Merge branch 'content_revision5' into 'master'

Content revision5

See merge request !61

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

@@ -17,7 +17,7 @@ fi
 alias qs='qstat -a'
 module load PrgEnv-gnu
 
-# Display informations to standard output - only in interactive ssh session
+# Display information to standard output - only in interactive ssh session
 if [ -n "$SSH_TTY" ]
 then
  module list # Display loaded modules

docs.it4i/anselm-cluster-documentation/shell-and-data-access.md

@@ -207,4 +207,4 @@ Graphical User Interface
 VPN Access
 ----------
 
--   Access to IT4Innovations internal resources via [VPN](../get-started-with-it4innovations/vpn-access/).
+-   Access to IT4Innovations internal resources via [VPN](../get-started-with-it4innovations/accessing-the-clusters/vpn-access/).

docs.it4i/anselm-cluster-documentation/software/compilers.md

@@ -40,7 +40,7 @@ With the module loaded two environment variables are predefined. One for maximum
     -O0 -g
 ```
 
-For more informations about the possibilities of the compilers, please see the man pages.
+For more information about the possibilities of the compilers, please see the man pages.
 
 Unified Parallel C
 ------------------
@@ -90,7 +90,7 @@ To run the example with 5 threads issue
     $ ./count.upc.x -fupc-threads-5
 ```
 
-For more informations see the man pages.
+For more information see the man pages.
 
 ### Berkley UPC Compiler
 
@@ -144,7 +144,7 @@ To run the example on two compute nodes using all 32 cores, with 32 threads, iss
     $ upcrun -n 32 ./hello.upc.x
 ```
 
-For more informations see the man pages.
+For more information see the man pages.
 
 Java
 ----

docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab.md

@@ -22,7 +22,7 @@ By default the EDU variant is marked as default. If you need other version or va
 
 If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.
 
-If you require the Matlab GUI, please follow the general informations about [running graphical applications](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/).
+If you require the Matlab GUI, please follow the general information about [running graphical applications](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/).
 
 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/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-system/)) is recommended.
 

docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md

@@ -25,7 +25,7 @@ By default the EDU variant is marked as default. If you need other version or va
 
 If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.
 
-If you require the Matlab GUI, please follow the general informations about running graphical applications
+If you require the Matlab GUI, please follow the general information about running graphical applications
 
 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) is recommended.
 

docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md

-Cygwin and X11 forwarding
-=========================
-
-**If no able to forward X11 using PuTTY to CygwinX**
-
-```bash
-[usename@login1.anselm ~]$ gnome-session &
-[1] 23691
-[usename@login1.anselm ~]$ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused
-PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused
-
-  (gnome-session:23691): WARNING **: Cannot open display:**
-```
-
-1. Locate and modify Cygwin shortcut that uses [startxwin](http://x.cygwin.com/docs/man1/startxwin.1.html)
-    locate
-    C:cygwin64binXWin.exe
-    change it
-    to
-    C:*cygwin64binXWin.exe -listen tcp*
-
-![XWin-listen-tcp.png](../../../img/XWinlistentcp.png "XWin-listen-tcp.png")
-
-2. Check Putty settings:
-     Enable X11 forwarding
-
-    ![](../../../img/cygwinX11forwarding.png)

docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md

@@ -52,7 +52,7 @@ There are variety of X servers available for Windows environment. The commercial
 
  |How to use Xwin |How to use Xming |
  | --- | --- |
- |[Install Cygwin](http://x.cygwin.com/) Find and execute XWin.exeto start the X server on Windows desktop computer.[If no able to forward X11 using PuTTY to CygwinX](cygwin-and-x11-forwarding/) |<p>Use Xlaunch to configure the Xming.<p>Run Xmingto start the X server on Windows desktop computer.|
+ |[Install Cygwin](http://x.cygwin.com/) Find and execute XWin.exeto start the X server on Windows desktop computer.[If no able to forward X11 using PuTTY to CygwinX](#if-no-able-to-forward-x11-using-putty-to-cygwinx) |<p>Use Xlaunch to configure the Xming.<p>Run Xmingto start the X server on Windows desktop computer.|
 
 Read more on [http://www.math.umn.edu/systems_guide/putty_xwin32.html](http://www.math.umn.edu/systems_guide/putty_xwin32.shtml)
 
@@ -140,3 +140,29 @@ $ gnome-session &
 In this way, we run remote gnome session on the cluster, displaying it in the local X server
 
 Use System-&gt;Log Out to close the gnome-session
+
+
+### If no able to forward X11 using PuTTY to CygwinX
+
+```bash
+[usename@login1.anselm ~]$ gnome-session &
+[1] 23691
+[usename@login1.anselm ~]$ PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused
+PuTTY X11 proxy: unable to connect to forwarded X server: Network error: Connection refused
+
+  (gnome-session:23691): WARNING **: Cannot open display:**
+```
+
+1. Locate and modify Cygwin shortcut that uses [startxwin](http://x.cygwin.com/docs/man1/startxwin.1.html)
+    locate
+    C:cygwin64binXWin.exe
+    change it
+    to
+    C:*cygwin64binXWin.exe -listen tcp*
+
+![XWin-listen-tcp.png](../../../img/XWinlistentcp.png "XWin-listen-tcp.png")
+
+2. Check Putty settings:
+     Enable X11 forwarding
+
+    ![](../../../img/cygwinX11forwarding.png)

docs.it4i/get-started-with-it4innovations/accessing-the-clusters/introduction.md

@@ -22,3 +22,9 @@ Graphical User Interface
 Read more about [X Window System](./graphical-user-interface/x-window-system/).
 
 Read more about [Virtual Network Computing (VNC)](./graphical-user-interface/vnc/).
+
+
+Accessing IT4Innovations internal resources via VPN
+---------------------------------------------------
+
+Read more about [VPN Access](vpn-access/).

docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md

-PuTTY
-=====
-
-!!! Note "Note"
-	PuTTY -  before we start SSH connection
+# PuTTY (Windows)
 
 Windows PuTTY Installer
 -----------------------

docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md

-SSH keys
-========
+# OpenSSH Keys (UN\*X)
 
-Key management
---------------
+## Key management
 
 After logging in, you can see .ssh/ directory with SSH keys and authorized_keys file:
 
@@ -18,8 +16,8 @@ After logging in, you can see .ssh/ directory with SSH keys and authorized_keys
     -rw-r--r-- 1 username username  392 May 21  2014 id_rsa.pub
 ```
 
-!!! Note "Note"
-    Please note that private keys in .ssh directory are without passphrase and allow you to connect within the cluster.
+!!! Hint
+    Private keys in .ssh directory are without passphrase and allow you to connect within the cluster.
 
 Access privileges on .ssh folder
 --------------------------------
@@ -44,7 +42,7 @@ Private key
 !!! Note "Note"
     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 Pageant (for Windows users). The private key should always be kept in a safe place.
+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 Pageant (for Windows users). The private key should always be kept in a safe place.
 
 An example of private key format:
 

docs.it4i/salomon/environment-and-modules.md

@@ -17,7 +17,7 @@ fi
 alias qs='qstat -a'
 module load intel/2015b
 
-# Display informations to standard output - only in interactive ssh session
+# Display information to standard output - only in interactive ssh session
 if [ -n "$SSH_TTY" ]
 then
  module list # Display loaded modules

docs.it4i/salomon/shell-and-data-access.md

@@ -200,4 +200,4 @@ Graphical User Interface
 VPN Access
 ----------
 
--   Access to IT4Innovations internal resources via [VPN](../get-started-with-it4innovations/vpn-access/).
+-   Access to IT4Innovations internal resources via [VPN](../get-started-with-it4innovations/accessing-the-clusters/vpn-access/).

docs.it4i/salomon/software/numerical-languages/matlab.md

@@ -22,7 +22,7 @@ By default the EDU variant is marked as default. If you need other version or va
 
 If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.
 
-If you require the Matlab GUI, please follow the general informations about [running graphical applications](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/).
+If you require the Matlab GUI, please follow the general information about [running graphical applications](../../../get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system/).
 
 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/accessing-the-clusters/graphical-user-interface/x-window-system/)) is recommended.
 

mkdocs.yml

@@ -20,14 +20,14 @@ pages:
     - Applying for Resources: get-started-with-it4innovations/applying-for-resources.md
     - Obtaining Login Credentials: get-started-with-it4innovations/obtaining-login-credentials/obtaining-login-credentials.md
     - Certificates FAQ: get-started-with-it4innovations/obtaining-login-credentials/certificates-faq.md
-    - Accessing the Clusters: get-started-with-it4innovations/accessing-the-clusters/introduction.md
+    - Accessing the Clusters:
+      #- Introduction: get-started-with-it4innovations/accessing-the-clusters/introduction.md
+      - OpenSSH Keys (UN*X): get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
+      - PuTTY (Windows): get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
+      - X Window System: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
+      - VNC: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
+      - VPN Access: get-started-with-it4innovations/accessing-the-clusters/vpn-access.md
 #    - VPN-Connection-Fail-in-Win-8.1: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/vpn-connection-fail-in-win-8.1.md
-    - SSH Keys: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md
-    - PuTTY: get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md
-    - X Window System: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md
-    - X Window System Using Cygwin: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md
-    - VNC: get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md
-    - VPN Access: get-started-with-it4innovations/vpn-access.md
   - Anselm Cluster:
     - Introduction: anselm-cluster-documentation/introduction.md
     - Hardware Overview: anselm-cluster-documentation/hardware-overview.md