfo
The output of the "micinfo" utility executed on one of the cluster node
-is as follows. (noteto get PCIe related details the command has to be
+is as follows. (note: to get PCIe related details the command has to be
run with root privileges)
MicInfo Utility Log
@@ -38,109 +38,109 @@ run with root privileges)
System Info
- HOST OS Linux
- OS Version 2.6.32-504.16.2.el6.x86_64
- Driver Version 3.4.1-1
- MPSS Version 3.4.1
- Host Physical Memory 131930 MB
+ HOST OS : Linux
+ OS Version : 2.6.32-504.16.2.el6.x86_64
+ Driver Version : 3.4.1-1
+ MPSS Version : 3.4.1
+ Host Physical Memory : 131930 MB
- Device No0, Device Namemic0
+ Device No: 0, Device Name: mic0
Version
- Flash Version 2.1.02.0390
- SMC Firmware Version 1.16.5078
- SMC Boot Loader Version 1.8.4326
- uOS Version 2.6.38.8+mpss3.4.1
- Device Serial Number ADKC44601414
+ Flash Version : 2.1.02.0390
+ SMC Firmware Version : 1.16.5078
+ SMC Boot Loader Version : 1.8.4326
+ uOS Version : 2.6.38.8+mpss3.4.1
+ Device Serial Number : ADKC44601414
Board
- Vendor ID 0x8086
- Device ID 0x225c
- Subsystem ID 0x7d95
- Coprocessor Stepping ID 2
- PCIe Width x16
- PCIe Speed 5 GT/s
- PCIe Max payload size 256 bytes
- PCIe Max read req size 512 bytes
- Coprocessor Model 0x01
- Coprocessor Model Ext 0x00
- Coprocessor Type 0x00
- Coprocessor Family 0x0b
- Coprocessor Family Ext 0x00
- Coprocessor Stepping C0
- Board SKU C0PRQ-7120 P/A/X/D
- ECC Mode Enabled
- SMC HW Revision Product 300W Passive CS
+ Vendor ID : 0x8086
+ Device ID : 0x225c
+ Subsystem ID : 0x7d95
+ Coprocessor Stepping ID : 2
+ PCIe Width : x16
+ PCIe Speed : 5 GT/s
+ PCIe Max payload size : 256 bytes
+ PCIe Max read req size : 512 bytes
+ Coprocessor Model : 0x01
+ Coprocessor Model Ext : 0x00
+ Coprocessor Type : 0x00
+ Coprocessor Family : 0x0b
+ Coprocessor Family Ext : 0x00
+ Coprocessor Stepping : C0
+ Board SKU : C0PRQ-7120 P/A/X/D
+ ECC Mode : Enabled
+ SMC HW Revision : Product 300W Passive CS
Cores
- Total No of Active Cores 61
- Voltage 1007000 uV
- Frequency 1238095 kHz
+ Total No of Active Cores : 61
+ Voltage : 1007000 uV
+ Frequency : 1238095 kHz
Thermal
- Fan Speed Control N/A
- Fan RPM N/A
- Fan PWM N/A
- Die Temp 60 C
+ Fan Speed Control : N/A
+ Fan RPM : N/A
+ Fan PWM : N/A
+ Die Temp : 60 C
GDDR
- GDDR Vendor Samsung
- GDDR Version 0x6
- GDDR Density 4096 Mb
- GDDR Size 15872 MB
- GDDR Technology GDDR5
- GDDR Speed 5.500000 GT/s
- GDDR Frequency 2750000 kHz
- GDDR Voltage 1501000 uV
+ GDDR Vendor : Samsung
+ GDDR Version : 0x6
+ GDDR Density : 4096 Mb
+ GDDR Size : 15872 MB
+ GDDR Technology : GDDR5
+ GDDR Speed : 5.500000 GT/s
+ GDDR Frequency : 2750000 kHz
+ GDDR Voltage : 1501000 uV
- Device No1, Device Namemic1
+ Device No: 1, Device Name: mic1
Version
- Flash Version 2.1.02.0390
- SMC Firmware Version 1.16.5078
- SMC Boot Loader Version 1.8.4326
- uOS Version 2.6.38.8+mpss3.4.1
- Device Serial Number ADKC44500454
+ Flash Version : 2.1.02.0390
+ SMC Firmware Version : 1.16.5078
+ SMC Boot Loader Version : 1.8.4326
+ uOS Version : 2.6.38.8+mpss3.4.1
+ Device Serial Number : ADKC44500454
Board
- Vendor ID 0x8086
- Device ID 0x225c
- Subsystem ID 0x7d95
- Coprocessor Stepping ID 2
- PCIe Width x16
- PCIe Speed 5 GT/s
- PCIe Max payload size 256 bytes
- PCIe Max read req size 512 bytes
- Coprocessor Model 0x01
- Coprocessor Model Ext 0x00
- Coprocessor Type 0x00
- Coprocessor Family 0x0b
- Coprocessor Family Ext 0x00
- Coprocessor Stepping C0
- Board SKU C0PRQ-7120 P/A/X/D
- ECC Mode Enabled
- SMC HW Revision Product 300W Passive CS
+ Vendor ID : 0x8086
+ Device ID : 0x225c
+ Subsystem ID : 0x7d95
+ Coprocessor Stepping ID : 2
+ PCIe Width : x16
+ PCIe Speed : 5 GT/s
+ PCIe Max payload size : 256 bytes
+ PCIe Max read req size : 512 bytes
+ Coprocessor Model : 0x01
+ Coprocessor Model Ext : 0x00
+ Coprocessor Type : 0x00
+ Coprocessor Family : 0x0b
+ Coprocessor Family Ext : 0x00
+ Coprocessor Stepping : C0
+ Board SKU : C0PRQ-7120 P/A/X/D
+ ECC Mode : Enabled
+ SMC HW Revision : Product 300W Passive CS
Cores
- Total No of Active Cores 61
- Voltage 998000 uV
- Frequency 1238095 kHz
+ Total No of Active Cores : 61
+ Voltage : 998000 uV
+ Frequency : 1238095 kHz
Thermal
- Fan Speed Control N/A
- Fan RPM N/A
- Fan PWM N/A
- Die Temp 59 C
+ Fan Speed Control : N/A
+ Fan RPM : N/A
+ Fan PWM : N/A
+ Die Temp : 59 C
GDDR
- GDDR Vendor Samsung
- GDDR Version 0x6
- GDDR Density 4096 Mb
- GDDR Size 15872 MB
- GDDR Technology GDDR5
- GDDR Speed 5.500000 GT/s
- GDDR Frequency 2750000 kHz
- GDDR Voltage 1501000 uV
+ GDDR Vendor : Samsung
+ GDDR Version : 0x6
+ GDDR Density : 4096 Mb
+ GDDR Size : 15872 MB
+ GDDR Technology : GDDR5
+ GDDR Speed : 5.500000 GT/s
+ GDDR Frequency : 2750000 kHz
+ GDDR Voltage : 1501000 uV
Offload Mode
------------
@@ -378,7 +378,7 @@ int main(int argc, char **argv)
       mkl_mic_enable();
      Â
       int ndevices = mkl_mic_get_device_count(); /* Number of MIC devices */
-       printf("Automatic Offload enabled%d MIC devices presentn",  ndevices);
+       printf("Automatic Offload enabled: %d MIC devices presentn",  ndevices);
       printf("Computing SGEMM with automatic workdivisionn");
       sgemm(&transa, &transb, &N, &N, &N, &alpha, A, &N, B, &N, &beta, C, &N);
@@ -392,7 +392,7 @@ int main(int argc, char **argv)
}
```
-Please noteThis example is simplified version of an example from MKL.
+Please note: This example is simplified version of an example from MKL.
The expanded version can be found here:
**$MKL_EXAMPLES/mic_ao/blasc/source/sgemm.c**
@@ -411,7 +411,7 @@ lines starting with [MKL] are generated by offload reporting:
[user@r31u03n799 ~]$ ./sgemm
Computing SGEMM on the host
Enabling Automatic Offload
- Automatic Offload enabled2 MIC devices present
+ Automatic Offload enabled: 2 MIC devices present
Computing SGEMM with automatic workdivision
[MKL] [MIC --] [AO Function]Â Â Â SGEMM
[MKL] [MIC --] [AO SGEMM Workdivision]Â Â Â 0.44 0.28 0.28
@@ -554,7 +554,7 @@ libirng.so
libintlc.so.5
</span>
-<span>Finally, to run the compiled code use</span>
+<span>Finally, to run the compiled code use: </span>
$ ~/path_to_binary/vect-add-mic
@@ -581,7 +581,7 @@ and link OpenCL code. Load "opencl-rt" for running your compiled code.
</span>
<span>There are two basic examples of OpenCL code in the following
-directory</span>
+directory: </span>
/apps/intel/opencl-examples/
@@ -601,7 +601,7 @@ be compiled on Anselm. </span>
$ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
$ make
-<span>The compilation command for this example is</span>
+<span>The compilation command for this example is: </span>
$ g++ capsbasic.cpp -lOpenCL -o capsbasic -I/apps/intel/opencl/include/
@@ -611,25 +611,25 @@ be displayed.
./capsbasic
- Number of available platforms1
+ Number of available platforms: 1
Platform names:
   [0] Intel(R) OpenCL [Selected]
Number of devices available for each type:
- Â Â Â CL_DEVICE_TYPE_CPU1
- Â Â Â CL_DEVICE_TYPE_GPU0
- Â Â Â CL_DEVICE_TYPE_ACCELERATOR1
+ Â Â Â CL_DEVICE_TYPE_CPU: 1
+ Â Â Â CL_DEVICE_TYPE_GPU: 0
+ Â Â Â CL_DEVICE_TYPE_ACCELERATOR: 1
*** Detailed information for each device ***
CL_DEVICE_TYPE_CPU[0]
   CL_DEVICE_NAME:       Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
- Â Â Â CL_DEVICE_AVAILABLE1
+ Â Â Â CL_DEVICE_AVAILABLE: 1
...
CL_DEVICE_TYPE_ACCELERATOR[0]
- Â Â Â CL_DEVICE_NAMEIntel(R) Many Integrated Core Acceleration Card
- Â Â Â CL_DEVICE_AVAILABLE1
+ Â Â Â CL_DEVICE_NAME: Intel(R) Many Integrated Core Acceleration Card
+ Â Â Â CL_DEVICE_AVAILABLE: 1
...
@@ -648,12 +648,12 @@ to your directory and compile it.Â
$ cd GEMM
$ make
-<span>The compilation command for this example is</span>
+<span>The compilation command for this example is: </span>
$ g++ cmdoptions.cpp gemm.cpp ../common/basic.cpp ../common/cmdparser.cpp ../common/oclobject.cpp -I../common -lOpenCL -o gemm -I/apps/intel/opencl/include/
<span>To see the performance of Intel Xeon Phi performing the DGEMM run
-the example as follows</span>
+the example as follows: </span>
./gemm -d 1
Platforms (1):
@@ -661,19 +661,19 @@ the example as follows</span>
Devices (2):
[0] Intel(R) Xeon(R) CPU E5-2470 0 @ 2.30GHz
[1] Intel(R) Many Integrated Core Acceleration Card [Selected]
- Build program options"-DT=float -DTILE_SIZE_M=1 -DTILE_GROUP_M=16 -DTILE_SIZE_N=128 -DTILE_GROUP_N=1 -DTILE_SIZE_K=8"
- Running gemm_nn kernel with matrix size3968x3968
- Memory row stride to ensure necessary alignment15872 bytes
- Size of memory region for one matrix62980096 bytes
+ Build program options: "-DT=float -DTILE_SIZE_M=1 -DTILE_GROUP_M=16 -DTILE_SIZE_N=128 -DTILE_GROUP_N=1 -DTILE_SIZE_K=8"
+ Running gemm_nn kernel with matrix size: 3968x3968
+ Memory row stride to ensure necessary alignment: 15872 bytes
+ Size of memory region for one matrix: 62980096 bytes
Using alpha = 0.57599 and beta = 0.872412
...
- Host time0.292953 sec.
- Host perf426.635 GFLOPS
- Host time0.293334 sec.
- Host perf426.081 GFLOPS
+ Host time: 0.292953 sec.
+ Host perf: 426.635 GFLOPS
+ Host time: 0.293334 sec.
+ Host perf: 426.081 GFLOPS
...
-<span>Please noteGNU compiler is used to compile the OpenCL codes for
+<span>Please note: GNU compiler is used to compile the OpenCL codes for
Intel MIC. You do not need to load Intel compiler module.
</span>
@@ -692,7 +692,7 @@ This ensures, that MPI inside node will use SHMEM communication, between
HOST and Phi the IB SCIF will be used and between different nodes or
Phi's on diferent nodes a CCL-Direct proxy will be used.
-Please noteOther FABRICS like tcp,ofa may be used (even combined with
+Please note: Other FABRICS like tcp,ofa may be used (even combined with
shm) but there's severe loss of performance (by order of magnitude).
Usage of single DAPL PROVIDER (e. g.
I_MPI_DAPL_PROVIDER=ofa-v2-mlx4_0-1u) will cause failure of
@@ -788,7 +788,7 @@ The output should be similar to:
### Coprocessor-only model
<span>There are two ways how to execute an MPI code on a single
-coprocessor1.) lunch the program using "**mpirun**" from the
+coprocessor: 1.) lunch the program using "**mpirun**" from the
coprocessor; or 2.) lunch the task using "**mpiexec.hydra**" from a
host.
</span>
@@ -901,7 +901,7 @@ accelerators on multiple nodes**
<span>To get access to multiple nodes with MIC accelerator, user has to
use PBS to allocate the resources. To start interactive session, that
allocates 2 compute nodes = 2 MIC accelerators run qsub command with
-following parameters</span>
+following parameters: </span>
$ qsub -I -q qprod -l select=2:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
@@ -913,7 +913,7 @@ immediately. To see the other nodes that have been allocated use:
$ cat $PBS_NODEFILE
-<span>For example</span>
+<span>For example: </span>
r38u31n1000.bullx
r38u32n1001.bullx
@@ -923,16 +923,16 @@ r38u32n1001, which means that user has direct access to
"**r38u31n1000-mic0**" and "**<span>r38u32n1001</span>-mic0**"
accelerators.</span>
-<span>Please noteAt this point user can connect to any of the
+<span>Please note: At this point user can connect to any of the
allocated nodes or any of the allocated MIC accelerators using ssh:
-- to connect to the second node **<span class="monospace">$
+- to connect to the second node : **<span class="monospace">$
ssh <span>r38u32n1001</span></span>**
<span>- to connect to the accelerator on the first node from the first
-node<span class="monospace">**$ ssh
+node: <span class="monospace">**$ ssh
<span>r38u31n1000</span>-mic0**</span></span> or **<span
class="monospace">$ ssh mic0</span>**
**-** to connect to the accelerator on the second node from the first
-node<span class="monospace">**$ ssh
+node: <span class="monospace">**$ ssh
<span>r38u32n1001</span>-mic0**</span>
</span>
@@ -950,13 +950,13 @@ don't forget to have correct FABRIC and PROVIDER defined.
$ mpirun -genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH
-host r38u31n1000-mic0 -n 4 ~/mpi-test-mic
- -host r38u32n1001-mic0 -n 6 ~/mpi-test-mic
+ : -host r38u32n1001-mic0 -n 6 ~/mpi-test-mic
or using mpirun:
$ mpirun -genv LD_LIBRARY_PATH
-host r38u31n1000-mic0 -n 4 ~/mpi-test-mic
- -host r38u32n1001-mic0 -n 6 ~/mpi-test-mic
+ : -host r38u32n1001-mic0 -n 6 ~/mpi-test-mic
In this case four MPI processes are executed on accelerator
r38u31n1000-mic and six processes are executed on accelerator
@@ -977,7 +977,7 @@ The same way MPI program can be executed on multiple hosts:Â
$ mpirun -genv LD_LIBRARY_PATH $MIC_LD_LIBRARY_PATH
-host r38u31n1000 -n 4 ~/mpi-test
- -host r38u32n1001 -n 6 ~/mpi-test
+ : -host r38u32n1001 -n 6 ~/mpi-test
### <span>Symmetric model </span>
@@ -995,14 +995,14 @@ These two binaries can be executed at once using mpiexec.hydra:
$ mpirun
-genv $MIC_LD_LIBRARY_PATH
-host r38u32n1001 -n 2 ~/mpi-test
- -host r38u32n1001-mic0 -n 2 ~/mpi-test-mic
+ : -host r38u32n1001-mic0 -n 2 ~/mpi-test-mic
In this example the first two parameters (line 2 and 3) sets up required
environment variables for execution. The third line specifies binary
that is executed on host (here r38u32n1001) and the last line specifies
the binary that is execute on the accelerator (here r38u32n1001-mic0).
-<span>The output of the program is</span>
+<span>The output of the program is: </span>
Hello world from process 0 of 4 on host r38u32n1001
Hello world from process 1 of 4 on host r38u32n1001
diff --git a/docs.it4i.cz/salomon/software/isv_licenses.html b/docs.it4i.cz/salomon/software/isv_licenses.html
new file mode 100644
index 000000000..c7e5adfd1
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/isv_licenses.html
@@ -0,0 +1,351 @@
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diff --git a/docs.it4i.cz/salomon/software/java.html b/docs.it4i.cz/salomon/software/java.html
new file mode 100644
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@@ -0,0 +1,884 @@
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+ <div id="parent-fieldname-text-08627913df094d7a9fa9317ec34129a3" class="">
+ <p>Java is available on the cluster. Activate java by loading the Java module</p>
+<pre class=" ">$ module load Java</pre>
+<p>Note that the Java module must be loaded on the compute nodes as well, in order to run java on compute nodes.</p>
+<p>Check for java version and path</p>
+<pre class=" ">$ java -version<br />$ which java</pre>
+<p class=" ">With the module loaded, not only the runtime environment (JRE), but also the development environment (JDK) with the compiler is available.</p>
+<pre class=" ">$ javac -version<br />$ which javac</pre>
+<p class=" ">Java applications may use MPI for interprocess communication, in conjunction with OpenMPI. Read more on <a class="external-link" href="http://www.open-mpi.org/faq/?category=java" target="_self" title="">http://www.open-mpi.org/faq/?category=java</a>.<br />This functionality is currently not supported on Anselm cluster. In case you require the java interface to MPI, please contact <a class="external-link" href="https://support.it4i.cz/rt/" target="_self" title="">cluster support</a>.</p>
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+ <h2 class=" ">Setting up MPI Environment</h2>
+<p>The Salomon cluster provides several implementations of the MPI library:</p>
+<table class="listing">
+<tbody>
+<tr><th>MPI Library</th><th>Thread support</th></tr>
+<tr class="odd">
+<td><strong>Intel MPI 4.1</strong></td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE</td>
+</tr>
+<tr class="odd">
+<td><strong>Intel MPI 5.0</strong></td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE</td>
+</tr>
+<tr class="even">
+<td>OpenMPI 1.8.6</td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE, MPI-3.0 support</td>
+</tr>
+<tr class="even">
+<td>SGI MPT 2.12</td>
+<td></td>
+</tr>
+</tbody>
+</table>
+<ul></ul>
+<p class="callout">MPI libraries are activated via the environment modules.</p>
+<p>Look up section modulefiles/mpi in module avail</p>
+<pre class=" ">$ module avail<br />------------------------------ /apps/modules/mpi -------------------------------<br />impi/4.1.1.036-iccifort-2013.5.192<br />impi/4.1.1.036-iccifort-2013.5.192-GCC-4.8.3<br />impi/5.0.3.048-iccifort-2015.3.187<br />impi/5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25<br />MPT/2.12<br />OpenMPI/1.8.6-GNU-5.1.0-2.25<br /><br /></pre>
+<p>There are default compilers associated with any particular MPI implementation. The defaults may be changed, the MPI libraries may be used in conjunction with any compiler.<br />The defaults are selected via the modules in following way</p>
+<table class="listing" summary="Modules selecting the MPI environment">
+<tbody>
+<tr><th>Module</th><th>MPI</th><th>Compiler suite</th></tr>
+<tr class="odd">
+<td>impi-5.0.3.048-iccifort-2015.3.187</td>
+<td>Intel MPI 5.0.3</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>OpenMP-1.8.6-GNU-5.1.0-2.25</td>
+<td>OpenMPI 1.8.6</td>
+<td></td>
+</tr>
+</tbody>
+</table>
+<p>Examples:</p>
+<pre class=" ">$ module load gompi/2015b</pre>
+<p>In this example, we activate the latest OpenMPI with latest GNU compilers (OpenMPI 1.8.6 and GCC 5.1). Please see more information about toolchains in section <a href="../environment-and-modules.html">Environment and Modules</a> .</p>
+<p>To use OpenMPI with the intel compiler suite, use</p>
+<pre class=" ">$ module load iompi/2015.03</pre>
+<p>In this example, the openmpi 1.8.6 using intel compilers is activated. It's used "iompi" toolchain.</p>
+<h2 class=" ">Compiling MPI Programs</h2>
+<p class="callout">After setting up your MPI environment, compile your program using one of the mpi wrappers</p>
+<pre class=" ">$ mpicc -v<br />$ mpif77 -v<br />$ mpif90 -v</pre>
+<p>When using Intel MPI, use the following MPI wrappers:</p>
+<pre class=" ">$ mpicc<br />$ mpiifort </pre>
+<p>Wrappers mpif90, mpif77 that are provided by Intel MPI are designed for gcc and gfortran. You might be able to compile MPI code by them even with Intel compilers, but you might run into problems (for example, native MIC compilation with -mmic does not work with mpif90).</p>
+<p>Example program:</p>
+<pre class=" ">// helloworld_mpi.c<br />#include <stdio.h><br /><br />#include<mpi.h><br /><br />int main(int argc, char **argv) {<br /><br />int len;<br />int rank, size;<br />char node[MPI_MAX_PROCESSOR_NAME];<br /><br />// Initiate MPI<br />MPI_Init(&argc, &argv);<br />MPI_Comm_rank(MPI_COMM_WORLD,&rank);<br />MPI_Comm_size(MPI_COMM_WORLD,&size);<br /><br />// Get hostame and print<br />MPI_Get_processor_name(node,&len);<br />printf("Hello world! from rank %d of %d on host %s\n",rank,size,node);<br /><br />// Finalize and exit<br />MPI_Finalize();<br /><br />return 0;<br />}</pre>
+<p>Compile the above example with</p>
+<pre class=" ">$ mpicc helloworld_mpi.c -o helloworld_mpi.x</pre>
+<h2 class=" ">Running MPI Programs</h2>
+<p class="callout">The MPI program executable must be compatible with the loaded MPI module. <br />Always compile and execute using the very same MPI module.</p>
+<p>It is strongly discouraged to mix mpi implementations. Linking an application with one MPI implementation and running mpirun/mpiexec form other implementation may result in unexpected errors.</p>
+<p>The MPI program executable must be available within the same path on all nodes. This is automatically fulfilled on the /home and /scratch filesystem. You need to preload the executable, if running on the local scratch /lscratch filesystem.</p>
+<h3 class=" ">Ways to run MPI programs</h3>
+<p>Optimal way to run an MPI program depends on its memory requirements, memory access pattern and communication pattern.</p>
+<p class="callout">Consider these ways to run an MPI program:<br />1. One MPI process per node, 24 threads per process<br />2. Two MPI processes per node, 12 threads per process<br />3. 24 MPI processes per node, 1 thread per process.</p>
+<p class=" "><strong>One MPI</strong> process per node, using 24 threads, is most useful for memory demanding applications, that make good use of processor cache memory and are not memory bound. This is also a preferred way for communication intensive applications as one process per node enjoys full bandwidth access to the network interface. </p>
+<p class=" "><strong>Two MPI</strong> processes per node, using 12 threads each, bound to processor socket is most useful for memory bandwidth bound applications such as BLAS1 or FFT, with scalable memory demand. However, note that the two processes will share access to the network interface. The 12 threads and socket binding should ensure maximum memory access bandwidth and minimize communication, migration and numa effect overheads.</p>
+<p class="callout">Important! Bind every OpenMP thread to a core!</p>
+<p>In the previous two cases with one or two MPI processes per node, the operating system might still migrate OpenMP threads between cores. You want to avoid this by setting the KMP_AFFINITY or GOMP_CPU_AFFINITY environment variables.</p>
+<p class=" "><strong class=" ">24 MPI</strong> processes per node, using 1 thread each bound to processor core is most suitable for highly scalable applications with low communication demand.</p>
+<h3 class=" ">Running OpenMPI</h3>
+<p>The <a class="external-link" href="http://www.open-mpi.org/" target="_self" title=""><strong>OpenMPI 1.8.6</strong></a> is based on OpenMPI. Read more on <a href="mpi-1/Running_OpenMPI.html" title="" target="_self" class="internal-link">how to run OpenMPI</a> based MPI.</p>
+<p>Â </p>
+<p>The Intel MPI may run on the<a href="intel-xeon-phi.html" title="" target="_self" class="internal-link"> Intel Xeon Ph</a>i accelerators as well. Read more on <a href="intel-xeon-phi.html" title="" target="_self" class="internal-link">how to run Intel MPI on accelerators</a>.</p>
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+ <h2 class=" ">OpenMPI program execution</h2>
+<p>The OpenMPI programs may be executed only via the PBS Workload manager, by entering an appropriate queue. On the cluster, the <strong>OpenMPI 1.8.6</strong> is OpenMPI based MPI implementation.</p>
+<h3 class=" ">Basic usage</h3>
+<p class="callout">Use the mpiexec to run the OpenMPI code.</p>
+<p>Example:</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=24 -I<br />qsub: waiting for job 15210.isrv5 to start<br />qsub: job 15210.isrv5 ready<br /><br />$ pwd<br />/home/username<br /><br />$ module load OpenMPI<br />$ mpiexec -pernode ./helloworld_mpi.x<br />Hello world! from rank 0 of 4 on host r1i0n17<br />Hello world! from rank 1 of 4 on host r1i0n5<br />Hello world! from rank 2 of 4 on host r1i0n6<br />Hello world! from rank 3 of 4 on host r1i0n7</pre>
+<p class="callout">Please be aware, that in this example, the directive<strong> -pernode</strong> is used to run only <strong>one task per node</strong>, which is normally an unwanted behaviour (unless you want to run hybrid code with just one MPI and 24 OpenMP tasks per node). In normal MPI programs <strong>omit the -pernode directive</strong> to run up to 24 MPI tasks per each node.</p>
+<p class=" ">In this example, we allocate 4 nodes via the express queue interactively. We set up the openmpi environment and interactively run the helloworld_mpi.x program.<br />Note that the executable <span class="monospace">helloworld_mpi.x</span> must be available within the same path on all nodes. This is automatically fulfilled on the /home and /scratch filesystem.</p>
+<p class=" ">You need to preload the executable, if running on the local ramdisk /tmp filesystem</p>
+<pre class=" ">$ pwd<br /><span><span><span class="pun">/<strong>tmp</strong></span><strong><span class="pun">/</span></strong><span class="pun"></span><span class="pln"></span><span class="pun"></span></span></span>pbs.15210.isrv5<br /><br />$ mpiexec -pernode --preload-binary ./helloworld_mpi.x<br />Hello world! from rank 0 of 4 on host r1i0n17<br />Hello world! from rank 1 of 4 on host r1i0n5<br />Hello world! from rank 2 of 4 on host r1i0n6<br />Hello world! from rank 3 of 4 on host r1i0n7</pre>
+<p class=" ">In this example, we assume the executable <span class="monospace">helloworld_mpi.x</span> is present on compute node r1i0n17 on ramdisk. We call the mpiexec whith the <strong>--preload-binary</strong> argument (valid for openmpi). The mpiexec will copy the executable from r1i0n17 to the <span class="monospace">/tmp/pbs.15210.isrv5</span> directory on r1i0n5, r1i0n6 and r1i0n7 and execute the program.</p>
+<p class="callout">MPI process mapping may be controlled by PBS parameters.</p>
+<p class=" ">The mpiprocs and ompthreads parameters allow for selection of number of running MPI processes per node as well as number of OpenMP threads per MPI process.</p>
+<h3 class=" ">One MPI process per node</h3>
+<p class=" ">Follow this example to run one MPI process per node, 24 threads per process. </p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=24:mpiprocs=1:ompthreads=24 -I<br /><br />$ module load OpenMPI<br /><br />$ mpiexec --bind-to-none ./helloworld_mpi.x</pre>
+<p>In this example, we demonstrate recommended way to run an MPI application, using 1 MPI processes per node and 24 threads per socket, on 4 nodes.</p>
+<h3 class=" ">Two MPI processes per node</h3>
+<p class=" ">Follow this example to run two MPI processes per node, 8 threads per process. Note the options to mpiexec.</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=24:mpiprocs=2:ompthreads=12 -I<br /><br />$ module load OpenMPI<br /><br />$ mpiexec -bysocket -bind-to-socket ./helloworld_mpi.x</pre>
+<p>In this example, we demonstrate recommended way to run an MPI application, using 2 MPI processes per node and 12 threads per socket, each process and its threads bound to a separate processor socket of the node, on 4 nodes</p>
+<h3 class=" ">24 MPI processes per node</h3>
+<p class=" ">Follow this example to run 24 MPI processes per node, 1 thread per process. Note the options to mpiexec.</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=24:mpiprocs=24:ompthreads=1 -I<br /><br />$ module load OpenMPI<br /><br />$ mpiexec -bycore -bind-to-core ./helloworld_mpi.x</pre>
+<p>In this example, we demonstrate recommended way to run an MPI application, using 24 MPI processes per node, single threaded. Each process is bound to separate processor core, on 4 nodes.</p>
+<h3 class=" ">OpenMP thread affinity</h3>
+<p class="callout">Important! Bind every OpenMP thread to a core!</p>
+<p>In the previous two examples with one or two MPI processes per node, the operating system might still migrate OpenMP threads between cores. You might want to avoid this by setting these environment variable for GCC OpenMP:</p>
+<pre class=" "><span class="s1">$ export GOMP_CPU_AFFINITY="0-23"</span></pre>
+<p>or this one for Intel OpenMP:</p>
+<pre class=" ">$ export KMP_AFFINITY=granularity=fine,compact,1,0</pre>
+<p class=" ">As of OpenMP 4.0 (supported by GCC 4.9 and later and Intel 14.0 and later) the following variables may be used for Intel or GCC:</p>
+<pre class=" ">$ export OMP_PROC_BIND=true<br />$ export OMP_PLACES=cores </pre>
+<h2 class=" "><span>OpenMPI Process Mapping and Binding</span></h2>
+<p>The mpiexec allows for precise selection of how the MPI processes will be mapped to the computational nodes and how these processes will bind to particular processor sockets and cores.</p>
+<p>MPI process mapping may be specified by a hostfile or rankfile input to the mpiexec program. Altough all implementations of MPI provide means for process mapping and binding, following examples are valid for the openmpi only.</p>
+<h3 class=" ">Hostfile</h3>
+<p>Example hostfile</p>
+<pre class=" ">r1i0n17.smc.salomon.it4i.cz<br />r1i0n5.smc.salomon.it4i.cz<br />r1i0n6.smc.salomon.it4i.cz<br />r1i0n7.smc.salomon.it4i.cz</pre>
+<p class=" ">Use the hostfile to control process placement</p>
+<pre class=" ">$ mpiexec -hostfile hostfile ./helloworld_mpi.x<br />Hello world! from rank 0 of 4 on host r1i0n17<br />Hello world! from rank 1 of 4 on host r1i0n5<br />Hello world! from rank 2 of 4 on host r1i0n6<br />Hello world! from rank 3 of 4 on host r1i0n7</pre>
+<p>In this example, we see that ranks have been mapped on nodes according to the order in which nodes show in the hostfile</p>
+<h3 class=" ">Rankfile</h3>
+<p>Exact control of MPI process placement and resource binding is provided by specifying a rankfile</p>
+<p class="callout">Appropriate binding may boost performance of your application.</p>
+<p>Example rankfile</p>
+<pre class=" ">rank 0=r1i0n7.smc.salomon.it4i.cz slot=1:0,1<br />rank 1=r1i0n6.smc.salomon.it4i.cz slot=0:*<br />rank 2=r1i0n5.smc.salomon.it4i.cz slot=1:1-2<br />rank 3=r1i0n17.smc.salomon slot=0:1,1:0-2<br />rank 4=r1i0n6.smc.salomon.it4i.cz slot=0:*,1:*</pre>
+<p>This rankfile assumes 5 ranks will be running on 4 nodes and provides exact mapping and binding of the processes to the processor sockets and cores</p>
+<p>Explanation: <br /> rank 0 will be bounded to r1i0n7, socket1 core0 and core1 <br /> rank 1 will be bounded to r1i0n6, socket0, all cores <br /> rank 2 will be bounded to r1i0n5, socket1, core1 and core2<br /> rank 3 will be bounded to r1i0n17, socket0 core1, socket1 core0, core1, core2<br /> rank 4 will be bounded to r1i0n6, all cores on both sockets</p>
+<pre class=" ">$ mpiexec -n 5 -rf rankfile --report-bindings ./helloworld_mpi.x<br />[r1i0n17:11180] MCW rank 3 bound to socket 0[core 1] socket 1[core 0-2]: [. B . . . . . . . . . .][B B B . . . . . . . . .] (slot list 0:1,1:0-2)<br />[r1i0n7:09928] MCW rank 0 bound to socket 1[core 0-1]: [. . . . . . . . . . . .][B B . . . . . . . . . .] (slot list 1:0,1)<br />[r1i0n6:10395] MCW rank 1 bound to socket 0[core 0-7]: [B B B B B B B B B B B B][. . . . . . . . . . . .] (slot list 0:*)<br />[r1i0n5:10406] MCW rank 2 bound to socket 1[core 1-2]: [. . . . . . . . . . . .][. B B . . . . . . . . .] (slot list 1:1-2)<br />[r1i0n6:10406] MCW rank 4 bound to socket 0[core 0-7] socket 1[core 0-7]: [B B B B B B B B B B B B][B B B B B B B B B B B B] (slot list 0:*,1:*)<br />Hello world! from rank 3 of 5 on host r1i0n17<br />Hello world! from rank 1 of 5 on host r1i0n6<br />Hello world! from rank 0 of 5 on host r1i0n7<br />Hello world! from rank 4 of 5 on host r1i0n6<br />Hello world! from rank 2 of 5 on host r1i0n5</pre>
+<p>In this example we run 5 MPI processes (5 ranks) on four nodes. The rankfile defines how the processes will be mapped on the nodes, sockets and cores. The <strong>--report-bindings</strong> option was used to print out the actual process location and bindings. Note that ranks 1 and 4 run on the same node and their core binding overlaps.</p>
+<p>It is users responsibility to provide correct number of ranks, sockets and cores.</p>
+<h3 class=" ">Bindings verification</h3>
+<p>In all cases, binding and threading may be verified by executing for example:</p>
+<pre class=" ">$ mpiexec -bysocket -bind-to-socket --report-bindings echo<br />$ mpiexec -bysocket -bind-to-socket numactl --show<br />$ mpiexec -bysocket -bind-to-socket echo $OMP_NUM_THREADS</pre>
+<h2 class=" ">Changes in OpenMPI 1.8</h2>
+<p>Some options have changed in OpenMPI version 1.8.</p>
+<table class="plain">
+<tbody>
+<tr><th>version 1.6.5</th><th>version 1.8.1</th></tr>
+<tr>
+<td>--bind-to-none</td>
+<td>--bind-to none</td>
+</tr>
+<tr>
+<td>--bind-to-core</td>
+<td>--bind-to core</td>
+</tr>
+<tr>
+<td>--bind-to-socket</td>
+<td>--bind-to socket</td>
+</tr>
+<tr>
+<td>-bysocket</td>
+<td>--map-by socket</td>
+</tr>
+<tr>
+<td>-bycore</td>
+<td>--map-by core</td>
+</tr>
+<tr>
+<td>-pernode</td>
+<td>
+<p class="p1"><span class="s1">--map-by ppr:1:node</span></p>
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diff --git a/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md b/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
index addff07ee..3d15d224f 100644
--- a/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
+++ b/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
@@ -19,8 +19,8 @@ Use the mpiexec to run the OpenMPI code.
Example:
$ qsub -q qexp -l select=4:ncpus=24 -I
- qsubwaiting for job 15210.isrv5 to start
- qsubjob 15210.isrv5 ready
+ qsub: waiting for job 15210.isrv5 to start
+ qsub: job 15210.isrv5 ready
$ pwd
/home/username
@@ -198,11 +198,11 @@ core2
rank 4 will be bounded to r1i0n6, all cores on both sockets
$ mpiexec -n 5 -rf rankfile --report-bindings ./helloworld_mpi.x
- [r1i0n17:11180] MCW rank 3 bound to socket 0[core 1] socket 1[core 0-2][. B . . . . . . . . . .][B B B . . . . . . . . .] (slot list 0:1,1:0-2)
- [r1i0n7:09928] MCW rank 0 bound to socket 1[core 0-1][. . . . . . . . . . . .][B B . . . . . . . . . .] (slot list 1:0,1)
- [r1i0n6:10395] MCW rank 1 bound to socket 0[core 0-7][B B B B B B B B B B B B][. . . . . . . . . . . .] (slot list 0:*)
- [r1i0n5:10406] MCW rank 2 bound to socket 1[core 1-2][. . . . . . . . . . . .][. B B . . . . . . . . .] (slot list 1:1-2)
- [r1i0n6:10406] MCW rank 4 bound to socket 0[core 0-7] socket 1[core 0-7][B B B B B B B B B B B B][B B B B B B B B B B B B] (slot list 0:*,1:*)
+ [r1i0n17:11180] MCW rank 3 bound to socket 0[core 1] socket 1[core 0-2]: [. B . . . . . . . . . .][B B B . . . . . . . . .] (slot list 0:1,1:0-2)
+ [r1i0n7:09928] MCW rank 0 bound to socket 1[core 0-1]: [. . . . . . . . . . . .][B B . . . . . . . . . .] (slot list 1:0,1)
+ [r1i0n6:10395] MCW rank 1 bound to socket 0[core 0-7]: [B B B B B B B B B B B B][. . . . . . . . . . . .] (slot list 0:*)
+ [r1i0n5:10406] MCW rank 2 bound to socket 1[core 1-2]: [. . . . . . . . . . . .][. B B . . . . . . . . .] (slot list 1:1-2)
+ [r1i0n6:10406] MCW rank 4 bound to socket 0[core 0-7] socket 1[core 0-7]: [B B B B B B B B B B B B][B B B B B B B B B B B B] (slot list 0:*,1:*)
Hello world! from rank 3 of 5 on host r1i0n17
Hello world! from rank 1 of 5 on host r1i0n6
Hello world! from rank 0 of 5 on host r1i0n7
diff --git a/docs.it4i.cz/salomon/software/mpi-1/mpi.html b/docs.it4i.cz/salomon/software/mpi-1/mpi.html
new file mode 100644
index 000000000..c53d7ff18
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+ MPI
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+ <h2 class=" ">Setting up MPI Environment</h2>
+<p>The Salomon cluster provides several implementations of the MPI library:</p>
+<table class="listing">
+<tbody>
+<tr><th>MPI Library</th><th>Thread support</th></tr>
+<tr class="odd">
+<td><strong>Intel MPI 4.1</strong></td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE</td>
+</tr>
+<tr class="odd">
+<td><strong>Intel MPI 5.0</strong></td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE</td>
+</tr>
+<tr class="even">
+<td>OpenMPI 1.8.6</td>
+<td>Full thread support up to MPI_THREAD_MULTIPLE, MPI-3.0 support</td>
+</tr>
+<tr class="even">
+<td>SGI MPT 2.12</td>
+<td></td>
+</tr>
+</tbody>
+</table>
+<ul></ul>
+<p class="callout">MPI libraries are activated via the environment modules.</p>
+<p>Look up section modulefiles/mpi in module avail</p>
+<pre class=" ">$ module avail<br />------------------------------ /apps/modules/mpi -------------------------------<br />impi/4.1.1.036-iccifort-2013.5.192<br />impi/4.1.1.036-iccifort-2013.5.192-GCC-4.8.3<br />impi/5.0.3.048-iccifort-2015.3.187<br />impi/5.0.3.048-iccifort-2015.3.187-GNU-5.1.0-2.25<br />MPT/2.12<br />OpenMPI/1.8.6-GNU-5.1.0-2.25<br /><br /></pre>
+<p>There are default compilers associated with any particular MPI implementation. The defaults may be changed, the MPI libraries may be used in conjunction with any compiler.<br />The defaults are selected via the modules in following way</p>
+<table class="listing" summary="Modules selecting the MPI environment">
+<tbody>
+<tr><th>Module</th><th>MPI</th><th>Compiler suite</th></tr>
+<tr class="odd">
+<td>impi-5.0.3.048-iccifort-2015.3.187</td>
+<td>Intel MPI 5.0.3</td>
+<td></td>
+</tr>
+<tr class="even">
+<td>OpenMP-1.8.6-GNU-5.1.0-2.25</td>
+<td>OpenMPI 1.8.6</td>
+<td></td>
+</tr>
+</tbody>
+</table>
+<p>Examples:</p>
+<pre class=" ">$ module load gompi/2015b</pre>
+<p>In this example, we activate the latest OpenMPI with latest GNU compilers (OpenMPI 1.8.6 and GCC 5.1). Please see more information about toolchains in section <a href="../../environment-and-modules.html">Environment and Modules</a> .</p>
+<p>To use OpenMPI with the intel compiler suite, use</p>
+<pre class=" ">$ module load iompi/2015.03</pre>
+<p>In this example, the openmpi 1.8.6 using intel compilers is activated. It's used "iompi" toolchain.</p>
+<h2 class=" ">Compiling MPI Programs</h2>
+<p class="callout">After setting up your MPI environment, compile your program using one of the mpi wrappers</p>
+<pre class=" ">$ mpicc -v<br />$ mpif77 -v<br />$ mpif90 -v</pre>
+<p>When using Intel MPI, use the following MPI wrappers:</p>
+<pre class=" ">$ mpicc<br />$ mpiifort </pre>
+<p>Wrappers mpif90, mpif77 that are provided by Intel MPI are designed for gcc and gfortran. You might be able to compile MPI code by them even with Intel compilers, but you might run into problems (for example, native MIC compilation with -mmic does not work with mpif90).</p>
+<p>Example program:</p>
+<pre class=" ">// helloworld_mpi.c<br />#include <stdio.h><br /><br />#include<mpi.h><br /><br />int main(int argc, char **argv) {<br /><br />int len;<br />int rank, size;<br />char node[MPI_MAX_PROCESSOR_NAME];<br /><br />// Initiate MPI<br />MPI_Init(&argc, &argv);<br />MPI_Comm_rank(MPI_COMM_WORLD,&rank);<br />MPI_Comm_size(MPI_COMM_WORLD,&size);<br /><br />// Get hostame and print<br />MPI_Get_processor_name(node,&len);<br />printf("Hello world! from rank %d of %d on host %s\n",rank,size,node);<br /><br />// Finalize and exit<br />MPI_Finalize();<br /><br />return 0;<br />}</pre>
+<p>Compile the above example with</p>
+<pre class=" ">$ mpicc helloworld_mpi.c -o helloworld_mpi.x</pre>
+<h2 class=" ">Running MPI Programs</h2>
+<p class="callout">The MPI program executable must be compatible with the loaded MPI module. <br />Always compile and execute using the very same MPI module.</p>
+<p>It is strongly discouraged to mix mpi implementations. Linking an application with one MPI implementation and running mpirun/mpiexec form other implementation may result in unexpected errors.</p>
+<p>The MPI program executable must be available within the same path on all nodes. This is automatically fulfilled on the /home and /scratch filesystem. You need to preload the executable, if running on the local scratch /lscratch filesystem.</p>
+<h3 class=" ">Ways to run MPI programs</h3>
+<p>Optimal way to run an MPI program depends on its memory requirements, memory access pattern and communication pattern.</p>
+<p class="callout">Consider these ways to run an MPI program:<br />1. One MPI process per node, 24 threads per process<br />2. Two MPI processes per node, 12 threads per process<br />3. 24 MPI processes per node, 1 thread per process.</p>
+<p class=" "><strong>One MPI</strong> process per node, using 24 threads, is most useful for memory demanding applications, that make good use of processor cache memory and are not memory bound. This is also a preferred way for communication intensive applications as one process per node enjoys full bandwidth access to the network interface. </p>
+<p class=" "><strong>Two MPI</strong> processes per node, using 12 threads each, bound to processor socket is most useful for memory bandwidth bound applications such as BLAS1 or FFT, with scalable memory demand. However, note that the two processes will share access to the network interface. The 12 threads and socket binding should ensure maximum memory access bandwidth and minimize communication, migration and numa effect overheads.</p>
+<p class="callout">Important! Bind every OpenMP thread to a core!</p>
+<p>In the previous two cases with one or two MPI processes per node, the operating system might still migrate OpenMP threads between cores. You want to avoid this by setting the KMP_AFFINITY or GOMP_CPU_AFFINITY environment variables.</p>
+<p class=" "><strong class=" ">24 MPI</strong> processes per node, using 1 thread each bound to processor core is most suitable for highly scalable applications with low communication demand.</p>
+<h3 class=" ">Running OpenMPI</h3>
+<p>The <a class="external-link" href="http://www.open-mpi.org/" target="_self" title=""><strong>OpenMPI 1.8.6</strong></a> is based on OpenMPI. Read more on <a href="Running_OpenMPI.html" title="" target="_self" class="internal-link">how to run OpenMPI</a> based MPI.</p>
+<p>Â </p>
+<p>The Intel MPI may run on the<a href="../intel-xeon-phi.html" title="" target="_self" class="internal-link"> Intel Xeon Ph</a>i accelerators as well. Read more on <a href="../intel-xeon-phi.html" title="" target="_self" class="internal-link">how to run Intel MPI on accelerators</a>.</p>
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+ <h2 class=" ">Introduction</h2>
+<p>MPI for Python provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.</p>
+<p>This package is constructed on top of the MPI-1/2 specifications and provides an object oriented interface which closely follows MPI-2 C++ bindings. It supports point-to-point (sends, receives) and collective (broadcasts, scatters, gathers) communications of any picklable Python object, as well as optimized communications of Python object exposing the single-segment buffer interface (NumPy arrays, builtin bytes/string/array objects).</p>
+<p>On Anselm MPI4Py is available in standard Python modules.</p>
+<h2 class=" ">Modules</h2>
+<p>MPI4Py is build for OpenMPI. Before you start with MPI4Py you need to load Python and OpenMPI modules. You can use toolchain, that loads Python and OpenMPI at once.</p>
+<pre><span>$ module load Python/2.7.9-foss-2015g</span><span><br /></span></pre>
+<h2 class=" ">Execution</h2>
+<p>You need to import MPI to your python program. Include the following line to the python script:</p>
+<pre class=" ">from mpi4py import MPI</pre>
+<p>The MPI4Py enabled python programs <a href="Running_OpenMPI.html" title="" target="_self" class="internal-link">execute as any other OpenMPI</a> code.The simpliest way is to run</p>
+<pre><span>$ mpiexec python <script>.py</span></pre>
+<p><span>For example</span></p>
+<pre>$ mpiexec python hello_world.py</pre>
+<h2 class=" ">Examples</h2>
+<h3 class=" ">Hello world!</h3>
+<pre><span class="kn">from</span> <span class="nn">mpi4py</span> <span class="kn">import</span> <span class="n">MPI<br /><br />comm = MPI.COMM_WORLD<br /><br />print "Hello! I'm rank %d from %d running in total..." % (comm.rank, comm.size)<br /><br />comm.Barrier() Â # wait for everybody to synchronize<br /></span></pre>
+<h3 class=" "><span>Collective Communication with NumPy arrays</span></h3>
+<pre class=" "><span class="kn">from __future__ import division<br />from</span> <span class="nn">mpi4py</span> <span class="kn">import</span> <span class="n">MPI<br /></span>import numpy as np<br /><br />comm = MPI.COMM_WORLD<br /><br />print("-"*78)<br />print(" Running on %d cores" % comm.size)<br />print("-"*78)<br /><br />comm.Barrier()<br /><br /># Prepare a vector of N=5 elements to be broadcasted...<br />N = 5<br />if comm.rank == 0:<br />Â Â A = np.arange(N, dtype=np.float64) Â Â # rank 0 has proper data<br />else:<br />Â Â A = np.empty(N, dtype=np.float64) Â Â # all other just an empty array<br /><br /># Broadcast A from rank 0 to everybody<br />comm.Bcast( [A, MPI.DOUBLE] )<br /><br /># Everybody should now have the same...<br />print "[%02d] %s" % (comm.rank, A)</pre>
+<p class=" ">Execute the above code as:</p>
+<pre class=" ">$ qsub -q qexp -l select=4:ncpus=24:mpiprocs=24:ompthreads=1 -I<br /><br />$ module load Python/2.7.9-foss-2015g<br /><br />$ mpiexec --map-by core --bind-to core python hello_world.py</pre>
+<p class=" ">In this example, we run MPI4Py enabled code on 4 nodes, 24 cores per node (total of 96 processes), each python process is bound to a different core.<br />More examples and documentation can be found on <a class="external-link" href="https://pythonhosted.org/mpi4py/usrman/index.html" target="_blank" title="">MPI for Python webpage</a>.</p>
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+<p>This section contains a collection of high-level interpreted languages, primarily intended for numerical computations.</p>
+<h2 class=" ">Matlab</h2>
+<p>MATLAB<sup>®</sup> is a high-level language and interactive environment for numerical computation, visualization, and programming.</p>
+<pre class=" ">$ module load MATLAB<br />$ matlab</pre>
+<p>Read more at the <a href="numerical-languages/matlab.html" title="" target="_self" class="internal-link">Matlab<span class="internal-link"></span> page</a>.</p>
+<h2 class=" ">Octave</h2>
+<p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.</p>
+<pre class=" ">$ module load Octave<br />$ octave</pre>
+<p>Read more at the <a href="numerical-languages/octave.html" title="" target="_self" class="internal-link">Octave page</a>.</p>
+<h2 class=" ">R</h2>
+<p>The R is an interpreted language and environment for statistical computing and graphics.</p>
+<pre class=" ">$ module load R<br />$ R</pre>
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+ <h2 class=" ">Introduction</h2>
+<p>This section contains a collection of high-level interpreted languages, primarily intended for numerical computations.</p>
+<h2 class=" ">Matlab</h2>
+<p>MATLAB<sup>®</sup> is a high-level language and interactive environment for numerical computation, visualization, and programming.</p>
+<pre class=" ">$ module load MATLAB<br />$ matlab</pre>
+<p>Read more at the <a href="matlab.html" title="" target="_self" class="internal-link">Matlab<span class="internal-link"></span> page</a>.</p>
+<h2 class=" ">Octave</h2>
+<p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. The Octave language is quite similar to Matlab so that most programs are easily portable.</p>
+<pre class=" ">$ module load Octave<br />$ octave</pre>
+<p>Read more at the <a href="octave.html" title="" target="_self" class="internal-link">Octave page</a>.</p>
+<h2 class=" ">R</h2>
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+ Matlab
+ </h1>
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+ <div id="parent-fieldname-text-2efd48d0282d45b7b8fb11393c96d853" class="">
+ <h2 class=" ">Introduction</h2>
+<p>Matlab is available in versions R2015a and R2015b. There are always two variants of the release:</p>
+<ul>
+<li>Non commercial or so called EDU variant, which can be used for common research and educational purposes.</li>
+<li>Commercial or so called COM variant, which can used also for commercial activities. The licenses for commercial variant are much more expensive, so usually the commercial variant has only subset of features compared to the EDU available.</li>
+</ul>
+<p>Â </p>
+<p>To load the latest version of Matlab load the module</p>
+<pre class=" ">$ module load MATLAB</pre>
+<p>By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use</p>
+<pre class=" ">$ module avail MATLAB</pre>
+<p>If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.</p>
+<p>If you require the Matlab GUI, please follow the general informations about <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">running graphical applications</a>.</p>
+<p>Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">here</a>) is recommended.</p>
+<p>To run Matlab with GUI, use</p>
+<pre class=" ">$ matlab</pre>
+<p>To run Matlab in text mode, without the Matlab Desktop GUI environment, use</p>
+<pre class=" ">$ matlab -nodesktop -nosplash</pre>
+<p>plots, images, etc... will be still available.</p>
+<h2 class=" "><a name="running-parallel-matlab-using-distributed-computing-toolbox---engine"></a>Running parallel Matlab using Distributed Computing Toolbox / Engine</h2>
+<p class="exclamation">Distributed toolbox is available only for the EDU variant</p>
+<p class=" ">The MPIEXEC mode available in previous versions is no longer available in MATLAB 2015. Also, the programming interface has changed. Refer to <a class="external-link" href="http://www.mathworks.com/help/distcomp/release-notes.html#buanp9e-1" target="_self" title="">Release Notes</a>.</p>
+<p class=" ">Delete previously used file mpiLibConf.m, we have observed crashes when using Intel MPI.</p>
+<p class=" ">To use Distributed Computing, you first need to setup a parallel profile. We have provided the profile for you, you can either import it in MATLAB command line:</p>
+<pre class=" ">>> parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings')<br /><br />ans = <br /><br />SalomonPBSPro </pre>
+<p class=" ">Or in the GUI, go to tab HOME -> Parallel -> Manage Cluster Profiles..., click Import and navigate to :</p>
+<p class=" ">/apps/all/MATLAB/2015b-EDU/SalomonPBSPro.settings</p>
+<p class=" ">With the new mode, MATLAB itself launches the workers via PBS, so you can either use interactive mode or a batch mode on one node, but the actual parallel processing will be done in a separate job started by MATLAB itself. Alternatively, you can use "local" mode to run parallel code on just a single node.</p>
+<h3 class=" ">Parallel Matlab interactive session</h3>
+<p>Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see <a href="../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html" title="" target="_self" class="internal-link">this page</a>.</p>
+<pre class=" ">$ xhost +<br />$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00 \<br />-l feature__matlab__MATLAB=1 </pre>
+<p>This qsub command example shows how to run Matlab on a single node.</p>
+<p>The second part of the command shows how to request all necessary licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing Engines licenses.</p>
+<p>Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:Â </p>
+<pre class=" ">r1i0n17$ module load MATLAB/2015a-EDU<br />r1i0n17$ matlab &</pre>
+<h3 class=" "><a name="parallel-matlab-batch-job-in-local-mode"></a>Parallel Matlab batch job in Local mode</h3>
+<p>To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.</p>
+<pre class=" ">#!/bin/bash<br />#PBS -A PROJECT ID<br />#PBS -q qprod<br />#PBS -l select=1:ncpus=24:mpiprocs=24:ompthreads=1<br /><br /># change to shared scratch directory<br />SCR=/scratch/work/user/$USER/$PBS_JOBID<br />mkdir -p $SCR ; cd $SCR || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/matlabcode.m .<br /><br /># load modules<br />module load MATLAB/2015a-EDU<br /><br /># execute the calculation<br />matlab -nodisplay -r matlabcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.</pre>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, <strong>the .m must not be included</strong>. Note that the <strong>shared /scratch must be used</strong>. Further, it is <strong>important to include quit</strong> statement at the end of the matlabcode.m script.</p>
+<p>Submit the jobscript using qsub</p>
+<pre class=" ">$ qsub ./jobscript</pre>
+<h3 class=" ">Parallel Matlab Local mode program example</h3>
+<p>The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.</p>
+<pre class=" ">cluster = parcluster('local')</pre>
+<p class=" ">This script creates scheduler object "cluster" of type "local" that starts workers locally. </p>
+<p class="callout">Please note: Every Matlab script that needs to initialize/use matlabpool has to contain these three lines prior to calling parpool(sched, ...) function. </p>
+<p class=" ">The last step is to start matlabpool with "cluster" object and correct number of workers. We have 24 cores per node, so we start 24 workers.</p>
+<pre class=" ">parpool(cluster,24);<br /> <br /> <br />... parallel code ...<br /> <br /> <br />parpool close</pre>
+<p>The complete example showing how to use Distributed Computing Toolbox in local mode is shown here. </p>
+<pre class=" ">cluster = parcluster('local');<br />cluster<br /><br />parpool(cluster,24);<br /><br />n=2000;<br /><br />W = rand(n,n);<br />W = distributed(W);<br />x = (1:n)';<br />x = distributed(x);<br />spmd<br />[~, name] = system('hostname')<br />   <br />   T = W*x; % Calculation performed on labs, in parallel.<br />            % T and W are both codistributed arrays here.<br />end<br />T;<br />whos        % T and W are both distributed arrays here.<br /><br />parpool close<br />quit</pre>
+<p>You can copy and paste the example in a .m file and execute. Note that the parpool size should correspond to <strong>total number of cores</strong> available on allocated nodes.</p>
+<h3 class=" ">Parallel Matlab Batch job using PBS mode (workers spawned in a separate job)</h3>
+<p>This mode uses PBS scheduler to launch the parallel pool. It uses the SalomonPBSPro profile that needs to be imported to Cluster Manager, as mentioned before. This methodod uses MATLAB's PBS Scheduler interface - it spawns the workers in a separate job submitted by MATLAB using qsub.</p>
+<p>This is an example of m-script using PBS mode:</p>
+<pre class=" ">cluster = parcluster('SalomonPBSPro');
+set(cluster, 'SubmitArguments', '-A OPEN-0-0');
+set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=24');
+set(cluster, 'NumWorkers', 240);
+
+pool = parpool(cluster,240);
+
+n=2000;
+
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
+
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
+
+% shut down parallel pool
+delete(pool)
+</pre>
+<p class=" ">Note that we first construct a cluster object using the imported profile, then set some important options, namely : SubmitArguments, where you need to specify accounting id, and ResourceTemplate, where you need to specify number of nodes to run the job. </p>
+<p class=" ">You can start this script using batch mode the same way as in Local mode example.</p>
+<h3 class=" ">Parallel Matlab Batch with direct launch (workers spawned within the existing job)</h3>
+<p>This method is a "hack" invented by us to emulate the mpiexec functionality found in previous MATLAB versions. We leverage the MATLAB Generic Scheduler interface, but instead of submitting the workers to PBS, we launch the workers directly within the running job, thus we avoid the issues with master script and workers running in separate jobs (issues with license not available, waiting for the worker's job to spawn etc.)</p>
+<p>Please note that this method is experimental.</p>
+<p>For this method, you need to use SalomonDirect profile, import it using <a class="anchor-link" href="matlab.html#running-parallel-matlab-using-distributed-computing-toolbox---engine" target="_self" title="">the same way as SalomonPBSPro</a> </p>
+<p>This is an example of m-script using direct mode:</p>
+<pre class=" "><br />parallel.importProfile('/apps/all/MATLAB/2015b-EDU/SalomonDirect.settings')<br />cluster = parcluster('SalomonDirect');
+set(cluster, 'NumWorkers', 48);
+
+pool = parpool(cluster, 48);
+
+n=2000;
+
+W = rand(n,n);
+W = distributed(W);
+x = (1:n)';
+x = distributed(x);
+spmd
+[~, name] = system('hostname')
+
+ T = W*x; % Calculation performed on labs, in parallel.
+ % T and W are both codistributed arrays here.
+end
+whos % T and W are both distributed arrays here.
+
+% shut down parallel pool
+delete(pool)</pre>
+<h3 class=" ">Non-interactive Session and Licenses</h3>
+<p>If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the " -l __feature__matlab__MATLAB=1" for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please <a href="../../../anselm-cluster-documentation/software/isv_licenses.html" title="" target="_self" class="internal-link">look here</a>.</p>
+<p class="exclamation">The licensing feature of PBS is currently disabled.</p>
+<p>In case of non-interactive session please read the <a href="../../../anselm-cluster-documentation/software/isv_licenses.html" title="" target="_self" class="internal-link">following information</a> on how to modify the qsub command to test for available licenses prior getting the resource allocation.</p>
+<h3 class=" ">Matlab Distributed Computing Engines start up time</h3>
+<p>Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:</p>
+<table class="plain">
+<tbody>
+<tr><th>compute nodes</th><th>number of workers</th><th>start-up time[s]</th></tr>
+<tr>
+<td>16</td>
+<td>384</td>
+<td>831</td>
+</tr>
+<tr>
+<td>8</td>
+<td>192</td>
+<td>807</td>
+</tr>
+<tr>
+<td>4</td>
+<td>96</td>
+<td>483</td>
+</tr>
+<tr>
+<td>2</td>
+<td>48</td>
+<td>16</td>
+</tr>
+</tbody>
+</table>
+<h2>MATLAB on UV2000Â </h2>
+<p>UV2000 machine available in queue "qfat" can be used for MATLAB computations. This is a SMP NUMA machine with large amount of RAM, which can be beneficial for certain types of MATLAB jobs. CPU cores are allocated in chunks of 8 for this machine.</p>
+<p>You can use MATLAB on UV2000 in two parallel modes :</p>
+<h3>Threaded mode</h3>
+<p class=" ">Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set <span class="monospace">maxNumCompThreads </span>accordingly and certain operations, such as <span class="monospace">fft, \, eig, svd</span>, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.<span class="monospace"><br /></span></p>
+<h3 class=" ">Local cluster mode</h3>
+<p>You can also use Parallel Toolbox on UV2000. Use l<a class="anchor-link" href="matlab.html#parallel-matlab-batch-job-in-local-mode" target="_self" title="">ocal cluster mode</a>, "SalomonPBSPro" profile will not work.</p>
+<p>Â </p>
+<p>Â </p>
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diff --git a/docs.it4i.cz/salomon/software/numerical-languages/matlab.md b/docs.it4i.cz/salomon/software/numerical-languages/matlab.md
index 90a2dbae7..32e0f3e37 100644
--- a/docs.it4i.cz/salomon/software/numerical-languages/matlab.md
+++ b/docs.it4i.cz/salomon/software/numerical-languages/matlab.md
@@ -160,7 +160,7 @@ script before Distributed Computing Toolbox is started.
This script creates scheduler object "cluster" of type "local" that
starts workers locally.Â
-Please noteEvery Matlab script that needs to initialize/use matlabpool
+Please note: Every Matlab script that needs to initialize/use matlabpool
has to contain these three lines prior to calling parpool(sched, ...)
function.Â
@@ -239,7 +239,7 @@ This is an example of m-script using PBS mode:
delete(pool)
Note that we first construct a cluster object using the imported
-profile, then set some important options, namely SubmitArguments,
+profile, then set some important options, namely : SubmitArguments,
where you need to specify accounting id, and ResourceTemplate, where you
need to specify number of nodes to run the job.Â
diff --git a/docs.it4i.cz/salomon/software/numerical-languages/octave.html b/docs.it4i.cz/salomon/software/numerical-languages/octave.html
new file mode 100644
index 000000000..19c8736ec
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/numerical-languages/octave.html
@@ -0,0 +1,964 @@
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+ <p>GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable. Read more on <a class="external-link" href="http://www.gnu.org/software/octave/" target="_self" title="">http://www.gnu.org/software/octave/</a><strong></strong></p>
+<p><strong><br /></strong>Two versions of octave are available on the cluster, via module</p>
+<table class="listing">
+<tbody>
+<tr><th style="text-align: left; ">Status</th><th style="text-align: left; ">Version</th><th style="text-align: left; ">module</th></tr>
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+<td><strong>Stable</strong></td>
+<td>Octave 3.8.2</td>
+<td>Octave</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<pre class=" ">$ module load Octave</pre>
+<p>The octave on the cluster is linked to highly optimized MKL mathematical library. This provides threaded parallelization to many octave kernels, notably the linear algebra subroutines. Octave runs these heavy calculation kernels without any penalty. By default, octave would parallelize to 24 threads. You may control the threads by setting the OMP_NUM_THREADS environment variable.</p>
+<p>To run octave interactively, log in with ssh -X parameter for X11 forwarding. Run octave:</p>
+<pre class=" ">$ octave</pre>
+<p>To run octave in batch mode, write an octave script, then write a bash jobscript and execute via the qsub command. By default, octave will use 16 threads when running MKL kernels.</p>
+<pre class=" ">#!/bin/bash<br /><br /># change to local scratch directory<br />mkdir -p /scratch/work/user/$USER/$PBS_JOBID<br />cd /scratch/work/user/$USER/$PBS_JOBID || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/octcode.m .<br /><br /># load octave module<br />module load Octave<br /><br /># execute the calculation<br />octave -q --eval octcode > output.out<br /><br /># copy output file to home<br />cp output.out $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in octcode.m file, outputs in output.out file. See the single node jobscript example in the <a href="../../resource-allocation-and-job-execution.html" title="" target="_self" class="internal-link">Job execution section</a>.</p>
+<p class="hiddenForView">The octave c compiler mkoctfile calls the GNU gcc 4.8.1 for compiling native c code. This is very useful for running native c subroutines in octave environment.</p>
+<p class="hiddenForView">$ mkoctfile -v</p>
+<p class="hiddenForView">Octave may use MPI for interprocess communication<br />This functionality is currently not supported on the cluster cluster. In case you require the octave interface to MPI, please contact our <a class="external-link" href="https://support.it4i.cz/rt/" target="_self" title="">cluster support</a>.</p>
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+ <h2 class=" " id="parent-fieldname-title">Introduction</h2>
+<p class=" ">The R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible.</p>
+<div id="content-core">
+<div id="parent-fieldname-text-4a9d341ec7e54eecbc6b9c0d8f470ebc">
+<p>One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.</p>
+<p>Another convenience is the ease with which the C code or third party libraries may be integrated within R.</p>
+<p>Extensive support for parallel computing is available within R.</p>
+<p>Read more on <a class="external-link" href="http://www.r-project.org/" target="_self" title="">http://www.r-project.org/</a>, <a class="external-link" href="http://cran.r-project.org/doc/manuals/r-release/R-lang.html" target="_self" title="">http://cran.r-project.org/doc/manuals/r-release/R-lang.html</a></p>
+<h2 class=" ">Modules</h2>
+<p><strong></strong>The R version 3.1.1 is available on the cluster, along with GUI interface Rstudio</p>
+<table class="listing">
+<tbody>
+<tr><th style="text-align: left; ">Application</th><th style="text-align: left; ">Version</th><th style="text-align: left; ">module</th></tr>
+<tr class="even">
+<td><strong>R</strong></td>
+<td>R 3.1.1</td>
+<td>R/3.1.1-intel-2015b</td>
+</tr>
+<tr class="odd">
+<td><strong>Rstudio</strong></td>
+<td>Rstudio 0.97</td>
+<td>Rstudio</td>
+</tr>
+</tbody>
+</table>
+<pre class=" ">$ module load R</pre>
+<h2 class=" ">Execution</h2>
+<p><a name="interactive-execution"></a>The R on Anselm is linked to highly optimized MKL mathematical library. This provides threaded parallelization to many R kernels, notably the linear algebra subroutines. The R runs these heavy calculation kernels without any penalty. By default, the R would parallelize to 24 threads. You may control the threads by setting the OMP_NUM_THREADS environment variable.</p>
+<h3 class=" ">Interactive execution</h3>
+<p>To run R interactively, using Rstudio GUI, log in with ssh -X parameter for X11 forwarding. Run rstudio:</p>
+<pre class=" ">$ module load Rstudio<br />$ rstudio</pre>
+<h3 class=" ">Batch execution</h3>
+<p>To run R in batch mode, write an R script, then write a bash jobscript and execute via the qsub command. By default, R will use 24 threads when running MKL kernels.</p>
+<p>Example jobscript:</p>
+<pre class=" ">#!/bin/bash<br /><br /># change to local scratch directory<br />cd /lscratch/$PBS_JOBID || exit<br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/rscript.R .<br /><br /># load R module<br />module load R<br /><br /># execute the calculation<br />R CMD BATCH rscript.R routput.out<br /><br /># copy output file to home<br />cp routput.out $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
+<p>This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_self" class="internal-link">Job execution section</a>.</p>
+<h2 class=" ">Parallel R</h2>
+<p>Parallel execution of R may be achieved in many ways. One approach is the implied parallelization due to linked libraries or specially enabled functions, as <a class="anchor-link" href="r.html#interactive-execution" target="_self" title="">described above</a>. In the following sections, we focus on explicit parallelization, where parallel constructs are directly stated within the R script.</p>
+<h2 class=" "><a name="package-parallel"></a>Package parallel</h2>
+<p class=" ">The package parallel provides support for parallel computation, including by forking (taken from package multicore), by sockets (taken from package snow) and random-number generation.</p>
+<p class=" ">The package is activated this way:</p>
+<pre class=" ">$ R<br />> library(parallel)</pre>
+<p class=" ">More information and examples may be obtained directly by reading the documentation available in R</p>
+<pre class=" ">> ?parallel<br />> library(help = "parallel")<br />> <span class="internal-link">vignette("parallel")</span></pre>
+<p class=" ">Download the package <a href="package-parallel-vignette" title="" target="_self" class="internal-link">parallell</a> vignette.</p>
+<p class=" ">The forking is the most simple to use. Forking family of functions provide parallelized, drop in replacement for the serial apply() family of functions.</p>
+<p class="callout">Forking via package parallel provides functionality similar to OpenMP construct<br />#omp parallel for <br /><br />Only cores of single node can be utilized this way!</p>
+<p class=" ">Forking example:</p>
+<pre class=" ">library(parallel)<br /><br />#integrand function<br />f <- function(i,h) {<br />x <- h*(i-0.5)<br />return (4/(1 + x*x))<br />}<br /><br />#initialize<br />size <- detectCores()<br /><br />while (TRUE)<br />{<br /> #read number of intervals<br /> cat("Enter the number of intervals: (0 quits) ")<br /> fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)<br /><br /> if(n<=0) break<br /><br /> #run the calculation<br /> n <- max(n,size)<br /> h <- 1.0/n<br /><br /> i <- seq(1,n);<br /> pi3 <- h*sum(simplify2array(mclapply(i,f,h,mc.cores=size)));<br /><br /> #print results<br /> cat(sprintf("Value of PI %16.14f, diff= %16.14f\n",pi3,pi3-pi))<br />}<br /><br /></pre>
+<p>The above example is the classic parallel example for calculating the number π. Note the <strong>detectCores()</strong> and <strong>mclapply()</strong> functions.<br />Execute the example as:</p>
+<pre class=" ">$ R --slave --no-save --no-restore -f pi3p.R</pre>
+<p>Every evaluation of the integrad function runs in parallel on different process.</p>
+<h2 class=" ">Package Rmpi</h2>
+<p class="callout">package Rmpi provides an interface (wrapper) to MPI APIs.</p>
+<p>It also provides interactive R slave environment. On the cluster, Rmpi provides interface to the <a href="../mpi-1/Running_OpenMPI.html" title="" target="_self" class="internal-link">OpenMPI</a>.</p>
+<p>Read more on Rmpi at <a class="external-link" href="http://cran.r-project.org/web/packages/Rmpi/" target="_self" title="">http://cran.r-project.org/web/packages/Rmpi/</a>, reference manual is available at <a class="external-link" href="http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf" target="_self" title="">http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf</a></p>
+<p>When using package Rmpi, both openmpi and R modules must be loaded</p>
+<pre class=" ">$ module load OpenMPI<br />$ module load R</pre>
+<p>Rmpi may be used in three basic ways. The static approach is identical to executing any other MPI programm. In addition, there is Rslaves dynamic MPI approach and the mpi.apply approach. In the following section, we will use the number π integration example, to illustrate all these concepts.</p>
+<h3 class=" "><a name="static-rmpi"></a>static Rmpi</h3>
+<p>Static Rmpi programs are executed via mpiexec, as any other MPI programs. Number of processes is static - given at the launch time.</p>
+<p>Static Rmpi example:</p>
+<pre class=" ">library(Rmpi)<br /><br />#integrand function<br />f <- function(i,h) {<br />x <- h*(i-0.5)<br />return (4/(1 + x*x))<br />}<br /><br />#initialize<br />invisible(mpi.comm.dup(0,1))<br />rank <- mpi.comm.rank()<br />size <- mpi.comm.size()<br />n<-0<br /><br />while (TRUE)<br />{<br /> #read number of intervals<br /> if (rank==0) {<br /> cat("Enter the number of intervals: (0 quits) ")<br /> fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)<br /> }<br /><br /> #broadcat the intervals<br /> n <- mpi.bcast(as.integer(n),type=1)<br /><br /> if(n<=0) break<br /><br /> #run the calculation<br /> n <- max(n,size)<br /> h <- 1.0/n<br /><br /> i <- seq(rank+1,n,size);<br /> mypi <- h*sum(sapply(i,f,h));<br /><br /> pi3 <- mpi.reduce(mypi)<br /><br /> #print results<br /> if (rank==0) cat(sprintf("Value of PI %16.14f, diff= %16.14f\n",pi3,pi3-pi))<br />}<br /><br />mpi.quit()</pre>
+<p>The above is the static MPI example for calculating the number π. Note the <strong>library(Rmpi) </strong>and<strong> mpi.comm.dup()</strong> function calls.<br />Execute the example as:</p>
+<pre class=" ">$ mpirun R --slave --no-save --no-restore -f pi3.R</pre>
+<h3 class=" ">dynamic Rmpi</h3>
+<p>Dynamic Rmpi programs are executed by calling the R directly. OpenMPI module must be still loaded. The R slave processes will be spawned by a function call within the Rmpi program.</p>
+<p>Dynamic Rmpi example:</p>
+<pre class=" ">#integrand function<br />f <- function(i,h) {<br />x <- h*(i-0.5)<br />return (4/(1 + x*x))<br />}<br /><br />#the worker function<br />workerpi <- function()<br />{<br />#initialize<br />rank <- mpi.comm.rank()<br />size <- mpi.comm.size()<br />n<-0<br /><br />while (TRUE)<br />{<br /> #read number of intervals<br /> if (rank==0) {<br /> cat("Enter the number of intervals: (0 quits) ")<br /> fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)<br /> }<br /><br /> #broadcat the intervals<br /> n <- mpi.bcast(as.integer(n),type=1)<br /><br /> if(n<=0) break<br /><br /> #run the calculation<br /> n <- max(n,size)<br /> h <- 1.0/n<br /><br /> i <- seq(rank+1,n,size);<br /> mypi <- h*sum(sapply(i,f,h));<br /><br /> pi3 <- mpi.reduce(mypi)<br /><br /> #print results<br /> if (rank==0) cat(sprintf("Value of PI %16.14f, diff= %16.14f\n",pi3,pi3-pi))<br />}<br />}<br /><br />#main<br />library(Rmpi)<br /><br />cat("Enter the number of slaves: ")<br />fp<-file("stdin"); ns<-scan(fp,nmax=1); close(fp)<br /><br />mpi.spawn.Rslaves(nslaves=ns)<br />mpi.bcast.Robj2slave(f)<br />mpi.bcast.Robj2slave(workerpi)<br /><br />mpi.bcast.cmd(workerpi())<br />workerpi()<br /><br /><br />mpi.quit()</pre>
+<p>The above example is the dynamic MPI example for calculating the number π. Both master and slave processes carry out the calculation. Note the <strong>mpi.spawn.Rslaves(), mpi.bcast.Robj2slave() </strong>and the<strong> mpi.bcast.cmd()</strong> function calls.<br />Execute the example as:</p>
+<pre class=" ">$ mpirun -np 1 R --slave --no-save --no-restore -f pi3Rslaves.R</pre>
+Note that this method uses MPI_Comm_spawn (Dynamic process feature of MPI-2) to start the slave processes - the master process needs to be launched with MPI. In general, Dynamic processes are not well supported among MPI implementations, some issues might arise. Also, environment variables are not propagated to spawned processes, so they will not see paths from modules.
+<h3 class=" ">mpi.apply Rmpi</h3>
+<p>mpi.apply is a specific way of executing Dynamic Rmpi programs.</p>
+<p class="callout">mpi.apply() family of functions provide MPI parallelized, drop in replacement for the serial apply() family of functions.</p>
+<p>Execution is identical to other dynamic Rmpi programs.</p>
+<p>mpi.apply Rmpi example:</p>
+<pre class=" ">#integrand function<br />f <- function(i,h) {<br />x <- h*(i-0.5)<br />return (4/(1 + x*x))<br />}<br /><br />#the worker function<br />workerpi <- function(rank,size,n)<br />{<br /> #run the calculation<br /> n <- max(n,size)<br /> h <- 1.0/n<br /><br /> i <- seq(rank,n,size);<br /> mypi <- h*sum(sapply(i,f,h));<br /><br /> return(mypi)<br />}<br /><br />#main<br />library(Rmpi)<br /><br />cat("Enter the number of slaves: ")<br />fp<-file("stdin"); ns<-scan(fp,nmax=1); close(fp)<br /><br />mpi.spawn.Rslaves(nslaves=ns)<br />mpi.bcast.Robj2slave(f)<br />mpi.bcast.Robj2slave(workerpi)<br /><br />while (TRUE)<br />{<br /> #read number of intervals<br /> cat("Enter the number of intervals: (0 quits) ")<br /> fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)<br /> if(n<=0) break<br /><br /> #run workerpi<br /> i=seq(1,2*ns)<br /> pi3=sum(mpi.parSapply(i,workerpi,2*ns,n))<br /><br /> #print results<br /> cat(sprintf("Value of PI %16.14f, diff= %16.14f\n",pi3,pi3-pi))<br />}<br /><br />mpi.quit()</pre>
+<p>The above is the mpi.apply MPI example for calculating the number π. Only the slave processes carry out the calculation. Note the <strong>mpi.parSapply(), </strong> function call. The package <span class="anchor-link">parallel <a class="anchor-link" href="r.html#package-parallel" target="_self" title="">example</a></span><a class="anchor-link" href="r.html#package-parallel" target="_self" title=""> above</a> may be trivially adapted (for much better performance) to this structure using the mclapply() in place of mpi.parSapply().</p>
+<p>Execute the example as:</p>
+<pre class=" ">$ mpirun -np 1 R --slave --no-save --no-restore -f pi3parSapply.R</pre>
+<h2 class=" ">Combining parallel and Rmpi</h2>
+<p>Currently, the two packages can not be combined for hybrid calculations.</p>
+<h2 class=" ">Parallel execution</h2>
+<p>The R parallel jobs are executed via the PBS queue system exactly as any other parallel jobs. User must create an appropriate jobscript and submit via the <strong>qsub</strong></p>
+<p>Example jobscript for <a class="anchor-link" href="r.html#static-rmpi" target="_self" title="">static Rmpi</a> parallel R execution, running 1 process per core:</p>
+<pre class=" ">#!/bin/bash<br />#PBS -q qprod<br />#PBS -N Rjob<br />#PBS -l select=100:ncpus=24:mpiprocs=24:ompthreads=1<br /><br /># change to scratch directory<span class="pln"><br />SCRDIR</span><span class="pun">=/</span><span class="pln">scratch</span><span class="pun">/</span><span class="pln">work/user/$USER</span><span class="pun">/</span><span class="pln">myjob</span><br /><span class="pln">cd $SCRDIR </span><span class="pun">||</span><span class="pln"> exit</span><br /><br /># copy input file to scratch <br />cp $PBS_O_WORKDIR/rscript.R .<br /><br /># load R and openmpi module<br />module load R<br />module load OpenMPI<br /><br /># execute the calculation<br />mpiexec -bycore -bind-to-core R --slave --no-save --no-restore -f rscript.R<br /><br /># copy output file to home<br />cp routput.out $PBS_O_WORKDIR/.<br /><br />#exit<br />exit</pre>
+For more information about jobscripts and MPI execution refer to the <a href="../../resource-allocation-and-job-execution/job-submission-and-execution.html" title="" target="_self" class="internal-link">Job submission</a> and general <a href="../mpi-1.html" title="" target="_self" class="internal-link">MPI</a> sections.</div>
+<div></div>
+<div>
+<h2>Xeon Phi Offload</h2>
+<p>By leveraging MKL, R can accelerate certain computations, most notably linear algebra operations on the Xeon Phi accelerator by using Automated Offload. To use MKL Automated Offload, you need to first set this environment variable before R execution :</p>
+<pre>$ export MKL_MIC_ENABLE=1</pre>
+<p class=" "><a href="../intel-xeon-phi.html" title="" target="_self" class="internal-link">Read more about automatic offload</a></p>
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diff --git a/docs.it4i.cz/salomon/software/numerical-languages/r.md b/docs.it4i.cz/salomon/software/numerical-languages/r.md
index a66404d41..f1ac55755 100644
--- a/docs.it4i.cz/salomon/software/numerical-languages/r.md
+++ b/docs.it4i.cz/salomon/software/numerical-languages/r.md
@@ -153,7 +153,7 @@ Forking example:
while (TRUE)
{
#read number of intervals
- cat("Enter the number of intervals(0 quits) ")
+ cat("Enter the number of intervals: (0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
if(n<=0) break
@@ -227,7 +227,7 @@ Static Rmpi example:
{
#read number of intervals
if (rank==0) {
- cat("Enter the number of intervals(0 quits) ")
+ cat("Enter the number of intervals: (0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
}
@@ -283,7 +283,7 @@ Dynamic Rmpi example:
{
#read number of intervals
if (rank==0) {
- cat("Enter the number of intervals(0 quits) ")
+ cat("Enter the number of intervals: (0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
}
@@ -309,7 +309,7 @@ Dynamic Rmpi example:
#main
library(Rmpi)
- cat("Enter the number of slaves")
+ cat("Enter the number of slaves: ")
fp<-file("stdin"); ns<-scan(fp,nmax=1); close(fp)
mpi.spawn.Rslaves(nslaves=ns)
@@ -369,7 +369,7 @@ mpi.apply Rmpi example:
#main
library(Rmpi)
- cat("Enter the number of slaves")
+ cat("Enter the number of slaves: ")
fp<-file("stdin"); ns<-scan(fp,nmax=1); close(fp)
mpi.spawn.Rslaves(nslaves=ns)
@@ -379,7 +379,7 @@ mpi.apply Rmpi example:
while (TRUE)
{
#read number of intervals
- cat("Enter the number of intervals(0 quits) ")
+ cat("Enter the number of intervals: (0 quits) ")
fp<-file("stdin"); n<-scan(fp,nmax=1); close(fp)
if(n<=0) break
diff --git a/docs.it4i.cz/salomon/software/operating-system.html b/docs.it4i.cz/salomon/software/operating-system.html
new file mode 100644
index 000000000..a933ce2d5
--- /dev/null
+++ b/docs.it4i.cz/salomon/software/operating-system.html
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+ <h2 class=" ">Introduction</h2>
+<p>There are two main shared file systems on Salomon cluster, the <a class="anchor-link" href="storage/storage.html#home" target="_self" title=""><span class="anchor-link"><span class="anchor-link">HOME</span></span></a> and <a class="anchor-link" href="storage/storage.html#shared-filesystems" target="_self" title=""><span class="anchor-link"><span class="anchor-link">SCRATCH</span></span></a>. All login and compute nodes may access same data on shared filesystems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp filesystems.</p>
+<h2 class=" ">Policy (in a nutshell)</h2>
+<p class="callout">Use <a class="anchor-link" href="storage/storage.html#home" target="_self" title="">HOME</a> for your most valuable data and programs.<br />Use <a class="anchor-link" href="storage/storage.html#work" target="_self" title="">WORK</a> for your large project files<br />Use <a class="anchor-link" href="storage/storage.html#temp" target="_self" title="">TEMP</a> for large scratch data.</p>
+<p class="callout">Do not use for <a class="anchor-link" href="storage/storage.html#archiving" target="_self" title="">archiving</a>!</p>
+<h2 class=" "><a name="archiving"></a>Archiving</h2>
+<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a href="../anselm-cluster-documentation/storage-1/cesnet-data-storage.html" title="" target="_self" class="internal-link">CESNET storage service</a>, which is available via SSHFS.</p>
+<h2 class=" "><a name="shared-filesystems"></a>Shared Filesystems</h2>
+<p class=" ">Salomon computer provides two main shared filesystems, the <a class="anchor-link" href="storage/storage.html#home-filesystem" target="_self" title=""><span class="anchor-link">HOME filesystem</span></a> and the <a class="anchor-link" href="storage/storage.html#scratch-filesystem" target="_self" title="">SCRATCH filesystem</a>. The SCRATCH filesystem is partitioned to <a class="anchor-link" href="storage/storage.html#shared-workspaces" target="_self" title="">WORK and TEMP workspaces</a>. The HOME filesystem is realized as a tiered NFSÂ disk storage. The SCRATCH filesystem is realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both HOME/SCRATCH filesystems for the purpose of sharing data with other users using fine-grained control.</p>
+<h3 class=" "><a name="home-filesystem"></a><a name="home-filesystem"></a>HOME filesystem</h3>
+<p class=" ">The HOME filesystem is realized as a Tiered filesystem, exported via NFS. The first tier has capacity 100TB, second tier has capacity 400TB. The filesystem is available on all login and computational nodes. The Home filesystem hosts the <a class="anchor-link" href="storage/storage.html#home" target="_self" title="">HOME workspace</a>.</p>
+<h3 class=" "><a name="scratch-filesystem"></a><a name="the-scratch-filesystem"></a>SCRATCH filesystem</h3>
+<p>The architecture of Lustre on Salomon is composed of two metadata servers (MDS) and six data/object storage servers (OSS). Accessible capacity is 1.69 PB, shared among all users. The SCRATCH filesystem hosts the <a class="anchor-link" href="storage/storage.html#shared-workspaces" target="_self" title="">WORK and TEMP workspaces</a>.</p>
+<p class=" "><span class="listitem">Configuration of the SCRATCH Lustre storage<br /></span></p>
+<div class="itemizedlist"><span class="emphasis"></span><span class="emphasis"></span>
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem"><span class="emphasis">SCRATCH Lustre object storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">Disk array SFA12KX</li>
+<li class="listitem">540 4TB SAS 7.2krpm disks</li>
+<li class="listitem">54 OSTs of 10 disks in RAID6 (8+2)</li>
+<li class="listitem">15 hot-spare disks</li>
+<li class="listitem">4x 400GB SSD cache</li>
+</ul>
+</div>
+</li>
+<li class="listitem"><span class="emphasis">SCRATCH Lustre metadata storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">Disk array EF3015</li>
+<li class="listitem">12 600GB SAS 15krpm disks</li>
+</ul>
+</div>
+</li>
+</ul>
+</div>
+<h3 class=" ">Understanding the Lustre Filesystems</h3>
+<p>(source <a class="external-link" href="http://www.nas.nasa.gov" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
+<p>A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.</p>
+<p>When a client (a <span class="glossaryItem">compute <span class="glossaryItem">node</span></span> from your job) needs to create or access a file, the client queries the metadata server (<span class="glossaryItem">MDS</span>) and the metadata target (<span class="glossaryItem">MDT</span>) for the layout and location of the <a href="http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping">file's stripes</a>. Once the file is opened and the client obtains the striping information, the <span class="glossaryItem">MDS</span> is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.</p>
+<p>If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.</p>
+<p>There is default stripe configuration for Salomon Lustre filesystems. However, users can set the following stripe parameters for their own directories or files to get optimum I/O performance:</p>
+<ol><ol>
+<li>stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Salomon Lustre filesystems</li>
+<li>stripe_count the number of OSTs to stripe across; default is 1 for Salomon Lustre filesystems one can specify -1 to use all OSTs in the filesystem.</li>
+<li>stripe_offset The index of the <span class="glossaryItem">OST</span> where the first stripe is to be placed; default is -1 which results in random selection; using a non-default value is NOT recommended.</li>
+</ol></ol>
+<p class=" ">Â </p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<p class=" ">Use the lfs getstripe for getting the stripe parameters. Use the lfs setstripe command for setting the stripe parameters to get optimal I/O performance The correct stripe setting depends on your needs and file access patterns. </p>
+<pre class="prettyprint lang-sh"><code>$ lfs getstripe dir|filename <br />$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename </code></pre>
+<p>Example:</p>
+<pre class="prettyprint lang-sh">$ lfs getstripe /scratch/work/user/username<br />/scratch/work/user/username<br />stripe_count: 1 stripe_size: 1048576 stripe_offset: -1<br /><br />$ lfs setstripe -c -1 /scratch/work/user/username/<br />$ lfs getstripe /scratch/work/user/username/<br />/scratch/work/user/username/<br />stripe_count: -1 stripe_size: 1048576 stripe_offset: -1</pre>
+<p>In this example, we view current stripe setting of the /scratch/username/ directory. The stripe count is changed to all OSTs, and verified. All files written to this directory will be striped over all (54) OSTs</p>
+<p>Use lfs check OSTs to see the number and status of active OSTs for each filesystem on Salomon. Learn more by reading the man page</p>
+<pre class="prettyprint lang-sh">$ lfs check osts<br />$ man lfs</pre>
+<h3 class=" ">Hints on Lustre Stripping</h3>
+<p class="callout">Increase the stripe_count for parallel I/O to the same file.</p>
+<p>When multiple processes are writing blocks of data to the same file in parallel, the I/O performance for large files will improve when the stripe_count is set to a larger value. The stripe count sets the number of OSTs the file will be written to. By default, the stripe count is set to 1. While this default setting provides for efficient access of metadata (for example to support the ls -l command), large files should use stripe counts of greater than 1. This will increase the aggregate I/O bandwidth by using multiple OSTs in parallel instead of just one. A rule of thumb is to use a stripe count approximately equal to the number of gigabytes in the file.</p>
+<p>Another good practice is to make the stripe count be an integral factor of the number of processes performing the write in parallel, so that you achieve load balance among the OSTs. For example, set the stripe count to 16 instead of 15 when you have 64 processes performing the writes.</p>
+<p class="callout">Using a large stripe size can improve performance when accessing very large files</p>
+<p>Large stripe size allows each client to have exclusive access to its own part of a file. However, it can be counterproductive in some cases if it does not match your I/O pattern. The choice of stripe size has no effect on a single-stripe file.</p>
+<p>Read more on <a class="external-link" href="http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html" target="_self" title="">http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html</a></p>
+<h2 class=" "><span>Disk usage and quota commands</span></h2>
+<p><span>User quotas on the Lustre file systems (SCRATCH) can be checked and reviewed using following command:</span></p>
+<pre class="prettyprint lang-sh">$ lfs quota dir</pre>
+<p>Example for Lustre SCRATCH directory:</p>
+<pre class="prettyprint lang-sh">$ lfs quota /scratch<br />Disk quotas for user user001 (uid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br />  /scratch    8    0 100000000000    -    3    0    0    -<br />Disk quotas for gro<span>up user001 (gid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /scratch    8    0    0    -    3    0    0    -<br /></span></pre>
+<p>In this example, we view current quota size limit of 100TB and 8KB currently used by user001.</p>
+<p>HOME directory is mounted via NFS, so a different command must be used to obtain quota information:</p>
+<pre class=" ">Â $ quota</pre>
+<p class=" ">Example output:</p>
+<pre class=" ">$ quota<br />Disk quotas for user vop999 (uid 1025):<br /> Filesystem blocks quota limit grace files quota limit grace<br />home-nfs-ib.salomon.it4i.cz:/home<br /> 28 0 250000000 10 0 500000</pre>
+<p>To have a better understanding of where the space is exactly used, you can use following command to find out.</p>
+<pre class="prettyprint lang-sh">$ du -hs dir</pre>
+<p>Example for your HOME directory:</p>
+<pre class="prettyprint lang-sh">$ cd /home<br />$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr<br />258M cuda-samples<br />15M .cache<br />13M .mozilla<br />5,5M .eclipse<br />2,7M .idb_13.0_linux_intel64_app</pre>
+<p>This will list all directories which are having MegaBytes or GigaBytes of consumed space in your actual (in this example HOME) directory. List is sorted in descending order from largest to smallest files/directories.</p>
+<p><br /> <span>To have a better understanding of previous commands, you can read manpages.</span></p>
+<pre class="prettyprint lang-sh">$ man lfs</pre>
+<pre class="prettyprint lang-sh">$ man du </pre>
+<h2 class=" ">Extended Access Control List (ACL)</h2>
+<p class=" ">Extended ACLs provide another security mechanism beside the standard POSIX ACLs which are defined by three entries (for owner/group/others). Extended ACLs have more than the three basic entries. In addition, they also contain a mask entry and may contain any number of named user and named group entries.</p>
+<p class=" ">ACLs on a Lustre file system work exactly like ACLs on any Linux file system. They are manipulated with the standard tools in the standard manner. Below, we create a directory and allow a specific user access.</p>
+<pre class="prettyprint lang-sh">[vop999@login1.salomon ~]$ umask 027<br />[vop999@login1.salomon ~]$ mkdir test<br />[vop999@login1.salomon ~]$ ls -ld test<br />drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.salomon ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />group::r-x<br />other::---<br /><br />[vop999@login1.salomon ~]$ setfacl -m user:johnsm:rwx test<br />[vop999@login1.salomon ~]$ ls -ld test<br />drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.salomon ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />user:johnsm:rwx<br />group::r-x<br />mask::rwx<br />other::---</pre>
+<p class=" ">Default ACL mechanism can be used to replace setuid/setgid permissions on directories. Setting a default ACL on a directory (-d flag to setfacl) will cause the ACL permissions to be inherited by any newly created file or subdirectory within the directory. Refer to this page for more information on Linux ACL:</p>
+<p><a class="external-link" href="http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html" target="_self" title="">http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html </a></p>
+<div class="itemizedlist">
+<h2 class=" "><a name="shared-workspaces"></a>Shared Workspaces</h2>
+</div>
+<h3><a name="home"></a><a name="home"></a>HOME</h3>
+<p>Users home directories /home/username reside on HOME filesystem. Accessible capacity is 0.5PB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. <span>If 250GB should prove as insufficient for particular user, please contact</span>Â <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request.</p>
+<p class="callout">The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.</p>
+<p>The HOMEÂ should not be used to archive data of past Projects or other unrelated data.</p>
+<p>The files on HOME will not be deleted until end of the <a href="../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html" title="" target="_self" class="internal-link">users lifecycle</a>.</p>
+<p class=" ">The workspace is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files. <br /><br /></p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">HOME workspace</th></tr>
+<tr class="even">
+<td>Accesspoint</td>
+<td>/home/username</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>0.5PB</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>6GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>250GB</td>
+</tr>
+<tr class="odd">
+<td>Protocol</td>
+<td>NFS, 2-Tier</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><a name="work"></a>WORK</h3>
+<p>The WORK workspace resides on SCRATCH filesystem. Users may create subdirectories and files in directories <strong>/scratch/work/user/username</strong> and <strong>/scratch/work/project/projectid. </strong>The /scratch/work/user/username is private to user, much like the home directory. The /scratch/work/project/projectid is accessible to all users involved in project projectid. <span></span></p>
+<p class="callout">The WORK workspace is intended to store users project data as well as for high performance access to input and output files. All project data should be removed once the project is finished. The data on the WORK workspace are not backed up.<br /><br />Files on the WORK filesystem are<strong> persistent </strong>(not automatically deleted) throughout duration of the project.</p>
+<p>The WORK workspace is hosted on SCRATCH filesystem. The SCRATCH is realized as Lustre parallel filesystem and is available from all login and computational nodes. Default stripe size is 1MB, stripe count is 1. There are 54 OSTs dedicated for the SCRATCH filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">WORK workspace</th></tr>
+<tr class="even">
+<td>Accesspoints</td>
+<td>/scratch/work/user/username<br />/scratch/work/user/projectid</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>1.6P</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>30GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>100TB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>54</td>
+</tr>
+<tr class="even">
+<td>Protocol</td>
+<td>Lustre</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><a name="temp"></a>TEMP</h3>
+<p>The TEMP workspace resides on SCRATCH filesystem. The TEMP workspace accesspoint is /scratch/temp. Users may freely create subdirectories and files on the workspace. Accessible capacity is 1.6P, shared among all users on TEMP and WORK. Individual users are restricted by filesystem usage quotas, set to 100TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. <span>If 100TB should prove as insufficient for particular user, please contact <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request. </span></p>
+<p class="callout">The TEMP workspace is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the TEMP workspace as their working directory.<br /><br />Users are advised to save the necessary data from the TEMP workspace to HOME or WORK after the calculations and clean up the scratch files.<br /><br />Files on the TEMP filesystem that are <strong>not accessed for more than 90 days</strong> will be automatically <strong>deleted</strong>.</p>
+<p>The TEMP workspace is hosted on SCRATCH filesystem. The SCRATCH is realized as Lustre parallel filesystem and is available from all login and computational nodes. Default stripe size is 1MB, stripe count is 1. There are 54 OSTs dedicated for the SCRATCH filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">TEMP workspace</th></tr>
+<tr class="even">
+<td>Accesspoint</td>
+<td>/scratch/temp</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>1.6P</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>30GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>100TB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>54</td>
+</tr>
+<tr class="even">
+<td>Protocol</td>
+<td>Lustre</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<h2 class=" ">RAM disk</h2>
+<p>Every computational node is equipped with filesystem realized in memory, so called RAM disk.</p>
+<p class="callout">Use RAM disk in case you need really fast access to your data of limited size during your calculation.<br />Be very careful, use of RAM disk filesystem is at the expense of operational memory.</p>
+<p><a name="LocalScratch"></a>The local RAM disk is mounted as /ramdisk and is accessible to user at /ramdisk/$PBS_JOBID directory.</p>
+<p class=" ">The local RAM disk filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. Size of RAM disk filesystem is limited. Be very careful, use of RAM disk filesystem is at the expense of operational memory. It is not recommended to allocate large amount of memory and use large amount of data in RAM disk filesystem at the same time.</p>
+<p class="callout">The local RAM disk directory /ramdisk/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">RAM disk</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td><span class="monospace">/ramdisk</span></td>
+</tr>
+<tr class="odd">
+<td>Accesspoint</td>
+<td><span class="monospace">/ramdisk/$PBS_JOBID</span></td>
+</tr>
+<tr class="even">
+<td>Capacity</td>
+<td>120 GB</td>
+</tr>
+<tr class="odd">
+<td>Throughput</td>
+<td>
+<p>over 1.5 GB/s write, over 5 GB/s read, single thread<br />over 10 GB/s write, over 50 GB/s read, 16 threads</p>
+</td>
+</tr>
+<tr class="even">
+<td>User quota</td>
+<td>none</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<div class="table">
+<h2 class=" "><strong>Summary<br /></strong></h2>
+<div class="table-contents">
+<table class="listing" summary="Best usage of the file systems"><colgroup><col><col><col><col><col><col><col><col></colgroup>
+<thead>
+<tr><th align="center" style="text-align: center; ">Mountpoint</th><th align="center" style="text-align: center; ">Usage</th><th align="center" style="text-align: center; ">Protocol</th><th align="center" style="text-align: center; ">Net Capacity</th><th align="center" style="text-align: center; ">Throughput</th><th align="center" style="text-align: center; ">Limitations</th><th align="center" style="text-align: center; ">Access</th><th align="center" style="text-align: center; ">Services</th></tr>
+</thead>
+<tbody>
+<tr class="even">
+<td><span class="monospace">/home</span></td>
+<td align="center">home directory</td>
+<td align="center">NFS, 2-Tier</td>
+<td align="center">0.5 PB</td>
+<td align="center">6 GB/s</td>
+<td align="center">Quota 250GB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">backed up</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/scratch/work</span></td>
+<td align="center">large project files</td>
+<td align="center">Lustre</td>
+<td align="center">1.69 PB</td>
+<td align="center">30 GB/s</td>
+<td align="center">Quota<br />1TB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">none</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/scratch/temp</span></td>
+<td align="center">job temporary data</td>
+<td align="center">Lustre</td>
+<td align="center">1.69 PB</td>
+<td align="center">30 GB/s</td>
+<td align="center">Quota 100TB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">files older 90 days removed</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/ramdisk</span></td>
+<td align="center">job temporary data, node local</td>
+<td align="center">local</td>
+<td align="center">120GB</td>
+<td align="center">90 GB/s</td>
+<td align="center">none</td>
+<td align="center">Compute nodes</td>
+<td align="center">purged after job ends</td>
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diff --git a/docs.it4i.cz/salomon/storage.md b/docs.it4i.cz/salomon/storage.md
index dc9c39fb2..bcc57a6b7 100644
--- a/docs.it4i.cz/salomon/storage.md
+++ b/docs.it4i.cz/salomon/storage.md
@@ -127,7 +127,7 @@ There is default stripe configuration for Salomon Lustre filesystems.
However, users can set the following stripe parameters for their own
directories or files to get optimum I/O performance:
-1. stripe_sizethe size of the chunk in bytes; specify with k, m, or
+1. stripe_size: the size of the chunk in bytes; specify with k, m, or
g to use units of KB, MB, or GB, respectively; the size must be an
even multiple of 65,536 bytes; default is 1MB for all Salomon Lustre
filesystems
@@ -159,12 +159,12 @@ Example:
```
$ lfs getstripe /scratch/work/user/username
/scratch/work/user/username
-stripe_count 1 stripe_size 1048576 stripe_offset -1
+stripe_count: 1 stripe_size: 1048576 stripe_offset: -1
$ lfs setstripe -c -1 /scratch/work/user/username/
$ lfs getstripe /scratch/work/user/username/
/scratch/work/user/username/
-stripe_count -1 stripe_size 1048576 stripe_offset -1
+stripe_count: -1 stripe_size: 1048576 stripe_offset: -1
```
In this example, we view current stripe setting of the
@@ -304,9 +304,9 @@ manner. Below, we create a directory and allow a specific user access.
[vop999@login1.salomon ~]$ ls -ld test
drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.salomon ~]$ getfacl test
-# filetest
-# ownervop999
-# groupvop999
+# file: test
+# owner: vop999
+# group: vop999
user::rwx
group::r-x
other::---
@@ -315,9 +315,9 @@ other::---
[vop999@login1.salomon ~]$ ls -ld test
drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.salomon ~]$ getfacl test
-# filetest
-# ownervop999
-# groupvop999
+# file: test
+# owner: vop999
+# group: vop999
user::rwx
user:johnsm:rwx
group::r-x
@@ -532,4 +532,3 @@ none
-
diff --git a/docs.it4i.cz/salomon/storage/cesnet-data-storage.html b/docs.it4i.cz/salomon/storage/cesnet-data-storage.html
new file mode 100644
index 000000000..a044be945
--- /dev/null
+++ b/docs.it4i.cz/salomon/storage/cesnet-data-storage.html
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+
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+
+ <div id="parent-fieldname-text-1707485f61744664987f59c9a05a6767" class="">
+ <h2 class=" ">Introduction</h2>
+<p class="external-link" title="">Do not use shared filesystems at IT4Innovations as a backup for large amount of data or long-term archiving purposes.</p>
+<p class="callout" title="">The IT4Innovations does not provide storage capacity for data archiving. Academic staff and students of research institutions in the Czech Republic can use <a class="external-link" href="https://du.cesnet.cz/" target="_self" title="">CESNET Storage service</a>.</p>
+<p class=" ">The CESNET Storage service can be used for research purposes, mainly by academic staff and students of research institutions in the Czech Republic.<br /><br />User of data storage CESNET (DU) association can become organizations or an individual person who is either in the current employment relationship (employees) or the current study relationship (students) to a legal entity (organization) that meets the “Principles for access to CESNET Large infrastructure (Access Policy)”.<br /><br />User may only use data storage CESNET for data transfer and storage which are associated with activities in science, research, development, the spread of education, culture and prosperity. In detail see “Acceptable Use Policy CESNET Large Infrastructure (Acceptable Use Policy, AUP)”.</p>
+<p class=" ">The service is documented at <a class="external-link" href="https://du.cesnet.cz/wiki/doku.php/en/start" target="_self" title="">https://du.cesnet.cz/wiki/doku.php/en/start</a>. For special requirements please contact directly CESNET Storage Department via e-mail <a class="email-link" href="mailto:du-support@cesnet.cz" target="_self" title="">du-support(at)cesnet.cz</a>.</p>
+<p class=" ">The procedure to obtain the CESNET access is quick and trouble-free.</p>
+<p class=" ">(source <a class="external-link" href="https://du.cesnet.cz/wiki/doku.php/en/start" target="_self" title="CESNET Data Storage">https://du.cesnet.cz/</a>)</p>
+<h2 class=" ">CESNET storage access</h2>
+<h3 class=" ">Understanding Cesnet storage</h3>
+<p class="callout">It is very important to understand the Cesnet storage before uploading data. Please read <a class="external-link" href="https://du.cesnet.cz/en/navody/home-migrace-plzen/start" target="_self" title="">https://du.cesnet.cz/en/navody/home-migrace-plzen/start</a> first.</p>
+<p class=" ">Once registered for CESNET Storage, you may <a class="external-link" href="https://du.cesnet.cz/en/navody/faq/start" target="_self" title="">access the storage</a> in number of ways. We recommend the SSHFS and RSYNC methods.</p>
+<h3 class=" ">SSHFS Access</h3>
+<p class="callout">SSHFS: The storage will be mounted like a local hard drive</p>
+<p>The SSHFSÂ provides a very convenient way to access the CESNET Storage. The storage will be mounted onto a local directory, exposing the vast CESNET Storage as if it was a local removable harddrive. Files can be than copied in and out in a usual fashion.</p>
+<p>First, create the mountpoint</p>
+<pre class=" ">$ mkdir cesnet</pre>
+<p>Mount the storage. Note that you can choose among the ssh.du1.cesnet.cz (Plzen), ssh.du2.cesnet.cz (Jihlava), ssh.du3.cesnet.cz (Brno)<br />Mount tier1_home <strong>(only 5120M !)</strong>:</p>
+<pre class=" ">$ sshfs username@ssh.du1.cesnet.cz:. cesnet/</pre>
+<p class=" ">For easy future access from Anselm, install your public key</p>
+<pre class=" ">$ cp .ssh/id_rsa.pub cesnet/.ssh/authorized_keys</pre>
+<p class=" ">Mount tier1_cache_tape for the Storage VO:</p>
+<pre class=" ">$ sshfs username@ssh.du1.cesnet.cz:/cache_tape/VO_storage/home/username cesnet/</pre>
+<p class=" ">View the archive, copy the files and directories in and out</p>
+<pre class=" ">$ ls cesnet/ <br />$ cp -a mydir cesnet/.<br />$ cp cesnet/myfile .</pre>
+<p class=" ">Once done, please remember to unmount the storage</p>
+<pre class=" ">$ fusermount -u cesnet</pre>
+<h3 class=" ">Rsync access</h3>
+<p class="callout">Rsync provides delta transfer for best performance, can resume interrupted transfers</p>
+<p>Rsync is a fast and extraordinarily versatile file copying tool. It is famous for its delta-transfer algorithm, which reduces the amount of data sent over the network by sending only the differences between the source files and the existing files in the destination. Rsync is widely used for backups and mirroring and as an improved copy command for everyday use.<br /><br />Rsync finds files that need to be transferred using a "quick check" algorithm (by default) that looks for files that have changed in size or in last-modified time. Any changes in the other preserved attributes (as requested by options) are made on the destination file directly when the quick check indicates that the file's data does not need to be updated.</p>
+<p class=" ">More about Rsync at <a class="external-link" href="https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele" target="_self" title="">https://du.cesnet.cz/en/navody/rsync/start#pro_bezne_uzivatele</a></p>
+<p class=" ">Transfer large files to/from Cesnet storage, assuming membership in the Storage VO</p>
+<pre class=" ">$ rsync --progress datafile username@ssh.du1.cesnet.cz:VO_storage-cache_tape/.<br />$ rsync --progress username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafile .</pre>
+<p class=" ">Transfer large directories to/from Cesnet storage, assuming membership in the Storage VO</p>
+<pre class=" ">$ rsync --progress -av datafolder username@ssh.du1.cesnet.cz:VO_storage-cache_tape/.<br />$ rsync --progress -av username@ssh.du1.cesnet.cz:VO_storage-cache_tape/datafolder .</pre>
+<p class=" ">Transfer rates of about 28MB/s can be expected.</p>
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diff --git a/docs.it4i.cz/salomon/storage/cesnet-data-storage.md b/docs.it4i.cz/salomon/storage/cesnet-data-storage.md
index 2eeffcb3b..2f65b5a9b 100644
--- a/docs.it4i.cz/salomon/storage/cesnet-data-storage.md
+++ b/docs.it4i.cz/salomon/storage/cesnet-data-storage.md
@@ -57,7 +57,7 @@ number of ways. We recommend the SSHFS and RSYNC methods.
### SSHFS Access
-SSHFSThe storage will be mounted like a local hard drive
+SSHFS: The storage will be mounted like a local hard drive
The SSHFSÂ provides a very convenient way to access the CESNET Storage.
The storage will be mounted onto a local directory, exposing the vast
diff --git a/docs.it4i.cz/salomon/storage/storage.html b/docs.it4i.cz/salomon/storage/storage.html
new file mode 100644
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+ <h2 class=" ">Introduction</h2>
+<p>There are two main shared file systems on Salomon cluster, the <a class="anchor-link" href="storage.html#home" target="_self" title=""><span class="anchor-link"><span class="anchor-link">HOME</span></span></a> and <a class="anchor-link" href="storage.html#shared-filesystems" target="_self" title=""><span class="anchor-link"><span class="anchor-link">SCRATCH</span></span></a>. All login and compute nodes may access same data on shared filesystems. Compute nodes are also equipped with local (non-shared) scratch, ramdisk and tmp filesystems.</p>
+<h2 class=" ">Policy (in a nutshell)</h2>
+<p class="callout">Use <a class="anchor-link" href="storage.html#home" target="_self" title="">HOME</a> for your most valuable data and programs.<br />Use <a class="anchor-link" href="storage.html#work" target="_self" title="">WORK</a> for your large project files<br />Use <a class="anchor-link" href="storage.html#temp" target="_self" title="">TEMP</a> for large scratch data.</p>
+<p class="callout">Do not use for <a class="anchor-link" href="storage.html#archiving" target="_self" title="">archiving</a>!</p>
+<h2 class=" "><a name="archiving"></a>Archiving</h2>
+<p>Please don't use shared filesystems as a backup for large amount of data or long-term archiving mean. The academic staff and students of research institutions in the Czech Republic can use <a href="../../anselm-cluster-documentation/storage-1/cesnet-data-storage.html" title="" target="_self" class="internal-link">CESNET storage service</a>, which is available via SSHFS.</p>
+<h2 class=" "><a name="shared-filesystems"></a>Shared Filesystems</h2>
+<p class=" ">Salomon computer provides two main shared filesystems, the <a class="anchor-link" href="storage.html#home-filesystem" target="_self" title=""><span class="anchor-link">HOME filesystem</span></a> and the <a class="anchor-link" href="storage.html#scratch-filesystem" target="_self" title="">SCRATCH filesystem</a>. The SCRATCH filesystem is partitioned to <a class="anchor-link" href="storage.html#shared-workspaces" target="_self" title="">WORK and TEMP workspaces</a>. The HOME filesystem is realized as a tiered NFSÂ disk storage. The SCRATCH filesystem is realized as a parallel Lustre filesystem. Both shared file systems are accessible via the Infiniband network. Extended ACLs are provided on both HOME/SCRATCH filesystems for the purpose of sharing data with other users using fine-grained control.</p>
+<h3 class=" "><a name="home-filesystem"></a><a name="home-filesystem"></a>HOME filesystem</h3>
+<p class=" ">The HOME filesystem is realized as a Tiered filesystem, exported via NFS. The first tier has capacity 100TB, second tier has capacity 400TB. The filesystem is available on all login and computational nodes. The Home filesystem hosts the <a class="anchor-link" href="storage.html#home" target="_self" title="">HOME workspace</a>.</p>
+<h3 class=" "><a name="scratch-filesystem"></a><a name="the-scratch-filesystem"></a>SCRATCH filesystem</h3>
+<p>The architecture of Lustre on Salomon is composed of two metadata servers (MDS) and six data/object storage servers (OSS). Accessible capacity is 1.69 PB, shared among all users. The SCRATCH filesystem hosts the <a class="anchor-link" href="storage.html#shared-workspaces" target="_self" title="">WORK and TEMP workspaces</a>.</p>
+<p class=" "><span class="listitem">Configuration of the SCRATCH Lustre storage<br /></span></p>
+<div class="itemizedlist"><span class="emphasis"></span><span class="emphasis"></span>
+<ul class="itemizedlist" style="list-style-type: disc; ">
+<li class="listitem"><span class="emphasis">SCRATCH Lustre object storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">Disk array SFA12KX</li>
+<li class="listitem">540 4TB SAS 7.2krpm disks</li>
+<li class="listitem">54 OSTs of 10 disks in RAID6 (8+2)</li>
+<li class="listitem">15 hot-spare disks</li>
+<li class="listitem">4x 400GB SSD cache</li>
+</ul>
+</div>
+</li>
+<li class="listitem"><span class="emphasis">SCRATCH Lustre metadata storage</span>
+<div class="itemizedlist">
+<ul class="itemizedlist" style="list-style-type: circle; ">
+<li class="listitem">Disk array EF3015</li>
+<li class="listitem">12 600GB SAS 15krpm disks</li>
+</ul>
+</div>
+</li>
+</ul>
+</div>
+<h3 class=" ">Understanding the Lustre Filesystems</h3>
+<p>(source <a class="external-link" href="http://www.nas.nasa.gov" target="_self" title="">http://www.nas.nasa.gov</a>)</p>
+<p>A user file on the Lustre filesystem can be divided into multiple chunks (stripes) and stored across a subset of the object storage targets (OSTs) (disks). The stripes are distributed among the OSTs in a round-robin fashion to ensure load balancing.</p>
+<p>When a client (a <span class="glossaryItem">compute <span class="glossaryItem">node</span></span> from your job) needs to create or access a file, the client queries the metadata server (<span class="glossaryItem">MDS</span>) and the metadata target (<span class="glossaryItem">MDT</span>) for the layout and location of the <a href="http://www.nas.nasa.gov/hecc/support/kb/Lustre_Basics_224.html#striping">file's stripes</a>. Once the file is opened and the client obtains the striping information, the <span class="glossaryItem">MDS</span> is no longer involved in the file I/O process. The client interacts directly with the object storage servers (OSSes) and OSTs to perform I/O operations such as locking, disk allocation, storage, and retrieval.</p>
+<p>If multiple clients try to read and write the same part of a file at the same time, the Lustre distributed lock manager enforces coherency so that all clients see consistent results.</p>
+<p>There is default stripe configuration for Salomon Lustre filesystems. However, users can set the following stripe parameters for their own directories or files to get optimum I/O performance:</p>
+<ol><ol>
+<li>stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Salomon Lustre filesystems</li>
+<li>stripe_count the number of OSTs to stripe across; default is 1 for Salomon Lustre filesystems one can specify -1 to use all OSTs in the filesystem.</li>
+<li>stripe_offset The index of the <span class="glossaryItem">OST</span> where the first stripe is to be placed; default is -1 which results in random selection; using a non-default value is NOT recommended.</li>
+</ol></ol>
+<p class=" ">Â </p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<p class=" ">Use the lfs getstripe for getting the stripe parameters. Use the lfs setstripe command for setting the stripe parameters to get optimal I/O performance The correct stripe setting depends on your needs and file access patterns. </p>
+<pre class="prettyprint lang-sh"><code>$ lfs getstripe dir|filename <br />$ lfs setstripe -s stripe_size -c stripe_count -o stripe_offset dir|filename </code></pre>
+<p>Example:</p>
+<pre class="prettyprint lang-sh">$ lfs getstripe /scratch/work/user/username<br />/scratch/work/user/username<br />stripe_count: 1 stripe_size: 1048576 stripe_offset: -1<br /><br />$ lfs setstripe -c -1 /scratch/work/user/username/<br />$ lfs getstripe /scratch/work/user/username/<br />/scratch/work/user/username/<br />stripe_count: -1 stripe_size: 1048576 stripe_offset: -1</pre>
+<p>In this example, we view current stripe setting of the /scratch/username/ directory. The stripe count is changed to all OSTs, and verified. All files written to this directory will be striped over all (54) OSTs</p>
+<p>Use lfs check OSTs to see the number and status of active OSTs for each filesystem on Salomon. Learn more by reading the man page</p>
+<pre class="prettyprint lang-sh">$ lfs check osts<br />$ man lfs</pre>
+<h3 class=" ">Hints on Lustre Stripping</h3>
+<p class="callout">Increase the stripe_count for parallel I/O to the same file.</p>
+<p>When multiple processes are writing blocks of data to the same file in parallel, the I/O performance for large files will improve when the stripe_count is set to a larger value. The stripe count sets the number of OSTs the file will be written to. By default, the stripe count is set to 1. While this default setting provides for efficient access of metadata (for example to support the ls -l command), large files should use stripe counts of greater than 1. This will increase the aggregate I/O bandwidth by using multiple OSTs in parallel instead of just one. A rule of thumb is to use a stripe count approximately equal to the number of gigabytes in the file.</p>
+<p>Another good practice is to make the stripe count be an integral factor of the number of processes performing the write in parallel, so that you achieve load balance among the OSTs. For example, set the stripe count to 16 instead of 15 when you have 64 processes performing the writes.</p>
+<p class="callout">Using a large stripe size can improve performance when accessing very large files</p>
+<p>Large stripe size allows each client to have exclusive access to its own part of a file. However, it can be counterproductive in some cases if it does not match your I/O pattern. The choice of stripe size has no effect on a single-stripe file.</p>
+<p>Read more on <a class="external-link" href="http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html" target="_self" title="">http://wiki.lustre.org/manual/LustreManual20_HTML/ManagingStripingFreeSpace.html</a></p>
+<h2 class=" "><span>Disk usage and quota commands</span></h2>
+<p><span>User quotas on the Lustre file systems (SCRATCH) can be checked and reviewed using following command:</span></p>
+<pre class="prettyprint lang-sh">$ lfs quota dir</pre>
+<p>Example for Lustre SCRATCH directory:</p>
+<pre class="prettyprint lang-sh">$ lfs quota /scratch<br />Disk quotas for user user001 (uid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br />  /scratch    8    0 100000000000    -    3    0    0    -<br />Disk quotas for gro<span>up user001 (gid 1234):<br /> Filesystem kbytes quota limit grace files quota limit grace<br /> /scratch    8    0    0    -    3    0    0    -<br /></span></pre>
+<p>In this example, we view current quota size limit of 100TB and 8KB currently used by user001.</p>
+<p>HOME directory is mounted via NFS, so a different command must be used to obtain quota information:</p>
+<pre class=" ">Â $ quota</pre>
+<p class=" ">Example output:</p>
+<pre class=" ">$ quota<br />Disk quotas for user vop999 (uid 1025):<br /> Filesystem blocks quota limit grace files quota limit grace<br />home-nfs-ib.salomon.it4i.cz:/home<br /> 28 0 250000000 10 0 500000</pre>
+<p>To have a better understanding of where the space is exactly used, you can use following command to find out.</p>
+<pre class="prettyprint lang-sh">$ du -hs dir</pre>
+<p>Example for your HOME directory:</p>
+<pre class="prettyprint lang-sh">$ cd /home<br />$ du -hs * .[a-zA-z0-9]* | grep -E "[0-9]*G|[0-9]*M" | sort -hr<br />258M cuda-samples<br />15M .cache<br />13M .mozilla<br />5,5M .eclipse<br />2,7M .idb_13.0_linux_intel64_app</pre>
+<p>This will list all directories which are having MegaBytes or GigaBytes of consumed space in your actual (in this example HOME) directory. List is sorted in descending order from largest to smallest files/directories.</p>
+<p><br /> <span>To have a better understanding of previous commands, you can read manpages.</span></p>
+<pre class="prettyprint lang-sh">$ man lfs</pre>
+<pre class="prettyprint lang-sh">$ man du </pre>
+<h2 class=" ">Extended Access Control List (ACL)</h2>
+<p class=" ">Extended ACLs provide another security mechanism beside the standard POSIX ACLs which are defined by three entries (for owner/group/others). Extended ACLs have more than the three basic entries. In addition, they also contain a mask entry and may contain any number of named user and named group entries.</p>
+<p class=" ">ACLs on a Lustre file system work exactly like ACLs on any Linux file system. They are manipulated with the standard tools in the standard manner. Below, we create a directory and allow a specific user access.</p>
+<pre class="prettyprint lang-sh">[vop999@login1.salomon ~]$ umask 027<br />[vop999@login1.salomon ~]$ mkdir test<br />[vop999@login1.salomon ~]$ ls -ld test<br />drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.salomon ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />group::r-x<br />other::---<br /><br />[vop999@login1.salomon ~]$ setfacl -m user:johnsm:rwx test<br />[vop999@login1.salomon ~]$ ls -ld test<br />drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test<br />[vop999@login1.salomon ~]$ getfacl test<br /># file: test<br /># owner: vop999<br /># group: vop999<br />user::rwx<br />user:johnsm:rwx<br />group::r-x<br />mask::rwx<br />other::---</pre>
+<p class=" ">Default ACL mechanism can be used to replace setuid/setgid permissions on directories. Setting a default ACL on a directory (-d flag to setfacl) will cause the ACL permissions to be inherited by any newly created file or subdirectory within the directory. Refer to this page for more information on Linux ACL:</p>
+<p><a class="external-link" href="http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html" target="_self" title="">http://www.vanemery.com/Linux/ACL/POSIX_ACL_on_Linux.html </a></p>
+<div class="itemizedlist">
+<h2 class=" "><a name="shared-workspaces"></a>Shared Workspaces</h2>
+</div>
+<h3><a name="home"></a><a name="home"></a>HOME</h3>
+<p>Users home directories /home/username reside on HOME filesystem. Accessible capacity is 0.5PB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. <span>If 250GB should prove as insufficient for particular user, please contact</span>Â <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request.</p>
+<p class="callout">The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.</p>
+<p>The HOMEÂ should not be used to archive data of past Projects or other unrelated data.</p>
+<p>The files on HOME will not be deleted until end of the <a href="../../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html" title="" target="_self" class="internal-link">users lifecycle</a>.</p>
+<p class=" ">The workspace is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files. <br /><br /></p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">HOME workspace</th></tr>
+<tr class="even">
+<td>Accesspoint</td>
+<td>/home/username</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>0.5PB</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>6GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>250GB</td>
+</tr>
+<tr class="odd">
+<td>Protocol</td>
+<td>NFS, 2-Tier</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><a name="work"></a>WORK</h3>
+<p>The WORK workspace resides on SCRATCH filesystem. Users may create subdirectories and files in directories <strong>/scratch/work/user/username</strong> and <strong>/scratch/work/project/projectid. </strong>The /scratch/work/user/username is private to user, much like the home directory. The /scratch/work/project/projectid is accessible to all users involved in project projectid. <span></span></p>
+<p class="callout">The WORK workspace is intended to store users project data as well as for high performance access to input and output files. All project data should be removed once the project is finished. The data on the WORK workspace are not backed up.<br /><br />Files on the WORK filesystem are<strong> persistent </strong>(not automatically deleted) throughout duration of the project.</p>
+<p>The WORK workspace is hosted on SCRATCH filesystem. The SCRATCH is realized as Lustre parallel filesystem and is available from all login and computational nodes. Default stripe size is 1MB, stripe count is 1. There are 54 OSTs dedicated for the SCRATCH filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">WORK workspace</th></tr>
+<tr class="even">
+<td>Accesspoints</td>
+<td>/scratch/work/user/username<br />/scratch/work/user/projectid</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>1.6P</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>30GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>100TB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>54</td>
+</tr>
+<tr class="even">
+<td>Protocol</td>
+<td>Lustre</td>
+</tr>
+</tbody>
+</table>
+<h3 class=" "><a name="temp"></a>TEMP</h3>
+<p>The TEMP workspace resides on SCRATCH filesystem. The TEMP workspace accesspoint is /scratch/temp. Users may freely create subdirectories and files on the workspace. Accessible capacity is 1.6P, shared among all users on TEMP and WORK. Individual users are restricted by filesystem usage quotas, set to 100TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. <span>If 100TB should prove as insufficient for particular user, please contact <a class="external-link" href="https://support.it4i.cz/rt" target="_self" title="">support</a>, the quota may be lifted upon request. </span></p>
+<p class="callout">The TEMP workspace is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the TEMP workspace as their working directory.<br /><br />Users are advised to save the necessary data from the TEMP workspace to HOME or WORK after the calculations and clean up the scratch files.<br /><br />Files on the TEMP filesystem that are <strong>not accessed for more than 90 days</strong> will be automatically <strong>deleted</strong>.</p>
+<p>The TEMP workspace is hosted on SCRATCH filesystem. The SCRATCH is realized as Lustre parallel filesystem and is available from all login and computational nodes. Default stripe size is 1MB, stripe count is 1. There are 54 OSTs dedicated for the SCRATCH filesystem.</p>
+<p class="callout">Setting stripe size and stripe count correctly for your needs may significantly impact the I/O performance you experience.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">TEMP workspace</th></tr>
+<tr class="even">
+<td>Accesspoint</td>
+<td>/scratch/temp</td>
+</tr>
+<tr class="odd">
+<td>Capacity</td>
+<td>1.6P</td>
+</tr>
+<tr class="even">
+<td>Throughput</td>
+<td>30GB/s</td>
+</tr>
+<tr class="odd">
+<td>User quota</td>
+<td>100TB</td>
+</tr>
+<tr class="even">
+<td>Default stripe size</td>
+<td>1MB</td>
+</tr>
+<tr class="odd">
+<td>Default stripe count</td>
+<td>1</td>
+</tr>
+<tr class="even">
+<td>Number of OSTs</td>
+<td>54</td>
+</tr>
+<tr class="even">
+<td>Protocol</td>
+<td>Lustre</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<h2 class=" ">RAM disk</h2>
+<p>Every computational node is equipped with filesystem realized in memory, so called RAM disk.</p>
+<p class="callout">Use RAM disk in case you need really fast access to your data of limited size during your calculation.<br />Be very careful, use of RAM disk filesystem is at the expense of operational memory.</p>
+<p><a name="LocalScratch"></a>The local RAM disk is mounted as /ramdisk and is accessible to user at /ramdisk/$PBS_JOBID directory.</p>
+<p class=" ">The local RAM disk filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. Size of RAM disk filesystem is limited. Be very careful, use of RAM disk filesystem is at the expense of operational memory. It is not recommended to allocate large amount of memory and use large amount of data in RAM disk filesystem at the same time.</p>
+<p class="callout">The local RAM disk directory /ramdisk/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.</p>
+<table class="listing">
+<tbody>
+<tr><th colspan="2">RAM disk</th></tr>
+<tr class="even">
+<td>Mountpoint</td>
+<td><span class="monospace">/ramdisk</span></td>
+</tr>
+<tr class="odd">
+<td>Accesspoint</td>
+<td><span class="monospace">/ramdisk/$PBS_JOBID</span></td>
+</tr>
+<tr class="even">
+<td>Capacity</td>
+<td>120 GB</td>
+</tr>
+<tr class="odd">
+<td>Throughput</td>
+<td>
+<p>over 1.5 GB/s write, over 5 GB/s read, single thread<br />over 10 GB/s write, over 50 GB/s read, 16 threads</p>
+</td>
+</tr>
+<tr class="even">
+<td>User quota</td>
+<td>none</td>
+</tr>
+</tbody>
+</table>
+<p>Â </p>
+<div class="table">
+<h2 class=" "><strong>Summary<br /></strong></h2>
+<div class="table-contents">
+<table class="listing" summary="Best usage of the file systems"><colgroup><col><col><col><col><col><col><col><col></colgroup>
+<thead>
+<tr><th align="center" style="text-align: center; ">Mountpoint</th><th align="center" style="text-align: center; ">Usage</th><th align="center" style="text-align: center; ">Protocol</th><th align="center" style="text-align: center; ">Net Capacity</th><th align="center" style="text-align: center; ">Throughput</th><th align="center" style="text-align: center; ">Limitations</th><th align="center" style="text-align: center; ">Access</th><th align="center" style="text-align: center; ">Services</th></tr>
+</thead>
+<tbody>
+<tr class="even">
+<td><span class="monospace">/home</span></td>
+<td align="center">home directory</td>
+<td align="center">NFS, 2-Tier</td>
+<td align="center">0.5 PB</td>
+<td align="center">6 GB/s</td>
+<td align="center">Quota 250GB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">backed up</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/scratch/work</span></td>
+<td align="center">large project files</td>
+<td align="center">Lustre</td>
+<td align="center">1.69 PB</td>
+<td align="center">30 GB/s</td>
+<td align="center">Quota<br />1TB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">none</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/scratch/temp</span></td>
+<td align="center">job temporary data</td>
+<td align="center">Lustre</td>
+<td align="center">1.69 PB</td>
+<td align="center">30 GB/s</td>
+<td align="center">Quota 100TB</td>
+<td align="center">Compute and login nodes</td>
+<td align="center">files older 90 days removed</td>
+</tr>
+<tr class="odd">
+<td><span class="monospace">/ramdisk</span></td>
+<td align="center">job temporary data, node local</td>
+<td align="center">local</td>
+<td align="center">120GB</td>
+<td align="center">90 GB/s</td>
+<td align="center">none</td>
+<td align="center">Compute nodes</td>
+<td align="center">purged after job ends</td>
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diff --git a/docs.it4i.cz/salomon/storage/storage.md b/docs.it4i.cz/salomon/storage/storage.md
index aed3dae07..7b85a45db 100644
--- a/docs.it4i.cz/salomon/storage/storage.md
+++ b/docs.it4i.cz/salomon/storage/storage.md
@@ -124,7 +124,7 @@ There is default stripe configuration for Salomon Lustre filesystems.
However, users can set the following stripe parameters for their own
directories or files to get optimum I/O performance:
-1. stripe_sizethe size of the chunk in bytes; specify with k, m, or
+1. stripe_size: the size of the chunk in bytes; specify with k, m, or
g to use units of KB, MB, or GB, respectively; the size must be an
even multiple of 65,536 bytes; default is 1MB for all Salomon Lustre
filesystems
@@ -156,12 +156,12 @@ Example:
```
$ lfs getstripe /scratch/work/user/username
/scratch/work/user/username
-stripe_count 1 stripe_size 1048576 stripe_offset -1
+stripe_count: 1 stripe_size: 1048576 stripe_offset: -1
$ lfs setstripe -c -1 /scratch/work/user/username/
$ lfs getstripe /scratch/work/user/username/
/scratch/work/user/username/
-stripe_count -1 stripe_size 1048576 stripe_offset -1
+stripe_count: -1 stripe_size: 1048576 stripe_offset: -1
```
In this example, we view current stripe setting of the
@@ -301,9 +301,9 @@ manner. Below, we create a directory and allow a specific user access.
[vop999@login1.salomon ~]$ ls -ld test
drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.salomon ~]$ getfacl test
-# filetest
-# ownervop999
-# groupvop999
+# file: test
+# owner: vop999
+# group: vop999
user::rwx
group::r-x
other::---
@@ -312,9 +312,9 @@ other::---
[vop999@login1.salomon ~]$ ls -ld test
drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
[vop999@login1.salomon ~]$ getfacl test
-# filetest
-# ownervop999
-# groupvop999
+# file: test
+# owner: vop999
+# group: vop999
user::rwx
user:johnsm:rwx
group::r-x
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+<div>
+
+ <a href="get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.html" title="FAQ about certificates in general" class="state-published contenttype-document">
+
+ <span>Certificates FAQ</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="get-started-with-it4innovations/accessing-the-clusters.html" title="" class="state-published contenttype-folder">
+
+ <span>Accessing the Clusters</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="get-started-with-it4innovations/accessing-the-clusters.html" title="" class="state-published contenttype-folder">
+
+ <span>Shell access and data transfer</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.html" title="" class="state-published contenttype-folder">
+
+ <span>Graphical User Interface</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon.html" title="" class="state-published contenttype-folder">
+
+ <span>Salomon Cluster Documentation</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel2">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/hardware-overview-1.1.html" title="" class="state-published contenttype-folder">
+
+ <span>Hardware Overview</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/accessing-the-cluster.html" title="" class="state-published contenttype-folder">
+
+ <span>Accessing the Cluster</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/accessing-the-cluster.html" title="" class="state-published contenttype-folder">
+
+ <span>Shell access and data transfer</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/accessing-the-cluster/graphical-user-interface.html" title="" class="state-published contenttype-folder">
+
+ <span>Graphical User Interface</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/accessing-the-cluster/vpn-access.html" title="" class="state-published contenttype-document">
+
+ <span>VPN Access</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/accessing-the-cluster/outgoing-connections.html" title="" class="state-published contenttype-document">
+
+ <span>Outgoing connections</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/environment-and-modules.html" title="" class="state-published contenttype-document">
+
+ <span>Environment and Modules</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/list_of_modules.html" title="List of Available Modules on Salomon Cluster" class="state-published contenttype-document">
+
+ <span>List of Available Modules</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/resource-allocation-and-job-execution.html" title="" class="state-published contenttype-folder">
+
+ <span>Resource Allocation and Job Execution</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/resource-allocation-and-job-execution/resources-allocation-policy.html" title="" class="state-published contenttype-document">
+
+ <span>Resources Allocation Policy</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/resource-allocation-and-job-execution/job-submission-and-execution.html" title="" class="state-published contenttype-document">
+
+ <span>Job submission and execution</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/resource-allocation-and-job-execution/job-priority.html" title="" class="state-published contenttype-document">
+
+ <span>Job scheduling</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/resource-allocation-and-job-execution/capacity-computing.html" title="" class="state-published contenttype-document">
+
+ <span>Capacity computing</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/compute-nodes.html" title="" class="state-published contenttype-document">
+
+ <span>Compute Nodes</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/storage.html" title="" class="state-published contenttype-folder">
+
+ <span>Storage</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/storage/cesnet-data-storage.html" title="" class="state-published contenttype-document">
+
+ <span>CESNET Data Storage</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/network-1.html" title="" class="state-published contenttype-folder">
+
+ <span>Network</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/network-1/7d-enhanced-hypercube.html" title="" class="state-published contenttype-document">
+
+ <span>7D Enhanced Hypercube</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/network-1/ib-single-plane-topology.html" title="" class="state-published contenttype-folder">
+
+ <span>IB single-plane topology</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/software.html" title="In this section we provide overview of installed software and its usage.
+
+
+" class="state-published contenttype-folder">
+
+ <span>Software</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/software/ansys.html" title="An engineering simulation software " class="state-published contenttype-folder">
+
+ <span>ANSYS</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/software/comsol.html" title=" A finite element analysis, solver and Simulation software" class="state-published contenttype-folder">
+
+ <span>COMSOL</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/software/debuggers.1.html" title="A collection of development tools" class="state-published contenttype-folder">
+
+ <span>Debuggers and profilers</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/software/chemistry.html" title="Tools for computational chemistry." class="state-published contenttype-folder">
+
+ <span>Chemistry, Physics and Materials science</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/software/intel-suite.html" title="The Intel Parallel Studio XE" class="state-published contenttype-folder">
+
+ <span>Intel Parallel studio</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/software/mpi-1.html" title="Message Passing Interface libraries on ANSELM" class="state-published contenttype-folder">
+
+ <span>MPI</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/software/numerical-languages.1.html" title="Interpreted languages for numerical computations" class="state-published contenttype-folder">
+
+ <span>Numerical languages</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/software/compilers.html" title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document">
+
+ <span>Compilers</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/software/intel-xeon-phi.html" title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document">
+
+ <span>Intel Xeon Phi</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/software/java.html" title="Java on the cluster" class="state-published contenttype-document">
+
+ <span>Java</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/software/operating-system.html" title="The operating system, deployed on Salomon cluster" class="state-published contenttype-document">
+
+ <span>Operating System</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="salomon/prace.html" title="" class="state-published contenttype-document">
+
+ <span>PRACE User Support</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm.html" title="" class="state-published contenttype-folder">
+
+ <span>Anselm Cluster Documentation</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel2">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/hardware-overview.html" title="" class="state-published contenttype-document">
+
+ <span>Hardware Overview</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/accessing-the-cluster.html" title="" class="state-published contenttype-folder">
+
+ <span>Accessing the Cluster</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/accessing-the-cluster.html" title="" class="state-published contenttype-folder">
+
+ <span>Shell access and data transfer</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.html" title="" class="state-published contenttype-link">
+
+ <span>Graphical User Interface</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/accessing-the-cluster/vpn-access.html" title="" class="state-published contenttype-document">
+
+ <span>VPN Access</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.html" title="" class="state-published contenttype-document">
+
+ <span>Outgoing connections</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/environment-and-modules.html" title="" class="state-published contenttype-document">
+
+ <span>Environment and Modules</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/resource-allocation-and-job-execution.html" title="" class="state-published contenttype-folder">
+
+ <span>Resource Allocation and Job Execution</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.html" title="" class="state-published contenttype-document">
+
+ <span>Resources Allocation Policy</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.html" title="" class="state-published contenttype-document">
+
+ <span>Job submission and execution</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.html" title="" class="state-published contenttype-document">
+
+ <span>Job scheduling</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.html" title="" class="state-published contenttype-document">
+
+ <span>Capacity computing</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/compute-nodes.html" title="" class="state-published contenttype-document">
+
+ <span>Compute Nodes</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/storage-1.html" title="" class="state-published contenttype-folder">
+
+ <span>Storage</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/storage-1/cesnet-data-storage.html" title="" class="state-published contenttype-document">
+
+ <span>CESNET Data Storage</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/network.html" title="" class="state-published contenttype-document">
+
+ <span>Network</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software.1.html" title="In this section we provide overview of installed software and its usage.
+
+
+" class="state-published contenttype-folder">
+
+ <span>Software</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel3">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/ansys.html" title="An engineering simulation software " class="state-published contenttype-folder">
+
+ <span>ANSYS</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/comsol.html" title=" A finite element analysis, solver and Simulation software" class="state-published contenttype-folder">
+
+ <span>COMSOL</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/debuggers.1.html" title="A collection of development tools" class="state-published contenttype-folder">
+
+ <span>Debuggers and profilers</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/chemistry.html" title="Tools for computational chemistry." class="state-published contenttype-folder">
+
+ <span>Chemistry and Materials science</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/intel-suite.html" title="The Intel Parallel Studio XE" class="state-published contenttype-folder">
+
+ <span>Intel Parallel studio</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/mpi-1.html" title="Message Passing Interface libraries on ANSELM" class="state-published contenttype-folder">
+
+ <span>MPI</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/numerical-libraries.html" title="Libraries for numerical computations" class="state-published contenttype-folder">
+
+ <span>Numerical Libraries</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/numerical-languages.1.html" title="Interpreted languages for numerical computations" class="state-published contenttype-folder">
+
+ <span>Numerical languages</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/virtualization.html" title="" class="state-published contenttype-folder">
+
+ <span>Virtualization</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/compilers.html" title="Available compilers, including GNU, INTEL and UPC compilers" class="state-published contenttype-document">
+
+ <span>Compilers</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/intel-xeon-phi.html" title="A guide to Intel Xeon Phi usage" class="state-published contenttype-document">
+
+ <span>Intel Xeon Phi</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/isv_licenses.html" title="A guide to managing Independent Software Vendor licences" class="state-published contenttype-document">
+
+ <span>ISV Licenses</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/java.html" title="Java on ANSELM" class="state-published contenttype-document">
+
+ <span>Java</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/nvidia-cuda.html" title="A guide to nVidia CUDA programming and GPU usage" class="state-published contenttype-document">
+
+ <span>nVidia CUDA</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/omics-master-1.html" title="" class="state-published contenttype-folder">
+
+ <span>OMICS Master</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/openfoam.html" title="A free, open source CFD software package" class="state-published contenttype-document">
+
+ <span>OpenFOAM</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/operating-system.html" title="The operating system, deployed on ANSELM" class="state-published contenttype-document">
+
+ <span>Operating System</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/paraview.html" title="An open-source, multi-platform data analysis and visualization application " class="state-published contenttype-document">
+
+ <span>ParaView</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/software/gpi2.html" title="A library that implements the GASPI specification" class="state-published contenttype-document">
+
+ <span>GPI-2</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/remote-visualization.html" title="" class="state-published contenttype-document">
+
+ <span>Remote visualization service</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="anselm-cluster-documentation/prace.html" title="" class="state-published contenttype-document">
+
+ <span>PRACE User Support</span>
+ </a>
+
+</div>
+</li>
+
+</ul>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="links.html" title="" class="state-published contenttype-document">
+
+ <span>Links</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="changelog.html" title="" class="state-published contenttype-collection">
+
+ <span>Changelog</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="pbspro-documentation.html" title="PBSPro Quick Start Guide, User's Guide, Reference Guide, Programmers Guide" class="state-published contenttype-folder">
+
+ <span>PBSPro Documentation</span>
+ </a>
+
+</div>
+<ul class="navTree navTreeLevel2">
+<li class="navTreeItem visualNoMarker">
+<div>
+
+ <a href="pbspro-documentation/pbspro-programmers-guide/view.html" title="Version 12." class="state-missing-value contenttype-file">
+ <img width="16" height="16" src="https://docs.it4i.cz/pdf.png" alt="Soubor" />
+ <span>PBSPro Programmer's Guide</span>
+ </a>
+
+</div>
+</li>
+<li class="navTreeItem visualNoMarker">
+<div>
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+ <p>AnyConnect users on Windows 8.1 will receive a "Failed to initialize connection subsystem" error after installing the Windows 8.1 02/10/15<br />security patch. This OS defect introduced with the 02/10/15 patch update will also impact WIndows 7 users with IE11. Windows Server<br />2008/2012 are also impacted by this defect, but neither is a supported OS for AnyConnect.<br /><br /><strong>Workaround:</strong></p>
+<ul>
+<li>Close the Cisco AnyConnect Window and the taskbar mini-icon</li>
+<li>Right click vpnui.exe in the 'Cisco AnyConnect Secure Mobility Client' folder. (C:\Program Files (x86)\Cisco\Cisco AnyConnect Secure Mobility</li>
+<li>Client\)</li>
+<li>Click on the 'Run compatibility troubleshooter' button</li>
+<li>Choose 'Try recommended settings'</li>
+<li>The wizard suggests Windows 8 compatibility.</li>
+<li>Click 'Test Program'. This will open the program.</li>
+<li>Close</li>
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+
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+ <!-- nagios_check_http_expect_string -->
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diff --git a/docs.it4i.cz/vpn-connection-fail-in-win-8.1.md b/docs.it4i.cz/vpn-connection-fail-in-win-8.1.md
index 6c7858129..335f333d9 100644
--- a/docs.it4i.cz/vpn-connection-fail-in-win-8.1.md
+++ b/docs.it4i.cz/vpn-connection-fail-in-win-8.1.md
@@ -25,4 +25,3 @@ OS for AnyConnect.
-
diff --git a/docs.it4i.cz/whats-new.html b/docs.it4i.cz/whats-new.html
new file mode 100644
index 000000000..80a61134e
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+ News
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+ <thead>
+ <tr>
+ <th class="listing-header-EffectiveDate">Datum účinnosti</th>
+ <th class="listing-header-Title">Nadpis</th>
+ </tr>
+ </thead>
+ <tbody>
+
+ <tr class="odd">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Středa 13.07.2016 15:40
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/matlab-2015b" title="MATLAB 2015b">MATLAB 2015b</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="even">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Pátek 08.07.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/vampir-installed" title="Vampir installed">Vampir installed</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="odd">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ ÄŚtvrtek 30.06.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/allinea-tools-updated-to-6-0.6" title="Allinea Tools updated to 6.0.6">Allinea Tools updated to 6.0.6</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="even">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ ÄŚtvrtek 30.06.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/intel-vtune-amplifier-support-for-xeon-phi-on-salomon" title="Intel VTune Amplifier support for Xeon Phi on Salomon">Intel VTune Amplifier support for Xeon Phi on Salomon</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="odd">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ ÄŚtvrtek 23.06.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/new-method-to-execute-parallel-matlab-jobs" title="New method to execute parallel MATLAB jobs">New method to execute parallel MATLAB jobs</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="even">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Středa 08.06.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/new-versions-of-allinea-forge-and-performance-version" title="New versions of Allinea Forge and Performance Reports">New versions of Allinea Forge and Performance Reports</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="odd">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Pondělà 06.06.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/intel-vtune-is-working" title="Intel VTune is working">Intel VTune is working</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="even">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ ĂšterĂ˝ 31.05.2016 14:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/intel-parallel-studio-2016-update-3" title="Intel Parallel Studio 2016 update 3">Intel Parallel Studio 2016 update 3</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="odd">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ ÄŚtvrtek 05.05.2016 15:58
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/ansys-17-0-installed" title="ANSYS 17.0 Installed">ANSYS 17.0 Installed</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="even">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Pátek 29.04.2016 14:25
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/allinea-forge-6.0" title="Allinea Forge 6.0">Allinea Forge 6.0</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="odd">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Pátek 29.04.2016 14:23
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/issue-with-intel-mpi-4-1-1-on-salomon" title="Issue with Intel MPI 4.1.1 on Salomon">Issue with Intel MPI 4.1.1 on Salomon</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="even">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Pátek 22.04.2016 14:35
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/new-modules-for-parallel-programming-in-modern-fortran-course" title="New modules for Parallel programming in modern Fortran course">New modules for Parallel programming in modern Fortran course</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="odd">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Středa 13.04.2016 14:20
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/octave-updated-to-4-0-1-on-anselm" title="Octave updated to 4.0.1 on Anselm">Octave updated to 4.0.1 on Anselm</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="even">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Pátek 01.04.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/allinea-forge-5-1-installed-on-anselm" title="Allinea Forge 5.1 installed on Anselm">Allinea Forge 5.1 installed on Anselm</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="odd">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Pondělà 07.03.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/cuda-7-5-is-now-installed-on-anselm" title="Cuda 7.5 is now installed on Anselm">Cuda 7.5 is now installed on Anselm</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="even">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Středa 24.02.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector" title="Added basic documentation for Intel Advisor and Intel Inspector">Added basic documentation for Intel Advisor and Intel Inspector</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="odd">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Středa 24.02.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/anselm-downtime-has-been-extended-to-feb-26th" title="Anselm downtime has been extended to Feb 26th.">Anselm downtime has been extended to Feb 26th.</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="even">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ ÄŚtvrtek 11.02.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/allinea-forge-documentation-updated" title="Allinea Forge documentation updated">Allinea Forge documentation updated</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="odd">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ ĂšterĂ˝ 09.02.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/new-bioinformatic-tools-installed-fastqc-0-11-3-gatk-3-5-java-1-7-0_79-picard-2-1-0-samtools-1-3-foss-2015g-snpeff-4-1_g-trimmomatic-0-35-java-1-7.0_79" title="New bioinformatic tools installed: FastQC/0.11.3, GATK/3.5-Java-1.7.0_79, picard/2.1.0, SAMtools/1.3-foss-2015g, SnpEff/4.1_G, Trimmomatic/0.35-Java-1.7.0_79">New bioinformatic tools installed: FastQC/0.11.3, GATK/3.5-Java-1.7.0_79, picard/2.1.0, SAMtools/1.3-foss-2015g, SnpEff/4.1_G, Trimmomatic/0.35-Java-1.7.0_79</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="even">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ ĂšterĂ˝ 26.01.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/salomon-pbs-changes" title="Salomon PBS changes">Salomon PBS changes</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="odd">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Pátek 15.01.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/capacity-computing-updated-for-salomon" title="Capacity computing updated for Salomon">Capacity computing updated for Salomon</a>
+ </td>
+
+
+
+
+
+ </tr>
+
+
+ <tr class="even">
+
+
+
+
+
+ <td class="listing-body-EffectiveDate">
+ Středa 13.01.2016 00:00
+ </td>
+
+
+
+
+ <td class="listing-body-Title">
+ <a href="https://docs.it4i.cz/whats-new/news-feed/mono-4-2-2-and-mpi-net-1-2-on-salomon" title="Mono 4.2.2 and MPI.NET 1.2 on Salomon">Mono 4.2.2 and MPI.NET 1.2 on Salomon</a>
+ </td>
+
+
+
+
+
+ </tr>
+
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+<div id="viewlet-cookiepolicy" style="display:none">
+ <h1 id="tlspu_cookiepolicy_title">This Site Uses Cookies</h1>
+ <p id="tlspu_cookiepolicy_message">We may use cookies to record some preference settings and to analyse how you use our web site. We may also use external analysis systems which may set additional cookies to perform their analysis. These cookies are integral to our web site. You can delete or disable these cookies in your web browser if you wish but then our site may not work correctly.</p>
+ <form id="tlspu_cookiepolicy_form">
+ <input type="checkbox" id="tlspu_cookiepolicy_agreed" value="confirmed" />
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+ <a href="anselm.html">Dokumentace pro Anselm</a>
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+ <a href="https://extranet.it4i.cz">Extranet</a>
+ <a href="http://prace.it4i.cz/">HPC & PRACE</a>
+ <a href="http://study.it4i.cz/">HPC Study</a>
+ <a href="salomon.html">Dokumentace pro Salomon</a>
+ <a href="http://industry.it4i.cz/en/">SuperpoÄŤĂtánĂ pro prĹŻmysl</a>
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diff --git a/docs.it4i.cz/whats-new/downtimes_history.md b/docs.it4i.cz/whats-new/downtimes_history.md
deleted file mode 100644
index 8f9727cb4..000000000
--- a/docs.it4i.cz/whats-new/downtimes_history.md
+++ /dev/null
@@ -1,464 +0,0 @@
-History of Downtimes
-====================
-
-Full history of important announcements related to IT4I infrastructure,
-planned downtimes, outages etc.
-
-
-<table>
-<colgroup>
-<col width="50%" />
-<col width="50%" />
-</colgroup>
-<thead>
-<tr class="header">
-<th align="left">Date and time</th>
-<th align="left">Title and description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td align="left">2016-07-19 10:51:02</td>
-<td align="left"><strong>Anselm planned downtime</strong>
-<p></p>
-<p>There's a planned maintenance window from 2016-08-16 07:00 till 2016-06-18 20:00 CEST.</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2016-07-15 08:20:00</td>
-<td align="left"><strong>Salomon cluster maintenance outage</strong>
-<p></p>
-<p>From 2016-07-20 09:00 till  2016-07-21 12:00 CEST will be maintenance outage for Salomon.</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2016-06-29 13:50:00</td>
-<td align="left"><strong>Salomon cluster maintenance outage prolonged</strong>
-<p></p>
-<p>Important! Salomon cluster maintenance outage will be prolonged till 2016-06-29 20:00 CEST.</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2016-06-16 00:00:00</td>
-<td align="left"><strong>Salomon planned downtime</strong>
-<p></p>
-<p>There's a planned maintenance window from 2016-06-28 09:00 till 2016-06-29 20:00 CEST.</p>
-<p>Thank you for understanding,<br />
-the IT4Innovations team</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2016-05-26 10:31:44</td>
-<td align="left"><strong>Salomon planned downtime</strong>
-<p></p>
-<p>There's a planned maintenance window from 2016-06-08 09:00 till 2016-06-09 09:00 CEST.</p>
-<p>Thank you for understanding,<br />
-the IT4Innovations team</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2016-04-27 15:57:28</td>
-<td align="left"><strong>Salomon cluster maintenance outage prolonged</strong>
-<p></p>
-<p>Important! Salomon cluster maintenance outage will be prolonged till 2016-04-28 14:00 CEST</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2016-03-31 19:03:25</td>
-<td align="left"><strong>Failure on Salomon Cooling System</strong>
-<p></p>
-<p>We have very serious issue with Salomon cooling system since 2016-03-31 10:00. We are working to resolve the issue.</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2016-03-31 18:59:04</td>
-<td align="left"><strong>Salomon Back in Production</strong>
-<p></p>
-<p>As of 2016-03-31 19:30 CET, the Salomon is back in production. The outage was caused by an issue in cooling system.</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2016-03-30 15:57:57</td>
-<td align="left"><strong>PBS malfunction</strong>
-<p></p>
-<p>We've had several issues with PBS scheduler since 2016-03-30 13:00 CEST. We are still working on it.</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2016-03-26 09:52:41</td>
-<td align="left"><strong>Salomon back to production</strong>
-<p></p>
-<p>We have recovered all the issues with the Salomon cluster.</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2016-03-26 09:51:16</td>
-<td align="left"><strong>Failure on Salomon Cooling Infrastructure</strong>
-<p></p>
-<p>We had an issue with the cooling infra of Salomon. This issue led to InfiniBand and storage outage. We are working to resolve the issue.</p>
-
-
-</td>
-</tr>
-<tr class="even">
-<td align="left">2016-03-14 14:57:51</td>
-<td align="left"><strong>Infrastructure Maintenance</strong>
-<p></p>
-<p>The Salomon supercomputer will be down for the maintenance from 2016-03-22 10:00 CEST to 2016-03-22 17:00 CEST.</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2016-02-24 12:30:00</td>
-<td align="left"><strong>Anselm Upgrade</strong>
-<p></p>
-<p>The Anselm supercomputer will be down for the updates from 2016-02-01 to 2016-02-29.</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2016-02-23 08:45:45</td>
-<td align="left"><strong>Anselm Upgrade</strong>
-<p></p>
-<p>The Anselm supercomputer will be down for the updates from 2016-02-01 to 2016-02-29.</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2016-02-14 08:07:46</td>
-<td align="left"><strong>Failure on Salomon Infiniband Network</strong>
-<p></p>
-<p>We have very serious issue with Salomon Infiniband network since 2016-02-11 10:18. We are working to resolve the issue as quickly as possible and apologize for any inconvenience.</p>
-
-
-</td>
-</tr>
-<tr class="even">
-<td align="left">2016-02-04 11:53:30</td>
-<td align="left"><strong>Short network outage</strong>
-<p></p>
-<p>We need to apply some changes in network devices settings which may cause short network outage for Anselm Login nodes. This work will start around 6 am 2016-01-26.</p>
-<p>Thanks for your understanding.</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2016-02-04 11:52:37</td>
-<td align="left"><strong>Salomon Upgrade</strong>
-<p></p>
-<p>The Salomon supercomputer will be down for the updates from 2016-02-16 09:00 CEST to 2016-02-16 13:00 CEST.</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2016-02-04 11:52:25</td>
-<td align="left"><strong>Salomon Upgrade</strong>
-<p></p>
-<p>The Salomon supercomputer will be down for the updates from 2016-02-16 09:00 CEST to 2016-02-16 13:00 CEST.</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2015-11-26 08:11:25</td>
-<td align="left"><strong>/home downtime</strong>
-<p></p>
-<p>Dear HPC users<br />
-<br />
-There's a /home downtime on the Salomon supercomputer planned for 25th November. The reason is a maintenance of the underlying CXFS filesystem. Your jobs will be scheduled with respect to this maintenance window.<br />
-<br />
-Thank you for understanding,<br />
-the IT4I team</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2015-11-24 09:10:15</td>
-<td align="left"><strong>The /home filesystem was down</strong>
-<p></p>
-<p><span>On 23.11.2015, 13:55 - 14:55, the /home filesystem was down due to acute technical problems.</span><br />
-<span>We apologize for inconvenience.</span></p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2015-09-04 16:14:12</td>
-<td align="left"><strong>SCRATCH downtime</strong>
-<p></p>
-<p>Dear IT4I users<br />
-<br />
-Salomon's SCRATCH will *not* be accessible on Thursday (10th September 2015) from 13:00 till 18:00 CEST.<br />
-<br />
-Thank you for understanding,<br />
-the IT4Innovations team</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2015-08-27 00:00:00</td>
-<td align="left"><strong>Today's SCRATCH downtime</strong>
-<p></p>
-<p>Dear IT4I users<br />
-<br />
-We are sorry for today's (27th August) inaccessibility of SCRATCH filesystem due to a broken service which normally provides mapping for user/group IDs (UIDs/GIDs). The issue has been fixed. No data were lost.<br />
-<br />
-Thank you for understanding,<br />
-the IT4Innovations team</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2015-08-12 00:00:00</td>
-<td align="left"><strong>Unplanned downtime</strong>
-<p></p>
-<p>Dear Salomon users,<br />
-<br />
-there was an unplanned downtime of the non-accelerated nodes. At this moment, systems are booting and we are revising consequences. Temporarily inaccessible SCRATCH filesystem is one of them.<br />
-<br />
-We're sorry for the inconvenience,<br />
-the IT4I team</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2015-08-06 00:00:00</td>
-<td align="left"><strong>SCRATCH downtime</strong>
-<p></p>
-<p>Dear IT4I users<br />
-<br />
-Salomon's SCRATCH will not be accessible tomorrow (7th August 2015) from 08:30 till 11:00 CEST.<br />
-<br />
-Thank you for understanding,<br />
-the IT4Innovations team</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2014-11-14 10:27:51</td>
-<td align="left"><strong>Unplanned PBS Downtime</strong>
-<p></p>
-<p>Dear Anselm users,<br />
-<br />
-we apologize for the unavailability of our PBS scheduler during the last weekend. However, running jobs shouldn't have been affected at that time.<br />
-<br />
-Thank you for understanding,<br />
-Anselm Admins</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2014-11-14 10:27:50</td>
-<td align="left"><strong>Login1 troubles</strong>
-<p></p>
-<p>Login1 had a short unplanned downtime. Sorry for the troubles.</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2014-10-14 20:30:00</td>
-<td align="left"><strong>Unexpected power failure</strong>
-<p></p>
-<p><span>Dear Anselm users,</span></p>
-<p><span><br />
-</span></p>
-<p><span>on Tuesday 14th approximately at 17:20 CEST we encountered power failure during service operation on backup diesel generator. The system shut down. Additional checks after the shutdown took more time than what would expect.</span><span><span> The system was back on-line with all services approximately at 21:00 CEST.</span> We are very sorry for any troubles, this matter may caused you. If some of your jobs ended in incorrect state, please feel free to reclaim your core hours.</span></p>
-<p><span><br />
-</span></p>
-<p><span>Thank you for understanding, <br />
-Anselm Administrators</span></p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2014-07-17 13:50:00</td>
-<td align="left"><strong>Login2(!) downtime</strong>
-<p></p>
-<p>Dear Anselm users,<br />
-<br />
-there's an upgrade planned on Friday, 18th July from 13:00 till 16:00 CEST. Please, take in mind that login2.anselm.it4i.cz will be unavailable at the given time-frame. We are sorry for the inconvenience.<br />
-<br />
-Thank you for understanding,<br />
-Anselm Admins</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2014-07-16 13:11:34</td>
-<td align="left"><strong>Login1 downtime</strong>
-<p></p>
-<p>Dear Anselm users,<br />
-<br />
-there's an upgrade planned on Thursday, 17th July from 13:00 till 16:00 CEST. Please, take in mind that login1.anselm.it4i.cz will be unavailable at the given time-frame. We are sorry for the inconvenience.<br />
-<br />
-Thank you for understanding,<br />
-Anselm Admins</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2014-06-18 10:51:56</td>
-<td align="left"><strong>Login2 downtime</strong>
-<p></p>
-<p>Dear Anselm users,<br />
-<br />
-there's an upgrade planned on Wednesday, 18th June from 11:20 till 14:20 CEST. Please, take in mind that login2.anselm.it4i.cz will be unavailable at the given time-frame. We are sorry for the inconvenience.<br />
-<br />
-Thank you for understanding,<br />
-Anselm Admins</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2014-05-22 00:00:00</td>
-<td align="left"><strong>Outage</strong>
-<p></p>
-<p>Dear Anselm users.<br />
-<br />
-As of today (20140523 10:45) we had an unmanaged outage of a few nodes. Affected nodes were cn[117-126,193-195].<br />
-<br />
-Sorry for the inconveniences,<br />
-Anselm admins</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2014-04-11 11:30:00</td>
-<td align="left"><strong>Heartbleed bug</strong>
-<p></p>
-<p>Dear users of the Anselm cluster,<br />
-<br />
-A serious bug in the OpenSSL library, known as the "Heartbleed bug" has been recently discovered. <span>We would like to ensure you that IT4I has taken all necessary steps to fix the OpenSSL library on all the systems.</span><br />
-The bug in OpenSSL library affected many sites worldwide for nearly two years. At this moment, there is no evidence that any abuse of data took place at IT4I.<br />
-In order to ensure the security and integrity of IT4I systems, all users will be issued new login credentials, including password and ssh keys.<br />
-<span>For more informations about the Heartbleed bug, please see</span><a href="../heartbleed-bug.html" class="moz-txt-link-freetext external-link">https://docs.it4i.cz/heartbleed-bug</a><br />
-<br />
-Thank you for your understanding.<br />
-IT4Innovations team</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2014-04-02 13:05:00</td>
-<td align="left"><strong>Scheduler is Down</strong>
-<p></p>
-<p>We are sorry for the current scheduler issues which are caused by an inconsistency of the internal PBS database. Thus it's not possible to interact with the scheduler now. In addition, some jobs may be affected and some job outputs may not be retrieved at this moment.</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2014-03-26 15:50:00</td>
-<td align="left"><strong>Temporary Scratch Mount on Login1</strong>
-<p></p>
-<p>Because of the Lustre issues (mentioned in previous announcements) there's a temporary mount point for Scratch filesystem on login1 node. Please, follow this path to access your data:</p>
-<p>/scratch_nfs/</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2014-03-26 13:10:00</td>
-<td align="left"><strong>Both Login Nodes Inaccessible</strong>
-<p></p>
-<p>We are sorry for the inaccessibility of both login nodes. We are co-operating with our supplier and trying hard to solve this problem as soon as possible.</p>
-<p>Thank you for understanding.</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2014-03-25 22:05:00</td>
-<td align="left"><strong>Login1(!) Not Responding</strong>
-<p></p>
-<p>Currently, if you're having trouble while accessing Anselm, please use address login2.anselm.it4i.cz instead of anselm.it4i.cz. There's a Lustre issue with the login1 node, which causes it to not respond.</p>
-<p>We'll let you know by MOTD when login1 comes back online.</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2013-12-03 00:00:00</td>
-<td align="left"><strong>Planned Downtime</strong>
-<p></p>
-<p>On 17th December 08:00 to 18:00 CET Anselm will be down for maintenance. Power supply upgrade will take place, as well as system maintenance and software updates.<br />
-<br />
-Prior to the period:<br />
-- Jobs will be scheduled for running with a respect to the downtime.<br />
-<br />
-During the period:<br />
-- No Anselm HPC service will be available.<br />
-- Following web applications will not be accessibleRequest Tracker, Anselm cluster documentation, Anselm Allocation.<br />
-- Submitting tickets through the e-mail address <script type="text/javascript">
-<!--
-h='';a='@';n='support%5Bat%5Dit4i.cz';e=n+a+h;
-document.write('<a h'+'ref'+'="ma'+'ilto'+':'+e+'" clas'+'s="em' + 'ail">'+'support[at]it4i.cz'+'</'+'a'+'>');
-// -->
-</script><noscript>support[at]it4i.cz (support%5Bat%5Dit4i.cz at )</noscript> will be delayed.<br />
-<br />
-After the period:<br />
-- All service will be brought back to normal.<br />
-- Jobs in a 'Q' state will be scheduled for running.<br />
-<br />
-We are sorry for the inconvenience.</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2013-10-14 00:00:00</td>
-<td align="left"><strong>Cooling system unstable</strong>
-<p></p>
-<p>Dear Anselm users,<br />
-<br />
-there was an unplanned downtime due to severe issues with the cold doors today. We are trying hard to bring all services up. We assume that we will finish the maintenance at about 13:30 CEST.<br />
-<br />
-Thank you for understanding.<br />
-<br />
-Sincerely yours,<br />
-Anselm admins</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2013-09-17 15:50:00</td>
-<td align="left"><strong>A Fair Amount of Nodes Down</strong>
-<p></p>
-<p>Dear Anselm users,<br />
-<br />
-We had an outage on the Anselm Cluster. A fair amount of the nodes was unavailable to production.<br />
-<br />
-Consider terminated job resubmission.<br />
-<br />
-We are sorry for the troubles,<br />
-Anselm admins</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2013-08-23 15:25:00</td>
-<td align="left"><strong>Infiniband Maintenance Window</strong>
-<p></p>
-<p>Dear Anselm users,<br />
-<br />
-We would like to inform you about a planned Infiniband maintenance window, on Wednesday, 28th August from 09:00 till 16:30 CEST.<br />
-No Anselm service will be available during this outage.<br />
-<br />
-New batch jobs will not be scheduled for running during this time. Consider altering the job walltime, to achieve job execution prior to the downtime (See Job Submission in the Anselm Documentation).<br />
-<br />
-Sincerely yours,<br />
-Anselm Admins</p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2013-08-14 17:10:00</td>
-<td align="left"><strong>Planned Upgrade / Scheduler Downtime</strong>
-<p></p>
-<p>Dear Anselm users,<br />
-<br />
-there's an upgrade planned on Thursday, 15th August from 18:00 till 22:00 CEST. Please, take in mind that PBS scheduler won't accept your jobs at the given timeframe. We are sorry for the inconvenience.<br />
-<br />
-Thank you for understanding,<br />
-Anselm Admins</p>
-</td>
-</tr>
-<tr class="even">
-<td align="left">2013-07-16 13:45:00</td>
-<td align="left"><strong>Anselm Cluster Upgrade - July 23rd</strong>
-<p></p>
-<p>Dear Anselm users.<br />
-<br />
-We would like to inform you that Anselm cluster will be unavailable due to upgrades on Tuesday, July 23rd from 07:00 to 20:00 CEST.<br />
-<br />
-Sorry for the inconvenience,<br />
-Anselm admins<br />
-<br />
---<br />
-<br />
-Anselm cluster documentation can be found at:<br />
-<a href="http://support.it4i.cz/docs/anselm-cluster-documentation/" class="uri" class="external-link">http://support.it4i.cz/docs/anselm-cluster-documentation/</a></p>
-</td>
-</tr>
-<tr class="odd">
-<td align="left">2013-06-27 09:35:00</td>
-<td align="left"><strong>SSH Password Authentication</strong>
-<p></p>
-<p>Dear Anselm users.<br />
-<br />
-If you are experiencing some troubles when using SSH PasswordAuthentication on the client side, please switch to PubkeyAuthentication instead.<br />
-<br />
-We are trying hard to resolve this issue.<br />
-<br />
-Sincerely yours,<br />
-Anselm admins</p>
-</td>
-</tr>
-</tbody>
-</table>
-
diff --git a/docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector.md b/docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector.md
deleted file mode 100644
index 91678df68..000000000
--- a/docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector.md
+++ /dev/null
@@ -1,106 +0,0 @@
-Intel Parallel Studio
-=====================
-
-
-
-
-
-The Salomon cluster provides following elements of the Intel Parallel
-Studio XE
-
- Intel Parallel Studio XE
- -------------------------------------------------
- Intel Compilers
- Intel Debugger
- Intel MKL Library
- Intel Integrated Performance Primitives Library
- Intel Threading Building Blocks Library
- Intel Trace Analyzer and Collector
- Intel Advisor
- Intel Inspector
-
-Intel compilers
----------------
-
-The Intel compilers version 131.3 are available, via module
-iccifort/2013.5.192-GCC-4.8.3. The compilers include the icc C and C++
-compiler and the ifort fortran 77/90/95 compiler.
-
- $ module load intel
- $ icc -v
- $ ifort -v
-
-Read more at the [Intel
-Compilers](../../salomon/software/intel-suite/intel-compilers.html)
-page.
-
-Intel debugger
---------------
-
-IDB is no longer available since Parallel Studio 2015.
-
-Â The intel debugger version 13.0 is available, via module intel. The
-debugger works for applications compiled with C and C++ compiler and the
-ifort fortran 77/90/95 compiler. The debugger provides java GUI
-environment. Use [X
-display](../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
-for running the GUI.
-
- $ module load intel
- $ idb
-
-Read more at the [Intel
-Debugger](../../salomon/software/intel-suite/intel-debugger.html)
-page.
-
-Intel Math Kernel Library
--------------------------
-
-Intel Math Kernel Library (Intel MKL) is a library of math kernel
-subroutines, extensively threaded and optimized for maximum performance.
-Intel MKL unites and provides these basic componentsBLAS, LAPACK,
-ScaLapack, PARDISO, FFT, VML, VSL, Data fitting, Feast Eigensolver and
-many more.
-
- $ module load imkl
-
-Read more at the [Intel
-MKL](../../salomon/software/intel-suite/intel-mkl.html)
-page.
-
-Intel Integrated Performance Primitives
----------------------------------------
-
-Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX
-is available, via module ipp. The IPP is a library of highly optimized
-algorithmic building blocks for media and data applications. This
-includes signal, image and frame processing algorithms, such as FFT,
-FIR, Convolution, Optical Flow, Hough transform, Sum, MinMax and many
-more.
-
- $ module load ipp
-
-Read more at the [Intel
-IPP](../../salomon/software/intel-suite/intel-integrated-performance-primitives.html)
-page.
-
-Intel Threading Building Blocks
--------------------------------
-
-Intel Threading Building Blocks (Intel TBB) is a library that supports
-scalable parallel programming using standard ISO C++ code. It does not
-require special languages or compilers. It is designed to promote
-scalable data parallel programming. Additionally, it fully supports
-nested parallelism, so you can build larger parallel components from
-smaller parallel components. To use the library, you specify tasks, not
-threads, and let the library map tasks onto threads in an efficient
-manner.
-
- $ module load tbb
-
-Read more at the [Intel
-TBB](../../salomon/software/intel-suite/intel-tbb.html)
-page.
-
-
-
diff --git a/html_md.sh b/html_md.sh
index 57c5c6385..c82b635d0 100755
--- a/html_md.sh
+++ b/html_md.sh
@@ -45,7 +45,7 @@ if [ "$1" = "-i" ]; then
fi
if [ "$1" = "-w" ]; then
# download html pages
- wget -X changelog,portal_css,portal_javascripts,++resource++jquery-ui-themes,anselm-cluster-documentation/icon.jpg -R favicon.ico,pdf.png,logo.png,background.png,application.png,search_icon.png,png.png,sh.png,touch_icon.png,anselm-cluster-documentation/icon.jpg,*js,robots.txt,*xml,RSS,download_icon.png,*zip,*rar,@@*,anselm-cluster-documentation/icon.jpg.1 --mirror --convert-links --adjust-extension --page-requisites --no-parent https://docs.it4i.cz;
+ wget -X changelog,whats-new,portal_css,portal_javascripts,++resource++jquery-ui-themes,anselm-cluster-documentation/icon.jpg -R favicon.ico,pdf.png,logo.png,background.png,application.png,search_icon.png,png.png,sh.png,touch_icon.png,anselm-cluster-documentation/icon.jpg,*js,robots.txt,*xml,RSS,download_icon.png,*zip,*rar,@@*,anselm-cluster-documentation/icon.jpg.1 --mirror --convert-links --adjust-extension --page-requisites --no-parent https://docs.it4i.cz;
fi
if [ "$1" = "-c" ]; then
# delete all .md files
@@ -95,7 +95,7 @@ if [ "$1" = "-c" ]; then
(while read y;
do
# search and delete according with filter_auto
- sed -e 's/{'"$y"'}//g' "${i%.*}.md" | sed -e 's/\\//g' | sed -e 's/^Q//g' | sed -e 's/: //g' | sed -e 's/<\/div>//g' | sed '/^<div/d' | sed -e 's/^Obsah//g' | awk -v RS='\n\n\n\n\n' 1 > "${i%.*}TMP.md";
+ sed -e 's/{'"$y"'}//g' "${i%.*}.md" | sed -e 's/\\//g' | sed -e 's/^: //g' | sed -e 's/<\/div>//g' | sed '/^<div/d' | sed -e 's/^Obsah//g' | sed -e 's/{#putty---before-we-start-//g' | sed -e 's/ssh-connection style="text-alignstart; "}//g'| awk -v RS='\n\n\n\n\n' 1 > "${i%.*}TMP.md";
cat "${i%.*}TMP.md" > "${i%.*}.md";
done) < filter_auto
diff --git a/info/list_md.txt b/info/list_md.txt
index 830aa713a..aa84c1bec 100644
--- a/info/list_md.txt
+++ b/info/list_md.txt
@@ -1,6 +1,3 @@
-./docs.it4i.cz/whats-new/downtimes_history.md
-./docs.it4i.cz/whats-new/news-feed/added-basic-documentation-for-intel-advisor-and-intel-inspector.md
-./docs.it4i.cz/whats-new/news-feed/allinea-forge-documentation-updated.md
./docs.it4i.cz/links.md
./docs.it4i.cz/get-started-with-it4innovations/introduction.md
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters.md
@@ -44,6 +41,7 @@
./docs.it4i.cz/salomon/software/debuggers/summary.md
./docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md
./docs.it4i.cz/salomon/software/debuggers/valgrind.md
+./docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md
./docs.it4i.cz/salomon/software/debuggers/aislinn.md
./docs.it4i.cz/salomon/software/debuggers/vampir.md
./docs.it4i.cz/salomon/software/debuggers/total-view.md
@@ -95,7 +93,6 @@
./docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md
./docs.it4i.cz/salomon/network-1.md
./docs.it4i.cz/anselm.md
-./docs.it4i.cz/heartbleed-bug.md
./docs.it4i.cz/anselm-cluster-documentation/introduction.md
./docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
./docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.md
@@ -187,3 +184,4 @@
./docs.it4i.cz/vpn-connection-fail-in-win-8.1.md
./docs.it4i.cz/anselm-cluster-documentation.md
./docs.it4i.cz/index.md
+./README.md
diff --git a/info/list_png.txt b/info/list_png.txt
index c00dbb9ba..92f556b66 100644
--- a/info/list_png.txt
+++ b/info/list_png.txt
@@ -2,7 +2,7 @@
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-terminal.png
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmscreensaver.png
-./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmscreensaver.png/@@images/44048cfa-e854-4cb4-902b-c173821c2db1.png
+./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmscreensaver.png/@@images/8e80a92f-f691-4d92-8e62-344128dcc00b.png
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gnome-compute-nodes-over-vnc.png
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png
./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/cygwin-and-x11-forwarding/cygwinX11forwarding.png
--
GitLab