version 0.36

converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/outgoing-connections.md

@@ -44,7 +44,7 @@ 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 accessing
+Anselm and  port 1234 on the remote.host.com. By ing
 localhost:6000 on Anselm, an application will see response of
 remote.host.com:1234. The traffic will run via users local workstation.
 
@@ -55,7 +55,7 @@ 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 access to remote.host.com
+this requires that user has ssh  to remote.host.com
 
 ```
 $ ssh -L 6000:localhost:1234 remote.host.com
@@ -66,7 +66,7 @@ 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 access hosts outside Anselm Cluster.
+the compute nodes to  hosts outside Anselm Cluster.
 
 First, establish the remote port forwarding form the login node, as
 [described
@@ -80,7 +80,7 @@ $ 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 accessing
+remote.host.com:1234 has been established beforehand. By ing
 localhost:6000, an application running on a compute node will see
 response of remote.host.com:1234
 
@@ -90,7 +90,7 @@ 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 access to
+Applications with inbuilt proxy support, experience unlimited  to
 remote hosts, via single proxy server.
 
 To establish local proxy server on your workstation, install and run
@@ -114,6 +114,6 @@ local $ ssh -R 6000:localhost:1080 anselm.it4i.cz
 ```
 
 Now, configure the applications proxy settings to **localhost:6000**.
-Use port forwarding  to access the [proxy server from compute
+Use port forwarding  to  the [proxy server from compute
 nodes](outgoing-connections.html#port-forwarding-from-compute-nodes)
 as well .

converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/shell-and-data-access/shell-and-data-access.md

-Shell access and data transfer 
+Shell  and data transfer 
 ==============================
 
 
@@ -8,7 +8,7 @@ Shell access and data transfer
 Interactive Login
 -----------------
 
-The Anselm cluster is accessed by SSH protocol via login nodes login1
+The Anselm cluster is ed 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 +19,7 @@ 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/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](../../../get-started-with-it4innovations/ing-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 +44,7 @@ local $ chmod 600 /path/to/id_rsa
 ```
 
 On **Windows**, use [PuTTY ssh
-client](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
+client](../../../get-started-with-it4innovations/ing-the-clusters/shell-access-and-data-transfer/putty/putty.html).
 
 After logging in, you will see the command prompt:
 
@@ -79,10 +79,10 @@ 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   <span class="discreet">scp, sftp</span>
+ class="discreet">dm1.anselm.it4i.cz    class="discreet">22    class="discreet">scp, sftp</span>
 
  The authentication is by the [private
-key](../../../get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.html)
+key](../../../get-started-with-it4innovations/ing-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.

converted/docs.it4i.cz/anselm-cluster-documentation/accessing-the-cluster/vpn-access.md

@@ -35,37 +35,37 @@ It is impossible to connect to VPN from other operating systems.
 You can install VPN client from web interface after successful login
 with LDAP credentials on address <https://vpn1.it4i.cz/anselm>
 
-![](../login.jpg/@@images/30271119-b392-4db9-a212-309fb41925d6.jpeg)
+![](login.jpeg)
 
 According to the Java settings after login, the client either
 automatically installs, or downloads installation file for your
 operating system. It is necessary to allow start of installation tool
 for automatic installation.
 
-![Java
-detection](../java_detection.jpg/@@images/5498e1ba-2242-4b9c-a799-0377a73f779e.jpeg "Java detection")
 
-![Execution
-access](../executionaccess.jpg/@@images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpeg "Execution access")![Execution
-access
-2](../executionaccess2.jpg/@@images/bed3998c-4b82-4b40-83bd-c3528dde2425.jpeg "Execution access 2")
+![](java_detection.jpeg)
+
+
+](../executionaccess.jpg/@@images/4d6e7cb7-9aa7-419c-9583-6dfd92b2c015.jpeg "Execution access")
+
+![](execution2.jpeg)
 
 After successful installation, VPN connection will be established and
 you can use available resources from IT4I network.
 
-![Successfull
-instalation](../successfullinstalation.jpg/@@images/c6d69ffe-da75-4cb6-972a-0cf4c686b6e1.jpeg "Successfull instalation")
+
+![](successfullinstalation.jpeg)
 
 If your Java setting doesn't allow automatic installation, you can
 download installation file and install VPN client manually.
 
-![Installation
-file](../instalationfile.jpg/@@images/202d14e9-e2e1-450b-a584-e78c018d6b6a.jpeg "Installation file")
+
+![](instalationfile.jpeg)
 
 After you click on the link, download of installation file will start.
 
-![Download file
-successfull](../downloadfilesuccessfull.jpg/@@images/69842481-634a-484e-90cd-d65e0ddca1e8.jpeg "Download file successfull")
+
+![](downloadfilesuccessfull.jpeg)
 
 After successful download of installation file, you have to execute this
 tool with administrator's rights and install VPN client manually.
@@ -76,22 +76,22 @@ Working with VPN client
 You can use graphical user interface or command line interface to run
 VPN client on all supported operating systems. We suggest using GUI.
 
-![Icon](../icon.jpg "Icon")
+
 
 Before the first login to VPN, you have to fill
 URL **https://vpn1.it4i.cz/anselm** into the text field.
 
-![First run](../firstrun.jpg "First run")
+![](firstrun.jpg)
 
 After you click on the Connect button, you must fill your login
 credentials.
 
-![Login - GUI](../logingui.jpg "Login - GUI")
+![](logingui.jpg)
 
 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.
 
-![Successfull
+
 connection](../anyconnecticon.jpg "Successfull connection")
 
 If you right-click on this icon, you will see a context menu in which
@@ -105,18 +105,18 @@ profile and creates a new item "ANSELM" in the connection list. For
 subsequent connections, it is not necessary to re-enter the URL address,
 but just select the corresponding item.
 
-![Anselm profile](../Anselmprofile.jpg "Anselm profile")
+![](Anselmprofile.jpg)
 
 Then AnyConnect automatically proceeds like in the case of first logon.
 
-![Login with
-profile](../loginwithprofile.jpg/@@images/a6fd5f3f-bce4-45c9-85e1-8d93c6395eee.jpeg "Login with profile")
+
+![](loginwithprofile.jpeg)
 
 After a successful logon, you can see a green circle with a tick mark on
 the lock icon.
 
-![successful
-login](../successfullconnection.jpg "successful login")
+
+![](successfullconnection.jpg)
 
 For disconnecting, right-click on the AnyConnect client icon in the
 system tray and select **VPN Disconnect**.

converted/docs.it4i.cz/anselm-cluster-documentation/compute-nodes.md

@@ -15,38 +15,38 @@ nodes.****
 ###Compute Nodes Without Accelerator**
 
 
-- <div class="itemizedlist">
+- 
 
   180 nodes
 
   
 
-- <div class="itemizedlist">
+- 
 
   2880 cores in total
 
   
 
-- <div class="itemizedlist">
+- 
 
   two Intel Sandy Bridge E5-2665, 8-core, 2.4GHz processors per node
 
   
 
-- <div class="itemizedlist">
+- 
 
   64 GB of physical memory per node
 
   
 
 - one 500GB SATA 2,5” 7,2 krpm HDD per node
-- <div class="itemizedlist">
+- 
 
   bullx B510 blade servers
 
   
 
-- <div class="itemizedlist">
+- 
 
   cn[1-180]
 
@@ -54,44 +54,44 @@ nodes.****
 
 ###Compute Nodes With GPU Accelerator**
 
-- <div class="itemizedlist">
+- 
 
   23 nodes
 
   
 
-- <div class="itemizedlist">
+- 
 
   368 cores in total
 
   
 
-- <div class="itemizedlist">
+- 
 
   two Intel Sandy Bridge E5-2470, 8-core, 2.3GHz processors per node
 
   
 
-- <div class="itemizedlist">
+- 
 
   96 GB of physical memory per node
 
   
 
 - one 500GB SATA 2,5” 7,2 krpm HDD per node
-- <div class="itemizedlist">
+- 
 
   GPU accelerator 1x NVIDIA Tesla Kepler K20 per node
 
   
 
-- <div class="itemizedlist">
+- 
 
   bullx B515 blade servers
 
   
 
-- <div class="itemizedlist">
+- 
 
   cn[181-203]
 
@@ -99,44 +99,44 @@ nodes.****
 
 ###Compute Nodes With MIC Accelerator**
 
-- <div class="itemizedlist">
+- 
 
   4 nodes
 
   
 
-- <div class="itemizedlist">
+- 
 
   64 cores in total
 
   
 
-- <div class="itemizedlist">
+- 
 
   two Intel Sandy Bridge E5-2470, 8-core, 2.3GHz processors per node
 
   
 
-- <div class="itemizedlist">
+- 
 
   96 GB of physical memory per node
 
   
 
 - one 500GB SATA 2,5” 7,2 krpm HDD per node
-- <div class="itemizedlist">
+- 
 
   MIC accelerator 1x Intel Phi 5110P per node
 
   
 
-- <div class="itemizedlist">
+- 
 
   bullx B515 blade servers
 
   
 
-- <div class="itemizedlist">
+- 
 
   cn[204-207]
 
@@ -144,44 +144,44 @@ nodes.****
 
 ###Fat Compute Nodes**
 
-- <div>
+- 
 
   2 nodes
 
   
 
-- <div>
+- 
 
   32 cores in total
 
   
 
-- <div>
+- 
 
   2 Intel Sandy Bridge E5-2665, 8-core, 2.4GHz processors per node
 
   
 
-- <div>
+- 
 
   512 GB of physical memory per node
 
   
 
 - two 300GB SAS 3,5”15krpm HDD (RAID1) per node
-- <div>
+- 
 
   two 100GB SLC SSD per node
 
   
 
-- <div>
+- 
 
   bullx R423-E3 servers
 
   
 
-- <div>
+- 
 
   cn[208-209]
 
@@ -220,10 +220,10 @@ with accelerator). Processors support Advanced Vector Extensions (AVX)
 ### Intel Sandy Bridge E5-2665 Processor
 - eight-core
 - speed: 2.4 GHz, up to 3.1 GHz using Turbo Boost Technology
-- peak performance:  class="emphasis">19.2 Gflop/s per
+- peak performance:  19.2 Gflop/s per
   core
 - caches:
-  <div class="itemizedlist">
+  
 
   -   L2: 256 KB per core
   -   L3: 20 MB per processor
@@ -235,10 +235,10 @@ with accelerator). Processors support Advanced Vector Extensions (AVX)
 ### Intel Sandy Bridge E5-2470 Processor
 - eight-core
 - speed: 2.3 GHz, up to 3.1 GHz using Turbo Boost Technology
-- peak performance:  class="emphasis">18.4 Gflop/s per
+- peak performance:  18.4 Gflop/s per
   core
 - caches:
-  <div class="itemizedlist">
+  
 
   -   L2: 256 KB per core
   -   L3: 20 MB per processor
@@ -277,7 +277,7 @@ Memory Architecture
 ### Compute Node Without Accelerator
 - 2 sockets
 - Memory Controllers are integrated into processors.
-  <div class="itemizedlist">
+  
 
   -   8 DDR3 DIMMS per node
   -   4 DDR3 DIMMS per CPU
@@ -291,7 +291,7 @@ Memory Architecture
 ### Compute Node With GPU or MIC Accelerator
 - 2 sockets
 - Memory Controllers are integrated into processors.
-  <div class="itemizedlist">
+  
 
   -   6 DDR3 DIMMS per node
   -   3 DDR3 DIMMS per CPU
@@ -305,7 +305,7 @@ Memory Architecture
 ### Fat Compute Node
 - 2 sockets
 - Memory Controllers are integrated into processors.
-  <div class="itemizedlist">
+  
 
   -   16 DDR3 DIMMS per node
   -   8 DDR3 DIMMS per CPU

converted/docs.it4i.cz/anselm-cluster-documentation/environment-and-modules.md

@@ -35,7 +35,7 @@ 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">in the previous example.
+in the previous example.
 
 ### Application Modules
 

converted/docs.it4i.cz/anselm-cluster-documentation/hardware-overview.md

@@ -10,7 +10,7 @@ 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 access to the Anselm
+at least 64GB RAM, and local hard drive. The user  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 +19,7 @@ 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
-access 45 TB of dedicated block storage. Accelerated nodes, fat nodes,
+ 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 +348,9 @@ disk storage available on all compute nodes /lscratch.  [More about
 
 class="WYSIWYG_LINK">Storage](storage.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 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 parameters are summarized in the following tables:
 

converted/docs.it4i.cz/anselm-cluster-documentation/introduction.md

@@ -23,7 +23,7 @@ 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 accessible via the
+different scientific domains. These packages are ible via the
 [modules environment](environment-and-modules.html).
 
 User data shared file-system (HOME, 320TB) and job data shared
@@ -37,4 +37,4 @@ 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 [access the cluster](accessing-the-cluster.html).
+and [ the cluster](accessing-the-cluster.html).

converted/docs.it4i.cz/anselm-cluster-documentation/network.md

@@ -20,7 +20,7 @@ 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 accessed via the Infiniband network using ib0
+The compute nodes may be ed 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 +34,7 @@ other nodes concurrently.
 Ethernet Network
 ----------------
 
-The compute nodes may be accessed via the regular Gigabit Ethernet
+The compute nodes may be ed 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 +55,5 @@ $ ssh 10.2.1.110
 $ ssh 10.1.1.108
 ```
 
-In this example, we access the node cn110 by Infiniband network via the
+In this example, we  the node cn110 by Infiniband network via the
 ib0 interface, then from cn110 to cn108 by Ethernet network.