diff --git a/docs.it4i/anselm-cluster-documentation/environment-and-modules.md b/docs.it4i/anselm-cluster-documentation/environment-and-modules.md index 0835ce008f277e982ecf3a297f40c43ecb60a46c..45b23263a0a2f5b0f49c8c41279b716ee043621b 100644 --- a/docs.it4i/anselm-cluster-documentation/environment-and-modules.md +++ b/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 diff --git a/docs.it4i/anselm-cluster-documentation/shell-and-data-access.md b/docs.it4i/anselm-cluster-documentation/shell-and-data-access.md index 912e49a165705ad5ec1d234b8618b0f6fec50051..a72995bb0fb5e73c8518c31a6f94aedd56042d9d 100644 --- a/docs.it4i/anselm-cluster-documentation/shell-and-data-access.md +++ b/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/). diff --git a/docs.it4i/anselm-cluster-documentation/software/compilers.md b/docs.it4i/anselm-cluster-documentation/software/compilers.md index ab8935abfffc8d3c973975bf007cf7f697d7e340..8d5cabd42ea244a6ef2eea78251d0d50bb905e64 100644 --- a/docs.it4i/anselm-cluster-documentation/software/compilers.md +++ b/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 ---- diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab.md b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab.md index dbe107990dfa538f177344017b77a58a80117c5a..27dd6bb6e7def484ba4847d8ce7c67fb99a06b25 100644 --- a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab.md +++ b/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. diff --git a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md b/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md index 84b2897ea299701773c9d9736d2af4ed52e2ed3a..d28bb29cb4d9bbb2bec23336b4dc61a7b7710d81 100644 --- a/docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md +++ b/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. diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md deleted file mode 100644 index e98bf9f04e64354e965d02ac4cbc15ae531636c0..0000000000000000000000000000000000000000 --- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/cygwin-and-x11-forwarding.md +++ /dev/null @@ -1,27 +0,0 @@ -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* - - - -2. Check Putty settings: - Enable X11 forwarding - -  diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md index 3c6b877ca9821559517f89bf2459fd83b009fcb5..e4a3c023cbb78cc9071c8440501aacb277d43106 100644 --- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md +++ b/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->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* + + + +2. Check Putty settings: + Enable X11 forwarding + +  diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/introduction.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/introduction.md index 6ebeac33092d3ae6ce76ca7cc9aac6ba2c1cf825..696b2fc41a7a84f06e4d690ac01259d4bd448cd4 100644 --- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/introduction.md +++ b/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/). diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md index 352165097d8d405281e8f67862f40e5074dd2881..394184946dce39df963d18d64997f355843c7ebe 100644 --- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md +++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/putty.md @@ -1,8 +1,4 @@ -PuTTY -===== - -!!! Note "Note" - PuTTY - before we start SSH connection +# PuTTY (Windows) Windows PuTTY Installer ----------------------- diff --git a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md index ba5c29fdbe097438b4cc4eb158422c8fb8ec4137..9cb17c16b47f81a0e7022acbc48128e1b3acc51c 100644 --- a/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md +++ b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys.md @@ -1,8 +1,6 @@ -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: diff --git a/docs.it4i/get-started-with-it4innovations/vpn-access.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/vpn-access.md similarity index 100% rename from docs.it4i/get-started-with-it4innovations/vpn-access.md rename to docs.it4i/get-started-with-it4innovations/accessing-the-clusters/vpn-access.md diff --git a/docs.it4i/get-started-with-it4innovations/vpn1-access.md b/docs.it4i/get-started-with-it4innovations/accessing-the-clusters/vpn1-access.md similarity index 100% rename from docs.it4i/get-started-with-it4innovations/vpn1-access.md rename to docs.it4i/get-started-with-it4innovations/accessing-the-clusters/vpn1-access.md diff --git a/docs.it4i/salomon/environment-and-modules.md b/docs.it4i/salomon/environment-and-modules.md index b6ae85042866e704d9e5d67e58ffbc9c1c3207c4..e5e33007f53f259da21f29ac2f1de8386fc0dedf 100644 --- a/docs.it4i/salomon/environment-and-modules.md +++ b/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 diff --git a/docs.it4i/salomon/shell-and-data-access.md b/docs.it4i/salomon/shell-and-data-access.md index b214bd5f18ea08c33a0fc3ce4c02a9f30af06ed5..a779c8697062b30056e3a0a49c873eb8c3e681d5 100644 --- a/docs.it4i/salomon/shell-and-data-access.md +++ b/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/). diff --git a/docs.it4i/salomon/software/numerical-languages/matlab.md b/docs.it4i/salomon/software/numerical-languages/matlab.md index 7eebf17ad0d31a7737dddb75923a9a9244bf98c3..4347f5874a7d8a99d9c1c4540c9c32d45db53ed7 100644 --- a/docs.it4i/salomon/software/numerical-languages/matlab.md +++ b/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. diff --git a/mkdocs.yml b/mkdocs.yml index e621a2a11b385b07d5d194a4f9637da917edbfcb..cef21c6110fd759b03282037552df48b6c8871ce 100644 --- a/mkdocs.yml +++ b/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