diff --git a/README.md b/README.md
index 5842d66fe83c2c15107e6e14470fc091a0bcc451..9cd2312d512e18e74aa7b79a4cca6fd259df96fd 100755
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-Převod html dokumentace do md formátu (version 0.36) - BETA
+Převod html dokumentace do md formátu (version 0.4) - BETA
===========================================================
Výsledkem projektu by měl být skript pro stažení a převod stávající dokumentace na docs.it4i.cz do md formátu
@@ -18,11 +18,12 @@ Pro svou práci si naklonujete Gitem repozitář do svého pracovního adresář
> * interní a externí odkazy
> * formátování tabulek
> * formátovámí textu v některých místech
+> * doba převodu ~24min
>**Změny v nové verzi**
->* oprava odkazu na obrázky
->* vylepšené filtrování
->* přidání testovacího parametru t1 pro kontrolu změn, v následující verzi bude sloučen...
+> * oprava odkazu na obrázky a vylepšené filtrování
+> * přehled o počtu souboru a stavu převodu
+> * optimalizace, začlenění testovacích funkcí do hlavní větve programu
### Funkce skriptu
@@ -42,4 +43,4 @@ Testování
```bash
html_md.sh -t
-```
\ No newline at end of file
+```
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
index 342fc28f43616c0e2c6b7b7f394e4551ba15cad5..77868ae930afb0f767464f6fe548887309919770 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md
@@ -5,6 +5,14 @@ Outgoing connections
+
+
+
+
+
+
+
+
Connection restrictions
-----------------------
@@ -44,7 +52,7 @@ local $ ssh -R 6000:remote.host.com:1234 anselm.it4i.cz
```
In this example, we establish port forwarding between port 6000 on
-Anselm and port 1234 on the remote.host.com. By ing
+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.
@@ -55,7 +63,7 @@ Remote radio button. Insert 6000 to Source port textbox. Insert
remote.host.com:1234. Click Add button, then Open.
Port forwarding may be established directly to the remote host. However,
-this requires that user has ssh to remote.host.com
+this requires that user has ssh access to remote.host.com
```
$ ssh -L 6000:localhost:1234 remote.host.com
@@ -66,7 +74,7 @@ Note: Port number 6000 is chosen as an example only. Pick any free port.
### Port forwarding from compute nodes
Remote port forwarding from compute nodes allows applications running on
-the compute nodes to hosts outside Anselm Cluster.
+the compute nodes to access hosts outside Anselm Cluster.
First, establish the remote port forwarding form the login node, as
[described
@@ -80,7 +88,7 @@ $ ssh -TN -f -L 6000:localhost:6000 login1
```
In this example, we assume that port forwarding from login1:6000 to
-remote.host.com:1234 has been established beforehand. By ing
+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
@@ -90,7 +98,7 @@ Port forwarding is static, each single port is mapped to a particular
port on remote host. Connection to other remote host, requires new
forward.
-Applications with inbuilt proxy support, experience unlimited to
+Applications with inbuilt proxy support, experience unlimited access to
remote hosts, via single proxy server.
To establish local proxy server on your workstation, install and run
@@ -114,6 +122,10 @@ local $ ssh -R 6000:localhost:1080 anselm.it4i.cz
```
Now, configure the applications proxy settings to **localhost:6000**.
-Use port forwarding to the [proxy server from compute
+Use port forwarding to access the [proxy server from compute
nodes](outgoing-connections.html#port-forwarding-from-compute-nodes)
as well .
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
index 82f3ae4121b2b45c4f9d86253fcd0f1d0b683578..8bcf8a55f344b590d6050d009aba6f91576ca524 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md
@@ -1,14 +1,22 @@
-Shell and data transfer
+Shell access and data transfer
==============================
+
+
+
+
+
+
+
+
Interactive Login
-----------------
-The Anselm cluster is ed by SSH protocol via login nodes login1
+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.
@@ -19,7 +27,7 @@ login1.anselm.it4i.cz 22 ssh login1
login2.anselm.it4i.cz 22 ssh login2
The authentication is by the [private
-key](../../../get-started-with-it4innovations/ing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
Please verify SSH fingerprints during the first logon. They are
identical on all login nodes:
@@ -44,7 +52,7 @@ local $ chmod 600 /path/to/id_rsa
```
On **Windows**, use [PuTTY ssh
-client](../../../get-started-with-it4innovations/ing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
+client](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
After logging in, you will see the command prompt:
@@ -79,10 +87,10 @@ Address Port
anselm.it4i.cz 22 scp, sftp
login1.anselm.it4i.cz 22 scp, sftp
login2.anselm.it4i.cz 22 scp, sftp
- class="discreet">dm1.anselm.it4i.cz class="discreet">22 class="discreet">scp, sftp</span>
+ class="discreet">dm1.anselm.it4i.cz 22 class="discreet">scp, sftp</span>
The authentication is by the [private
-key](../../../get-started-with-it4innovations/ing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
Data transfer rates up to **160MB/s** can be achieved with scp or sftp.
1TB may be transferred in 1:50h.
@@ -138,3 +146,7 @@ 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/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
index e245539bcb98ad2b3b4613b5e866ea3b8c9d55c3..99df6595cdd44a8601f68f266c5aa9f61a17dcad 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md
@@ -5,6 +5,14 @@ VPN Access
+
+
+
+
+
+
+
+
Accessing IT4Innovations internal resources via VPN
---------------------------------------------------
@@ -46,9 +54,9 @@ for automatic installation.
-](../executionaccess.jpg/@@images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpeg "Execution access")
-
-
+access](../executionaccess.jpg/@@images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpeg "Execution access")
+access
+
After successful installation, VPN connection will be established and
you can use available resources from IT4I network.
@@ -92,13 +100,13 @@ 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.
-connection](../anyconnecticon.jpg "Successfull connection")
+
If you right-click on this icon, you will see a context menu in which
you can control the VPN connection.
-
+
+
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
@@ -110,7 +118,7 @@ but just select the corresponding item.
Then AnyConnect automatically proceeds like in the case of first logon.
-
+
After a successful logon, you can see a green circle with a tick mark on
the lock icon.
@@ -120,3 +128,7 @@ the lock icon.
For disconnecting, right-click on the AnyConnect client icon in the
system tray and select **VPN Disconnect**.
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md b/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
index 46675a0775ca8a61a59bbcade72aaed9c9d0dcd8..ae39e5e769fdd011dc8053e092bb80ceac0f33bf 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md
@@ -5,6 +5,14 @@ Compute Nodes
+
+
+
+
+
+
+
+
Nodes Configuration
-------------------
@@ -192,7 +200,7 @@ nodes.****
-**
+
**Figure Anselm bullx B510 servers****
@@ -207,17 +215,37 @@ Fat compute nodes 2 cn[208-209] 512GB 16 @ 2.4GHz qfat,
+
+
+
+
Processor Architecture
----------------------
+
+
+
+
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.
+
+
+
+
### Intel Sandy Bridge E5-2665 Processor
+
+
+
+
+
+
+
+
- eight-core
- speed: 2.4 GHz, up to 3.1 GHz using Turbo Boost Technology
- peak performance: 19.2 Gflop/s per
@@ -232,7 +260,23 @@ with accelerator). Processors support Advanced Vector Extensions (AVX)
- memory bandwidth at the level of the processor: 51.2 GB/s
+
+
+
+
+
+
+
+
### Intel Sandy Bridge E5-2470 Processor
+
+
+
+
+
+
+
+
- eight-core
- speed: 2.3 GHz, up to 3.1 GHz using Turbo Boost Technology
- peak performance: 18.4 Gflop/s per
@@ -262,8 +306,20 @@ $ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16:cpu_freq=24 -I
```
+
+
+
+
In this example, we allocate 4 nodes, 16 cores at 2.4GHhz per node.
+
+
+
+
+
+
+
+
Intel Turbo Boost Technology is used by default, you can disable it for
all nodes of job by using resource attribute cpu_turbo_boost.
@@ -274,7 +330,19 @@ all nodes of job by using resource attribute cpu_turbo_boost.
Memory Architecture
-------------------
+
+
+
+
### Compute Node Without Accelerator
+
+
+
+
+
+
+
+
- 2 sockets
- Memory Controllers are integrated into processors.
@@ -288,7 +356,23 @@ Memory Architecture
- Populated memory: 8x 8GB DDR3 DIMM 1600Mhz
+
+
+
+
+
+
+
+
### Compute Node With GPU or MIC Accelerator
+
+
+
+
+
+
+
+
- 2 sockets
- Memory Controllers are integrated into processors.
@@ -302,7 +386,23 @@ Memory Architecture
- Populated memory: 6x 16GB DDR3 DIMM 1600Mhz
+
+
+
+
+
+
+
+
### Fat Compute Node
+
+
+
+
+
+
+
+
- 2 sockets
- Memory Controllers are integrated into processors.
@@ -318,3 +418,10 @@ Memory Architecture
+
+
+
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md b/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
index b4a02b88b8ef2d6f8bbc99808b9a4293f4c3d58c..c8ee979a47335834690571edf265e70d11698538 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md
@@ -5,6 +5,14 @@ Environment and Modules
+
+
+
+
+
+
+
+
### Environment Customization
After logging in, you may want to configure the environment. Write your
@@ -34,7 +42,7 @@ 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 id="result_box"
-class="short_text"> class="hps alt-edited">stated
+ class="hps alt-edited">stated
in the previous example.
### Application Modules
@@ -113,3 +121,7 @@ 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/converted/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md b/converted/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
index 39af24ff18fd30782488e6cb8783e51a794989a2..e47a9f9f49a945cdfcf4ea51bb69093405cc3168 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md
@@ -5,12 +5,20 @@ Hardware Overview
+
+
+
+
+
+
+
+
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 class="WYSIWYG_LINK">powerful x86-64 computer,
equipped with 16 cores (two eight-core Intel Sandy Bridge processors),
-at least 64GB RAM, and local hard drive. The user to the Anselm
+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
@@ -19,7 +27,7 @@ share 320TB /home disk storage to store the user files. The 146TB shared
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
- 45 TB of dedicated block storage. Accelerated nodes, fat nodes,
+access 45 TB of dedicated block storage. Accelerated nodes, fat nodes,
and virtualization infrastructure are available [upon
request](https://support.it4i.cz/rt) made by a PI.
@@ -348,9 +356,9 @@ disk storage available on all compute nodes /lscratch. [More about
class="WYSIWYG_LINK">Storage](storage.html).
-The user to the Anselm cluster is provided by two login nodes
-login1, login2, and data mover node dm1. [More about ing
-cluster.](ing-the-cluster.html)
+The user access to the Anselm cluster is provided by two login nodes
+login1, login2, and data mover node dm1. [More about accessing
+cluster.](accessing-the-cluster.html)
The parameters are summarized in the following tables:
@@ -398,3 +406,7 @@ Fat compute node 2x Intel Sandy Bridge E5-2665, 2.4GHz 512GB -
nodes](compute-nodes.html),
[Storage](storage.html), and
[Network](network.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/introduction.md b/converted/docs.it4i.cz/anselm-cluster-documentation/introduction.md
index 39979bff8e9c120e08cd3a5833e8ebcdbb72d8f8..8c5f98f717909377ef1b1b7e361067114cec815f 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/introduction.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/introduction.md
@@ -5,6 +5,14 @@ Introduction
+
+
+
+
+
+
+
+
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
@@ -23,7 +31,7 @@ class="WYSIWYG_LINK">Linux
family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
We have installed a wide range of
[software](software.1.html) packages targeted at
-different scientific domains. These packages are ible via the
+different scientific domains. These packages are accessible via the
[modules environment](environment-and-modules.html).
User data shared file-system (HOME, 320TB) and job data shared
@@ -37,4 +45,8 @@ Read more on how to [apply for
resources](../get-started-with-it4innovations/applying-for-resources.html),
[obtain login
credentials,](../get-started-with-it4innovations/obtaining-login-credentials.html)
-and [ the cluster](accessing-the-cluster.html).
+and [access the cluster](accessing-the-cluster.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/network.md b/converted/docs.it4i.cz/anselm-cluster-documentation/network.md
index 673a16d793e7cc1e1a87bbc08beb76fd020a1020..375b9fd49ee16ac3a947776e748d87dbd084c038 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/network.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/network.md
@@ -5,6 +5,14 @@ Network
+
+
+
+
+
+
+
+
All compute and login nodes of Anselm are interconnected by
[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
QDR network and by Gigabit
@@ -20,7 +28,7 @@ high-bandwidth, low-latency
QDR network (IB 4x QDR, 40 Gbps). The network topology is a fully
non-blocking fat-tree.
-The compute nodes may be ed via the Infiniband network using ib0
+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.
@@ -34,7 +42,7 @@ other nodes concurrently.
Ethernet Network
----------------
-The compute nodes may be ed via the regular Gigabit Ethernet
+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.
The network provides **114MB/s** transfer rates via the TCP connection.
@@ -55,5 +63,9 @@ $ ssh 10.2.1.110
$ ssh 10.1.1.108
```
-In this example, we the node cn110 by Infiniband network via the
+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/converted/docs.it4i.cz/anselm-cluster-documentation/prace.md b/converted/docs.it4i.cz/anselm-cluster-documentation/prace.md
index 22b199c7ee52c366b3d6cab076b50cd84568c57f..ba5c31d028772a50fec21a38790645257f8a1c27 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/prace.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/prace.md
@@ -5,6 +5,14 @@ PRACE User Support
+
+
+
+
+
+
+
+
Intro
-----
@@ -14,12 +22,12 @@ 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 to some services intended for
+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 [Obtaining
Login Credentials
section](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html),
-if the same level of is required.
+if the same level of access is required.
All general [PRACE User
Documentation](http://www.prace-ri.eu/user-documentation/)
@@ -35,7 +43,7 @@ Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
Information about the local services are provided in the [introduction
of general user documentation](introduction.html).
Please keep in mind, that standard PRACE accounts don't have a password
-to the web interface of the local (IT4Innovations) request
+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.
@@ -59,7 +67,7 @@ Accessing the cluster
### Access with GSI-SSH
-For all PRACE users the method for interactive (login) and data
+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.
@@ -67,14 +75,14 @@ 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).
-Most of the information needed by PRACE users ing the Anselm
+Most of the information needed by PRACE users accessing the Anselm
TIER-1 system can be found here:
- [General user's
FAQ](http://www.prace-ri.eu/Users-General-FAQs)
- [Certificates
FAQ](http://www.prace-ri.eu/Certificates-FAQ)
-- [Interactive using
+- [Interactive access using
GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)
- [Data transfer with
GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
@@ -95,9 +103,9 @@ valid 12 hours), use:
-To Anselm cluster, two login nodes running GSI SSH service are
+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 (ible only from other PRACE partners).
+the internal PRACE network (accessible only from other PRACE partners).
Access from PRACE network:**
@@ -162,12 +170,12 @@ gsiscp can be used:
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 , please see the [section in
+user is using regular SSH based access, please see the [section in
general
documentation](https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/11e53ad0d2fd4c5187537f4baeedff33).
-If the user uses GSI SSH based , then the procedure is similar to
-the SSH based ([look
+If the user uses GSI SSH based access, then the procedure is similar to
+the SSH based access ([look
here](https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/11e53ad0d2fd4c5187537f4baeedff33)),
only the port forwarding must be done using GSI SSH:
@@ -176,7 +184,7 @@ only the port forwarding must be done using GSI SSH:
### Access with SSH
After successful obtainment of login credentials for the local
-IT4Innovations account, the PRACE users can the cluster as
+IT4Innovations account, the PRACE users can access the cluster as
regular users using SSH. For more information please see the [section in
general
documentation](https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/5d3d6f3d873a42e584cbf4365c4e251b).
@@ -192,7 +200,7 @@ documentation](https://docs.it4i.cz/anselm-cluster-documentation/resolveuid/5d3d
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 (ible only from other
+well as from the internal PRACE network (accessible only from other
PRACE partners).
There's one control server and three backend servers for striping and/or
@@ -268,8 +276,8 @@ Usage of the cluster
--------------------
There are some limitations for PRACE user when using the cluster. By
-default PRACE users aren't allowed to special queues in the PBS
-Pro to have high priority or exclusive to some special equipment
+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
@@ -373,3 +381,7 @@ increase.
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md b/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
index 8cd088240eee54b66d4e89032f3de4f200b05ea7..41c9e40ed78e7ec6b1363e638d1ba5cbb1fda30e 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/remote-visualization.md
@@ -1,12 +1,20 @@
Remote visualization service
============================
+
+
+
+
+
+
+
+
Introduction
------------
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 to the
+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.
The service is based on integration of open source tools VirtualGL and
@@ -32,9 +40,9 @@ InfiniBand QDR
Schematic overview
------------------
-
+
-
+
How to use the service
----------------------
@@ -120,7 +128,7 @@ $ ssh login2.anselm.it4i.cz -L 5901:localhost:5901
*If you use Windows and Putty, please refer to port forwarding setup
in the documentation:*
-[https://docs.it4i.cz/anselm-cluster-documentation/ing-the-cluster/x-window-and-vnc#section-12](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](accessing-the-cluster/x-window-and-vnc.html#section-12)
#### 7. If you don't have Turbo VNC installed on your workstation. {#7-if-you-don-t-have-turbo-vnc-installed-on-your-workstation}
@@ -138,7 +146,7 @@ $ vncviewer localhost:5901
*If you use Windows version of TurboVNC Viewer, just run the Viewer and
use address **localhost:5901**.*
-#### 9. Proceed to the chapter "Access the visualization node." {#9-proceed-to-the-chapter--the-visualization-node}
+#### 9. Proceed to the chapter "Access the visualization node." {#9-proceed-to-the-chapter-access-the-visualization-node}
*Now you should have working TurboVNC session connected to your
workstation.*
@@ -155,7 +163,7 @@ $ vncserver -kill :1
Access the visualization node
-----------------------------
-To the node use a dedicated PBS Professional scheduler queue
+To access the node use a dedicated PBS Professional scheduler queue
qviz**. The queue has following properties:
<table>
@@ -196,7 +204,7 @@ default/max</th>
</tbody>
</table>
-Currently when ing the node, each user gets 4 cores of a CPU
+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.
*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
@@ -204,7 +212,7 @@ 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.*
-To the visualization node, follow these steps:
+To access the visualization node, follow these steps:
#### 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}
@@ -281,22 +289,25 @@ Tips and Tricks
If you want to increase the responsibility of the visualization, please
adjust your TurboVNC client settings in this way:
-
+
To have an idea how the settings are affecting the resulting picture
quality three levels of "JPEG image quality" are demonstrated:
1. JPEG image quality = 30
-
+
2. JPEG image quality = 15
-
+
3. JPEG image quality = 10
-
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
index 5ccce37c5c3721a9ed72a592f9e906b46dde435a..1c23802df2a42588316f0ce466925a47823a8578 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/capacity-computing.md
@@ -5,6 +5,14 @@ Capacity computing
+
+
+
+
+
+
+
+
Introduction
------------
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
index 4ba64d17e38dbb961b98d3975b9b17165e994f94..f914ccf6c9eeeb5428fd02948adad251315ee18f 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/introduction.md
@@ -5,6 +5,14 @@ Resource Allocation and Job Execution
+
+
+
+
+
+
+
+
To run a [job](../introduction.html), [computational
resources](../introduction.html) for this particular job
must be allocated. This is done via the PBS Pro job workload manager
@@ -22,8 +30,8 @@ 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](job-priority.html) at Anselm ensures
that individual users may consume approximately equal amount of
-resources per week. The resources are ible via several queues for
-queueing the jobs. The queues provide prioritized and exclusive
+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:
@@ -72,3 +80,5 @@ Read more on [Capacity
computing](capacity-computing.html) page.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
index e5a5d60ef558b5c3c85aa639cf01c60d74a93021..f51d9e4c5a8550f9a9c38acb908003ff9f89c55f 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-priority.md
@@ -1,6 +1,14 @@
Job scheduling
==============
+
+
+
+
+
+
+
+
Job execution priority
----------------------
@@ -104,3 +112,5 @@ execution times and better resource usage. Jobs with suitable (small)
walltime could be backfilled - and overtake job(s) with higher priority.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
index 41d61d31a128b689bd5317178335280ff99feef6..f80fb145d18b9900f9649675f58cbbc56479c532 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job-submission-and-execution.md
@@ -5,6 +5,14 @@ Job submission and execution
+
+
+
+
+
+
+
+
Job Submission
--------------
@@ -149,11 +157,19 @@ switch can communicate most efficiently. Sharing the same switch
prevents hops in the network and provides for unbiased, most efficient
network communication.
+
+
+
+
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 [Hardware
Overview](../hardware-overview.html) section.
+
+
+
+
We recommend allocating compute nodes of a single switch when best
possible computational network performance is required to run the job
efficiently:
@@ -176,9 +192,21 @@ Advanced job handling
Intel Turbo Boost Technology is on by default. We strongly recommend
keeping the default.
+
+
+
+
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
+
+
+
+
+
+
+
+
$ qsub -A OPEN-0-0 -q qprod -l select=4:ncpus=16 -l cpu_turbo_boost=0 -I
More about the Intel Turbo Boost in the TurboBoost section
@@ -369,11 +397,11 @@ $ pwd
In this example, 4 nodes were allocated interactively for 1 hour via the
qexp queue. The interactive shell is executed in the home directory.
-All nodes within the allocation may be ed via ssh. Unallocated
-nodes are not ible to user.
+All nodes within the allocation may be accessed via ssh. Unallocated
+nodes are not accessible to user.
-The allocated nodes are ible via ssh from login nodes. The nodes
-may each other via ssh as well.
+The allocated nodes are accessible via ssh from login nodes. The nodes
+may access each other via ssh as well.
Calculations on allocated nodes may be executed remotely via the MPI,
ssh, pdsh or clush. You may find out which nodes belong to the
@@ -542,3 +570,5 @@ computing](capacity-computing.html) section.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
index 881fa3149d70c6236022cbf7ecc94859b222808c..532ef20fd3afad9f7f7c0bc343586d65bdf39844 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -5,6 +5,14 @@ Resources Allocation Policy
+
+
+
+
+
+
+
+
Resources Allocation Policy
---------------------------
@@ -13,8 +21,8 @@ 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 [Job scheduling](job-priority.html) section. The
-resources are ible via several queues for queueing the jobs. The
-queues provide prioritized and exclusive to the computational
+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:
@@ -135,7 +143,7 @@ select the proper nodes during the PSB job submission.
- **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 ed via the qprod queue, except the reserved ones.
+ nodes may be accessed via the qprod queue, except the reserved ones.
>*>178 nodes without accelerator are
included.* Full nodes, 16 cores per node
are allocated. The queue runs with medium priority and no special
@@ -144,14 +152,14 @@ select the proper nodes during the PSB job submission.
- **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 ed via the qlong queue. Full
+ 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.>
*The maximum runtime in qlong is 144 hours (three times of the
standard qprod time - 3 * 48 h).*
- **qnvidia, qmic, qfat**, the Dedicated queues****: The queue qnvidia
- is dedicated to the Nvidia accelerated nodes, the qmic to
- MIC nodes and qfat the Fat nodes. It is required that active
+ 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>
@@ -168,7 +176,7 @@ select the proper nodes during the PSB job submission.
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 ed from
+ 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.
@@ -193,7 +201,7 @@ Anselm users may check current queue configuration at
Check the status of jobs, queues and compute nodes at
<https://extranet.it4i.cz/anselm/>
-
+
Display the queue status on Anselm:
@@ -297,3 +305,5 @@ Password:
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
index e1c2bba19ffee599b72d221151761dc1877428e1..1e398688cd97cb054d7c051f6c07c118367c33c0 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys.md
@@ -1,6 +1,14 @@
Overview of ANSYS Products
==========================
+
+
+
+
+
+
+
+
[SVS FEM](http://www.svsfem.cz/)** as ***[ANSYS
Channel partner](http://www.ansys.com/)*** for Czech
Republic provided all ANSYS licenses for ANSELM cluster and supports of
@@ -14,7 +22,7 @@ are distinguished by "**Academic...**" word in the name of license or
by two letter preposition "**aa_**" in the license feature name. Change
of license is realized on command line respectively directly in user's
pbs file (see individual products). [ id="result_box"
-class="short_text"> More about
+ More about
licensing
here](ansys/licensing.html)
@@ -32,3 +40,5 @@ solution to the Anselm directly from the client's Workbench project
(see ANSYS RSM service).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
index 6e40eaa7d90ea7ac9fc413ae080d1a6b27708de9..816d1fa6f9c27d28583f79bfc0e4f87eb4a200ed 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md
@@ -1,6 +1,14 @@
ANSYS CFX
=========
+
+
+
+
+
+
+
+
[ANSYS
CFX](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX)
software is a high-performance, general purpose fluid dynamics program
@@ -50,7 +58,7 @@ for host in `cat $PBS_NODEFILE`
do
if [ "$hl" = "" ]
then hl="$host:$procs_per_host"
- else hl="$:$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
fi
done
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
index e725ae6a0825b0163d7f45a36845fb7378ac9a23..95062db4fe65fd9892d8f9234408b65fcedbbbd0 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md
@@ -1,6 +1,14 @@
ANSYS Fluent
============
+
+
+
+
+
+
+
+
[ANSYS
Fluent](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent)
software contains the broad physical modeling capabilities needed to
@@ -148,6 +156,14 @@ execute the job across multiple processors.
+
+
+
+
+
+
+
+
>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.
@@ -180,7 +196,7 @@ command.
cpus=‘expr $num_nodes * $NCPUS‘
#Default arguments for mpp jobs, these should be changed to suit your
#needs.
- fluent_args="-t$ $fluent_args -cnf=$PBS_NODEFILE"
+ fluent_args="-t${cpus} $fluent_args -cnf=$PBS_NODEFILE"
;;
*)
#SMP case
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
index 0369b68dc705ed8169c19fc7c541c98f7a12bf37..e8b84ab2d78129dc1b5be7adf5c92227c5cc4b0d 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
@@ -1,9 +1,17 @@
ANSYS LS-DYNA
=============
+
+
+
+
+
+
+
+
[ANSYS
LS-DYNA](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)
-software provides convenient and easy-to-use to the
+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
@@ -59,7 +67,7 @@ for host in `cat $PBS_NODEFILE`
do
if [ "$hl" = "" ]
then hl="$host:$procs_per_host"
- else hl="$:$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
fi
done
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
index 37287cff5f75425ad7389c50c9a76ed0b9ba6cd5..84f086b26f34b0d49a8ff54224f1023619d57954 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
@@ -1,6 +1,14 @@
ANSYS MAPDL
===========
+
+
+
+
+
+
+
+
>**[ANSYS
Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
software offers a comprehensive product solution for both multiphysics
@@ -45,7 +53,7 @@ for host in `cat $PBS_NODEFILE`
do
if [ "$hl" = "" ]
then hl="$host:$procs_per_host"
- else hl="$:$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
fi
done
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
index 3591982a5c40125a683b4ecba68b777ed8e40e88..66362a0d2fc8eaf20f8d88bf47a9b00a3870d8bd 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md
@@ -1,6 +1,14 @@
LS-DYNA
=======
+
+
+
+
+
+
+
+
[LS-DYNA](http://www.lstc.com/) is a multi-purpose,
explicit and implicit finite element program used to analyze the
nonlinear dynamic response of structures. Its fully automated contact
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
index ade13a15fb0009d539bbcbd947aec8d052723a2c..b526aaea9f0762059906535a3dc318cd0631e3ac 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/molpro.md
@@ -1,8 +1,20 @@
Molpro
======
+
+
+
+
Molpro is a complete system of ab initio programs for molecular
electronic structure calculations.
+
+
+
+
+
+
+
+
About Molpro
------------
@@ -14,7 +26,7 @@ License
-------
Molpro software package is available only to users that have a valid
-license. Please contact support to enable to Molpro if you have a
+license. Please contact support to enable access to Molpro if you have a
valid license appropriate for running on our cluster (eg. >academic
research group licence, parallel execution).
@@ -89,3 +101,5 @@ these are placed in the fast scratch filesystem.
rm -rf /scratch/$USER/$PBS_JOBID
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
index 9ee1499e52d32ba15f616a75d9f090b051d96b38..c32bc8e5d0696cd7e7101f8180f387e39e66ed57 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md
@@ -1,7 +1,19 @@
NWChem
======
+
+
+
+
High-Performance Computational Chemistry
+
+
+
+
+
+
+
+
>Introduction
-------------------------
@@ -64,3 +76,5 @@ in the input file set the following directives :
"direct" mode, eg. "scf direct"
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/compilers.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/compilers.md
index dc8f123ef3d895c64576e841769332f48993fbcc..c088e8fbf79ec7dfccbf02e22dca6c3adb26d995 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/compilers.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/compilers.md
@@ -1,11 +1,23 @@
Compilers
=========
+
+
+
+
Available compilers, including GNU, INTEL and UPC compilers
+
+
+
+
+
+
+
+
Currently there are several compilers for different programming
languages available on the Anselm cluster:
@@ -32,7 +44,7 @@ GNU C/C++ and Fortran Compilers
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
-ible in the search path by default.
+accessible in the search path by default.
It is strongly recommended to use the up to date version (4.8.1) which
comes with the module gcc:
@@ -163,3 +175,5 @@ For information how to work with nVidia CUDA, please read the [nVidia
CUDA page](nvidia-cuda.html).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
index 8019d80332d82bdb4aee198eaa920f2794c9845b..0490ce301c319f492c73e0597c5105987352bc41 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/comsol/comsol-multiphysics.md
@@ -5,11 +5,19 @@ COMSOL Multiphysics®
+
+
+
+
+
+
+
+
>>Introduction
-------------------------
->>[COMSOL](http://www.comsol.com)><span>
+>>[COMSOL](http://www.comsol.com)
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
@@ -37,7 +45,7 @@ applications.
others](http://www.comsol.com/products)
>>COMSOL also allows an
->>><span>interface support for
+>>interface support for
equation-based modelling of
>>partial differential
equations.
@@ -49,18 +57,18 @@ equations.
>>On the Anselm cluster COMSOL is available in the latest
stable version. There are two variants of the release:
-- >>**Non commercial**><span> or so
+- >>**Non commercial** or so
called >>**EDU
variant**>>, which can be used for research
and educational purposes.
-- >>**Commercial**><span> or so called
- >>**COM variant**><span>,
+- >>**Commercial** or so called
+ >>**COM variant**,
which can used also for commercial activities.
- >>**COM variant**><span>
+ >>**COM variant**
has only subset of features compared to the
>>**EDU
- variant**>> available.
+ variant**>> available. <span
id="result_box"
More about
licensing will be posted here
@@ -73,7 +81,7 @@ stable version. There are two variants of the release:
$ module load comsol
```
->>By default the ><span>**EDU
+>>By default the **EDU
variant**>> will be loaded. If user needs other
version or variant, load the particular version. To obtain the list of
available versions use
@@ -121,7 +129,7 @@ module load comsol
ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn $ 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
+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
```
>>Working directory has to be created before sending the
@@ -130,25 +138,25 @@ 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).
-LiveLink™* *for MATLAB^®^
+LiveLink™* *for MATLAB®^
-------------------------
>>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>**®**</span></span></span></span></span>^
+COMSOL>><span><span><span><span><span>**®**</span></span></span></span></span>^
API (Application Programming Interface) with the benefits of the
programming language and computing environment of the MATLAB.
>>LiveLink for MATLAB is available in both
->>**EDU**><span> and
->>**COM**><span>
->>**variant**><span> of the
+>>**EDU** and
+>>**COM**
+>>**variant** of the
COMSOL release. On Anselm 1 commercial
-(>>**COM**><span>) license
+(>>**COM**) license
and the 5 educational
-(>>**EDU**><span>) licenses
+(>>**EDU**) licenses
of LiveLink for MATLAB (please see the [ISV
Licenses](../isv_licenses.html)) are available.
Following example shows how to start COMSOL model from MATLAB via
@@ -192,7 +200,7 @@ module load comsol/43b-EDU
ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn $ server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/$USER &
+comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/$USER &
cd /apps/engineering/comsol/comsol43b/mli
matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/$USER; test_job"
```
@@ -205,3 +213,7 @@ 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/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.md
index 50587938502afd4807ec7efd0a114397d819e82f..719aee666334faf9d4cd2a660d40bd590ddb659e 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.md
@@ -5,6 +5,14 @@ Debuggers and profilers summary
+
+
+
+
+
+
+
+
Introduction
------------
@@ -90,3 +98,5 @@ Read more at
the [Vampir](../../salomon/software/debuggers/vampir.html) page.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
index 6397524fa0e33cef52a94842136be5f410bf676a..10f994424f1bc11f845a6084c4210223654ae68c 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-ddt.md
@@ -5,6 +5,14 @@ Allinea Forge (DDT,MAP)
+
+
+
+
+
+
+
+
Allinea Forge consist of two tools - debugger DDT and profiler MAP.
Allinea DDT, is a commercial debugger primarily for debugging parallel
@@ -61,11 +69,11 @@ $ 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.**
@@ -77,7 +85,7 @@ forwarding enabled. This could mean using the -X in the ssh:
$ ssh -X username@anselm.it4i.cz
-Other options is to login node using VNC. Please see the detailed
+Other options is to access login node using VNC. Please see the detailed
information on how to [use graphic user interface on
Anselm](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
.
@@ -130,3 +138,5 @@ Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
index 16c147569aa4858f839491c5f22fd593a216ea86..77f9ce55724f609d80aba8277a12351cb064b384 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
@@ -1,11 +1,23 @@
Allinea Performance Reports
===========================
+
+
+
+
quick application profiling
+
+
+
+
+
+
+
+
Introduction
------------
@@ -75,3 +87,7 @@ 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/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.md
index d84e0da10ea5efee6fa7c4c797ff04a863b79841..80a5cdfd4cea121228385363eb51a2d93a1c150f 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/cube.md
@@ -1,6 +1,14 @@
CUBE
====
+
+
+
+
+
+
+
+
Introduction
------------
@@ -22,6 +30,10 @@ dimension is organized by files and routines in your source code etc.
+
+
+
+
@@ -70,3 +82,5 @@ performance data will be available.
1.<http://www.scalasca.org/software/cube-4.x/download.html>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
index 7ad500b8770fee3c14343c8c50b7941468ed9872..90174f56f9a68ebde1e28774baba3fc0b50633bb 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
@@ -1,6 +1,14 @@
Intel Performance Counter Monitor
=================================
+
+
+
+
+
+
+
+
Introduction
------------
@@ -85,7 +93,7 @@ Usage: > pcm-power.x <delay> |
### pcm
This command provides an overview of performance counters and memory
-usage. >Usage: > pcm.x
+usage. >Usage: > <span pcm.x
<delay> | <external program>
Sample output :
@@ -207,7 +215,7 @@ installed on Anselm.
API
---
-In a similar fashion to PAPI, PCM provides a C++ API to the
+In a similar fashion to PAPI, PCM provides a C++ API to access the
performance counter from within your application. Refer to the [doxygen
documentation](http://intel-pcm-api-documentation.github.io/classPCM.html)
for details of the API.
@@ -300,3 +308,5 @@ References
Documentation
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
index b4569b2834638dce7a55e929789c2ecee656aed9..eeffc7a7bef2e6d50aa2af1655ab6d88c360e806 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/intel-vtune-amplifier.md
@@ -5,6 +5,14 @@ Intel VTune Amplifier
+
+
+
+
+
+
+
+
Introduction
------------
@@ -19,7 +27,11 @@ highlight of the features:
bandwidth
- Power usage analysis - frequency and sleep states.
-
+
+
+
+
+
@@ -110,3 +122,7 @@ References
1.><https://www.rcac.purdue.edu/tutorials/phi/PerformanceTuningXeonPhi-Tullos.pdf> Performance
Tuning for Intel® Xeon Phi™ Coprocessors
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
index 580197aeba698265dc808e83147290662457b5b9..59406fda9ae68d8102e8db36cb386203552074fd 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/papi.md
@@ -5,11 +5,19 @@ PAPI
+
+
+
+
+
+
+
+
Introduction
------------
dir="auto">Performance Application Programming
-Interface >(PAPI) is a portable interface to
+Interface >(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
@@ -102,6 +110,10 @@ PAPI provides two kinds of events:
- **Native events **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.
+
+
+
+
To use PAPI in your application, you need to link the appropriate
include file.
@@ -110,6 +122,10 @@ include file.
- f90papi.h for Fortran 90
- fpapi.h for Fortran with preprocessor
+
+
+
+
The include path is automatically added by papi module to
$INCLUDE.
@@ -269,3 +285,5 @@ References
3.<http://icl.cs.utk.edu/papi/docs/> API Documentation
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
index 3fff2cf0633fabe011e55750d93fddf33b904966..697152de2c06699c6339144379c90d26cc88b232 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/scalasca.md
@@ -1,6 +1,14 @@
Scalasca
========
+
+
+
+
+
+
+
+
>Introduction
-------------------------
@@ -107,3 +115,5 @@ References
1.<http://www.scalasca.org/>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
index 15482da4c33f86faf39d5330f7fe7abb1c5385b3..1a8e7cd840896192907956ca2aa819faa0e502d8 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/score-p.md
@@ -1,6 +1,14 @@
Score-P
=======
+
+
+
+
+
+
+
+
Introduction
------------
@@ -21,7 +29,7 @@ on Anselm :
- class="s1">scorep/1.2.3-gcc-openmpi>, for usage
with [GNU
- Compiler](../compilers.html)> and [OpenMPI](../mpi-1/Running_OpenMPI.html)>,</span>
+ Compiler](../compilers.html)> and [OpenMPI](../mpi-1/Running_OpenMPI.html){.internal>,</span>
- class="s1">scorep/1.2.3-icc-impi>, for usage
with [Intel
@@ -146,3 +154,6 @@ Again, please refer to the
[documentation](https://silc.zih.tu-dresden.de/scorep-current/pdf/scorep.pdf)
for a more elaborate description.
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md
index b60cde8ff14bcce56f9f8f1c2ed8fa29489d5c25..b8bced0e624cab776a842f99452e84fb93ea10cb 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/summary.md
@@ -5,6 +5,14 @@ Debuggers and profilers summary
+
+
+
+
+
+
+
+
Introduction
------------
@@ -85,3 +93,7 @@ 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/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
index e7bb3eb1d6b0352b49d93ab9d906a72d3f091f7e..80c232cdcaf3ab25942b7484c71a1dac788b6329 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/total-view.md
@@ -1,8 +1,20 @@
Total View
==========
+
+
+
+
TotalView is a GUI-based source code multi-process, multi-thread
debugger.
+
+
+
+
+
+
+
+
License and Limitations for Anselm Users
----------------------------------------
@@ -51,11 +63,11 @@ 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
-----------------------------
@@ -65,7 +77,7 @@ using the -X in the ssh:
ssh -X username@anselm.it4i.cz
-Other options is to login node using VNC. Please see the detailed
+Other options is to access login node using VNC. Please see the detailed
information on how to use graphic user interface on Anselm
[here](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33#VNC).
@@ -92,8 +104,8 @@ Please note:** 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 **~/.tvdrc** file:
- proc mpi_auto_run_starter {
- set starter_programs
+ proc mpi_auto_run_starter {loaded_id} {
+ set starter_programs {mpirun mpiexec orterun}
set executable_name [TV::symbol get $loaded_id full_pathname]
set file_component [file tail $executable_name]
@@ -161,3 +173,7 @@ 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/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
index 77fcfe6acfa31ef2d2ff2bd7c33c9bcb5a9c06ca..2123bb937437a79292417f6a23270cdcb182fb25 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/valgrind.md
@@ -1,7 +1,19 @@
Valgrind
========
+
+
+
+
Valgrind is a tool for memory debugging and profiling.
+
+
+
+
+
+
+
+
About Valgrind
--------------
@@ -20,8 +32,8 @@ Valgrind run 5-100 times slower.
The main tools available in Valgrind are :
- **Memcheck**, the original, must used and default tool. Verifies
- memory in you program and can detect use of unitialized
- memory, out of bounds memory , memory leaks, double free, etc.
+ memory access in you program and can detect use of unitialized
+ memory, out of bounds memory access, memory leaks, double free, etc.
- **Massif**, a heap profiler.
- **Hellgrind** and **DRD** can detect race conditions in
multi-threaded applications.
@@ -116,7 +128,7 @@ description of command line options.
==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 at line 5 and a memory leak of 40 bytes. If we
+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 --leak-check=full option :
@@ -288,3 +300,7 @@ launched MPI process)
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/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md
index f073038c9a837b1a9bfbaa2edc258fbcc0ff280c..c61edbc82c8d06b3d2a24aae614df7eb35b5c8ab 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vampir.md
@@ -1,6 +1,14 @@
Vampir
======
+
+
+
+
+
+
+
+
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
@@ -32,3 +40,5 @@ References
1.<https://www.vampir.eu>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
index 954fbca278eb85a473dac2c93d6b307fd625d323..c4d0de9ce0fce04299c3d43e17636796a5f551f8 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/gpi2.md
@@ -1,11 +1,23 @@
GPI-2
=====
+
+
+
+
A library that implements the GASPI specification
+
+
+
+
+
+
+
+
Introduction
------------
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md
index 048a009a495954b6784cd7c3910f85adc24102de..16b07fefde0e9491c7f01acbd87d8da215f4ece2 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite.md
@@ -5,6 +5,14 @@ Intel Parallel Studio
+
+
+
+
+
+
+
+
The Anselm cluster provides following elements of the Intel Parallel
Studio XE
@@ -94,3 +102,5 @@ Read more at the [Intel TBB](intel-suite/intel-tbb.html)
page.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
index 92023bac7b1e1feda0fee4b4650a3185e9297a9a..790c716074245c5b3f1554a4c4aa1299225f0166 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-compilers.md
@@ -5,6 +5,14 @@ Intel Compilers
+
+
+
+
+
+
+
+
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.
@@ -67,3 +75,5 @@ doing >this:
will result in larger binaries.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
index 1b6fc1c222bbc0bbda21bee492b52f8fa29116c3..5199e1900d1f22ee1b181687343f527f4eae4de0 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-debugger.md
@@ -5,6 +5,14 @@ Intel Debugger
+
+
+
+
+
+
+
+
Debugging serial applications
-----------------------------
@@ -23,7 +31,7 @@ The debugger may run in text mode. To debug in text mode, use
$ idbc
To debug on the compute nodes, module intel must be loaded.
-The GUI on compute nodes may be ed using the same way as in [the
+The GUI on compute nodes may be accessed using the same way as in [the
GUI
section](https://docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
@@ -40,7 +48,7 @@ Example:
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 is via X11 port
+interactively on the myprog.x executable. The GUI access is via X11 port
forwarding provided by the PBS workload manager.
Debugging parallel applications
@@ -98,3 +106,5 @@ website,
<http://software.intel.com/sites/products/documentation/doclib/stdxe/2013/composerxe/debugger/user_guide/index.htm>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
index 0945105c13f75f85b49718e28fe65ab79759b2df..14d9e68d3f2303a9c250efa215c35894644ed349 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
@@ -5,6 +5,14 @@ Intel IPP
+
+
+
+
+
+
+
+
Intel Integrated Performance Primitives
---------------------------------------
@@ -95,3 +103,5 @@ in particular the [IPP Reference
manual.](http://software.intel.com/sites/products/documentation/doclib/ipp_sa/71/ipp_manual/index.htm)
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
index 2a84fe485e65fd935efe94267cb24a80346b1ddd..dfc8761d878962b3000249be0e915483618ce553 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-mkl.md
@@ -6,6 +6,14 @@ Intel MKL
+
+
+
+
+
+
+
+
Intel Math Kernel Library
-------------------------
@@ -87,7 +95,7 @@ With intel compiler use -mkl option to link default threaded MKL.
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 2^31^-1
+type (necessary for indexing large arrays, with more than 231^-1
elements), whereas the LP64 libraries index arrays with the 32-bit
integer type.
@@ -195,3 +203,5 @@ particular the [MKL users
guide](https://software.intel.com/en-us/intel-mkl/documentation/linux).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md
index d4a7b981037e8786a840f42381a49eb1a69cc35b..50600509cc0e53ae3a8412bd06c53f0a35315a34 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-parallel-studio-introduction.md
@@ -5,6 +5,14 @@ Intel Parallel Studio
+
+
+
+
+
+
+
+
The Anselm cluster provides following elements of the Intel Parallel
Studio XE
@@ -91,3 +99,5 @@ manner.
Read more at the [Intel TBB](intel-tbb.html) page.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.md
index c9dde88efb33bdc82cc2602d7aa8dcd8c4cf0f31..7a4cae0cbaaf12c4e5827e50a977d363c78a9801 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-suite/intel-tbb.md
@@ -5,6 +5,14 @@ Intel TBB
+
+
+
+
+
+
+
+
Intel Threading Building Blocks
-------------------------------
@@ -55,3 +63,5 @@ Read more on Intel website,
<http://software.intel.com/sites/products/documentation/doclib/tbb_sa/help/index.htm>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
index 21ac1ca8dc07ee5e3db8decedc6d389cb4b8d1e8..1a3933def2ebfaae3131607a59c2ac4fbf5efd0b 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/intel-xeon-phi.md
@@ -1,11 +1,23 @@
Intel Xeon Phi
==============
+
+
+
+
A guide to Intel Xeon Phi usage
+
+
+
+
+
+
+
+
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.
@@ -13,7 +25,7 @@ supported.
Intel Utilities for Xeon Phi
----------------------------
-To get to a compute node with Intel Xeon Phi accelerator, use the
+To get access to a compute node with Intel Xeon Phi accelerator, use the
PBS interactive session
$ qsub -I -q qmic -A NONE-0-0
@@ -404,7 +416,7 @@ Phi:
### Execution of the Program in Native Mode on Intel Xeon Phi
-The user to the Intel Xeon Phi is through the SSH. Since user
+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.
@@ -662,7 +674,7 @@ 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 "**.profile**" file in user's home directory. This file
-sets up the environment on the MIC automatically once user to the
+sets up the environment on the MIC automatically once user access to the
accelerator through the SSH.
$ vim ~/.profile
@@ -684,7 +696,7 @@ libraries.
library and particular version of an Intel compiler. These versions have
to match with loaded modules.
-To a MIC accelerator located on a node that user is currently
+To access a MIC accelerator located on a node that user is currently
connected to, use:
$ ssh mic0
@@ -756,7 +768,7 @@ execute:
Execution on host - MPI processes distributed over multiple
accelerators on multiple nodes**
->To get to multiple nodes with MIC accelerator, user has to
+>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:
@@ -777,7 +789,7 @@ immediately. To see the other nodes that have been allocated use:
cn205.bullx
>This output means that the PBS allocated nodes cn204 and cn205,
-which means that user has direct to "**cn204-mic0**" and
+which means that user has direct access to "**cn204-mic0**" and
"**cn-205-mic0**" accelerators.
>Please note: At this point user can connect to any of the
@@ -937,11 +949,11 @@ 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:
Host only node-file:**
- - /lscratch/$/nodefile-cn
+ - /lscratch/${PBS_JOBID}/nodefile-cn
MIC only node-file**:
- - /lscratch/$/nodefile-mic
+ - /lscratch/${PBS_JOBID}/nodefile-mic
Host and MIC node-file**:
- - /lscratch/$/nodefile-mix
+ - /lscratch/${PBS_JOBID}/nodefile-mix
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"
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
index 667b7c11659c80f838ec9df43f62260933c6af1f..75b279dbe07051363da9d94f25d14a9abb8e9277 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/isv_licenses.md
@@ -1,11 +1,23 @@
ISV Licenses
============
+
+
+
+
A guide to managing Independent Software Vendor licences
+
+
+
+
+
+
+
+
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
@@ -24,7 +36,7 @@ non-commercial version.
Overview of the licenses usage
------------------------------
-The overview is generated every minute and is ible from web or
+The overview is generated every minute and is accessible from web or
command line interface.
### Web interface
@@ -40,7 +52,7 @@ number of free license features
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
-ible from the Anselm command prompt.
+accessible from the Anselm command prompt.
Product File with license state Note
------------ ----------------------------------------------------- ---------------------
@@ -80,7 +92,7 @@ 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 id="result_box"
-class="short_text"> unavailability of the
+ unavailability of the
needed licenses.
The general format of the name is:
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/java.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/java.md
index 6bf87d7f92753e8ebdc89be81bde7e474c533c6c..294e7901f6b76bfa1aaacadb30c075a9ff94717a 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/java.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/java.md
@@ -1,11 +1,23 @@
Java
====
+
+
+
+
Java on ANSELM
+
+
+
+
+
+
+
+
Java is available on Anselm cluster. Activate java by loading the java
module
@@ -33,3 +45,5 @@ you require the java interface to MPI, please contact [Anselm
support](https://support.it4i.cz/rt/).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.md
index 38885466d057805df8e46874ca59ff0f65bfd075..9acb9278e7cb94df88b6c1d36f1e2488eb0d8c4d 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/kvirtualization.md
@@ -1,11 +1,23 @@
Virtualization
==============
+
+
+
+
Running virtual machines on compute nodes
+
+
+
+
+
+
+
+
Introduction
------------
@@ -18,7 +30,7 @@ needs.
tools
- Application requires specific setup (installation, configuration) of
complex software stack
-- Application requires privileged to operating system
+- Application requires privileged access to operating system
- ... and combinations of above cases
We offer solution for these cases - **virtualization**. Anselm's
@@ -85,7 +97,7 @@ running in their virtual machines.
We propose this job workflow:
-
+Workflow](virtualization-job-workflow "Virtualization Job Workflow")
Our recommended solution is that job script creates distinct shared job
directory, which makes a central point for data exchange between
@@ -223,7 +235,7 @@ for 5 minutes, then shutdown virtual machine.
### Create job script for executing virtual machine
Create job script according recommended id="result_box"
-class="short_text">
+
[Virtual Machine Job
Workflow](virtualization.html#virtual-machine-job-workflow).
@@ -231,7 +243,7 @@ Example job for Windows virtual machine:
#/bin/sh
- JOB_DIR=/scratch/$USER/win/$
+ JOB_DIR=/scratch/$USER/win/${PBS_JOBID}
#Virtual machine settings
VM_IMAGE=~/work/img/win.img
@@ -239,25 +251,25 @@ Example job for Windows virtual machine:
VM_SMP=16
# Prepare job dir
- mkdir -p $ && cd $ || exit 1
+ mkdir -p ${JOB_DIR} && cd ${JOB_DIR} || exit 1
ln -s ~/work/win .
ln -s /scratch/$USER/data .
ln -s ~/work/win/script/run/run-appl.bat run.bat
# Run virtual machine
- export TMPDIR=/lscratch/$
+ export TMPDIR=/lscratch/${PBS_JOBID}
module add qemu
qemu-system-x86_64
-enable-kvm
-cpu host
- -smp $
- -m $
+ -smp ${VM_SMP}
+ -m ${VM_MEMORY}
-vga std
-localtime
-usb -usbdevice tablet
-device virtio-net-pci,netdev=net0
- -netdev user,id=net0,smb=$,hostfwd=tcp::3389-:3389
- -drive file=$,media=disk,if=virtio
+ -netdev user,id=net0,smb=${JOB_DIR},hostfwd=tcp::3389-:3389
+ -drive file=${VM_IMAGE},media=disk,if=virtio
-snapshot
-nographic
@@ -299,9 +311,9 @@ Run virtual machine (simple)
$ qemu-system-x86_64 -hda win.img -enable-kvm -cpu host -smp 16 -m 32768 -vga std -localtime -usb -usbdevice tablet -vnc :0
-You can virtual machine by VNC viewer (option -vnc) connecting to
+You can access virtual machine by VNC viewer (option -vnc) connecting to
IP address of compute node. For VNC you must use [VPN
-network](../../ing-the-cluster/vpn-access.html).
+network](../../accessing-the-cluster/vpn-access.html).
Install virtual machine from iso file
@@ -316,10 +328,10 @@ sharing and port forwarding, in snapshot mode
$ 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
-Thanks to port forwarding you can virtual machine via SSH (Linux)
+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 [VPN
-network](../../ing-the-cluster/vpn-access.html).
+network](../../accessing-the-cluster/vpn-access.html).
Keep in mind, that if you use virtio devices, you must have virtio
drivers installed on your virtual machine.
@@ -334,7 +346,7 @@ SMB sharing, port forwarding.
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 to Anselm's network via NAT on compute node (host).
+have access to Anselm's network via NAT on compute node (host).
Simple network setup
@@ -353,9 +365,9 @@ Optimized network setup with sharing and port forwarding
### Advanced networking
-Internet **
+Internet access**
-Sometime your virtual machine needs to internet (install
+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
@@ -479,7 +491,7 @@ file (and discarded after virtual machine exits). **It is strongly
recommended mode for running your jobs.** Set TMPDIR environment
variable to local scratch directory for placement temporary files.
- $ export TMPDIR=/lscratch/$
+ $ export TMPDIR=/lscratch/${PBS_JOBID}
$ qemu-system-x86_64 ... -snapshot
### Windows guests
@@ -489,3 +501,5 @@ For Windows guests we recommend these options, life will be easier:
$ qemu-system-x86_64 ... -localtime -usb -usbdevice tablet
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
index c8ae48589fae957c6f96ebcd50fc26e12385f44e..94f4063b0c2bf6dac257d10178a9de894cb1ca1f 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/Running_OpenMPI.md
@@ -5,6 +5,14 @@ Running OpenMPI
+
+
+
+
+
+
+
+
OpenMPI program execution
-------------------------
@@ -273,3 +281,5 @@ Some options have changed in OpenMPI version 1.8.
</table>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
index c74b65cb3a84d8305ff638138371cdfbb4896f3c..52cd3f2d40b3f973c2c8b1084a54a3ba5bce569a 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi.md
@@ -5,6 +5,14 @@ MPI
+
+
+
+
+
+
+
+
Setting up MPI Environment
--------------------------
@@ -150,7 +158,7 @@ scratch /lscratch filesystem.
### Ways to run MPI programs
Optimal way to run an MPI program depends on its memory requirements,
-memory pattern and communication pattern.
+memory access pattern and communication pattern.
Consider these ways to run an MPI program:
1. One MPI process per node, 16 threads per process
@@ -161,13 +169,13 @@ One MPI** 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 to the network interface.
+bandwidth access to the network interface.
Two MPI** 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 to the network interface. The 8 threads and
-socket binding should ensure maximum memory bandwidth and
+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.
Important! Bind every OpenMP thread to a core!
@@ -199,3 +207,5 @@ more on [how to run Intel MPI on
accelerators](../intel-xeon-phi.html).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md
index 725ccf169440d30d429b1cd9cf7df5808fcdc69a..2eee46e17ddd7b46b7441cd6b2762bc75e9172ad 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/mpi4py-mpi-for-python.md
@@ -1,11 +1,23 @@
MPI4Py (MPI for Python)
=======================
+
+
+
+
OpenMPI interface to Python
+
+
+
+
+
+
+
+
Introduction
------------
@@ -105,3 +117,5 @@ More examples and documentation can be found on [MPI for Python
webpage](https://pythonhosted.org/mpi4py/usrman/index.html).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
index e228281a02b74b370943ba2598b3632fc6130d17..c8cd47ec62d1634c650b08c815ef32a2a0a1cb36 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
@@ -5,12 +5,20 @@ Running MPICH2
+
+
+
+
+
+
+
+
MPICH2 program execution
------------------------
The MPICH2 programs use mpd daemon or ssh connection to spawn processes,
no PBS support is needed. However the PBS allocation is required to
- compute nodes. On Anselm, the **Intel MPI** and **mpich2 1.9**
+access compute nodes. On Anselm, the **Intel MPI** and **mpich2 1.9**
are MPICH2 based MPI implementations.
### Basic usage
@@ -193,3 +201,5 @@ chapter](../intel-xeon-phi.html) provides details on how
to run Intel MPI code on Xeon Phi architecture.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
index 05905cd8be261ffabd8b40d69d2a8f102aaa6fd5..79a4d0e6a2caa9936d3c4427691aab41fae9362a 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/copy_of_matlab.md
@@ -5,6 +5,14 @@ Matlab
+
+
+
+
+
+
+
+
Introduction
------------
@@ -36,12 +44,12 @@ Matlab on the compute nodes via PBS Pro scheduler.
If you require the Matlab GUI, please follow the general informations
about [running graphical
-applications](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+applications](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
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
-[here](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html))
+[here](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html))
is recommended.
To run Matlab with GUI, use
@@ -97,7 +105,7 @@ Anselm.
Following example shows how to start interactive session with support
for Matlab GUI. For more information about GUI based applications on
Anselm see [this
-page](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+page](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
$ xhost +
$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00
@@ -109,7 +117,7 @@ The second part of the command shows how to request all necessary
licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing
Engines licenses.
-Once the to compute nodes is granted by PBS, user can load
+Once the access to compute nodes is granted by PBS, user can load
following modules and start Matlab:
r1i0n17$ module load MATLAB/2015b-EDU
@@ -349,3 +357,5 @@ mode](copy_of_matlab.html#parallel-matlab-batch-job-in-local-mode),
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md
index 320a56635a477f6c52b04e6a966ae1dcf7a20ceb..31eb11293d3d2e7bf90a8fe5416f39fd1b5c70de 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/introduction.md
@@ -1,11 +1,23 @@
Numerical languages
===================
+
+
+
+
Interpreted languages for numerical computations and analysis
+
+
+
+
+
+
+
+
Introduction
------------
@@ -15,7 +27,7 @@ primarily intended for numerical computations.
Matlab
------
-MATLAB^®^ is a high-level language and interactive environment for
+MATLAB®^ is a high-level language and interactive environment for
numerical computation, visualization, and programming.
$ module load MATLAB/2015b-EDU
@@ -48,3 +60,5 @@ computing and graphics.
Read more at the [R page](r.html).
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md
index ed43615d1e0f697ca6182e31f54b4a3474d6b695..386ed44ef6b485f6c8518ec0d1afb69e4550314e 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/matlab.md
@@ -5,6 +5,14 @@ Matlab 2013-2014
+
+
+
+
+
+
+
+
Introduction
------------
@@ -71,7 +79,7 @@ non-interactive PBS sessions. This mode guarantees that the data
processing is not performed on login nodes, but all processing is on
compute nodes.
-
+ 
For the performance reasons Matlab should use system MPI. On Anselm the
supported MPI implementation for Matlab is Intel MPI. To switch to
@@ -92,7 +100,7 @@ be exactly the same as in the following listing:
mpl = strcat(mpich, 'libmpl.so');
opa = strcat(mpich, 'libopa.so');
- extras = ;
+ extras = {};
System MPI library allows Matlab to communicate through 40Gbps
Infiniband QDR interconnect instead of slower 1Gb ethernet network.
@@ -124,7 +132,7 @@ 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.
-Once the to compute nodes is granted by PBS, user can load
+Once the access to compute nodes is granted by PBS, user can load
following modules and start Matlab:
cn79$ module load matlab/R2013a-EDU
@@ -264,3 +272,5 @@ compute nodes number of workers start-up time[s]
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md
index 04e38a45c03a925763de6e5ecddd87671cc96fc4..f4843c401de1567e462aac671f2b91a3e38f0d70 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/octave.md
@@ -5,6 +5,14 @@ Octave
+
+
+
+
+
+
+
+
Introduction
------------
@@ -150,3 +158,5 @@ other mechanism) will actually run slower than on host CPU.
>
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
index c507ac4f273457dc647052c568c23a74a4b341fc..a9edbe5286c885641ac2f1685d78596a514e1a46 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages/r.md
@@ -5,6 +5,14 @@ R
+
+
+
+
+
+
+
+
Introduction
------------
@@ -34,12 +42,12 @@ Modules
-------
**The R version 3.0.1 is available on Anselm, along with GUI interface
-Rstudio**
+Rstudio
Application Version module
------------- -------------- ---------
R** R 3.0.1 R
-Rstudio**** Rstudio 0.97 Rstudio
+Rstudio** Rstudio 0.97 Rstudio
$ module load R
@@ -55,10 +63,10 @@ OMP_NUM_THREADS environment variable.
### Interactive execution
-To run R interactively, using Rstudio** GUI, log in with ssh -X parameter
+To run R interactively, using Rstudio GUI, log in with ssh -X parameter
for X11 forwarding. Run rstudio:
- $ module load Rstudio**
+ $ module load Rstudio
$ rstudio
### Batch execution
@@ -391,7 +399,7 @@ The above is the mpi.apply MPI example for calculating the number π.
Only the slave processes carry out the calculation. Note the
mpi.parSapply(), ** function call. The package
parallel
-[example](r.html#package-parallel)[above](r.html#package-parallel)
+[example](r.html#package-parallel)[above](r.html#package-parallel){.anchor
may be trivially adapted (for much better performance) to this structure
using the mclapply() in place of mpi.parSapply().
@@ -446,3 +454,8 @@ and general [MPI](../mpi-1.html) sections.
+
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
index c35d9412de21656fb52ef417775e4550f7d8c97f..a5a568eeb18bec984cdf87dcecf70660a5353368 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/fftw.md
@@ -1,11 +1,23 @@
FFTW
====
+
+
+
+
The discrete Fourier transform in one or more dimensions, MPI parallel
+
+
+
+
+
+
+
+
FFTW is a C subroutine library for computing the discrete Fourier
@@ -153,3 +165,7 @@ program](../mpi-1/running-mpich2.html).
Read more on FFTW usage on the [FFTW
website.](http://www.fftw.org/fftw3_doc/)
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md
index 00ea8e8779ce195d586afb128ad1cce2d8a76ea9..1e7ef10da517a4be0f0e6f4bd9bf10cc587bb42d 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/gsl.md
@@ -1,12 +1,24 @@
GSL
===
+
+
+
+
The GNU Scientific Library. Provides a wide range of mathematical
routines.
+
+
+
+
+
+
+
+
Introduction
------------
@@ -164,3 +176,6 @@ library search path is compiled in, so that no modules are necessary to
run the code.
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
index 13b8f36700085de894f1ea2b551d9f84c83a8c48..5048c00cfce322ebfeae4d81433bea08b0857476 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/hdf5.md
@@ -1,7 +1,19 @@
HDF5
====
+
+
+
+
Hierarchical Data Format library. Serial and MPI parallel version.
+
+
+
+
+
+
+
+
[HDF5 (Hierarchical Data Format)](http://www.hdfgroup.org/HDF5/) is a
@@ -154,10 +166,10 @@ Example
status = H5Dread(dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
dset_data);
- /* End to the dataset and release resources used by it. */
+ /* End access to the dataset and release resources used by it. */
status = H5Dclose(dataset_id);
- /* Terminate to the data space. */
+ /* Terminate access to the data space. */
status = H5Sclose(dataspace_id);
/* Close the file. */
@@ -184,9 +196,13 @@ For further informations, please see the website:
-class="smarterwiki-popup-bubble smarterwiki-popup-bubble-active smarterwiki-popup-bubble-flipped">
+
class="smarterwiki-popup-bubble-tip">
-class="smarterwiki-popup-bubble-body">
-class="smarterwiki-popup-bubble-links-container">
-class="smarterwiki-popup-bubble-links">
-btnI=I'm+Feeling+Lucky&btnI=I'm+Feeling+Lucky&q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB+wikipedia "Search Wikipedia"){.smarterwiki-popup-bubble-link}</span>
+
+
+
+btnI=I'm+Feeling+Lucky&btnI=I'm+Feeling+Lucky&q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB+wikipedia "Search Wikipedia"){.smarterwiki-popup-bubble</span>
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
index 2304f2fd17fe219c72ae5157348c0ded0e64cb9d..3d307a110c59e89113dc1421b248fac3b41cac8c 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
@@ -1,11 +1,23 @@
Intel numerical libraries
=========================
+
+
+
+
Intel libraries for high performance in numerical computing
+
+
+
+
+
+
+
+
Intel Math Kernel Library
-------------------------
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
index 7fa0a444c23e6c29bef8b872bc843483cc5b153e..f0113b1ab34012b311ee9153b76a946f4dc8ac44 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
@@ -1,8 +1,20 @@
MAGMA for Intel Xeon Phi
========================
+
+
+
+
Next generation dense algebra library for heterogeneous systems with
accelerators
+
+
+
+
+
+
+
+
### Compiling and linking with MAGMA
To be able to compile and link code with MAGMA library user has to load
@@ -90,3 +102,7 @@ Jack Dongarra et. al,
[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/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md
index ebb0f189e6c78b162df95c989ae84f5f8715069d..42272de8096bf05c675bf8353751de681bdc801a 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/petsc.md
@@ -1,6 +1,10 @@
PETSc
=====
+
+
+
+
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
@@ -9,6 +13,14 @@ OpenCL, as well as hybrid MPI-shared memory or MPI-GPU parallelism.
+
+
+
+
+
+
+
+
Introduction
------------
@@ -47,7 +59,7 @@ names obey this pattern:
module load petsc/3.4.4-icc-impi-mkl-opt
where `variant` is replaced by one of
-``. The `opt` variant is compiled
+`{dbg, opt, threads-dbg, threads-opt}`. The `opt` variant is compiled
without debugging information (no `-g` option) and with aggressive
compiler optimizations (`-O3 -xAVX`). This variant is suitable for
performance measurements and production runs. In all other cases use the
@@ -104,3 +116,7 @@ petsc module loaded.
- [Trilinos ML](http://trilinos.sandia.gov/packages/ml/)
- [SPAI - Sparse Approximate
Inverse](https://bitbucket.org/petsc/pkg-spai)
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
index 81b90738dde4c7bcaade4303d5d719d10b80271c..63d7156885edd7a4c418295271653693135dcaa7 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/numerical-libraries/trilinos.md
@@ -1,8 +1,20 @@
Trilinos
========
+
+
+
+
Packages for large scale scientific and engineering problems. Provides
MPI and hybrid parallelization.
+
+
+
+
+
+
+
+
### Introduction
Trilinos is a collection of software packages for the numerical solution
@@ -66,7 +78,7 @@ or
include Makefile.export.<package>
if you are interested only in a specific Trilinos package. This will
-give you to the variables such as Trilinos_CXX_COMPILER,
+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/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
index 38f69e3838897254a1effc0d7d50752f7d956e30..952c928505bf204c8f70fe5db88be0257b2e4fa4 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/nvidia-cuda.md
@@ -1,11 +1,23 @@
nVidia CUDA
===========
+
+
+
+
A guide to nVidia CUDA programming and GPU usage
+
+
+
+
+
+
+
+
CUDA Programming on Anselm
--------------------------
@@ -41,7 +53,7 @@ the example used is deviceQuery) and run "make" to start the compilation
$ cd ~/cuda-samples/1_Utilities/deviceQuery
$ make
-To run the code user can use PBS interactive session to get to a
+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
@@ -185,7 +197,7 @@ This code can be compiled using following command
$ nvcc test.cu -o test_cuda
-To run the code use interactive PBS session to get to one of the
+To run the code use interactive PBS session to get access to one of the
GPU accelerated nodes
$ qsub -I -q qnvidia -A OPEN-0-0
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
index 994fc86aa850c6722b7e1c369cdd1c8c7dc2c380..c6c822b5ee3250a1f02860b3909557ecbaf1446b 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/diagnostic-component-team.md
@@ -6,15 +6,23 @@ Diagnostic component (TEAM)
+
+
+
+
+
+
+
+
### Access
TEAM is available at the following address
: <http://omics.it4i.cz/team/>
-The address is ible only via
-[VPN. ](../../ing-the-cluster/vpn-access.html)
+The address is accessible only via
+[VPN. ](../../accessing-the-cluster/vpn-access.html)
-### Diagnostic component (TEAM)
+### Diagnostic component (TEAM) {#diagnostic-component-team}
VCF files are scanned by this diagnostic tool for known diagnostic
disease-associated variants. When no diagnostic mutation is found, the
@@ -33,11 +41,11 @@ 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.
-
-
-
-
-
+
@@ -46,10 +54,15 @@ mutations can be added or discarded to adjust panel definitions.
*Figure 5. ****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
+panels can be interactively improved as the knowledge of the disease
increases.*
*
*
+
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
index a7b30eed8da0041c681d9066c831eb19eb3bd96b..01bfba86310b076c729e59499d06e45c537f1ff0 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/overview.md
@@ -1,11 +1,23 @@
Overview
========
+
+
+
+
The human NGS data processing solution
+
+
+
+
+
+
+
+
Introduction
------------
@@ -20,15 +32,15 @@ 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.
-
-
-
-
-
-
-
-
-
+
*Figure 1.*** *OMICS MASTER solution overview. Data is produced in the
external labs and comes to IT4I (represented by the blue dashed line).
@@ -37,7 +49,7 @@ 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
+that produced them, depending of the experimental design carried
out*. style="text-align: left; ">
Typical genomics pipelines are composed by several components that need
@@ -85,22 +97,22 @@ 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.
-Input:** FASTQ file.
+Input: FASTQ file.
-Output:** FASTQ file plus an HTML file containing statistics on the
+Output: FASTQ file plus an HTML file containing statistics on the
data.
FASTQ format
>It represents the nucleotide sequence and its corresponding
quality scores.
-
-*Figure 2.****** FASTQ file.***
+
+*Figure 2.**FASTQ file.**
#### Mapping
-Component:** Hpg-aligner.****
+Component:** Hpg-aligner.**
Sequence reads are mapped over the human reference genome. SOLiD reads
are not covered by this solution; they should be mapped with specific
@@ -113,7 +125,7 @@ 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.
-Input:** FASTQ file.
+Input: FASTQ file.
Output:** Aligned file in BAM format.****
@@ -124,7 +136,7 @@ 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.
->The SAM format ^(1)^> consists of one header
+>The SAM format (1)^> consists of one header
section and one alignment section. The lines in the header section start
with character ‘@’, and lines in the alignment section do not. All lines
are TAB delimited.
@@ -181,7 +193,7 @@ corresponding information is unavailable.
<tr class="even">
<td align="left"><p>7</p></td>
<td align="left"><p>MRNM </p></td>
-<td align="left"><p>Mate REference NaMe ('=^' if same RNAME)</p></td>
+<td align="left"><p>Mate REference NaMe ('=' if same RNAME)</p></td>
</tr>
<tr class="odd">
<td align="left"><p>8</p></td>
@@ -220,21 +232,21 @@ soft clipping, ‘H’ for hard clipping and ‘P’ for padding. These support
splicing, clipping, multi-part and padded alignments. Figure 3 shows
examples of CIGAR strings for different types of alignments.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
*
Figure 3.*** *SAM format file. The ‘@SQ’ line in the header section
gives the order of reference sequences. Notably, r001 is the name of a
@@ -279,7 +291,7 @@ Component:** GATK.
Identification of single nucleotide variants and indels on the
alignments is performed using the Genome Analysis Toolkit (GATK). GATK
-^(2)^ is a software package developed at the Broad Institute to analyze
+(2)^ 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.
@@ -290,7 +302,7 @@ Output:** VCF
Variant Call Format (VCF)**
->VCF ^(3)^> is a standardized format for storing the
+>VCF (3)^> 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
@@ -328,26 +340,26 @@ 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.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
Figure 4.**> (a) Example of valid VCF. The header lines
##fileformat and #CHROM are mandatory, the rest is optional but
@@ -363,11 +375,11 @@ 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
-
-
-
-
+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.
### >Annotating
@@ -379,7 +391,7 @@ using the HPG-Variant software, which extracts from CellBase**,** the
Knowledge database, all the information relevant on the predicted
pathologic effect of the variants.
-VARIANT (VARIant Analysis Tool) ^(4)^ reports information on the
+VARIANT (VARIant Analysis Tool) (4)^ 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
@@ -393,58 +405,58 @@ conventional reports beyond the coding regions and expands the knowledge
on the contribution of non-coding or synonymous variants to the
phenotype studied.
-Input:** VCF
+Input:** VCF**
Output:** 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.
+the corresponding QC and functional annotations.**
#### CellBase
-CellBase^(5)^ is a relational database integrates biological information
+CellBase(5)^ is a relational database integrates biological information
from different sources and includes:
-Core features:**
+**Core features:**
We took genome sequences, genes, transcripts, exons, cytobands or cross
references (xrefs) identifiers (IDs) >from Ensembl
-^(6)^>. Protein information including sequences, xrefs or
+(6)^>. Protein information including sequences, xrefs or
protein features (natural variants, mutagenesis sites,
post-translational modifications, etc.) were imported from UniProt
-^(7)^>.
+(7)^>.
-Regulatory:**
+**Regulatory:**
-CellBase imports miRNA from miRBase ^(8)^; curated and non-curated miRNA
-targets from miRecords ^(9)^, >miRTarBase ^(10)^>,
-TargetScan^(11)^> and microRNA.org ^(12)^> and
+CellBase imports miRNA from miRBase (8)^; curated and non-curated miRNA
+targets from miRecords (9)^, >miRTarBase ^(10)^>,
+TargetScan(11)^> and microRNA.org ^(12)^> and
CpG islands and conserved regions from the UCSC database
-^(13)^>.> </span>
+(13)^>.> </span>
-Functional annotation**
+**Functional annotation**
-OBO Foundry ^(14)^ develops many biomedical ontologies that are
+OBO Foundry (14)^ 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 ^(6)^. InterPro ^(15)^ annotations
+annotations were taken from Ensembl (6)^. InterPro ^(15)^ annotations
were also imported.
-Variation**
+**Variation**
-CellBase includes SNPs from dbSNP ^(16)^; SNP population frequencies
-from HapMap ^(17)^, 1000 genomes project ^(18)^ and Ensembl ^(6)^;
+CellBase includes SNPs from dbSNP (16)^; SNP population frequencies
+from HapMap (17)^, 1000 genomes project ^(18)^ and Ensembl ^(6)^;
phenotypically annotated SNPs were imported from NHRI GWAS Catalog
-^(19)^,^ ^>HGMD ^(20)^>, Open Access GWAS Database
-^(21)^>, UniProt ^(7)^> and OMIM
-^(22)^>; mutations from COSMIC ^(23)^> and
+(19)^,^ ^>HGMD ^(20)^>, Open Access GWAS Database
+(21)^>, UniProt ^(7)^> and OMIM
+(22)^>; mutations from COSMIC ^(23)^> and
structural variations from Ensembl
-^(6)^>.> </span>
+(6)^>.> </span>
-Systems biology**
+**Systems biology**
We also import systems biology information like interactome information
-from IntAct ^(24)^. Reactome ^(25)^> stores pathway and interaction
-information in BioPAX ^(26)^> format. BioPAX data exchange
+from IntAct (24)^. Reactome ^(25)^> stores pathway and interaction
+information in BioPAX (26)^> format. BioPAX data exchange
format >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
@@ -610,34 +622,38 @@ should use the next command:
speed-up mapping high-quality reads,
and *Smith-Waterman*> (SW) to increase sensitivity when
reads cannot be mapped using BWT.
-- >>>[hpg-fastq](http://docs.bioinfo.cipf.es/projects/fastqhpc/wiki), <span> a
+- >[hpg-fastq](http://docs.bioinfo.cipf.es/projects/fastqhpc/wiki), > a
quality control tool for high throughput
sequence data.
-- >>><span>[hpg-variant](http://wiki.opencb.org/projects/hpg/doku.php?id=variant:downloads), <span>The
+- >>[hpg-variant](http://wiki.opencb.org/projects/hpg/doku.php?id=variant:downloads), <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>[picard](http://picard.sourceforge.net/), <span>Picard
+- >>[picard](http://picard.sourceforge.net/), <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>[samtools](http://samtools.sourceforge.net/samtools-c.shtml), <span>SAM
+- >>[samtools](http://samtools.sourceforge.net/samtools-c.shtml), <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>
-- >>>[snpEff](http://snpeff.sourceforge.net/), <span>Genetic
+- >><span>[snpEff](http://snpeff.sourceforge.net/), <span>Genetic
variant annotation and effect
prediction toolbox.</span></span>
+
+
+
+
This listing show which tools are used in each step of the pipeline :
-<!-- -->
+
- >stage-00: fastqc
- >stage-01: hpg_fastq
@@ -692,9 +708,9 @@ button the diagnostic process starts.*
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 ^(20)^,
+databases: HGMD-public (20)^,
[HUMSAVAR](http://www.uniprot.org/docs/humsavar),
-ClinVar ^(29)^ and COSMIC ^(23)^.
+ClinVar (29)^ and COSMIC ^(23)^.
+The address is accessible only
+via [VPN. ](../../accessing-the-cluster/vpn-access.html)
### >BiERApp
@@ -31,11 +39,11 @@ 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.
-
-
-
-
-
+
*Figure 6***. *Web interface to the prioritization tool.* *This
figure* *shows the interface of the web tool for candidate gene
@@ -45,3 +53,4 @@ the variants in the corresponding genomic coordinates.*
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
index cc9609e7cbb0266f0454a7126a2a4727bfbcfd90..81b56414496bfbf959c7e8fe67fc87cf007a4aaf 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/openfoam.md
@@ -1,11 +1,23 @@
OpenFOAM
========
+
+
+
+
A free, open source CFD software package
+
+
+
+
+
+
+
+
Introduction**
----------------
@@ -29,21 +41,21 @@ For example syntax of available OpenFOAM module is:
>< openfoam/2.2.1-icc-openmpi1.6.5-DP >
this means openfoam version >2.2.1 compiled by
->ICC compiler with >openmpi1.6.5 in> double
+>ICC compiler with >openmpi1.6.5 in<span> double
precision.
Naming convection of the installed versions is following:
>
-openfoam/<>VERSION>>-<</span>>COMPILER</span><span>>-<</span><span>openmpiVERSION</span><span>>-<</span><span>PRECISION</span><span>></span>
+openfoam/<>VERSION>>-<</span><span>COMPILER</span><span>>-<</span><span>openmpiVERSION</span><span>>-<</span><span>PRECISION</span><span>></span>
-- ><>VERSION>> - version of
+- ><>VERSION<span>> - version of
openfoam
- ><>COMPILER> - version of used
compiler
- ><>openmpiVERSION> - version of used
openmpi/impi
-- ><>PRECISION> - DP/>SP –
+- ><>PRECISION> - DP/<span>SP –
double/single precision
###Available OpenFOAM modules**
@@ -118,6 +130,10 @@ Running Serial Applications**
>Create a Bash script >test.sh
+
+
+
+
>
>
@@ -160,8 +176,16 @@ here](../resource-allocation-and-job-execution/job-submission-and-execution.html
>Run the second case for example external incompressible turbulent
flow - case - motorBike.
+
+
+
+
>First we must run serial application bockMesh and decomposePar for
preparation of parallel computation.
+
+
+
+
>
@@ -206,7 +230,7 @@ preparation of parallel computation.
>>This job create simple block mesh and domain decomposition.
Check your decomposition, and submit parallel computation:
->>Create a PBS script>
+>>Create a PBS script<span>
testParallel.pbs:</span>
@@ -225,11 +249,11 @@ testParallel.pbs:</span>
nproc = 32
- mpirun -hostfile $ -np $nproc snappyHexMesh -overwrite -parallel | tee snappyHexMesh.log
+ mpirun -hostfile ${PBS_NODEFILE} -np $nproc snappyHexMesh -overwrite -parallel | tee snappyHexMesh.log
- mpirun -hostfile $ -np $nproc potentialFoam -noFunctionObject-writep -parallel | tee potentialFoam.log
+ mpirun -hostfile ${PBS_NODEFILE} -np $nproc potentialFoam -noFunctionObject-writep -parallel | tee potentialFoam.log
- mpirun -hostfile $ -np $nproc simpleFoam -parallel | tee simpleFoam.log
+ mpirun -hostfile ${PBS_NODEFILE} -np $nproc simpleFoam -parallel | tee simpleFoam.log
>
@@ -260,6 +284,10 @@ testParallel.pbs:</span>
$ cd $FOAM_RUN/
>Create directory applications/solvers in user directory
+
+
+
+
>
$ mkdir -p applications/solvers
$ cd applications/solvers
@@ -276,6 +304,10 @@ testParallel.pbs:</span>
$ cd My_icoFoam
+
+
+
+
>Rename icoFoam.C to My_icoFOAM.C
@@ -293,6 +325,10 @@ testParallel.pbs:</span>
icoFoam.C
EXE = $(FOAM_APPBIN)/icoFoam
+
+
+
+
>and change to:
@@ -318,8 +354,12 @@ testParallel.pbs:</span>
Have a fun with OpenFOAM :)**
- id="__caret"> id="__caret">
+ id="__caret">
+
+
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md
index 34467f1dad4fad0e346f323db9f71275d3fa5606..d20265f4e1d64ffe3e16a3719c10e0ad53e097dc 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/operating-system.md
@@ -1,11 +1,23 @@
Operating System
================
+
+
+
+
The operating system, deployed on ANSELM
+
+
+
+
+
+
+
+
The operating system on Anselm is Linux - bullx Linux Server release
6.3.
@@ -13,3 +25,5 @@ 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/converted/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md b/converted/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md
index 32970cd18379a79e2db0c02662394ccb2f107ca9..e0888d8fa2b7430b57ecb854ce78b9c0086c37a6 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/software/paraview.md
@@ -1,12 +1,24 @@
ParaView
========
+
+
+
+
An open-source, multi-platform data analysis and visualization
application
+
+
+
+
+
+
+
+
Introduction
------------
@@ -121,3 +133,5 @@ will not take advantage of accelerated nodes on Anselm. Support for GPU
acceleration might be added in the future.
+
+
diff --git a/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md b/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md
index be82b6fac217d54c30a7ea235c88437d4229ac0c..1f006bd53f57a9140ca4703d951b37e697d0017e 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/cesnet-data-storage.md
@@ -5,6 +5,14 @@ CESNET Data Storage
+
+
+
+
+
+
+
+
Introduction
------------
@@ -23,7 +31,7 @@ Republic.
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 to
+a legal entity (organization) that meets the “Principles for access to
CESNET Large infrastructure (Access Policy)”.
User may only use data storage CESNET for data transfer and storage
@@ -37,12 +45,12 @@ The service is documented at
please contact directly CESNET Storage Department via e-mail
[du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
-The procedure to obtain the CESNET is quick and trouble-free.
+The procedure to obtain the CESNET access is quick and trouble-free.
(source
[https://du.cesnet.cz/](https://du.cesnet.cz/wiki/doku.php/en/start "CESNET Data Storage"))
-CESNET storage
+CESNET storage access
---------------------
### Understanding Cesnet storage
@@ -51,7 +59,7 @@ It is very important to understand the Cesnet storage before uploading
data. Please read
<https://du.cesnet.cz/en/navody/home-migrace-plzen/start> first.
-Once registered for CESNET Storage, you may [ the
+Once registered for CESNET Storage, you may [access the
storage](https://du.cesnet.cz/en/navody/faq/start) in
number of ways. We recommend the SSHFS and RSYNC methods.
@@ -59,7 +67,7 @@ number of ways. We recommend the SSHFS and RSYNC methods.
SSHFS: The storage will be mounted like a local hard drive
-The SSHFS provides a very convenient way to the CESNET Storage.
+The SSHFS 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.
@@ -74,7 +82,7 @@ Mount tier1_home **(only 5120M !)**:
$ sshfs username@ssh.du1.cesnet.cz:. cesnet/
-For easy future from Anselm, install your public key
+For easy future access from Anselm, install your public key
$ cp .ssh/id_rsa.pub cesnet/.ssh/authorized_keys
@@ -92,7 +100,7 @@ Once done, please remember to unmount the storage
$ fusermount -u cesnet
-### Rsync
+### Rsync access
Rsync provides delta transfer for best performance, can resume
interrupted transfers
@@ -127,3 +135,7 @@ 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/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md b/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
index 5fa2b975c6d6fbcf34c669cd57bdb54b0a2a57b0..8bf8b095f575b5a397309226252bd106d82db084 100644
--- a/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
+++ b/converted/docs.it4i.cz/anselm-cluster-documentation/storage-1/storage.md
@@ -5,10 +5,18 @@ Storage
+
+
+
+
+
+
+
+
There are two main shared file systems on Anselm cluster, the
[HOME](../storage.html#home) and
[SCRATCH](../storage.html#scratch). All login and compute
-nodes may same data on shared filesystems. Compute nodes are also
+nodes may access same data on shared filesystems. Compute nodes are also
equipped with local (non-shared) scratch, ramdisk and tmp filesystems.
Archiving
@@ -27,7 +35,7 @@ Anselm computer provides two main shared filesystems, the [HOME
filesystem](../storage.html#home) and the [SCRATCH
filesystem](../storage.html#scratch). Both HOME and
SCRATCH filesystems are realized as a parallel Lustre filesystem. Both
-shared file systems are ible via the Infiniband network. Extended
+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.
@@ -42,7 +50,7 @@ round-robin fashion to ensure load balancing.
When a client (a compute
node from your job) needs to create
-or a file, the client queries the metadata server (
+or access a file, the client queries the metadata server (
MDS) and the metadata target (
MDT) for the layout and location of the
[file's
@@ -81,7 +89,7 @@ significantly impact the I/O performance you experience.
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
- patterns.
+access patterns.
```
$ lfs getstripe dir|filename
@@ -122,7 +130,7 @@ 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 of
+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
@@ -134,10 +142,10 @@ 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.
-Using a large stripe size can improve performance when ing very
+Using a large stripe size can improve performance when accessing very
large files
-Large stripe size allows each client to have exclusive to its own
+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.
@@ -249,7 +257,7 @@ prove as insufficient for particular user, please contact
lifted upon request.
The Scratch filesystem is intended for temporary scratch data generated
-during the calculation as well as for high performance to input
+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.
@@ -257,7 +265,7 @@ Users are advised to save the necessary data from the SCRATCH filesystem
to HOME filesystem after the calculations and clean up the scratch
files.
-Files on the SCRATCH filesystem that are **not ed for more than 90
+Files on the SCRATCH filesystem that are **not accessed for more than 90
days** will be automatically **deleted**.
The SCRATCH filesystem is realized as Lustre parallel filesystem and is
@@ -370,7 +378,7 @@ number of named user and named group entries.
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 .
+manner. Below, we create a directory and allow a specific user access.
```
[vop999@login1.anselm ~]$ umask 027
@@ -414,18 +422,18 @@ Local Filesystems
Every computational node is equipped with 330GB local scratch disk.
-Use local scratch in case you need to large amount of small files
+Use local scratch in case you need to access large amount of small files
during your calculation.
-The local scratch disk is mounted as /lscratch and is ible to
+The local scratch disk is mounted as /lscratch and is accessible to
user at /lscratch/$PBS_JOBID directory.
The local scratch filesystem is intended for temporary scratch data
-generated during the calculation as well as for high performance
-to input and output files. All I/O intensive jobs that large
+generated during the calculation as well as for high performance access
+to input and output files. All I/O intensive jobs that access large
number of small files within the calculation must use the local scratch
filesystem as their working directory. This is required for performance
-reasons, as frequent to number of small files may overload the
+reasons, as frequent access to number of small files may overload the
metadata servers (MDS) of the Lustre filesystem.
The local scratch directory /lscratch/$PBS_JOBID will be deleted
@@ -448,16 +456,16 @@ none
Every computational node is equipped with filesystem realized in memory,
so called RAM disk.
-Use RAM disk in case you need really fast to your data of limited
+Use RAM disk in case you need really fast access to your data of limited
size during your calculation.
Be very careful, use of RAM disk filesystem is at the expense of
operational memory.
-The local RAM disk is mounted as /ramdisk and is ible to user
+The local RAM disk is mounted as /ramdisk and is accessible to user
at /ramdisk/$PBS_JOBID directory.
The local RAM disk filesystem is intended for temporary scratch data
-generated during the calculation as well as for high performance
+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
@@ -504,6 +512,14 @@ Mountpoint Usage Protocol
/scratch cluster shared jobs' data Lustre 146 TiB 6 GB/s Quota 100TB Compute and login nodes files older 90 days removed
/lscratch node local jobs' data local 330 GB 100 MB/s none Compute nodes purged after job ends
/ramdisk node local jobs' data local 60, 90, 500 GB 5-50 GB/s none Compute nodes purged after job ends
- /tmp local temporary files local 100 MB/s none Compute and login nodes auto purged
+ /tmp local temporary files local 9.5 GB 100 MB/s none Compute and login nodes auto purged
+
+
+
+
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
index b8c46a60e5dd0e7d2272c55898245a142bd7f7a2..b4b6cb1639133926a77d84267ed8d70b1ef1dd30 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
@@ -1,6 +1,14 @@
Cygwin and X11 forwarding
=========================
+
+
+
+
+
+
+
+
### If no able to forward X11 using PuTTY to CygwinX
```
@@ -23,17 +31,17 @@ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connect
change it
-
+ to</span>
C:*cygwin64binXWin.exe -listen tcp*
- 
+ 
-2. Check Putty settings:
+2.
Check Putty settings:
Enable X11
-
+ forwarding
@@ -43,3 +51,5 @@ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connect
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
index 454ee5cd4ee844041a6cb3b7f0bc9faa678c3c13..6032500e06f4dd3dafdb496f215b5d296373f80c 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/graphical-user-interface.md
@@ -5,10 +5,18 @@ Graphical User Interface
+
+
+
+
+
+
+
+
X Window System
---------------
-The X Window system is a principal way to get GUI to the
+The X Window system is a principal way to get GUI access to the
clusters.
Read more about configuring [**X Window
@@ -27,6 +35,8 @@ to remotely control another
class="link-external">[computer](http://en.wikipedia.org/wiki/Computer "Computer").
Read more about configuring
-[VNC](../../../salomon/ing-the-cluster/graphical-user-interface/vnc.html)**.
+**[VNC](../../../salomon/accessing-the-cluster/graphical-user-interface/vnc.html)**.
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
index fa6db5525fa7e11d71874ddf9e609677218e8681..4309360c33449cd032131bfce05637d886cbd878 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
@@ -5,6 +5,14 @@ VNC
+
+
+
+
+
+
+
+
The **Virtual Network Computing** (**VNC**) is a graphical [desktop
sharing](http://en.wikipedia.org/wiki/Desktop_sharing "Desktop sharing")
system that uses the [Remote Frame Buffer protocol
@@ -18,7 +26,7 @@ and
events from one computer to another, relaying the graphical
[screen](http://en.wikipedia.org/wiki/Computer_screen "Computer screen")
updates back in the other direction, over a
-[network](http://en.wikipedia.org/wiki/Computer_network "Computer network").(http://en.wikipedia.org/wiki/Virtual_Network_Computing#cite_note-1)^
+[network](http://en.wikipedia.org/wiki/Computer_network "Computer network").(http://en.wikipedia.org/wiki/Virtual_Network_Computing#cite_note-1)
The recommended clients are
[TightVNC](http://www.tightvnc.com) or
@@ -40,13 +48,13 @@ Verify:
Start vncserver
---------------
-To VNC a local vncserver must be started first and also a tunnel
+To access VNC a local vncserver must be started first and also a tunnel
using SSH port forwarding must be established.
[See below](vnc.html#linux-example-of-creating-a-tunnel)
for the details on SSH tunnels. In this example we use port 61.
You can find ports which are already occupied. Here you can see that
-ports "/usr/bin/Xvnc :79" and "
+ports " /usr/bin/Xvnc :79" and "
/usr/bin/Xvnc :60" are occupied.
```
@@ -78,7 +86,7 @@ X DISPLAY # PROCESS ID
:61 18437
```
-Another command:
+Another command:
```
[username@login2 .vnc]$ ps aux | grep Xvnc
@@ -86,7 +94,7 @@ Another command:
username 10296 0.0 0.0 131772 21076 pts/29 SN 13:01 0:01 /usr/bin/Xvnc :61 -desktop login2:61 (username) -auth /home/jir13/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5961 -fp catalogue:/etc/X11/fontpath.d -pn
```
-To the VNC server you have to create a tunnel between the login
+To access the VNC server you have to create a tunnel between the login
node using TCP **port 5961** and your machine using a free TCP port (for
simplicity the very same, in this case).
@@ -163,7 +171,7 @@ Fill the Source port and Destination fields. **Do not forget to click
the Add button**.
-tunnel](https://docs.it4i.cz/get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/vnc/putty-tunnel.png/@@images/4c66cd51-c858-473b-98c2-8d901aea7118.png "PuTTY Tunnel")](putty-tunnel.png)
+
Run the VNC client of your choice, select VNC server 127.0.0.1, port
5961 and connect using VNC password.
@@ -199,12 +207,12 @@ You should see after the successful login.
Open Screensaver preferences dialog:
-
+
Uncheck both options below the slider:
-
+
### Kill screensaver if locked screen
@@ -239,7 +247,7 @@ GUI applications on compute nodes over VNC
------------------------------------------
The very [same methods as described
-above](https://docs.it4i.cz/get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-and-vnc#gui-applications-on-compute-nodes),
+above](https://docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-and-vnc#gui-applications-on-compute-nodes),
may be used to run the GUI applications on compute nodes. However, for
maximum performance**, proceed following these steps:
@@ -277,3 +285,5 @@ Example described above:
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vpnuiV.png b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vpnuiV.png
deleted file mode 100644
index 076e2c4f9873d72937ecab0bb542a7690f6a70dc..0000000000000000000000000000000000000000
Binary files a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vpnuiV.png and /dev/null differ
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
index 1f0b4eba84c91acdd76aae9a837293a7d430814b..2ce2407a6774d03862d8c5c29f49d30234ab3ace 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
@@ -5,7 +5,15 @@ X Window System
-The X Window system is a principal way to get GUI to the
+
+
+
+
+
+
+
+
+The X Window system is a principal way to get GUI access to the
clusters. The **X Window System** (commonly known as **X11**, based on
its current major version being 11, or shortened to simply **X**, and
sometimes informally **X-Windows**) is a computer software system and
@@ -200,3 +208,5 @@ in the local X server
Use System->Log Out to close the gnome-session
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/introduction.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/introduction.md
index 1bbcf5094d1d9c3a05588c92c17c35d62a688b4d..baee0ca1270ff8e6f3ae3ec4846edfb47394d56f 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/introduction.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/introduction.md
@@ -1,21 +1,33 @@
Accessing the Clusters
======================
-The IT4Innovations clusters are ed by SSH protocol via login
+
+
+
+
+
+
+
+
+The IT4Innovations clusters are accessed by SSH protocol via login
nodes.
Read more on [Accessing the Salomon
-Cluste](../salomon/ing-the-cluster.html)r or
+Cluste](../salomon/accessing-the-cluster.html)r or
[Accessing the Anselm
-Cluster](../anselm-cluster-documentation/ing-the-cluster.html)
+Cluster](../anselm-cluster-documentation/accessing-the-cluster.html)
pages.
### PuTTY
On **Windows**, use [PuTTY ssh
-client](ing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
+client](accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
### SSH keys
Read more about [SSH keys
-management](ing-the-clusters/shell-access-and-data-transfer/ssh-keys.html).
+management](accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/introduction.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/introduction.md
index cbfc29c5e95351cdbea0454da6c6620b1b8b8dbd..a5c02508dbe86cac7c092005f6143cb6109a4f5a 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/introduction.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/introduction.md
@@ -1,13 +1,21 @@
Accessing the Clusters
======================
-The IT4Innovations clusters are ed by SSH protocol via login
+
+
+
+
+
+
+
+
+The IT4Innovations clusters are accessed by SSH protocol via login
nodes.
Read more on [Accessing the Salomon
-Cluste](../../../salomon/ing-the-cluster.html)r or
+Cluste](../../../salomon/accessing-the-cluster.html)r or
[Accessing the Anselm
-Cluster](../../../anselm-cluster-documentation/ing-the-cluster.html)
+Cluster](../../../anselm-cluster-documentation/accessing-the-cluster.html)
pages.
### PuTTY
@@ -18,3 +26,7 @@ client](putty/putty.html).
### SSH keys
Read more about [SSH keys management](ssh-keys.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md
index 6e004088c57715819a313e4bae6ff1421185b309..1788502386229f8b8b46392048c3d57ea1752200 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/pageant.md
@@ -5,6 +5,14 @@ Pageant SSH agent
+
+
+
+
+
+
+
+
Pageant holds your private key in memory without needing to retype a
passphrase on every login.
@@ -15,6 +23,10 @@ passphrase on every login.
- Now you have your private key in memory without needing to retype a
passphrase on every login.
- [](PageantV.png)
+ 
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
index 72e0950e6d2ce3a3f447a6a765605ec7b601fcb1..7431f8cfa8096fa3f6f0c11e8295a353e5686c37 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
@@ -5,7 +5,15 @@ PuTTY
-PuTTY - before we start SSH connection ssh-connection style="text-align: start; "}
+
+
+
+
+
+
+
+
+PuTTY - before we start SSH connection
---------------------------------------------------------------------------------
### Windows PuTTY Installer
@@ -41,7 +49,7 @@ PuTTY - how to connect to the IT4Innovations cluster
- Run PuTTY
- Enter Host name and Save session fields with [Login
- address](../../../../salomon/ing-the-cluster/shell-and-data-access/shell-and-data-access.html)
+ address](../../../../salomon/accessing-the-cluster/shell-and-data-access/shell-and-data-access.html)
and browse Connection - > SSH -> Auth menu.
The *Host Name* input may be in the format
**"username@clustername.it4i.cz"** so you don't have to type your
@@ -49,7 +57,7 @@ PuTTY - how to connect to the IT4Innovations cluster
In this example we will connect to the Salomon cluster using
**"salomon.it4i.cz"**.
- [](PuTTY_host_Salomon.png)
+ 
@@ -59,16 +67,16 @@ PuTTY - how to connect to the IT4Innovations cluster
Browse and select your [private
key](../ssh-keys.html) file.
- [](PuTTY_keyV.png)
+ 
- Return to Session page and Save selected configuration with *Save*
button.
- [](PuTTY_save_Salomon.png)
+ 
- Now you can log in using *Open* button.
- [](PuTTY_open_Salomon.png)
+ 
- Enter your username if the *Host Name* input is not in the format
"username@salomon.it4i.cz".
@@ -84,9 +92,13 @@ Another PuTTY Settings
- Category -> Windows -> Translation -> Remote character set
and select **UTF-8**.
-<!-- -->
+
- Category -> Terminal -> Features and select **Disable
application keypad mode** (enable numpad)
- Save your configuration on Session page in to Default Settings with
*Save* button .
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
index f6e3ea2462bfb3b679905c9de01f1e44b7522b05..cde0d8094132a89951609b579cbf08b0adc3bf8a 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/puttygen.md
@@ -5,6 +5,14 @@ PuTTY key generator
+
+
+
+
+
+
+
+
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.
@@ -21,7 +29,7 @@ Make sure to backup the key.
- Confirm key passphrase.
- Save your private key with *Save private key* button.
- [](PuttyKeygeneratorV.png)
+ 
@@ -33,15 +41,15 @@ key into authorized_keys file for authentication with your own private
- Start with *Generate* button.
- [](PuttyKeygenerator_001V.png)
+ 
- Generate some randomness.
- [](PuttyKeygenerator_002V.png)
+ 
- Wait.
- [](20150312_143443.png)
+ 
- Enter a *comment* for your key using format
'username@organization.example.com'.
@@ -50,18 +58,18 @@ key into authorized_keys file for authentication with your own private
Save your new private key `in "*.ppk" `format with *Save private
key* button.
- [](PuttyKeygenerator_004V.png)
+ 
- Save the public key with *Save public key* button.
You can copy public key out of the ‘Public key for pasting into
authorized_keys file’ box.
- [](PuttyKeygenerator_005V.png)
+ 
- Export private key in OpenSSH format "id_rsa" using Conversion
-> Export OpenSSH key
- [](PuttyKeygenerator_006V.png)
+ 
- Now you can insert additional public key into authorized_keys file
for authentication with your own private >key.
@@ -69,3 +77,7 @@ key into authorized_keys file for authentication with your own private
proceed to [How to add your own
key](../ssh-keys.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
index 1fafc36c858ee4da7f81c5ae69727af74b6eeeda..739798403a467606535309caa7ec89e1cd3eb817 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
@@ -5,7 +5,15 @@ SSH keys
-
+
+
+
+
+
+
+
+
+ Key management
-------------------------------------------------------------------
After logging in, you can see .ssh/ directory with SSH keys and
@@ -52,7 +60,7 @@ the cluster.
-<!-- -->
+
cd /home/username/
chmod 700 .ssh/
@@ -70,8 +78,8 @@ 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.
Private key is present locally
-on local side and used for example in SSH agent
-. The private key should
+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.
An example of private key
@@ -113,7 +121,7 @@ verify a
digital signature. Public
key is present on the remote
-side and allows to
+side and allows access to
the owner of the matching private key.
An example of public key
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
index 604bdf27ee2135e02b164baef79b514f0e58b446..aa82e6f28a450962f26d409e4fe7499e59630078 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
@@ -1,7 +1,19 @@
VPN - Connection fail in Win 8.1
================================
+
+
+
+
Failed to initialize connection subsystem Win 8.1 - 02-10-15 MS patch
+
+
+
+
+
+
+
+
AnyConnect users on Windows 8.1 will receive a "Failed to initialize
connection subsystem" error after installing the Windows 8.1 02/10/15
security patch. This OS defect introduced with the 02/10/15 patch update
@@ -9,7 +21,7 @@ will also impact WIndows 7 users with IE11. Windows Server
2008/2012 are also impacted by this defect, but neither is a supported
OS for AnyConnect.
-Workaround:**
+**Workaround:**
- Close the Cisco AnyConnect Window and the taskbar mini-icon
- Right click vpnui.exe in the 'Cisco AnyConnect Secure Mobility
@@ -25,3 +37,5 @@ Workaround:**
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md b/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
index 8b592cb500b14f5dd8b6cc7d16269929252314c0..17af28e4d493c8984d302a14df1755d88e7eab44 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/applying-for-resources.md
@@ -5,6 +5,14 @@ Applying for Resources
+
+
+
+
+
+
+
+
Computational resources may be allocated by any of the following
[Computing resources
allocation](http://www.it4i.cz/computing-resources-allocation/?lang=en)
@@ -12,7 +20,7 @@ mechanisms.
Academic researchers can apply for computational resources via [Open
Access
-Competitions](http://www.it4i.cz/open--competition/?lang=en&lang=en).
+Competitions](http://www.it4i.cz/open-access-competition/?lang=en&lang=en).
Anyone is welcomed to apply via the [Directors
Discretion.](http://www.it4i.cz/obtaining-computational-resources-through-directors-discretion/?lang=en&lang=en)
@@ -21,7 +29,7 @@ Foreign (mostly European) users can obtain computational resources via
the [PRACE (DECI)
program](http://www.prace-ri.eu/DECI-Projects).
-In all cases, IT4Innovations’ mechanisms are aimed at
+In all cases, IT4Innovations’ access mechanisms are aimed at
distributing computational resources while taking into account the
development and application of supercomputing methods and their benefits
and usefulness for society. The applicants are expected to submit a
@@ -37,3 +45,7 @@ and [Obtaining Login
Credentials](obtaining-login-credentials.html) page.
+
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/introduction.md b/converted/docs.it4i.cz/get-started-with-it4innovations/introduction.md
index faec5ef5ff7604cdee2614a1a3f131ad1edcb9dd..b833142fb5b79280ac4c3f37c05d3a13506c889a 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/introduction.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/introduction.md
@@ -5,6 +5,14 @@ Documentation
+
+
+
+
+
+
+
+
Welcome to IT4Innovations documentation pages. The IT4Innovations
national supercomputing center operates supercomputers
[Salomon](../salomon.html) and
@@ -15,7 +23,7 @@ industrial community worldwide. The purpose of these pages is to provide
a comprehensive documentation on hardware, software and usage of the
computers.
- class="link-external"> class="WYSIWYG_LINK">How to read the documentation
+ class="link-external">How to read the documentation
--------------------------------------------------------------------------------------------------
1.Read the list in the left column. Select the subject of interest.
@@ -143,3 +151,6 @@ 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/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
index 493abbdafcaf9f578bbd72ea0ce1e1bc58206a1f..92ab874bf3ae6c94855a8408c6a5fe55a34cbd5e 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
@@ -1,12 +1,24 @@
Certificates FAQ
================
+
+
+
+
FAQ about certificates in general
+
+
+
+
+
+
+
+
Q: What are certificates?
-------------------------
@@ -20,15 +32,15 @@ of use. We mention here:
- User (Private) certificates
-<!-- -->
+
- Certificate Authority (CA) certificates
-<!-- -->
+
- Host certificates
-<!-- -->
+
- Service certificates
@@ -222,7 +234,7 @@ 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>
-Q: How do I use my certificate to 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
@@ -237,7 +249,7 @@ 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
[UNICORE6 in PRACE](http://www.prace-ri.eu/UNICORE6-in-PRACE){.spip_in
-.external-link}
+.external
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
@@ -294,7 +306,7 @@ Q: What is the MyProxy service?
-------------------------------
[The MyProxy Service](http://grid.ncsa.illinois.edu/myproxy/){.spip_in
-.external-link}, can be employed by gsissh-term and Globus tools, and is
+.external, 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
@@ -303,7 +315,7 @@ to carry their private keys and certificates when travelling; nor do
users have to install private keys and certificates on possibly insecure
computers.
-Q: Someone may have copied or had 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
@@ -313,3 +325,6 @@ team](https://support.it4i.cz/rt).
+
+
+
diff --git a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
index 82b0df2d5e8e610a4430ac32c9beda74e33d6c59..5748f4f776846e6309facf8779181eb34d2032ac 100644
--- a/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
+++ b/converted/docs.it4i.cz/get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
@@ -5,36 +5,44 @@ Obtaining Login Credentials
+
+
+
+
+
+
+
+
Obtaining Authorization
-----------------------
The computational resources of IT4I are allocated by the Allocation
Committee to a [Project](../introduction.html),
investigated by a Primary Investigator. By allocating the computational
-resources, the Allocation Committee is authorizing the PI to and
+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 and use the clusters, to consume the resources
+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:
-
+
You need to either [become the
PI](../applying-for-resources.html) or [be named as a
collaborator](obtaining-login-credentials.html#authorization-of-collaborator-by-pi)
-by a PI in order to and use the clusters.
+by a PI in order to access and use the clusters.
Head of Supercomputing Services acts as a PI of a project DD-13-5.
-Joining this project, you may ** and explore the clusters**, use
+Joining this project, you may **access and explore the clusters**, 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 **free to the
+Supercomputing Services in order to obtain **free access to the
clusters**.
### Authorization of PI by Allocation Committee
@@ -45,7 +53,7 @@ the Allocation Committee decision.
### Authorization by web
-This is a preferred way of granting to project resources.
+This is a preferred way of granting access to project resources.
Please, use this method whenever it's possible.
Log in to the [IT4I Extranet
@@ -69,7 +77,7 @@ following information:
2.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 already exists on the IT4I systems.
+ collaborator login access already exists on the IT4I systems.
3.Include "Authorization to IT4Innovations" into the subject line.
Example (except the subject line which must be in English, you may use
@@ -98,7 +106,7 @@ The Login Credentials
-------------------------
Once authorized by PI, every person (PI or Collaborator) wishing to
- the clusters, should contact the [IT4I
+access the clusters, should contact the [IT4I
support](https://support.it4i.cz/rt/) (E-mail: [support
[at] it4i.cz](mailto:support%20%5Bat%5D%20it4i.cz)) providing
following information:
@@ -144,7 +152,7 @@ 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
+login credentials (user name, key, passphrase and password) to access
the IT4I systems.
We accept certificates issued by any widely respected certification
@@ -160,8 +168,8 @@ The login credentials include:
2.ssh private key and private key passphrase
3.system password
-The clusters are ed by the [private
-key](../ing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+The clusters are accessed by the [private
+key](../accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
and username.
Username and password is used for login to the information systems
listed on <http://support.it4i.cz/>.
@@ -175,7 +183,7 @@ local $ ssh-keygen -f id_rsa -p
```
On Windows, use [PuTTY Key
-Generator](../ing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html).
+Generator](../accessing-the-clusters/shell-access-and-data-transfer/putty/puttygen.html).
### Change Password
@@ -270,3 +278,7 @@ pending removal:.
The messages will inform about the projected removal date and will
challenge the user to migrate her/his data
+
+
+
+
diff --git a/converted/docs.it4i.cz/index.md b/converted/docs.it4i.cz/index.md
index 42a6d692007d1cfb7b6b16f4e8a404bb925fc62a..682b5b5731f495e4c52cdc8055c7cce17351cf66 100644
--- a/converted/docs.it4i.cz/index.md
+++ b/converted/docs.it4i.cz/index.md
@@ -5,6 +5,14 @@ Documentation
+
+
+
+
+
+
+
+
Welcome to IT4Innovations documentation pages. The IT4Innovations
national supercomputing center operates supercomputers
[Salomon](salomon.html) and
@@ -15,7 +23,7 @@ industrial community worldwide. The purpose of these pages is to provide
a comprehensive documentation on hardware, software and usage of the
computers.
- class="link-external"> class="WYSIWYG_LINK">How to read the documentation
+ class="link-external">How to read the documentation
--------------------------------------------------------------------------------------------------
1.Read the list in the left column. Select the subject of interest.
@@ -143,3 +151,7 @@ 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.
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/accessing-the-cluster.md b/converted/docs.it4i.cz/salomon/accessing-the-cluster.md
index ecd7e8a605585f4edd6afd4d249e11e3c6597913..b7ad64bea8521f981030db81d815cb41b0d98399 100644
--- a/converted/docs.it4i.cz/salomon/accessing-the-cluster.md
+++ b/converted/docs.it4i.cz/salomon/accessing-the-cluster.md
@@ -1,14 +1,22 @@
-Shell and data transfer
+Shell access and data transfer
==============================
+
+
+
+
+
+
+
+
Interactive Login
-----------------
-The Salomon cluster is ed by SSH protocol via login nodes login1,
+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.
@@ -26,7 +34,7 @@ login3.salomon.it4i.cz 22 ssh login3
login4.salomon.it4i.cz 22 ssh login4
The authentication is by the [private
-key](../get-started-with-it4innovations/ing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
Please verify SSH fingerprints during the first logon. They are
identical on all login nodes:
@@ -51,7 +59,7 @@ local $ chmod 600 /path/to/id_rsa
```
On **Windows**, use [PuTTY ssh
-client](../get-started-with-it4innovations/ing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
+client](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
After logging in, you will see the command prompt:
@@ -91,11 +99,11 @@ Address Port Protocol
salomon.it4i.cz 22 scp, sftp
login1.salomon.it4i.cz 22 scp, sftp
login2.salomon.it4i.cz 22 scp, sftp
- class="discreet">login3.salomon.it4i.cz 22 class="discreet">scp, sftp
+ class="discreet">login3.salomon.it4i.cz 22 scp, sftp
login4.salomon.it4i.cz 22 scp, sftp
The authentication is by the [private
-key](../get-started-with-it4innovations/ing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
HTML commented section #2 (ssh transfer performance data need to be
verified)
@@ -143,3 +151,7 @@ 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/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md b/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
index 8d1d51104ff4f40e99475df6a22aeed5722a7f0d..4e538c6bbe71d5808dfe3b92af43d65e9a6b7cf2 100644
--- a/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
+++ b/converted/docs.it4i.cz/salomon/accessing-the-cluster/outgoing-connections.md
@@ -5,6 +5,14 @@ Outgoing connections
+
+
+
+
+
+
+
+
Connection restrictions
-----------------------
@@ -44,7 +52,7 @@ local $ ssh -R 6000:remote.host.com:1234 salomon.it4i.cz
```
In this example, we establish port forwarding between port 6000 on
-Salomon and port 1234 on the remote.host.com. By ing
+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.
@@ -55,7 +63,7 @@ Remote radio button. Insert 6000 to Source port textbox. Insert
remote.host.com:1234. Click Add button, then Open.
Port forwarding may be established directly to the remote host. However,
-this requires that user has ssh to remote.host.com
+this requires that user has ssh access to remote.host.com
```
$ ssh -L 6000:localhost:1234 remote.host.com
@@ -66,7 +74,7 @@ Note: Port number 6000 is chosen as an example only. Pick any free port.
### Port forwarding from compute nodes
Remote port forwarding from compute nodes allows applications running on
-the compute nodes to hosts outside Salomon Cluster.
+the compute nodes to access hosts outside Salomon Cluster.
First, establish the remote port forwarding form the login node, as
[described
@@ -80,7 +88,7 @@ $ ssh -TN -f -L 6000:localhost:6000 login1
```
In this example, we assume that port forwarding from login1:6000 to
-remote.host.com:1234 has been established beforehand. By ing
+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
@@ -90,7 +98,7 @@ Port forwarding is static, each single port is mapped to a particular
port on remote host. Connection to other remote host, requires new
forward.
-Applications with inbuilt proxy support, experience unlimited to
+Applications with inbuilt proxy support, experience unlimited access to
remote hosts, via single proxy server.
To establish local proxy server on your workstation, install and run
@@ -114,7 +122,7 @@ local $ ssh -R 6000:localhost:1080 salomon.it4i.cz
```
Now, configure the applications proxy settings to **localhost:6000**.
-Use port forwarding to the [proxy server from compute
+Use port forwarding to access the [proxy server from compute
nodes](outgoing-connections.html#port-forwarding-from-compute-nodes)
as well .
diff --git a/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md b/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
index b12c1d7669b946286da6c4a89f8c494f7e04c749..3a0b5b8d096d1c9ef7fd9ac78841d332529f6bc4 100644
--- a/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
+++ b/converted/docs.it4i.cz/salomon/accessing-the-cluster/vpn-access.md
@@ -5,6 +5,14 @@ VPN Access
+
+
+
+
+
+
+
+
Accessing IT4Innovations internal resources via VPN
---------------------------------------------------
@@ -40,7 +48,7 @@ for automatic installation.
-
+Install](https://docs.it4i.cz/salomon/vpn_web_install_2.png/@@images/c2baba93-824b-418d-b548-a73af8030320.png "VPN Install")](../vpn_web_install_2.png)
After successful installation, VPN connection will be established and
@@ -92,7 +100,7 @@ If everything works, you can see a lock in the Cisco tray icon.
If you right-click on this icon, you will see a context menu in which
you can control the VPN connection.
-
+[
When you connect to the VPN for the first time, the client downloads the
@@ -101,18 +109,18 @@ For subsequent connections, it is not necessary to re-enter the URL
address, but just select the corresponding item.
Contacting
-
+
Then AnyConnect automatically proceeds like in the case of first logon.
-
+
After a successful logon, you can see a green circle with a tick mark on
the lock icon.
Succesfull
-
+
For disconnecting, right-click on the AnyConnect client icon in the
system tray and select **VPN Disconnect**.
diff --git a/converted/docs.it4i.cz/salomon/environment-and-modules.md b/converted/docs.it4i.cz/salomon/environment-and-modules.md
index b8323d2f5ec2ccaae0e5b034d6bc2bd09c2be2e7..525d2a9d83659dc220f6392c4e18731d547b2edd 100644
--- a/converted/docs.it4i.cz/salomon/environment-and-modules.md
+++ b/converted/docs.it4i.cz/salomon/environment-and-modules.md
@@ -5,6 +5,14 @@ Environment and Modules
+
+
+
+
+
+
+
+
### Environment Customization
After logging in, you may want to configure the environment. Write your
@@ -34,7 +42,7 @@ 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 id="result_box"
-class="short_text"> class="hps alt-edited">stated
+ class="hps alt-edited">stated
in the previous example.
### Application Modules
@@ -131,7 +139,7 @@ The EasyBuild framework prepares the build environment for the different
toolchain components, by loading their respective modules and defining
environment variables to specify compiler commands (e.g.,
via `$F90`), compiler and linker options (e.g.,
-via `$CFLAGS` and `$LDFLAGS`),
+via `$CFLAGS` and `$LDFLAGS`{.docutils .literal}),
the list of library names to supply to the linker (via `$LIBS`{.docutils
.literal}), etc. This enables making easyblocks
largely toolchain-agnostic since they can simply rely on these
@@ -162,3 +170,5 @@ goolf BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK
iccifort icc, ifort
+
+
diff --git a/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md b/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md
index 9f246a4c281a1fb78bbb380f2f77e520a4e1f260..58e4577f66aeef637c8a5997ddb819114a3f8d01 100644
--- a/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md
+++ b/converted/docs.it4i.cz/salomon/hardware-overview-1/hardware-overview.md
@@ -5,6 +5,14 @@ Hardware Overview
+
+
+
+
+
+
+
+
Introduction
------------
@@ -15,7 +23,7 @@ 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 to the
+is available for the scratch project data. The user access to the
Salomon cluster is provided by four login nodes.
[More about schematic representation of the Salomon cluster compute
@@ -23,7 +31,7 @@ nodes IB
topology](../network-1/ib-single-plane-topology.html).
-
+
The parameters are summarized in the following tables:
@@ -121,3 +129,6 @@ available:
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/index.md b/converted/docs.it4i.cz/salomon/index.md
index 90a83ecda0d54f7ec8fad3b9c9bb954ed1b26736..1d945a17c3992ea0582644ec5d9c125e79035f2e 100644
--- a/converted/docs.it4i.cz/salomon/index.md
+++ b/converted/docs.it4i.cz/salomon/index.md
@@ -1,6 +1,14 @@
Introduction
============
+
+
+
+
+
+
+
+
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
@@ -19,15 +27,18 @@ the class="WYSIWYG_LINK">RedHat [
class="WYSIWYG_LINK">Linux
family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
-**Water-cooled Compute Nodes With MIC Accelerator**
-
+Water-cooled Compute Nodes With MIC Accelerator**
+[](salomon)
-
+
**Tape Library T950B**
-
+
+
+
+
+
-
diff --git a/converted/docs.it4i.cz/salomon/introduction.md b/converted/docs.it4i.cz/salomon/introduction.md
index 90a83ecda0d54f7ec8fad3b9c9bb954ed1b26736..820bd868cb403075fa92a0afe61372ab64acad5a 100644
--- a/converted/docs.it4i.cz/salomon/introduction.md
+++ b/converted/docs.it4i.cz/salomon/introduction.md
@@ -1,6 +1,14 @@
Introduction
============
+
+
+
+
+
+
+
+
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
@@ -19,9 +27,9 @@ the class="WYSIWYG_LINK">RedHat [
class="WYSIWYG_LINK">Linux
family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
-**Water-cooled Compute Nodes With MIC Accelerator**
-
+Water-cooled Compute Nodes With MIC Accelerator**
+
@@ -31,3 +39,6 @@ family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_T
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md b/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md
index 9487e731a7cb90eafc4c412f36bb33b424bb6d13..f676804ec709cde4ac22b74a0ecfc4288b883f8f 100644
--- a/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md
+++ b/converted/docs.it4i.cz/salomon/network-1/7d-enhanced-hypercube.md
@@ -1,6 +1,14 @@
7D Enhanced Hypercube
=====================
+
+
+
+
+
+
+
+
[More about Job submission - Placement by IB switch / Hypercube
dimension.](../resource-allocation-and-job-execution/job-submission-and-execution.html)
@@ -20,7 +28,7 @@ Hypercube dimension
topology represents hypercube
dimension 0](ib-single-plane-topology.html).
-### 7D Enhanced Hypercube
+### 7D Enhanced Hypercube {#d-enhanced-hypercube}
@@ -33,8 +41,8 @@ compute nodes MIC accelerated 432 cns577 - cns1008 r21u01n577 - r
### IB Topology
-
-
+ [](Salomon_IB_topology.png)
diff --git a/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md b/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
index 7e585bd38a3bfa06be87f38807f6fdd3bc8080d9..25f628f38121bf7f01a9a77e7cb0cd23bfccc6fa 100644
--- a/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
+++ b/converted/docs.it4i.cz/salomon/network-1/ib-single-plane-topology.md
@@ -5,6 +5,14 @@ IB single-plane topology
+
+
+
+
+
+
+
+
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
@@ -24,7 +32,7 @@ with connections as follows:
Each colour in each physical IRU represents one dual-switch ASIC switch.
-[](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf)
+
@@ -42,10 +50,11 @@ Topology](Salomon_IB_topology.png):
- Racks 27, 28, 29, 30, 31, 32 are equivalent to one Mcell rack.
- Racks 33, 34, 35, 36, 37, 38 are equivalent to one Mcell rack.
-[](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf)
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/network-1/network.md b/converted/docs.it4i.cz/salomon/network-1/network.md
index 235fb38c295e350e19bb2032e62ddf4ee770b516..56d876fc77c5cb3efb519bc3e0ee1349c09b3256 100644
--- a/converted/docs.it4i.cz/salomon/network-1/network.md
+++ b/converted/docs.it4i.cz/salomon/network-1/network.md
@@ -5,6 +5,14 @@ Network
+
+
+
+
+
+
+
+
All compute and login nodes of Salomon are interconnected by 7D Enhanced
hypercube
[Infiniband](http://en.wikipedia.org/wiki/InfiniBand)
@@ -27,11 +35,11 @@ Read more about schematic representation of the Salomon cluster [IB
single-plain topology](ib-single-plane-topology.html)
([hypercube dimension](7d-enhanced-hypercube.html)
0).[>](IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf/view.html){.state-missing-value
+.contenttype-file}
-
-The compute nodes may be ed via the Infiniband network using ib0
+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.
@@ -54,7 +62,7 @@ Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
r4i1n0/0*24+r4i1n1/0*24+r4i1n2/0*24+r4i1n3/0*24
```
-In this example, we the node r4i1n0 by Infiniband network via the
+In this example, we access the node r4i1n0 by Infiniband network via the
ib0 interface.
```
@@ -79,3 +87,4 @@ inet 10.17.35.19....
+
diff --git a/converted/docs.it4i.cz/salomon/prace.md b/converted/docs.it4i.cz/salomon/prace.md
index d2f8a2ad24d0b508c8830dc55b48cec7bb7ae7e0..2f1655599c2835574d1d16a572c99e83295ffe22 100644
--- a/converted/docs.it4i.cz/salomon/prace.md
+++ b/converted/docs.it4i.cz/salomon/prace.md
@@ -5,6 +5,14 @@ PRACE User Support
+
+
+
+
+
+
+
+
Intro
-----
@@ -14,12 +22,12 @@ 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 to some services intended for
+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 [Obtaining
Login Credentials
section](../get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.html),
-if the same level of is required.
+if the same level of access is required.
All general [PRACE User
Documentation](http://www.prace-ri.eu/user-documentation/)
@@ -35,7 +43,7 @@ Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
Information about the local services are provided in the [introduction
of general user documentation](introduction.html).
Please keep in mind, that standard PRACE accounts don't have a password
-to the web interface of the local (IT4Innovations) request
+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.
@@ -59,7 +67,7 @@ Accessing the cluster
### Access with GSI-SSH
-For all PRACE users the method for interactive (login) and data
+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.
@@ -67,14 +75,14 @@ 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).
-Most of the information needed by PRACE users ing the Salomon
+Most of the information needed by PRACE users accessing the Salomon
TIER-1 system can be found here:
- [General user's
FAQ](http://www.prace-ri.eu/Users-General-FAQs)
- [Certificates
FAQ](http://www.prace-ri.eu/Certificates-FAQ)
-- [Interactive using
+- [Interactive access using
GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)
- [Data transfer with
GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
@@ -95,9 +103,9 @@ valid 12 hours), use:
-To Salomon cluster, two login nodes running GSI SSH service are
+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 (ible only from other PRACE partners).
+the internal PRACE network (accessible only from other PRACE partners).
Access from PRACE network:**
@@ -166,13 +174,13 @@ gsiscp can be used:
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 , please see the [section in
+user is using regular SSH based access, please see the [section in
general
-documentation](../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+documentation](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
-If the user uses GSI SSH based , then the procedure is similar to
-the SSH based ([look
-here](../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)),
+If the user uses GSI SSH based access, then the procedure is similar to
+the SSH based access ([look
+here](../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)),
only the port forwarding must be done using GSI SSH:
$ gsissh -p 2222 salomon.it4i.cz -L 5961:localhost:5961
@@ -180,10 +188,10 @@ only the port forwarding must be done using GSI SSH:
### Access with SSH
After successful obtainment of login credentials for the local
-IT4Innovations account, the PRACE users can the cluster as
+IT4Innovations account, the PRACE users can access the cluster as
regular users using SSH. For more information please see the [section in
general
-documentation](ing-the-cluster/shell-and-data-access/shell-and-data-access.html).
+documentation](accessing-the-cluster/shell-and-data-access/shell-and-data-access.html).
File transfers
------------------
@@ -191,12 +199,12 @@ File transfers
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 [the section in the general
-documentation](ing-the-cluster/shell-and-data-access/shell-and-data-access.html).
+documentation](accessing-the-cluster/shell-and-data-access/shell-and-data-access.html).
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 (ible only from other
+well as from the internal PRACE network (accessible only from other
PRACE partners).
There's one control server and three backend servers for striping and/or
@@ -280,8 +288,8 @@ Usage of the cluster
--------------------
There are some limitations for PRACE user when using the cluster. By
-default PRACE users aren't allowed to special queues in the PBS
-Pro to have high priority or exclusive to some special equipment
+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
@@ -387,3 +395,4 @@ increase.
+
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
index 924cfbeff5667a28479254233eb057bf24f3393c..3b559fa7fa52c3e37831d5e06f2d888ffe8cf9de 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/capacity-computing.md
@@ -5,6 +5,14 @@ Capacity computing
+
+
+
+
+
+
+
+
Introduction
------------
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md
index 08c8e4151330890c54152951deae9b12711e6689..79011dfa38f944bff87d01aaf3716d3058e9b514 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/introduction.md
@@ -5,6 +5,14 @@ Resource Allocation and Job Execution
+
+
+
+
+
+
+
+
To run a [job](job-submission-and-execution.html),
[computational
resources](resources-allocation-policy.html) for this
@@ -23,8 +31,8 @@ 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](job-priority.html) at Salomon ensures
that individual users may consume approximately equal amount of
-resources per week. The resources are ible via several queues for
-queueing the jobs. The queues provide prioritized and exclusive
+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:
@@ -32,7 +40,7 @@ users:
- **qprod**, the Production queue****
- **qlong**, the Long queue
- **qmpp**, the Massively parallel queue
-- **qfat**, the queue to SMP UV2000 machine
+- **qfat**, the queue to access SMP UV2000 machine
- **qfree,** the Free resource utilization queue
Check the queue status at <https://extranet.it4i.cz/rsweb/salomon/>
@@ -60,3 +68,5 @@ HTML commented section #1 (removed Capacity computing section, this
will be optimized for Salomon)
+
+
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
index 0a0caaecc83507be4af55df289bc2311c6803754..ed77a237c50545a96689597a67016aa5de1a055a 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-priority.md
@@ -1,6 +1,14 @@
Job scheduling
==============
+
+
+
+
+
+
+
+
Job execution priority
----------------------
@@ -39,7 +47,7 @@ Fairshare priority is used for ranking jobs with equal queue priority.
Fairshare priority is calculated as
-
+
where MAX_FAIRSHARE has value 1E6,
usage~Project~ is cumulated usage by all members of selected project,
@@ -75,7 +83,7 @@ job.
Job execution priority (job sort formula) is calculated as:
-
+
### Job backfilling
@@ -109,3 +117,6 @@ 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/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
index d0af553ee539725b43dfb53622bc7c62f88100b5..fc8dc93f35be20f21788b5fe84777d6c3e1da176 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job-submission-and-execution.md
@@ -5,6 +5,14 @@ Job submission and execution
+
+
+
+
+
+
+
+
Job Submission
--------------
@@ -90,7 +98,7 @@ 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.
-The absence of specialized queue for ing the nodes with cards
+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
@@ -226,8 +234,16 @@ efficient network communication.
+
+
+
+
There are at most 9 nodes sharing the same Infiniband switch.
+
+
+
+
Infiniband switch list:
@@ -257,6 +273,10 @@ set node r37u32n970 resources_available.switch = r36sw3
set node r37u33n971 resources_available.switch = r36sw3
set node r37u34n972 resources_available.switch = r36sw3
```
+
+
+
+
Nodes sharing the same switch may be selected via the PBS resource
attribute switch.
@@ -274,13 +294,25 @@ $ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24:switch=r4i1s0sw1 ./myjob
In this example, we request all the 9 nodes sharing the r4i1s0sw1 switch
for 24 hours.
+
+
+
+
```
$ qsub -A OPEN-0-0 -q qprod -l select=9:ncpus=24 -l place=group=switch ./myjob
```
+
+
+
+
In this example, we request 9 nodes placed on the same switch using node
grouping placement for 24 hours.
+
+
+
+
HTML commented section #1 (turbo boost is to be implemented)
Job Management
@@ -447,11 +479,11 @@ $ pwd
In this example, 4 nodes were allocated interactively for 1 hour via the
qexp queue. The interactive shell is executed in the home directory.
-All nodes within the allocation may be ed via ssh. Unallocated
-nodes are not ible to user.
+All nodes within the allocation may be accessed via ssh. Unallocated
+nodes are not accessible to user.
-The allocated nodes are ible via ssh from login nodes. The nodes
-may each other via ssh as well.
+The allocated nodes are accessible via ssh from login nodes. The nodes
+may access each other via ssh as well.
Calculations on allocated nodes may be executed remotely via the MPI,
ssh, pdsh or clush. You may find out which nodes belong to the
@@ -614,3 +646,5 @@ may use threads.
HTML commented section #3 (Capacity computing need to be reworked)
+
+
diff --git a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
index 0281059a85aa10184fedfebff45540e90e8a9feb..685681fdd36fbcd9dee19b651ec9a02ec88bef3a 100644
--- a/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
+++ b/converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/resources-allocation-policy.md
@@ -5,6 +5,14 @@ Resources Allocation Policy
+
+
+
+
+
+
+
+
Resources Allocation Policy
---------------------------
@@ -13,8 +21,8 @@ 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 [Job scheduling](job-priority.html) section. The
-resources are ible via several queues for queueing the jobs. The
-queues provide prioritized and exclusive to the computational
+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:
@@ -148,14 +156,14 @@ is allowed after request for this queue.
- **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 ed via the qprod queue, however only 86 per job.
+ 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
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 ed via the qlong queue. Full
+ 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.>
*The maximum runtime in qlong is 144 hours (three times of the
@@ -163,7 +171,7 @@ is allowed after request for this queue.
- >****qmpp**, 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 ed via the qmpp queue. ** Full
+ the qmpp. All nodes may be accessed via the qmpp queue. ** 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> *needs explicitly*
@@ -172,7 +180,7 @@ is allowed after request for this queue.
her/his Project.
- >****qfat**, the UV2000 queue. This queue is dedicated
- to the fat SGI UV2000 SMP machine. The machine (uv1) has 112
+ 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> *needs
explicitly* ask
[support](https://support.it4i.cz/rt/) for
@@ -185,13 +193,13 @@ is allowed after request for this queue.
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 ed from
+ 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.
- **qviz**, the Visualization queue****: Intended for
pre-/post-processing using OpenGL accelerated graphics. Currently
- when ing the node, each user gets 4 cores of a CPU allocated,
+ 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"). *If more GPU power or RAM is required, it is
recommended to allocate more chunks (with 4 cores each) up to one
@@ -202,7 +210,7 @@ is allowed after request for this queue.
-To node with Xeon Phi co-processor user needs to specify that in
+To access node with Xeon Phi co-processor user needs to specify that in
[job submission select
statement](job-submission-and-execution.html).
@@ -228,7 +236,7 @@ Check the status of jobs, queues and compute nodes at
-
+
@@ -335,3 +343,5 @@ Password:
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
index e6d4672e1e07a5bddfc0d891c0fe1a9859aeb704..7710a02442ea319915219e7ba7a4a18355251543 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-cfx.md
@@ -1,6 +1,14 @@
ANSYS CFX
=========
+
+
+
+
+
+
+
+
[ANSYS
CFX](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX)
software is a high-performance, general purpose fluid dynamics program
@@ -48,7 +56,7 @@ cfx.pbs script and execute it via the qsub command.
do
if [ "$hl" = "" ]
then hl="$host:$procs_per_host"
- else hl="$:$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
fi
done
@@ -87,3 +95,4 @@ preferences](setting-license-preferences.html) instead.
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
index 8006674affb72aa794003bb4ef4dd0eb5c7fb3d3..7c1cb2e4e1eb122227e3d64c5131f90e711b492f 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-fluent.md
@@ -1,6 +1,14 @@
ANSYS Fluent
============
+
+
+
+
+
+
+
+
[ANSYS
Fluent](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent)
software contains the broad physical modeling capabilities needed to
@@ -144,6 +152,14 @@ execute the job across multiple processors.
+
+
+
+
+
+
+
+
>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.
@@ -176,7 +192,7 @@ command.
cpus=‘expr $num_nodes * $NCPUS‘
#Default arguments for mpp jobs, these should be changed to suit your
#needs.
- fluent_args="-t$ $fluent_args -cnf=$PBS_NODEFILE"
+ fluent_args="-t${cpus} $fluent_args -cnf=$PBS_NODEFILE"
;;
*)
#SMP case
@@ -215,3 +231,5 @@ run](setting-license-preferences.html).
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
index 9ff80553032d906a5f863d5faae1a4979029bd19..a118927458cb896bcd20ae6a92583ef55af0d51d 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-ls-dyna.md
@@ -1,9 +1,17 @@
ANSYS LS-DYNA
=============
+
+
+
+
+
+
+
+
[ANSYS
LS-DYNA](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)
-software provides convenient and easy-to-use to the
+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
@@ -52,7 +60,7 @@ default ansysdyna.pbs script and execute it via the qsub command.
do
if [ "$hl" = "" ]
then hl="$host:$procs_per_host"
- else hl="$:$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
fi
done
@@ -87,3 +95,4 @@ will fail.
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
index 7aac5b95c4eac9a6d3397a6b6f4ebf10e2db5eb4..0c3c6d9be6ddd041e49761e13b87ca127a9f9dee 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-mechanical-apdl.md
@@ -1,6 +1,14 @@
ANSYS MAPDL
===========
+
+
+
+
+
+
+
+
>**[ANSYS
Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
software offers a comprehensive product solution for both multiphysics
@@ -43,7 +51,7 @@ default mapdl.pbs script and execute it via the qsub command.
do
if [ "$hl" = "" ]
then hl="$host:$procs_per_host"
- else hl="$:$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
fi
done
@@ -80,3 +88,4 @@ AUTODYN)>
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
index 4e3c1f7353d4c75b43d55988b22735e04d3ccdeb..97420ddbe22552ea656fc01077b672f4eb6e924d 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
@@ -1,6 +1,14 @@
Overview of ANSYS Products
==========================
+
+
+
+
+
+
+
+
[SVS FEM](http://www.svsfem.cz/)** as ***[ANSYS
Channel partner](http://www.ansys.com/)*** for Czech
Republic provided all ANSYS licenses for all clusters and supports of
@@ -31,3 +39,4 @@ solution to the clusters directly from the client's Workbench project
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/ansys.md b/converted/docs.it4i.cz/salomon/software/ansys/ansys.md
index 6101ad911d4f90bf715b1540e23c2fdd6ded9612..82ff875b1ac1761a450cf58fb6312ab7ebab756f 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/ansys.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/ansys.md
@@ -1,6 +1,14 @@
Overview of ANSYS Products
==========================
+
+
+
+
+
+
+
+
[SVS FEM](http://www.svsfem.cz/)** as ***[ANSYS
Channel partner](http://www.ansys.com/)*** for Czech
Republic provided all ANSYS licenses for all clusters and supports of
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/licensing.md b/converted/docs.it4i.cz/salomon/software/ansys/licensing.md
index 5d09c5aeda8dc396ef1004bc7a3c11763a9b44f8..55a0acbe26e19526bc5827e77b80275776413a4e 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/licensing.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/licensing.md
@@ -1,6 +1,14 @@
Licensing and Available Versions
================================
+
+
+
+
+
+
+
+
ANSYS licence can be used by:
-----------------------------
@@ -42,3 +50,7 @@ Please [see this page to set license
preferences](setting-license-preferences.html).
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md b/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md
index b3c44f8f74a9bd9a8c684dafe078b086b274488c..e12e3b69fb6aec62a876d72dd4cc77c882d3e2a8 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/setting-license-preferences.md
@@ -1,6 +1,14 @@
Setting license preferences
===========================
+
+
+
+
+
+
+
+
Some ANSYS tools allow you to explicitly specify usage of academic or
commercial licenses in the command line (eg.
ansys161 -p aa_r to select Academic Research
@@ -17,11 +25,11 @@ Launch the ANSLIC_ADMIN utility in a graphical environment:
ANSLIC_ADMIN Utility will be run
-
+
-
+
-
+
@@ -30,7 +38,8 @@ the bottom of the list.
-
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/ansys/workbench.md b/converted/docs.it4i.cz/salomon/software/ansys/workbench.md
index 11091bd109f2d9db029501d3cbf459b3124603f5..34ce793bf1868078717c301f2adc03571963e8c7 100644
--- a/converted/docs.it4i.cz/salomon/software/ansys/workbench.md
+++ b/converted/docs.it4i.cz/salomon/software/ansys/workbench.md
@@ -1,6 +1,14 @@
Workbench
=========
+
+
+
+
+
+
+
+
Workbench Batch Mode
--------------------
@@ -74,3 +82,4 @@ uploading a project from your local computer.
+
diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/molpro.md b/converted/docs.it4i.cz/salomon/software/chemistry/molpro.md
index 77cf1643123f5d7ba4697a95eefa3e44353a0b71..80e64cdb72d5762e43eefff621bfe8acf7be0237 100644
--- a/converted/docs.it4i.cz/salomon/software/chemistry/molpro.md
+++ b/converted/docs.it4i.cz/salomon/software/chemistry/molpro.md
@@ -1,8 +1,20 @@
Molpro
======
+
+
+
+
Molpro is a complete system of ab initio programs for molecular
electronic structure calculations.
+
+
+
+
+
+
+
+
About Molpro
------------
@@ -14,7 +26,7 @@ License
-------
Molpro software package is available only to users that have a valid
-license. Please contact support to enable to Molpro if you have a
+license. Please contact support to enable access to Molpro if you have a
valid license appropriate for running on our cluster (eg. >academic
research group licence, parallel execution).
diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.md b/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.md
index 18d279ce916ab9625d37d7bd86332fb9bdf5e448..cda2a674e4ab3993eab0778eac389bae4d8b8206 100644
--- a/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.md
+++ b/converted/docs.it4i.cz/salomon/software/chemistry/nwchem.md
@@ -1,7 +1,19 @@
NWChem
======
+
+
+
+
High-Performance Computational Chemistry
+
+
+
+
+
+
+
+
>Introduction
-------------------------
diff --git a/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.md b/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.md
index 4aeb425767613523985a9de4324d3d011cc6f944..a508b6123673f0c4eb8af7f69b40b5f542c63c13 100644
--- a/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.md
+++ b/converted/docs.it4i.cz/salomon/software/chemistry/phono3py.md
@@ -4,6 +4,18 @@ Phono3py
+
+
+
+
+
+
+
+
+
+
+
+
Introduction
-------------
@@ -203,3 +215,7 @@ grouping single conductivity per grid calculations using
```
$ phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" --br --read_gamma
```
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/compilers.md b/converted/docs.it4i.cz/salomon/software/compilers.md
index 5dca15f3a6f31ad0b84f366ff7f749d2a6e12649..0967a0ff2d1c3a1b1a28af0bd97a9bc867c2cd81 100644
--- a/converted/docs.it4i.cz/salomon/software/compilers.md
+++ b/converted/docs.it4i.cz/salomon/software/compilers.md
@@ -1,11 +1,23 @@
Compilers
=========
+
+
+
+
Available compilers, including GNU, INTEL and UPC compilers
+
+
+
+
+
+
+
+
There are several compilers for different programming languages
available on the cluster:
@@ -63,7 +75,7 @@ GNU
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
-ible in the search path by default.
+accessible in the search path by default.
It is strongly recommended to use the up to date version which comes
with the module GCC:
diff --git a/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md b/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
index a4446f4149168757c1c627ddbe18193d9aebc88c..a2f4edd3f13e481b9e786b672610274e72d1d9f5 100644
--- a/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
+++ b/converted/docs.it4i.cz/salomon/software/comsol/comsol-multiphysics.md
@@ -5,11 +5,19 @@ COMSOL Multiphysics®
+
+
+
+
+
+
+
+
>>Introduction
-------------------------
->>[COMSOL](http://www.comsol.com)><span>
+>>[COMSOL](http://www.comsol.com)
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
@@ -37,7 +45,7 @@ applications.
others](http://www.comsol.com/products)
>>COMSOL also allows an
->>><span>interface support for
+>>interface support for
equation-based modelling of
>>partial differential
equations.
@@ -49,18 +57,18 @@ equations.
>>On the clusters COMSOL is available in the latest stable
version. There are two variants of the release:
-- >>**Non commercial**><span> or so
+- >>**Non commercial** or so
called >>**EDU
variant**>>, which can be used for research
and educational purposes.
-- >>**Commercial**><span> or so called
- >>**COM variant**><span>,
+- >>**Commercial** or so called
+ >>**COM variant**,
which can used also for commercial activities.
- >>**COM variant**><span>
+ >>**COM variant**
has only subset of features compared to the
>>**EDU
- variant**>> available.
+ variant**>> available. <span
id="result_box"
More about
licensing will be posted here
@@ -73,7 +81,7 @@ version. There are two variants of the release:
$ module load COMSOL/51-EDU
```
->>By default the ><span>**EDU
+>>By default the **EDU
variant**>> will be loaded. If user needs other
version or variant, load the particular version. To obtain the list of
available versions use
@@ -86,7 +94,7 @@ $ module avail COMSOL
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 [Virtual Network Computing
-(VNC)](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+(VNC)](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
```
$ xhost +
@@ -121,7 +129,7 @@ module load COMSOL
ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn $ 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
+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
```
>>Working directory has to be created before sending the
@@ -130,25 +138,25 @@ 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).
-LiveLink™* *for MATLAB^®^
+LiveLink™* *for MATLAB®^
-------------------------
>>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>**®**</span></span></span></span></span>^
+COMSOL>><span><span><span><span><span>**®**</span></span></span></span></span>^
API (Application Programming Interface) with the benefits of the
programming language and computing environment of the MATLAB.
>>LiveLink for MATLAB is available in both
->>**EDU**><span> and
->>**COM**><span>
->>**variant**><span> of the
+>>**EDU** and
+>>**COM**
+>>**variant** of the
COMSOL release. On the clusters 1 commercial
-(>>**COM**><span>) license
+(>>**COM**) license
and the 5 educational
-(>>**EDU**><span>) licenses
+(>>**EDU**) licenses
of LiveLink for MATLAB (please see the [ISV
Licenses](../isv_licenses.html)) are available.
Following example shows how to start COMSOL model from MATLAB via
@@ -192,7 +200,7 @@ module load COMSOL/51-EDU
ntask=$(wc -l $PBS_NODEFILE)
-comsol -nn $ server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/work/user/$USER/work &
+comsol -nn ${ntask} server -configuration /tmp -mpiarg -rmk -mpiarg pbs -tmpdir /scratch/work/user/$USER/work &
cd /apps/cae/COMSOL/51/mli
matlab -nodesktop -nosplash -r "mphstart; addpath /scratch/work/user/$USER/work; test_job"
```
@@ -206,3 +214,6 @@ path to input file has to be specified. The Matlab command option (-r
port number.
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md b/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md
index 4cd91829119228c196ce5d8c9569f01d0e79d211..22be0cc0eb97c1277bb3c567eed3d00f82506c9a 100644
--- a/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md
+++ b/converted/docs.it4i.cz/salomon/software/comsol/licensing-and-available-versions.md
@@ -1,6 +1,14 @@
Licensing and Available Versions
================================
+
+
+
+
+
+
+
+
Comsol licence can be used by:
------------------------------
@@ -27,7 +35,7 @@ Comsol COM Network Licence
The licence intended to be used for science and research, publications,
students’ projects, commercial research with no commercial use
-restrictions. id="result_box"> E
+restrictions. id="result_box"> E<span
nables the solution
of at least one job
by one user in one
@@ -37,3 +45,7 @@ Available Versions
------------------
- ver. 51
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers.md b/converted/docs.it4i.cz/salomon/software/debuggers.md
index 49d0dfc938e6a792bf7c471e2ed321efba319742..b2430cc67c532d654f8248ca0e6e4c809d670904 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers.md
@@ -5,6 +5,14 @@ Debuggers and profilers summary
+
+
+
+
+
+
+
+
Introduction
------------
@@ -22,7 +30,7 @@ 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/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+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
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/aislinn.md b/converted/docs.it4i.cz/salomon/software/debuggers/aislinn.md
index 451b73a0f81b07483b9960f496e6b5b24d33bdd7..339c5ebb68760a4de2afb006397681e868e48e43 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/aislinn.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/aislinn.md
@@ -1,11 +1,19 @@
Aislinn
=======
+
+
+
+
+
+
+
+
- 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.
-- Aislinn detects problems like invalid memory es, deadlocks,
+- Aislinn detects problems like invalid memory accesses, deadlocks,
misuse of MPI, and resource leaks.
- Aislinn is open-source software; you can use it without any
licensing limitations.
@@ -17,6 +25,10 @@ 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>.
+
+
+
+
### Usage
Let us have the following program that contains a bug that is not
@@ -112,6 +124,10 @@ It shows us:
> - 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.
+
+
+
+
### Limitations
Since the verification is a non-trivial process there are some of
@@ -148,3 +164,7 @@ will be removed in the future:
reads inputs and writes results, it is ok.
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md b/converted/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md
index 4e1b2df7e873ca9553332a021af0ed7654fa5830..64b4024a3acc3592788d5eefb32afb1fc35381c3 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/allinea-ddt.md
@@ -5,6 +5,14 @@ Allinea Forge (DDT,MAP)
+
+
+
+
+
+
+
+
Allinea Forge consist of two tools - debugger DDT and profiler MAP.
Allinea DDT, is a commercial debugger primarily for debugging parallel
@@ -59,11 +67,11 @@ $ 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.**
@@ -72,15 +80,15 @@ Direct starting a Job with Forge
Be sure to log in with an [ X window
forwarding
-enabled](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+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:
$ ssh -X username@clustername.it4i.cz
-Other options is to login node using VNC. Please see the detailed
+Other options is to access login node using VNC. Please see the detailed
information on [how to
use graphic user interface on the
-clusters](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+clusters](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
.
From the login node an interactive session **with X windows forwarding**
@@ -106,7 +114,7 @@ Command line arguments to a program can be entered to the
box.
-
+
To start the debugging directly without the submission window, user can
specify the debugging and execution parameters from the command line.
@@ -154,7 +162,7 @@ It is recommended to set the following environment values on the offload
host:
export MYO_WATCHDOG_MONITOR=-1 # To make sure the host process isn't killed when we enter a debugging session
- export AMPLXE_COI_DEBUG_SUPPORT=true # To make sure that debugging symbols are ible on the host and the card
+ export AMPLXE_COI_DEBUG_SUPPORT=true # To make sure that debugging symbols are accessible on the host and the card
unset OFFLOAD_MAIN # To make sure allinea DDT can attach to offloaded codes
Then use one of the above mentioned methods to launch Forge. (Reverse
@@ -223,3 +231,5 @@ Debugging with Allinea DDT, Workshop conducted at LLNL by Allinea on May
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md b/converted/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md
index 390af2892bf7c650fe8fbae991ccfcbc9abd616f..e1fffc40c47586e349774e0bc170b80798d4c28e 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/allinea-performance-reports.md
@@ -1,11 +1,23 @@
Allinea Performance Reports
===========================
+
+
+
+
quick application profiling
+
+
+
+
+
+
+
+
Introduction
------------
@@ -75,3 +87,6 @@ and
were created. We can see that the code is very efficient on MPI and is
CPU bounded.
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md b/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
index 51dbe43813b0a583fd3396a45eacb0351eb0d5fe..6a82738a95f48a77296f6d54f7362ecf7a245db8 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/intel-vtune-amplifier.md
@@ -5,6 +5,14 @@ Intel VTune Amplifier XE
+
+
+
+
+
+
+
+
Introduction
------------
@@ -19,7 +27,11 @@ highlight of the features:
bandwidth
- Power usage analysis - frequency and sleep states.
-
+
+
+
+
+
@@ -139,3 +151,6 @@ References
3.>><https://software.intel.com/en-us/amplifier_help_linux> Linux
user guide
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/report.png b/converted/docs.it4i.cz/salomon/software/debuggers/report.png
new file mode 100644
index 0000000000000000000000000000000000000000..d7614f04f06b8fb8b93e83225ad97e4210ea2c14
Binary files /dev/null and b/converted/docs.it4i.cz/salomon/software/debuggers/report.png differ
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/summary.md b/converted/docs.it4i.cz/salomon/software/debuggers/summary.md
index d649fa53c4a2d17b8ecb4cb3b24d93be00d2ac01..b1fe967768984e6e3581e6ded7d622a8dd38bb58 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/summary.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/summary.md
@@ -5,6 +5,14 @@ Debuggers and profilers summary
+
+
+
+
+
+
+
+
Introduction
------------
@@ -22,7 +30,7 @@ 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/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+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
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/total-view.md b/converted/docs.it4i.cz/salomon/software/debuggers/total-view.md
index db26eae9977e5fb5f38441c1f43ca12f5b310f35..9159d2e968710131aa5a8cd87816b45034003c2d 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/total-view.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/total-view.md
@@ -1,8 +1,20 @@
Total View
==========
+
+
+
+
TotalView is a GUI-based source code multi-process, multi-thread
debugger.
+
+
+
+
+
+
+
+
License and Limitations for cluster Users
-----------------------------------------
@@ -42,11 +54,11 @@ 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
-----------------------------
@@ -56,7 +68,7 @@ using the -X in the ssh:
ssh -X username@salomon.it4i.cz
-Other options is to login node using VNC. Please see the detailed
+Other options is to access login node using VNC. Please see the detailed
information on how to use graphic user interface on Anselm
[here](https://docs.it4i.cz/salomon/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33#VNC).
@@ -83,8 +95,8 @@ Please note:** 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 **~/.tvdrc** file:
- proc mpi_auto_run_starter {
- set starter_programs
+ proc mpi_auto_run_starter {loaded_id} {
+ set starter_programs {mpirun mpiexec orterun}
set executable_name [TV::symbol get $loaded_id full_pathname]
set file_component [file tail $executable_name]
@@ -124,7 +136,7 @@ When following dialog appears click on "Yes"
At this point the main TotalView GUI window will appear and you can
insert the breakpoints and start debugging:
-
+
### Debugging a parallel code - option 2
@@ -154,3 +166,6 @@ 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/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.md b/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.md
index 27c51bce32b23ee1db384fe5ce5b83ceb96709ed..de33465df60600745f7e52efb88667105cf5ff12 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/valgrind.md
@@ -1,7 +1,19 @@
Valgrind
========
+
+
+
+
Valgrind is a tool for memory debugging and profiling.
+
+
+
+
+
+
+
+
About Valgrind
--------------
@@ -20,8 +32,8 @@ Valgrind run 5-100 times slower.
The main tools available in Valgrind are :
- **Memcheck**, the original, must used and default tool. Verifies
- memory in you program and can detect use of unitialized
- memory, out of bounds memory , memory leaks, double free, etc.
+ memory access in you program and can detect use of unitialized
+ memory, out of bounds memory access, memory leaks, double free, etc.
- **Massif**, a heap profiler.
- **Hellgrind** and **DRD** can detect race conditions in
multi-threaded applications.
@@ -121,7 +133,7 @@ description of command line options.
==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 at line 5 and a memory leak of 40 bytes. If we
+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 --leak-check=full option :
diff --git a/converted/docs.it4i.cz/salomon/software/debuggers/vampir.md b/converted/docs.it4i.cz/salomon/software/debuggers/vampir.md
index 4fb7ad88a4b64c6abdebc1014cb936c1f5f4aefd..a0b44fbd63f3c26bfe408cd0edd00d91d0723f26 100644
--- a/converted/docs.it4i.cz/salomon/software/debuggers/vampir.md
+++ b/converted/docs.it4i.cz/salomon/software/debuggers/vampir.md
@@ -1,13 +1,21 @@
Vampir
======
+
+
+
+
+
+
+
+
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 [Score-P](score-p.html)) first to collect the
traces.
-
+
----------------------------------------------------------------------------------------------------------------------------------------------
Installed versions
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
index 12a07b716878a7d98fb7be22c56e0a5e7415fd9f..a2c1b218c7a832b87d2196bfa4164c1828687896 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-advisor.md
@@ -1,6 +1,14 @@
Intel Advisor
=============
+
+
+
+
+
+
+
+
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
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md
index 6dd1fa07a77fee58fe0bc8fe768fa11681b53209..5d8661a9b41737b540e806c4e20eff1e95aabc44 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-compilers.md
@@ -5,6 +5,14 @@ Intel Compilers
+
+
+
+
+
+
+
+
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.
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md
index 82f38d171627b66ce9e765e29f2b3f0ca50bf7b5..b1663cee8bccbdbaac6be71cd0d7efa791b9f531 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-debugger.md
@@ -5,6 +5,14 @@ Intel Debugger
+
+
+
+
+
+
+
+
IDB is no longer available since Intel Parallel Studio 2015
Debugging serial applications
@@ -14,7 +22,7 @@ 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/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+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/2014.06
@@ -26,9 +34,9 @@ The debugger may run in text mode. To debug in text mode, use
$ idbc
To debug on the compute nodes, module intel must be loaded.
-The GUI on compute nodes may be ed using the same way as in [the
+The GUI on compute nodes may be accessed using the same way as in [the
GUI
-section](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+section](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
Example:
@@ -43,7 +51,7 @@ Example:
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 is via X11 port
+interactively on the myprog.x executable. The GUI access is via X11 port
forwarding provided by the PBS workload manager.
Debugging parallel applications
@@ -56,7 +64,7 @@ programs as well.
For debugging small number of MPI ranks, you may execute and debug each
rank in separate xterm terminal (do not forget the [X
-display](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)).
+display](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)).
Using Intel MPI, this may be done in following way:
$ qsub -q qexp -l select=2:ncpus=24 -X -I
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md
index dce7067681a702f079b72943dfdd01d21a3c78fa..17209fd2ef83b4f378ff11b3ef64b96dde87c8bd 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-inspector.md
@@ -1,6 +1,14 @@
Intel Inspector
===============
+
+
+
+
+
+
+
+
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
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md
index e0b1bf13ba4b0fa90837c56f4e401a3e095df99d..d62f7400cf61afd7059e8edc0fea41d255856056 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-integrated-performance-primitives.md
@@ -5,6 +5,14 @@ Intel IPP
+
+
+
+
+
+
+
+
Intel Integrated Performance Primitives
---------------------------------------
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
index 43cb59ba1248fd8d93ea9eac1a579ef3c4c3a7e0..23e0781b99450a6d735131a66cdb4d6a710c6851 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-mkl.md
@@ -6,6 +6,14 @@ Intel MKL
+
+
+
+
+
+
+
+
Intel Math Kernel Library
-------------------------
@@ -88,7 +96,7 @@ With intel compiler use -mkl option to link default threaded MKL.
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
-2^31^-1 elements), whereas the LP64 libraries index arrays with the
+231^-1 elements), whereas the LP64 libraries index arrays with the
32-bit integer type.
Interface Integer type
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md
index 498b7c9d1a6f1367f77a40f41a370385627631ad..3a8c44f5715987349b8232d87497ec71ee989d3c 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-parallel-studio-introduction.md
@@ -5,6 +5,14 @@ Intel Parallel Studio
+
+
+
+
+
+
+
+
The Salomon cluster provides following elements of the Intel Parallel
Studio XE
@@ -42,7 +50,7 @@ IDB is no longer available since Parallel Studio 2015.
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/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+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
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.md
index bdc4e31e726b15ae2d8bbf2df5edbbec45a21744..84d45ce7e1d952deef2361d15e3f250256c3ace5 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-tbb.md
@@ -5,6 +5,14 @@ Intel TBB
+
+
+
+
+
+
+
+
Intel Threading Building Blocks
-------------------------------
diff --git a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
index 9f6cb95bb5edfe46b0f59dc4bcc29aed28009421..61dc40e4f319196ca355901b0f93e785b58e588a 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
@@ -1,6 +1,14 @@
Intel Trace Analyzer and Collector
==================================
+
+
+
+
+
+
+
+
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,
@@ -32,7 +40,7 @@ Viewing traces
--------------
To view and analyze the trace, open ITAC GUI in a [graphical
-environment](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
+environment](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html)
:
$ module load itac/9.1.2.024
diff --git a/converted/docs.it4i.cz/salomon/software/intel-xeon-phi.md b/converted/docs.it4i.cz/salomon/software/intel-xeon-phi.md
index c5684fdb9ba0c257211c190d3b04b2fb08dcf003..25b9b052f280160c7b192fc6e97cb143155f7094 100644
--- a/converted/docs.it4i.cz/salomon/software/intel-xeon-phi.md
+++ b/converted/docs.it4i.cz/salomon/software/intel-xeon-phi.md
@@ -1,11 +1,23 @@
Intel Xeon Phi
==============
+
+
+
+
A guide to Intel Xeon Phi usage
+
+
+
+
+
+
+
+
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.
@@ -13,7 +25,7 @@ this document are supported.
Intel Utilities for Xeon Phi
----------------------------
-To get to a compute node with Intel Xeon Phi accelerator, use the
+To get access to a compute node with Intel Xeon Phi accelerator, use the
PBS interactive session
$ qsub -I -q qprod -l select=1:ncpus=24:accelerator=True:naccelerators=2:accelerator_model=phi7120 -A NONE-0-0
@@ -510,7 +522,7 @@ Phi:
### Execution of the Program in Native Mode on Intel Xeon Phi
-The user to the Intel Xeon Phi is through the SSH. Since user
+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.
@@ -799,7 +811,7 @@ 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 "**.profile**" file in user's home directory. This file
-sets up the environment on the MIC automatically once user to the
+sets up the environment on the MIC automatically once user access to the
accelerator through the SSH.
At first get the LD_LIBRARY_PATH for currenty used Intel Compiler and
@@ -828,7 +840,7 @@ libraries.
library and particular version of an Intel compiler. These versions have
to match with loaded modules.
-To a MIC accelerator located on a node that user is currently
+To access a MIC accelerator located on a node that user is currently
connected to, use:
$ ssh mic0
@@ -898,7 +910,7 @@ execute:
Execution on host - MPI processes distributed over multiple
accelerators on multiple nodes**
->To get to multiple nodes with MIC accelerator, user has to
+>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:
@@ -919,7 +931,7 @@ immediately. To see the other nodes that have been allocated use:
r38u32n1001.bullx
>This output means that the PBS allocated nodes r38u31n1000 and
-r38u32n1001, which means that user has direct to
+r38u32n1001, which means that user has direct access to
"**r38u31n1000-mic0**" and "**>r38u32n1001-mic0**"
accelerators.
@@ -1067,11 +1079,11 @@ 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:
Host only node-file:**
- - /lscratch/$/nodefile-cn
+ - /lscratch/${PBS_JOBID}/nodefile-cn
MIC only node-file**:
- - /lscratch/$/nodefile-mic
+ - /lscratch/${PBS_JOBID}/nodefile-mic
Host and MIC node-file**:
- - /lscratch/$/nodefile-mix
+ - /lscratch/${PBS_JOBID}/nodefile-mix
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"
@@ -1084,3 +1096,7 @@ For more details about optimization techniques please read Intel
document [Optimization and Performance Tuning for Intel® Xeon Phi™
Coprocessors](http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization "http://software.intel.com/en-us/articles/optimization-and-performance-tuning-for-intel-xeon-phi-coprocessors-part-1-optimization")
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/java.md b/converted/docs.it4i.cz/salomon/software/java.md
index 2701936ebc099c312e5594c243f241a4d80b5dac..2ec6c2c80060181e7a7c7a93e32f54a7779f5466 100644
--- a/converted/docs.it4i.cz/salomon/software/java.md
+++ b/converted/docs.it4i.cz/salomon/software/java.md
@@ -1,11 +1,23 @@
Java
====
+
+
+
+
Java on the cluster
+
+
+
+
+
+
+
+
Java is available on the cluster. Activate java by loading the Java
module
diff --git a/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md b/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
index 504db7f2b0415a3ba8ff8468c4232663c0004563..fd29a09a2f0292cc251f7a9b6302133831855952 100644
--- a/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
+++ b/converted/docs.it4i.cz/salomon/software/mpi-1/Running_OpenMPI.md
@@ -5,6 +5,14 @@ Running OpenMPI
+
+
+
+
+
+
+
+
OpenMPI program execution
-------------------------
diff --git a/converted/docs.it4i.cz/salomon/software/mpi-1/mpi.md b/converted/docs.it4i.cz/salomon/software/mpi-1/mpi.md
index 990d65d85d444d618bf87ef18a1a099437fb56f0..51395ae3821b16d36d4fca8fb0eb67e583250649 100644
--- a/converted/docs.it4i.cz/salomon/software/mpi-1/mpi.md
+++ b/converted/docs.it4i.cz/salomon/software/mpi-1/mpi.md
@@ -5,6 +5,14 @@ MPI
+
+
+
+
+
+
+
+
Setting up MPI Environment
--------------------------
@@ -141,7 +149,7 @@ scratch /lscratch filesystem.
### Ways to run MPI programs
Optimal way to run an MPI program depends on its memory requirements,
-memory pattern and communication pattern.
+memory access pattern and communication pattern.
Consider these ways to run an MPI program:
1. One MPI process per node, 24 threads per process
@@ -152,13 +160,13 @@ One MPI** 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 to the network interface.
+bandwidth access to the network interface.
Two MPI** 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 to the network interface. The 12
-threads and socket binding should ensure maximum memory bandwidth
+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.
Important! Bind every OpenMP thread to a core!
diff --git a/converted/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md b/converted/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md
index fddc6f7d275e4ce7d56828271d4442eae5b0eb4f..ce10aacccedc7cbb413ec2a6f7d9b90e5517c72f 100644
--- a/converted/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md
+++ b/converted/docs.it4i.cz/salomon/software/mpi-1/mpi4py-mpi-for-python.md
@@ -1,11 +1,23 @@
MPI4Py (MPI for Python)
=======================
+
+
+
+
OpenMPI interface to Python
+
+
+
+
+
+
+
+
Introduction
------------
diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/introduction.md b/converted/docs.it4i.cz/salomon/software/numerical-languages/introduction.md
index 5dba41d7cb27d6e096013c34ef931f1fb81cf666..a64bd025143cb0926017a963b2ccb8d2ef27abf4 100644
--- a/converted/docs.it4i.cz/salomon/software/numerical-languages/introduction.md
+++ b/converted/docs.it4i.cz/salomon/software/numerical-languages/introduction.md
@@ -1,11 +1,23 @@
Numerical languages
===================
+
+
+
+
Interpreted languages for numerical computations and analysis
+
+
+
+
+
+
+
+
Introduction
------------
@@ -15,7 +27,7 @@ primarily intended for numerical computations.
Matlab
------
-MATLAB^®^ is a high-level language and interactive environment for
+MATLAB®^ is a high-level language and interactive environment for
numerical computation, visualization, and programming.
$ module load MATLAB
diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/matlab.md b/converted/docs.it4i.cz/salomon/software/numerical-languages/matlab.md
index 282ebca40f4b34ba664d5b7dc27a09ec511065c4..5ac2f70fd2d0e1b898efbaa962a6f908ca464419 100644
--- a/converted/docs.it4i.cz/salomon/software/numerical-languages/matlab.md
+++ b/converted/docs.it4i.cz/salomon/software/numerical-languages/matlab.md
@@ -5,6 +5,14 @@ Matlab
+
+
+
+
+
+
+
+
Introduction
------------
@@ -36,12 +44,12 @@ Matlab on the compute nodes via PBS Pro scheduler.
If you require the Matlab GUI, please follow the general informations
about [running graphical
-applications](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+applications](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
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
-[here](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html))
+[here](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html))
is recommended.
To run Matlab with GUI, use
@@ -94,7 +102,7 @@ code on just a single node.
Following example shows how to start interactive session with support
for Matlab GUI. For more information about GUI based applications on
Anselm see [this
-page](../../../get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
+page](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-and-vnc.html).
$ xhost +
$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00
@@ -106,7 +114,7 @@ The second part of the command shows how to request all necessary
licenses. In this case 1 Matlab-EDU license and 48 Distributed Computing
Engines licenses.
-Once the to compute nodes is granted by PBS, user can load
+Once the access to compute nodes is granted by PBS, user can load
following modules and start Matlab:
r1i0n17$ module load MATLAB/2015a-EDU
diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.md b/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.md
index 22465fc8dc9b74d0fcfe394e5f5b72ad7b00716f..8f89df5dcf3aaae6095fe528ecc8b6dcf26bb7ee 100644
--- a/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.md
+++ b/converted/docs.it4i.cz/salomon/software/numerical-languages/octave.md
@@ -5,6 +5,14 @@ Octave
+
+
+
+
+
+
+
+
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
diff --git a/converted/docs.it4i.cz/salomon/software/numerical-languages/r.md b/converted/docs.it4i.cz/salomon/software/numerical-languages/r.md
index 58bf5bb8c24d5e3eea5a049993cf702f085c8fb6..2044e92d0e1d8309722105294b2908491c9590a8 100644
--- a/converted/docs.it4i.cz/salomon/software/numerical-languages/r.md
+++ b/converted/docs.it4i.cz/salomon/software/numerical-languages/r.md
@@ -5,6 +5,14 @@ R
+
+
+
+
+
+
+
+
Introduction
------------
@@ -34,12 +42,12 @@ Modules
-------
**The R version 3.1.1 is available on the cluster, along with GUI
-interface Rstudio**
+interface Rstudio
Application Version module
------------- -------------- ---------------------
R** R 3.1.1 R/3.1.1-intel-2015b
-Rstudio**** Rstudio 0.97 Rstudio
+Rstudio** Rstudio 0.97 Rstudio
$ module load R
@@ -55,10 +63,10 @@ OMP_NUM_THREADS environment variable.
### Interactive execution
-To run R interactively, using Rstudio** GUI, log in with ssh -X parameter
+To run R interactively, using Rstudio GUI, log in with ssh -X parameter
for X11 forwarding. Run rstudio:
- $ module load Rstudio**
+ $ module load Rstudio
$ rstudio
### Batch execution
@@ -397,7 +405,7 @@ The above is the mpi.apply MPI example for calculating the number π.
Only the slave processes carry out the calculation. Note the
mpi.parSapply(), ** function call. The package
parallel
-[example](r.html#package-parallel)[above](r.html#package-parallel)
+[example](r.html#package-parallel)[above](r.html#package-parallel){.anchor
may be trivially adapted (for much better performance) to this structure
using the mclapply() in place of mpi.parSapply().
@@ -452,6 +460,10 @@ and general [MPI](../mpi-1.html) sections.
+
+
+
+
Xeon Phi Offload
----------------
@@ -464,3 +476,11 @@ environment variable before R execution :
[Read more about automatic
offload](../intel-xeon-phi.html)
+
+
+
+
+
+
+
+
diff --git a/converted/docs.it4i.cz/salomon/software/operating-system.md b/converted/docs.it4i.cz/salomon/software/operating-system.md
index 12519fd4a000dbf83ef13e7293a62d25d7150cca..ea18335236578c0ea54622d7e976eff8f809bb17 100644
--- a/converted/docs.it4i.cz/salomon/software/operating-system.md
+++ b/converted/docs.it4i.cz/salomon/software/operating-system.md
@@ -1,11 +1,23 @@
Operating System
================
+
+
+
+
The operating system, deployed on Salomon cluster
+
+
+
+
+
+
+
+
The operating system on Salomon is Linux - CentOS 6.6.
>The CentOS Linux distribution is a stable, predictable, manageable
diff --git a/converted/docs.it4i.cz/salomon/storage/cesnet-data-storage.md b/converted/docs.it4i.cz/salomon/storage/cesnet-data-storage.md
index be82b6fac217d54c30a7ea235c88437d4229ac0c..1f006bd53f57a9140ca4703d951b37e697d0017e 100644
--- a/converted/docs.it4i.cz/salomon/storage/cesnet-data-storage.md
+++ b/converted/docs.it4i.cz/salomon/storage/cesnet-data-storage.md
@@ -5,6 +5,14 @@ CESNET Data Storage
+
+
+
+
+
+
+
+
Introduction
------------
@@ -23,7 +31,7 @@ Republic.
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 to
+a legal entity (organization) that meets the “Principles for access to
CESNET Large infrastructure (Access Policy)”.
User may only use data storage CESNET for data transfer and storage
@@ -37,12 +45,12 @@ The service is documented at
please contact directly CESNET Storage Department via e-mail
[du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
-The procedure to obtain the CESNET is quick and trouble-free.
+The procedure to obtain the CESNET access is quick and trouble-free.
(source
[https://du.cesnet.cz/](https://du.cesnet.cz/wiki/doku.php/en/start "CESNET Data Storage"))
-CESNET storage
+CESNET storage access
---------------------
### Understanding Cesnet storage
@@ -51,7 +59,7 @@ It is very important to understand the Cesnet storage before uploading
data. Please read
<https://du.cesnet.cz/en/navody/home-migrace-plzen/start> first.
-Once registered for CESNET Storage, you may [ the
+Once registered for CESNET Storage, you may [access the
storage](https://du.cesnet.cz/en/navody/faq/start) in
number of ways. We recommend the SSHFS and RSYNC methods.
@@ -59,7 +67,7 @@ number of ways. We recommend the SSHFS and RSYNC methods.
SSHFS: The storage will be mounted like a local hard drive
-The SSHFS provides a very convenient way to the CESNET Storage.
+The SSHFS 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.
@@ -74,7 +82,7 @@ Mount tier1_home **(only 5120M !)**:
$ sshfs username@ssh.du1.cesnet.cz:. cesnet/
-For easy future from Anselm, install your public key
+For easy future access from Anselm, install your public key
$ cp .ssh/id_rsa.pub cesnet/.ssh/authorized_keys
@@ -92,7 +100,7 @@ Once done, please remember to unmount the storage
$ fusermount -u cesnet
-### Rsync
+### Rsync access
Rsync provides delta transfer for best performance, can resume
interrupted transfers
@@ -127,3 +135,7 @@ 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/converted/docs.it4i.cz/salomon/storage/storage.md b/converted/docs.it4i.cz/salomon/storage/storage.md
index 8cd9de885abc4336dfad2443b677e95ede76fa8f..fd56abedb3d6c7834496e0a7d2907401390843b5 100644
--- a/converted/docs.it4i.cz/salomon/storage/storage.md
+++ b/converted/docs.it4i.cz/salomon/storage/storage.md
@@ -5,6 +5,14 @@ Storage
+
+
+
+
+
+
+
+
Introduction
------------
@@ -13,7 +21,7 @@ There are two main shared file systems on Salomon cluster, the [
HOME](storage.html#home)
and [
SCRATCH](storage.html#shared-filesystems).
-All login and compute nodes may same data on shared filesystems.
+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.
@@ -48,7 +56,7 @@ SCRATCH filesystem is partitioned to [WORK and TEMP
workspaces](storage.html#shared-workspaces). The HOME
filesystem is realized as a tiered NFS disk storage. The SCRATCH
filesystem is realized as a parallel Lustre filesystem. Both shared file
-systems are ible via the Infiniband network. Extended ACLs are
+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.
@@ -105,7 +113,7 @@ round-robin fashion to ensure load balancing.
When a client (a compute
node from your job) needs to create
-or a file, the client queries the metadata server (
+or access a file, the client queries the metadata server (
MDS) and the metadata target (
MDT) for the layout and location of the
[file's
@@ -144,7 +152,7 @@ significantly impact the I/O performance you experience.
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
- patterns.
+access patterns.
```
$ lfs getstripe dir|filename
@@ -185,7 +193,7 @@ 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 of
+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
@@ -197,10 +205,10 @@ 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.
-Using a large stripe size can improve performance when ing very
+Using a large stripe size can improve performance when accessing very
large files
-Large stripe size allows each client to have exclusive to its own
+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.
@@ -293,7 +301,7 @@ number of named user and named group entries.
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 .
+manner. Below, we create a directory and allow a specific user access.
```
[vop999@login1.salomon ~]$ umask 027
@@ -377,11 +385,11 @@ The WORK workspace resides on SCRATCH filesystem. Users may create
subdirectories and files in directories **/scratch/work/user/username**
and **/scratch/work/project/projectid. **The /scratch/work/user/username
is private to user, much like the home directory. The
-/scratch/work/project/projectid is ible to all users involved in
+/scratch/work/project/projectid is accessible to all users involved in
project projectid. >
The WORK workspace is intended to store users project data as well as
-for high performance to input and output files. All project data
+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.
@@ -417,7 +425,7 @@ Lustre
### TEMP
The TEMP workspace resides on SCRATCH filesystem. The TEMP workspace
-point is /scratch/temp. Users may freely create subdirectories
+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
@@ -428,14 +436,14 @@ insufficient for particular user, please contact
lifted upon request.
The TEMP workspace is intended for temporary scratch data generated
-during the calculation as well as for high performance to input
+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.
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.
-Files on the TEMP filesystem that are **not ed for more than 90
+Files on the TEMP filesystem that are **not accessed for more than 90
days** will be automatically **deleted**.
The TEMP workspace is hosted on SCRATCH filesystem. The SCRATCH is
@@ -471,16 +479,16 @@ RAM disk
Every computational node is equipped with filesystem realized in memory,
so called RAM disk.
-Use RAM disk in case you need really fast to your data of limited
+Use RAM disk in case you need really fast access to your data of limited
size during your calculation.
Be very careful, use of RAM disk filesystem is at the expense of
operational memory.
-The local RAM disk is mounted as /ramdisk and is ible to user
+The local RAM disk is mounted as /ramdisk and is accessible to user
at /ramdisk/$PBS_JOBID directory.
The local RAM disk filesystem is intended for temporary scratch data
-generated during the calculation as well as for high performance
+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
@@ -525,4 +533,12 @@ Mountpoint Usage
/ramdisk job temporary data, node local local 120GB 90 GB/s none Compute nodes purged after job ends
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+
+
+
+
+
+
+
+
diff --git a/html_md.sh b/html_md.sh
index cb24f7b7f1c05dfd05797b392893b50035130b41..b9ee31f4360ced36bd5c4159892d555e2bf709f3 100755
--- a/html_md.sh
+++ b/html_md.sh
@@ -2,117 +2,59 @@
### DOWNLOAD AND CONVERT DOCUMENTATION
# autor: kru0052
-# version: 0.36
-# change: repair images bugs and add new filtering html and css elements
+# version: 0.4
+# change: repair bugs and optimalizations
# bugs: bad formatting tables, bad links for other files, stayed a few html elements, formatting bugs...
###
if [ "$1" = "-t" ]; then
# testing new function
- echo "Testing 1..."
-
- rm -rf ./converted
-
- # exists file for move?
- if [ -f ./info/list_md.txt ];
- then
- mkdir converted;
- (while read i;
- do
- mkdir "./converted/$i";
- done) < ./source/list_folder.txt
-
- # move md files to new folders
- while read a b ; do
- cp "$a" "./converted/$b";
-
- done < <(paste ./info/list_md.txt ./source/list_md_mv.txt)
- # copy jpg and jpeg to new folders
-
- #cat "${i%.*}TMP.md" > "${i%.*}.md";
-
- while read a b ; do cp "$a" "./converted/$b"; done < <(paste ./info/list_image.txt ./source/list_image_mv.txt)
-
- cp ./docs.it4i.cz/salomon/salomon ./converted/docs.it4i.cz/salomon/salomon
- cp ./docs.it4i.cz/salomon/salomon-2 ./converted/docs.it4i.cz/salomon/salomon-2
- cp ./converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/fairshare_formula.png ./converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png
- cp ./converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job_sort_formula.png ./converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png
- cp ./converted/docs.it4i.cz/salomon/software/debuggers/vtune-amplifier.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vtune-amplifier.png
- cp ./converted/docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20160708v12.33.35.png
-
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization-job-workflow
- mv ./virtualization-job-workflow ./converted/docs.it4i.cz/anselm-cluster-documentation/software/
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig6.png
- mv ./fig6.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig6.png
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig5.png
- mv ./fig5.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig5.png
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig1.png
- mv ./fig1.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig1.png
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig2.png
- mv ./fig2.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig2.png
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig4.png
- mv ./fig4.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig4.png
- wget https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig3.png
- mv ./fig3.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/fig3.png
-
-
-
- else
- echo "list_md.txt not exists!!!!!"
- fi
-
-
-fi
-if [ "$1" = "-t1" ]; then
- # testing new function
-
- echo "Testing 1..."
-
-
- while read a ; do
-
- echo "$a";
-
- sed -e 's/``` /```/' "./converted/$a" | sed -e 's/ //' | sed -e 's/<span class="pln">//' | sed -e 's/<span//' | sed -e 's/class="pln">//' | sed -e 's/<\/span>//' | sed -e 's/^\*\*//' | sed -e 's/\^\[>\[1<span>\]<\/span>\]//' > "./converted/${a%.*}TMP.md";
-
- while read x ; do
- arg1=`echo "$x" | cut -d"&" -f1 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
- arg2=`echo $x | cut -d"&" -f2 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
- #echo "$arg1";
- #echo ">$arg2";
-
- sed -e 's/'"$arg1"'/'"$arg2"'/' "./converted/${a%.*}TMP.md" > "./converted/${a%TMP.*}.TEST.md";
- cat "./converted/${a%TMP.*}.TEST.md" > "./converted/${a%.*}TMP.md";
- done < ./source/replace.txt
- cat "./converted/${a%.*}TMP.md" > "./converted/${a%.*}.md";
- rm "./converted/${a%.*}TMP.md";
- rm "./converted/${a%TMP.*}.TEST.md";
- done <./source/list_md_mv.txt
-
-
fi
if [ "$1" = "-w" ]; then
# download html pages
wget -X pbspro-documentation,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,pdf,*zip,*rar,@@*,anselm-cluster-documentation/icon.jpg.1 --mirror --convert-links --adjust-extension --page-requisites --no-parent https://docs.it4i.cz;
- wget http://verif.cs.vsb.cz/aislinn/doc/report.png
- mv report.png ./converted/salomon/software/debuggers/
+ wget --directory-prefix=./docs.it4i.cz/ http://verif.cs.vsb.cz/aislinn/doc/report.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/virtualization/virtualization-job-workflow
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig1.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig2.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig3.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig4.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig5.png
+ wget --directory-prefix=./docs.it4i.cz/ https://docs.it4i.cz/anselm-cluster-documentation/software/omics-master-1/images/fig6.png
+
fi
if [ "$1" = "-c" ]; then
### convert html to md
# erasing the previous transfer
+
rm -rf converted;
rm -rf info;
+ # erasing duplicate files and unwanted files
+ (while read i;
+ do
+ if [ -f "$i" ];
+ then
+ echo "$(tput setaf 9)$i deleted";
+ rm "$i";
+ fi
+
+ done) < ./source/list_rm
+
+ counter=1
+ count=$(find . -name "*.html" -type f | wc -l)
+
find . -name "*.ht*" |
while read i;
do
# first filtering html
- echo "$i";
- printf "\t\tfiltering html files...\n";
+ echo "$(tput setaf 12)($counter/$count)$(tput setaf 11)$i";
+ counter=$((counter+1))
+ printf "$(tput setaf 15)\t\tfirst filtering html files...\n";
HEAD=$(grep -n -m1 '<h1' "$i" |cut -f1 -d: | tr --delete '\n')
END=$(grep -n -m1 '<!-- <div tal:content=' "$i" |cut -f1 -d: | tr --delete '\n')
@@ -126,49 +68,42 @@ if [ "$1" = "-c" ]; then
pandoc -f html -t markdown+pipe_tables-grid_tables "${i%.*}TMP.html" -o "${i%.*}.md";
rm "${i%.*}TMP.html";
- # create filter_auto (css, html, ...)
- grep -o -P '(?<={).*(?=})' "${i%.*}.md" | sort -u | sed '/{/d' | sed '/\$/d' >> filter_auto;
- sort -u filter_auto -o filter_auto;
-
- # exceptions filter_auto
- (while read y;
- do
- # search and delete according with filter_auto
- sed -e 's/'"$y"'//g' filter_auto > filter_autoTMP;
- cat filter_autoTMP > filter_auto;
- done) < ./source/exceptions_filter_auto
-
- # text filtering of html, css, ...
- printf "\t\tautomatic filter...\n"
- (while read y;
- do
- # search and delete according with filter_auto and erase unwanted elements
- 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" > "${i%.*}.md";
- done) < filter_auto
-
+ # second filtering html and css elements...
+ printf "\t\tsecond filtering html and css elements...\n"
+ sed -e 's/``` /```/' "${i%.*}.md" | sed -e 's/ //' | sed -e 's/<\/div>//g' | sed '/^<div/d' | sed -e 's/<\/span>//' | sed -e 's/^\*\*//' | sed -e 's/\\//g' | sed -e 's/^: //g' | sed -e 's/^Obsah//g' > "${i%.*}TMP.md";
+ while read x ; do
+ arg1=`echo "$x" | cut -d"&" -f1 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
+ arg2=`echo "$x" | cut -d"&" -f2 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
+
+ sed -e 's/'"$arg1"'/'"$arg2"'/' "${i%.*}TMP.md" > "${i%.*}TMP.TEST.md";
+ cat "${i%.*}TMP.TEST.md" > "${i%.*}TMP.md";
+ done < ./source/replace
+
+ # repair image...
+ printf "\t\trepair images...\n"
+ while read x ; do
+ arg1=`echo "$x" | cut -d"&" -f1 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
+ arg2=`echo "$x" | cut -d"&" -f2 | sed 's:[]\[\^\$\.\*\/\"]:\\\\&:g'`;
+
+ sed -e 's/'"$arg1"'/'"$arg2"'/' "${i%.*}TMP.md" > "${i%.*}.md";
+ cat "${i%.*}.md" > "${i%.*}TMP.md";
+ done < ./source/repairIMG
+
+ cat "${i%.*}TMP.md" > "${i%.*}.md";
+
# delete temporary files
- rm "${i%.*}TMP.md";
+ rm "${i%.*}TMP.md";
+ rm "${i%.*}TMP.TEST.md";
done
- # delete empty files, duplicate files and unwanted files
+ # delete empty files
find -type f -size -10c |
while read i;
do
rm "$i";
- echo "$i deleted";
+ echo "$(tput setaf 9)$i deleted";
done
- rm filter_autoTMP
- rm filter_auto
- (while read i;
- do
- if [ -f "$i" ];
- then
- rm "$i";
- fi
-
- done) < ./source/list_rm.txt
### create new folder and move converted files
# create folder info and view all files and folder
@@ -179,20 +114,29 @@ if [ "$1" = "-c" ]; then
find ./docs.it4i.cz -name "*.md" -type f> ./info/list_md.txt;
find ./docs.it4i.cz -type d | sort > ./info/list_folder.txt
- # exists file for move?
- if [ -f ./info/list_md.txt ];
- then
- mkdir converted;
- (while read i;
- do
- mkdir "./converted/$i";
- done) < ./source/list_folder.txt
-
- # move md files to new folders
- while read a b ; do cp "$a" "./converted/$b"; done < <(paste ./info/list_md.txt ./source/list_md_mv.txt)
- # copy jpg and jpeg to new folders
- while read a b ; do cp "$a" "./converted/$b"; done < <(paste ./info/list_image.txt ./source/list_image_mv.txt)
- else
- echo "list_md.txt not exists!!!!!"
- fi
+ rm -rf ./converted
+
+ mkdir converted;
+ (while read i;
+ do
+ mkdir "./converted/$i";
+ done) < ./source/list_folder
+
+ # move md files to new folders
+ while read a b ; do
+ cp "$a" "./converted/$b";
+ done < <(paste ./info/list_md.txt ./source/list_md_mv)
+
+ # copy jpg and jpeg to new folders
+ while read a b ; do
+ cp "$a" "./converted/$b";
+ done < <(paste ./info/list_image.txt ./source/list_image_mv.txt)
+ cp ./docs.it4i.cz/salomon/salomon ./converted/docs.it4i.cz/salomon/salomon
+ cp ./docs.it4i.cz/salomon/salomon-2 ./converted/docs.it4i.cz/salomon/salomon-2
+ cp ./converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/fairshare_formula.png ./converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/fairshare_formula.png
+ cp ./converted/docs.it4i.cz/salomon/resource-allocation-and-job-execution/job_sort_formula.png ./converted/docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution/job_sort_formula.png
+ cp ./converted/docs.it4i.cz/salomon/software/debuggers/vtune-amplifier.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/vtune-amplifier.png
+ cp ./converted/docs.it4i.cz/salomon/software/debuggers/Snmekobrazovky20160708v12.33.35.png ./converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers/Snmekobrazovky20160708v12.33.35.png
+ cp ./docs.it4i.cz/virtualization-job-workflow ./converted/docs.it4i.cz/anselm-cluster-documentation/software/
+
fi
diff --git a/source/exceptions_filter_auto b/source/exceptions_filter_auto
deleted file mode 100644
index bbdc8036273b547df41a4cdbafe17a177e47cd9d..0000000000000000000000000000000000000000
--- a/source/exceptions_filter_auto
+++ /dev/null
@@ -1,18 +0,0 @@
-00001..00111
-#10-after-you-end-your-visualization-session
-#1-connect-to-a-login-node
-#1-in-your-vnc-session-open-a-terminal-and-allocate-a-node-using-pbspro-qsub-command
-#2-in-your-vnc-session-open-another-terminal-keep-the-one-with-interactive-pbspro-job-open
-#2-run-your-own-instance-of-turbovnc-server
-#3-load-the-virtualgl-module
-#3-remember-which-display-number-your-vnc-server-runs-you-will-need-it-in-the-future-to-stop-the-server
-#4-remember-the-exact-login-node-where-your-vnc-server-runs
-#4-run-your-desired-opengl-accelerated-application-using-virtualgl-script-vglrun
-#5-after-you-end-your-work-with-the-opengl-application
-#5-remember-on-which-tcp-port-your-own-vnc-server-is-running
-#6-connect-to-the-login-node-where-your-vnc-server-runs-with-ssh-to-tunnel-your-vnc-session
-#7-if-you-don-t-have-turbo-vnc-installed-on-your-workstation
-#8-run-turbovnc-viewer-from-your-workstation
-#9-proceed-to-the-chapter-access-the-visualization-node
-PBS_ARRAY_INDEX
-IDX
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-./docs.it4i.cz/salomon/accessing-the-cluster/graphical-user-interface.md
-./docs.it4i.cz/salomon/software/comsol.md
-./docs.it4i.cz/salomon/software/mpi-1.md
-./docs.it4i.cz/salomon/software/intel-suite.md
-./docs.it4i.cz/salomon/software/numerical-languages.1.md
-./docs.it4i.cz/salomon/hardware-overview-1.1.md
-./docs.it4i.cz/salomon/compute-nodes.md
-./docs.it4i.cz/salomon/network-1.md
-./docs.it4i.cz/anselm-cluster-documentation/resource-allocation-and-job-execution.md
-./docs.it4i.cz/anselm-cluster-documentation/storage.md
-./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/x-window-and-vnc.md
-./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/storage-1.md
-./docs.it4i.cz/anselm-cluster-documentation/software/comsol.md
-./docs.it4i.cz/anselm-cluster-documentation/software/anselm-cluster-documentation/software/mpi-1/running-mpich2.md
-./docs.it4i.cz/anselm-cluster-documentation/software/virtualization.md
-./docs.it4i.cz/anselm-cluster-documentation/software/mpi-1.md
-./docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-products-mechanical-fluent-cfx-mapdl.md
-./docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.1.md
-./docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster.md
-./docs.it4i.cz/anselm-cluster-documentation/storage-1.md
-./docs.it4i.cz/salomon.md
-./docs.it4i.cz/anselm-cluster-documentation.md
-./docs.it4i.cz/anselm.md
-./docs.it4i.cz/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.1.md
-./docs.it4i.cz/robots.txt
-./docs.it4i.cz/anselm-cluster-documentation/icon.jpg
-./docs.it4i.cz/salomon/software/numerical-languages.md
-./docs.it4i.cz/anselm-cluster-documentation/software/numerical-languages.md
diff --git a/source/repairIMG b/source/repairIMG
new file mode 100644
index 0000000000000000000000000000000000000000..f3705ba1a6024404c17d5402a7c03e4ce1a41ced
--- /dev/null
+++ b/source/repairIMG
@@ -0,0 +1,108 @@
+&
+&
+
+2](../executionaccess2.jpg/@@images/bed3998c-4b82-4b40-83bd-c3528dde2425.jpeg "Execution access 2")&
+&
+&
+&
+&
+&
+&
+&
+&
+&
+&
+&
+**&&
+&
+&
+ &increases.](fig5.png.1 "fig5.png")
+out.](fig1.png "Fig 1")&out.](fig1.png "Fig 1")
+&
+operation.](images/fig3.png "fig3.png")&operation.](fig3.png "fig3.png")&
+where the position is ambiguous.](images/fig4.png)&where the position is ambiguous.](fig4.png)
+genomic coordinates.](images/fig6.png.1 "fig6.png")&genomic coordinates.](fig6.png.1 "fig6.png")
+ [](cygwin-and-x11-forwarding.html)&
+[](putty-tunnel.png)&
+&
+[****](TightVNC_login.png)&
+[](https://docs.it4i.cz/get-started-with-it4innovations/gnome_screen.jpg)&
+[](gdmdisablescreensaver.png)&
+[](../../../../salomon/gnome_screen.jpg.1)&
+[](gnome-terminal.png)&
+[](gnome-compute-nodes-over-vnc.png)&
+ [](PageantV.png)&
+ [](PuTTY_host_Salomon.png)&
+ [](PuTTY_keyV.png)&
+ [](PuTTY_save_Salomon.png)&
+ [](PuTTY_open_Salomon.png)&
+ [](PuttyKeygeneratorV.png)&
+ [](PuttyKeygenerator_001V.png)&
+ [](PuttyKeygenerator_002V.png)&
+ [](20150312_143443.png)&
+ [](PuttyKeygenerator_004V.png)&
+ [](PuttyKeygenerator_005V.png)&
+ [](PuttyKeygenerator_006V.png)&
+[](../vpn_web_login.png)&
+Install](https://docs.it4i.cz/salomon/vpn_web_login_2.png/@@images/be923364-0175-4099-a363-79229b88e252.png "VPN Install")](../vpn_web_login_2.png)&
+Install](https://docs.it4i.cz/salomon/vpn_web_install_2.png/@@images/c2baba93-824b-418d-b548-a73af8030320.png "VPN Install")](../vpn_web_install_2.png)[
+Install](https://docs.it4i.cz/salomon/copy_of_vpn_web_install_3.png/@@images/9c34e8ad-64b1-4e1d-af3a-13c7a18fbca4.png "VPN Install")](../copy_of_vpn_web_install_3.png)&
+Install](https://docs.it4i.cz/salomon/vpn_web_install_4.png/@@images/4cc26b3b-399d-413b-9a6c-82ec47899585.png "VPN Install")](../vpn_web_install_4.png)&
+Install](https://docs.it4i.cz/salomon/vpn_web_download.png/@@images/06a88cce-5f51-42d3-8f0a-f615a245beef.png "VPN Install")](../vpn_web_download.png)&
+Install](https://docs.it4i.cz/salomon/vpn_web_download_2.png/@@images/3358d2ce-fe4d-447b-9e6c-b82285f9796e.png "VPN Install")](../vpn_web_download_2.png)&
+&
+[](../vpn_contacting_https_cluster.png)&
+Cluster](https://docs.it4i.cz/salomon/vpn_contacting_https.png/@@images/ff365499-d07c-4baf-abb8-ce3e15559210.png "VPN Contacting Cluster")](../vpn_contacting_https.png)&
+[](../../anselm-cluster-documentation/anyconnecticon.jpg)&
+[](../../anselm-cluster-documentation/anyconnectcontextmenu.jpg)&
+[](../vpn_contacting.png)&
+login](https://docs.it4i.cz/salomon/vpn_login.png/@@images/5102f29d-93cf-4cfd-8f55-c99c18f196ea.png "VPN login")](../vpn_login.png)&
+Connection](https://docs.it4i.cz/salomon/vpn_successfull_connection.png/@@images/45537053-a47f-48b2-aacd-3b519d6770e6.png "VPN Succesfull Connection")](../vpn_successfull_connection.png)&
+[](../salomon-2)&&
+&
+[](salomon)&
+&
+&
+&
+[](7D_Enhanced_hypercube.png)&
+[](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20ICEX%20Mcell.pdf)&
+[](https://docs.it4i.cz/salomon/network-1/ib-single-plane-topology/IB%20single-plane%20topology%20-%20Accelerated%20nodes.pdf)&
+[](Fluent_Licence_1.jpg)&
+[](Fluent_Licence_2.jpg)&
+[](Fluent_Licence_3.jpg)&
+[](Fluent_Licence_4.jpg)&
+&
+&
+[{.image-inline width="451"&
+height="513"}](ddt1.png)&
+&
+[](vtune-amplifier)&
+[](totalview1.png)&
+[](totalview2.png)&
+&
+&
diff --git a/source/replace b/source/replace
new file mode 100644
index 0000000000000000000000000000000000000000..b1c30cd98ffc0c7744f9f945fb2e686d05c29209
--- /dev/null
+++ b/source/replace
@@ -0,0 +1,148 @@
+ []()&
+ **[]()&**
+- - &
+.[]()&.
+### []()[]()&###
+### []()&###
+### **&###
+style="text-align: left; float: none; ">&
+class="anchor-link">&
+class="Apple-converted-space">&
+class="discreet visualHighlight">&
+class="emphasis">&
+class="glossaryItem">&
+class="highlightedSearchTerm">&
+class="highlightedSearchTerm">SSH</span><span>&highlightedSearchTerm
+class="hps">&
+class="hps">&
+class="hps">More</span> <span class="hps">&
+class="hps trans-target-highlight">&
+class="internal-link">&
+class="internal-link"><span id="result_box" class="short_text"><span&
+class="monospace">&
+class="monospace">LAPACKE</span> module, which includes Intel's LAPACKE&LAPACKE modelu, which includes Intel's LAPACKE
+class="n">&
+### class="n">&###
+class="n">&
+class="pre">&
+class="pun">node_group_key&
+class="short_text"><span&
+class="smarterwiki-popup-bubble-body"><span&
+class="smarterwiki-popup-bubble-links-container"><span&
+class="smarterwiki-popup-bubble-links-row">[{.smarterwiki-popup-bubble-link-favicon}](http://maps.google.com/maps?q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB "Search Google Maps"){.smarterwiki-popup-bubble-link}[{.smarterwiki-popup-bubble-link-favicon}](http://www.google.com/search?q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB "Search Google"){.smarterwiki-popup-bubble-link}[](http://www.google.com/search?hl=com&btnI=I'm+Feeling+Lucky&q=HDF5%20icc%20serial%09pthread%09hdf5%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09%24HDF5_INC%20%24HDF5_CPP_LIB%09%24HDF5_INC%20%24HDF5_F90_LIB%0A%0AHDF5%20icc%20parallel%20MPI%0A%09pthread%2C%20IntelMPI%09hdf5-parallel%2F1.8.13%09%24HDF5_INC%20%24HDF5_SHLIB%09Not%20supported%09%24HDF5_INC%20%24HDF5_F90_LIB+wikipedia "Search Wikipedia"){.smarterwiki-popup-bubble-link}</span></span></span></span></span>&
+class="smarterwiki-popup-bubble-links"><span&
+class="smarterwiki-popup-bubble smarterwiki-popup-bubble-active smarterwiki-popup-bubble-flipped"><span&&
+class="smarterwiki-popup-bubble-tip"></span><span
+</div>&
+<div>&
+<div class="itemizedlist">&
+<div id="d4841e18">&
+<div id="d4841e21">&
+<div id="d4841e24">&
+<div id="d4841e27">&
+<div id="d4841e30">&
+<div id="d4841e34">&
+<div id="d4841e37">&
+{.external&
+### Gnome on Windows**&### Gnome on Windows
+### Notes **&### Notes
+</span>&
+<span&
+[<span class="anchor-link">&
+<span class="discreet">&
+<span class="discreet"></span>&
+<span class="glossaryItem">&
+<span class="hps">&
+<span class="hps alt-edited">&
+<span class="listitem">&
+<span class="n">&
+<span class="s1">&
+<span class="WYSIWYG_LINK">&
+<span dir="auto">&
+<span id="__caret">&
+<span id="__caret"><span id="__caret"></span></span>&
+(<span id="result_box">&
+<span id="result_box" class="short_text"><span class="hps">&
+<span id="result_box"><span class="hps">&
+</span></span>&
+</span> <span&
+<span><span>&
+</span> <span class="hps">&
+</span> <span class="hps">who have a valid</span> <span&
+<span><span class="monospace">&
+<span><span>Introduction&###Introduction
+</span></span><span><span>&
+</span></span></span></span><span><span>&
+</span></span><span><span><span><span>&
+.<span style="text-align: left; "> </span>&
+<span style="text-align: start; ">&
+{.state-missing-value
+ style="text-align: left; float: none; ">&
+ style="text-align: left; float: none; ">&
+ style="text-align: left; float: none; ">change it&change it to
+ style="text-align: left; float: none; ">Check Putty settings:&
+ style="text-align: left; float: none; ">Enable X11&Enable X11
+ style="text-align: left; float: none; "> &
+style="text-align: start; ">&
+style="text-align: start; float: none; ">&
+**Summary&**Summary**
+Tape Library T950B**&**Tape Library T950B**
+.text}.&
+.text}&
+ ****The R version 3.0.1 is available on Anselm, along with GUI interface&**The R version 3.0.1 is available on Anselm, along with GUI interface
+ssh-connection style="text-alignstart; "}&
+<div&
+</div>&
+{.anchor-link}&
+{.code-basic style="text-align: start; "}&
+{.code .highlight .white .shell}&
+{.docutils .literal}&
+{.email-link}&
+{.external-link}&
+{.fragment}&
+{.image-inline}&
+{.image-inline width="451" height="513"}&
+{.internal-link}&
+{.literal-block}&
+{.mw-redirect}&
+{#parent-fieldname-title}&
+{#parent-fieldname-title .documentFirstHeading}&
+{.prettyprint}&
+{.prettyprint .lang-cpp}&
+{.prettyprint .lang-sh}&
+{.prettyprint .lang-sh .prettyprinted}&
+{#putty---before-we-start-ssh-connection style="text-align: start; "}&
+{#resources-allocation-policy}&
+{#schematic-overview}&
+{.screen}&
+{#setup-and-start-your-own-turbovnc-server}&
+{style="text-align: left; "}&
+ssh-connection style="text-alignstart; "}&
+{#putty---before-we-start-&
+<span class="pln">&
+class="pln">&
+id="parent-fieldname-text-5739e5d4b93b40a6b3d987bd4047d4e0">&
+id="content-core">&
+id="viewlet-above-content-body">&
+id="viewlet-below-content-title">&
+^[>[1<span>]]&
+^&
+-link}&
+<span&
+Input:** FASTQ file.&Input: FASTQ file.
+Output:** FASTQ file plus an HTML file containing statistics on the&Output: FASTQ file plus an HTML file containing statistics on the
+*Figure 2.****** FASTQ file.***&*Figure 2.**FASTQ file.**
+Component:** Hpg-aligner.****&Component:** Hpg-aligner.**
+Input:** VCF&Input:** VCF**
+the corresponding QC and functional annotations.&the corresponding QC and functional annotations.**
+Core features:**&**Core features:**
+Regulatory:**&**Regulatory:**
+Functional annotation**&**Functional annotation**
+Variation**&**Variation**
+Systems biology**&**Systems biology**
+[VNC](../../../salomon/accessing-the-cluster/graphical-user-interface/vnc.html)**.&**[VNC](../../../salomon/accessing-the-cluster/graphical-user-interface/vnc.html)**.
+<!-- -->&
+ id="Key_management" class="mw-headline">&
+Workaround:**&**Workaround:**
+-g** : Generates extra debugging information usable by GDB. -g3&-g** : Generates extra debugging information usable by GDB. -g3**
+-O0** : Suppress all optimizations.&-O0** : Suppress all optimizations.**
diff --git a/source/replace.txt b/source/replace.txt
deleted file mode 100644
index 5eaf20e394371db52e3e95aa748214e4208add27..0000000000000000000000000000000000000000
--- a/source/replace.txt
+++ /dev/null
@@ -1,280 +0,0 @@
- []()&
- **[]()&**
-- - &
-.[]()&.
-### []()[]()&###
-### []()&###
-### **&###
-1. style="text-align: left; float: none; ">Locate and modify&1. Locate and modify
-2000](../uv-2000/@@images/04ce7514-8d27-4cdb-bf0f-45d875c75df0.jpeg "UV 2000")&
-2](../executionaccess2.jpg/@@images/bed3998c-4b82-4b40-83bd-c3528dde2425.jpeg "Execution access 2")&
-2); its mate is mapped to 37 on the reverse strand (32). Read r002 has&
-2. style="text-align: left; float: none; ">&2. Check Putty settings:
-[](7D_Enhanced_hypercube.png)&
-access&
-access](../executionaccess.jpg/@@images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpeg "Execution access")
-According to FLAG 163 (=1+2+32+128), the read mapped to position 7 is&
-&
-Analyzer](Snmekobrazovky20151204v15.35.12.png/@@images/fb3b3ac2-a88f-4e55-a25e-23f1da2200cb.png "Intel Trace Analyzer")&
-and comes to IT4I (represented by the blue dashed line). The data&
-Anselm](../../anselm-cluster-documentation/Authorization_chain.png "Authorization chain")&
-&
-&
-&
-are mandatory, the rest is optional but strongly recommended. Each line&
-class="anchor-link">&
-class="Apple-converted-space">&
-class="discreet visualHighlight">&
-class="emphasis">&
-class="glossaryItem">&
-class="highlightedSearchTerm">&
-class="highlightedSearchTerm">SSH</span><span>&highlightedSearchTerm
- class="hps">&
-class="hps">&
- class="hps">More</span> <span class="hps">&
-class="hps trans-target-highlight">&
-class="internal-link">&
- class="internal-link"><span id="result_box" class="short_text"><span&
-class="monospace">&
-class="monospace">LAPACKE</span> module, which includes Intel's LAPACKE&LAPACKE modelu, which includes Intel's LAPACKE
- class="n">&
-### class="n">&###
-class="n">&
- class="pre">&
-class="pun">node_group_key&
-class="short_text"><span&
-class="smarterwiki-popup-bubble-body"><span&
-class="smarterwiki-popup-bubble-links-container"><span&
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-class="smarterwiki-popup-bubble-links"><span&
-class="smarterwiki-popup-bubble smarterwiki-popup-bubble-active smarterwiki-popup-bubble-flipped"><span&&
-class="smarterwiki-popup-bubble-tip"></span><span
-Cluster](https://docs.it4i.cz/salomon/vpn_contacting_https_cluster.png/@@images/22b15d8c-5d5f-4c5c-8973-fbc4e9a32128.png "VPN Contacting Cluster")](../vpn_contacting_https_cluster.png)&
-Cluster](https://docs.it4i.cz/salomon/vpn_contacting_https.png/@@images/ff365499-d07c-4baf-abb8-ce3e15559210.png "VPN Contacting Cluster")](../vpn_contacting_https.png)&
-Cluster](https://docs.it4i.cz/salomon/vpn_contacting.png/@@images/9ccabccf-581a-476a-8c24-ce9842c3e657.png "VPN Contacting Cluster")](../vpn_contacting.png)&&
-column and referenced from the genotype fields as 1-based indexes to&
-component where they can be analysed directly by the user that produced&
-connection](https://docs.it4i.cz/anselm-cluster-documentation/anyconnecticon.jpg/@@images/ebdd0e41-e839-497e-ab33-45162d00b03b.jpeg "Successfull connection")](../../anselm-cluster-documentation/anyconnecticon.jpg)&
-Connection](https://docs.it4i.cz/salomon/vpn_successfull_connection.png/@@images/45537053-a47f-48b2-aacd-3b519d6770e6.png "VPN Succesfull Connection")](../vpn_successfull_connection.png)&&
-Connect](Snmekobrazovky20160211v14.27.45.png/@@images/3550e4ae-2eab-4571-8387-11a112dd6ca8.png "Allinea Reverse Connect")&
-contains a P (padding) operation which correctly aligns the inserted&
-.contenttype-file}&
-[](cygwin-and-x11-forwarding.html)&
-data, the separator indicates whether the data are phased (|) or&
-[{.image-inline width="451"&
-[&
-[&
-file](../instalationfile.jpg/@@images/202d14e9-e2e1-450b-a584-e78c018d6b6a.jpeg "Installation file")&
-filters available. The tool includes a genomic viewer (Genome Maps 30)&
-&
-[](Fluent_Licence_1.jpg)&
-[](Fluent_Licence_2.jpg)&
-[](Fluent_Licence_3.jpg)&
-[](Fluent_Licence_4.jpg)&
-for each sequenced patient. These lists files together with primary and&
- forwarding style="text-align: left; float: none; ">&
-genomic coordinates.](images/fig6.png.1 "fig6.png")&
-genomic position or region. All alternate alleles are listed in the ALT&
-[](gnome-compute-nodes-over-vnc.png)&
-### Gnome on Windows**&### Gnome on Windows
-[](gnome-terminal.png)&
-height="513"}](ddt1.png)&
-[****](TightVNC_login.png)&
- [](PuTTY_host_Salomon.png)&
- [](PuTTY_open_Salomon.png)&
- [](PuTTY_save_Salomon.png)&
-[](totalview1.png)&
-&
-&
- id="Key_management" class="mw-headline">Key management&
-increases.](images/fig5.png.1 "fig5.png")&
-insertion; the third a SNP; the fourth a large structural variant&
-instalation](../successfullinstalation.jpg/@@images/c6d69ffe-da75-4cb6-972a-0cf4c686b6e1.jpeg "Successfull instalation")&
-](../copy_of_vpn_web_install_3.png)&
-Install](https://docs.it4i.cz/salomon/vpn_web_download_2.png/@@images/3358d2ce-fe4d-447b-9e6c-b82285f9796e.png "VPN Install")](../vpn_web_download_2.png)&
-Install](https://docs.it4i.cz/salomon/vpn_web_download.png/@@images/06a88cce-5f51-42d3-8f0a-f615a245beef.png "VPN Install")](../vpn_web_download.png)&
-Install](https://docs.it4i.cz/salomon/vpn_web_install_2.png/@@images/c2baba93-824b-418d-b548-a73af8030320.png "VPN Install")](../vpn_web_install_2.png)[
-Install](https://docs.it4i.cz/salomon/vpn_web_install_4.png/@@images/4cc26b3b-399d-413b-9a6c-82ec47899585.png "VPN Install")](../vpn_web_install_4.png)&
-Install](https://docs.it4i.cz/salomon/vpn_web_login_2.png/@@images/be923364-0175-4099-a363-79229b88e252.png "VPN Install")](../vpn_web_login_2.png)&
-Install](https://docs.it4i.cz/salomon/vpn_web_login.png/@@images/5eac6b9c-22e4-4abe-ab38-e4ccbe87b710.png "VPN Install")](../vpn_web_login.png)&
-&
-login](https://docs.it4i.cz/salomon/vpn_login.png/@@images/5102f29d-93cf-4cfd-8f55-c99c18f196ea.png "VPN login")](../vpn_login.png)&&
-&
-login](../successfullconnection.jpg "successful login")&
-](../../anselm-cluster-documentation/anyconnectcontextmenu.jpg)&&
-mismatches. Read r004 is aligned across an intron, indicated by the N&
-### Notes **&### Notes
-of reference sequences. Notably, r001 is the name of a read pair.&
-of the base before the variant. (b–f ) Alignments and VCF&
-of the body describes variants present in the sampled population at one&
-&
-out.](images/fig1.png "Fig 1")&
-[Pageant (for Windows&
- [](PageantV.png)&
-&
-position of the first aligned base. The CIGAR string for this alignment&
-Preferences](gdmscreensaver.png/@@images/44048cfa-e854-4cb4-902b-c173821c2db1.png "Screensaver Preferences")](../../../../salomon/gnome_screen.jpg.1)&
-pre-processor converts raw data into a list of variants and annotations&
-present in the sequence field. The NM tag gives the number of&
-profile](../loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpeg "Login with profile")&
-PuTTY - class="Apple-converted-space"> before we start SSH connection ssh-connection style="text-align: start; "}&
-[](PuttyKeygenerator_001V.png)&
- [](PuttyKeygenerator_002V.png)&
- [](20150312_143443.png)&
- [](PuttyKeygenerator_004V.png)&
- [](PuttyKeygenerator_005V.png)&
- [](PuttyKeygenerator_006V.png)&
- [](PuttyKeygeneratorV.png)&
- [](PuTTY_keyV.png)&
-reference bases replaced by the haplotype in the ALT column. The&
-&
-&
-&
-&
-&
-&
-representations of different sequence variants: SNP, insertion,&
-resources on&
-&
-Rstudio&Rstudio**
-&
-[](../salomon-2)&
-[](salomon)&
-[](salomon)&
-&
-&
-&![]](salomon-3.jpeg)
-&
-](gdmdisablescreensaver.png)&
-[](vtune-amplifier)&
-Screenshot](Snmekobrazovky20141204v12.56.36.png "CUBE Screenshot")&
-&
-secondary (alignment) data files are stored in IT4I sequence DB and&
-sequences. Padding operations can be absent when an aligner does not&
-session](../../../../salomon/gnome_screen.jpg/@@images/7758b792-24eb-48dc-bf72-618cda100fda.png "Default Gnome session")](https://docs.it4i.cz/get-started-with-it4innovations/gnome_screen.jpg)&
-shows an example of a deletion (present in SAMPLE1) and a replacement of&
-</span>&
-<span&
- <span&
- [<span class="anchor-link">&
-<span class="discreet">&
-<span class="discreet"></span>&
-<span class="glossaryItem">&
- <span class="glossaryItem">&
-<span class="hps">&
-<span class="hps alt-edited">&
-<span class="listitem">&
-<span class="n">&
-<span class="s1">&
- <span class="WYSIWYG_LINK">&
-<span dir="auto">&
-<span id="__caret">&
-<span id="__caret"><span id="__caret"></span></span>&
-(<span id="result_box">&
-<span id="result_box" class="short_text"><span class="hps">&
- <span id="result_box"><span class="hps">&
-</span></span>&
-</span> <span&
-<span><span>&
-</span> <span class="hps">&
- </span> <span class="hps">&
-</span> <span class="hps">who have a valid</span> <span&
-<span><span class="monospace">&
-<span><span>Introduction&###Introduction
-</span></span><span><span>&
-</span></span></span></span><span><span>&
-</span></span><span><span><span><span>&
-.<span style="text-align: left; "> </span>&
-<span style="text-align: start; ">&
-{.state-missing-value
- style="text-align: left; float: none; ">&
- style="text-align: left; float: none; ">&
- style="text-align: left; float: none; ">change it&change it to
- style="text-align: left; float: none; ">Check Putty settings:&
- style="text-align: left; float: none; ">Enable X11&Enable X11
- style="text-align: left; float: none; "> &
-style="text-align: start; ">&
-style="text-align: start; float: none; ">&
-&
-**Summary&**Summary**
-support multiple sequence alignment. The last six bases of read r003 map&
-Tape Library T950B**&**Tape Library T950B**
-.text}.&
-.text}&
-that enables the representation of the variants in the corresponding&
-]&![]
-to position 9, and the first five to position 29 on the reverse strand.&
- to</span>&
-[](totalview2.png)&
-tunnel](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 "PuTTY Tunnel")](putty-tunnel.png)&
-two bases by another base (SAMPLE2); the second line shows a SNP and an&
-unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in&
-uploaded to the discovery (candidate priorization) or diagnostic&
-users)](putty/PageantV.png)&
-use simplest representation possible and lowest coordinate in cases&
-&
-&
-vncviewer](../../../../anselm-cluster-documentation/vncviewer.png/@@images/bb4cedff-4cb6-402b-ac79-039186fe5df3.png "Vncviewer")&
-[&
-Workflow](virtualization-job-workflow "Virtualization Job Workflow")&
- &
-[]() &
- &
- [**](TightVNC_login.png)&
-[](gnome-terminal.png)&
-[](gnome-compute-nodes-over-vnc.png)&
-screensaver](https://docs.it4i.cz/get-started-with-it4innovations/ing-the-clusters/graphical-user-interface/vnc/gdmdisablescreensaver.png/@@images/8a4758d9-3027-4ce4-9a90-2d5e88197451.png "Disable lock screen and screensaver")](gdmdisablescreensaver.png)&