Visualization server

The r740visu server is dedicated to extensive visualization (OpenGL/Mesa/CUDA8) at PSMN.

It is equipped with 2 Intel processors Xeon Gold 5122 @3.6GHz (16 logical cores) with 192 GiB of RAM. It is accessible using x2go and has a hardware accelerator NVidia Quadro P4000©.

Finally, and most importantly, the server give access to the /scratch/E5N (scratch system common to E5-* queues.

1. Connect to clusters
2. Use SSH keys and ssh-agent (or PuTTY/KiTTY for Windows)
3. Doing hops with SSH
4. Install x2go (x2goclient) on user's workstation (Linux, Mac or Windows ⇒ http://wiki.x2go.org/)

• New session

• Parameters: Tab Session

WARNING : the Session type NEED to be SET TO XFCE

• Parameters: Tab Connection

• Parameters: Tab Input/Output

• Parameters : Tab Media

• Parameters: Tab Directory

Expected result:

This paragraph concerns a connection to the visualization machine from outside the School, from a Linux or Mac OSX client. SSH bounces must be active, make sure you have read (understood and tested) the related documentation.

• Minimal modification to be made in your ~/.ssh/config (on user station):

Host allo-psmn-multihop
  User $USER
  ProxyCommand ssh -qt $USER@ssh.psmn.ens-lyon.fr tcpconnect allo-psmn.psmn.ens-lyon.fr %p

Replace $USER by your PSMN login.

• Modification x2go :

In the tab Session, block Proxy server, box Host, replace allo-psmn.psmn.ens-lyon.fr by the new configuration : allo-psmn-multihop. You must get the same thing as in §3 at the login x2go.

This part is about connection to visualization server from a network outside of ENS de Lyon (see illustration).

The first step is to create an SSH tunnel to the visualization machine. :

• Copy the gateway session (allo-psmn, Load, rename, save).

Change the “Host Name” to that of the display machine (here, for the example, r740visu). So rename the session to r740visu (to follow the example) and save.

.

• In Connection→Proxy, select Local.
• In Connection→Proxy, set “Telnet command” as follows :

  plink.exe -load allo-psmn -nc %host:%port

• In Connection→SSH→Tunnels, set Source port on port 2222 and Destination sur

  r740visu.psmn.ens-lyon.fr:22

• Return to Session, save, then click Open. Your tunnel is now open.

Confirm with OK, then double-click the session icon on the right side of the X2Go client. You are now connected to the graphical interface of the machine.

Every application installed in the PSMN environment can be used as is.

If your numeric keypad is not recognized, in a terminal, run the program numlockx.

For every application requiring the loading of a modulefile, it is necessary to first load from a terminal the modulefile then run the application.

Sometimes, x2go sessions don't load the ~/.profile. You can force it, by hand, with source ~/.profile, or add this line to your ~/.bashrc :

source /usr/share/lmod/lmod/init/bash

MacOS X users must have X11 Mac server installed and running prior to use x2go-client, see x2goclient documentation

For every application requiring hardware acceleration (OpenGL / GLX / GLSL / …), after loading the corresponding modulefile, you must prefix the call to the application by calling the VirtualGL wrapper: vglrun MyApp

• VMD

In a terminal run:

source ~/.profile
module load VMD/1.9.2
vglrun vmd

• molden/gmolden

In a terminal run:

source ~/.profile
module load Molden/5.4
vglrun gmolden

• ParaView

In a terminal run:

source ~/.profile
module load ParaView/4.4.0
vglrun paraview

• Avogadro

In a terminal run:

source ~/.profile
vglrun avogadro