Local visualization

For local visualization, the files must be copied via SSH connection to the local computer. The visualization files can then be opened in Paraview.

Another option is to use sshfs, which integrates remote directories into the local system via SSH.

Visualization with VNC: One-off preparation

To prepare for using VNC we first need a password for the VNC sessions and a .vnc directory in your own Home:

$ mkdir $HOME/.vnc
$ vncpasswd

vncpasswd then asks for a password that you want to use for your VNC sessions and a confirmation of the same. You can also assign a password for read-only access, so others could join your session while watching. We don't need that here.

Note on the use of Putty for SSH tunnels

Below, we make use of ssh tunnels and the commands used are ssh, if you are using Putty, you use plink.exe instead.

Start a visualization session

To start a VNC session for visualization, run:

module load vis/VirtualGL
vis_via_vnc.sh -msmp 01:00:00

The script then tells you what you need to run on your local system to connect to the VNC session.

It should be something along these lines:

Connect to the VNC session via the vncviewer:

vncviewer -via username@training.hlrs.de n002701:1

If the vncviewer doesn't support -via, we need to create a separate SSH tunnel for the connection. The necessary command is provided by the vis_via_vnc.sh script, however the node name gets lost, you need to use the ports provided by the script and put the visualization node in between like this:

ssh -N -L <port>:n002701:<port> <user>@training.hlrs.de

With this tunnel, it should then be possible to start vncviewer with:

vncviewer localhost:port

Then open a terminal in this session and do the following:

module load system/amdgpu
module load vis/VirtualGL
module load vis/paraview/5.11.0-MPI-Linux
vglrun paraview

Note: ignore warnings about zink written by paraview.

Alternative with local Paraview and Paraview server

Instead of performing the visualization in a VNC session on the cluster, we can also use a local Paraview Client to connect with a pvserver on the visualization node.

For this we need a Paraview installation in version 5.11 on the local computer. The version is important, otherwise the server will refuse the connection. This approach tends to be slower than using the VNC session, but takes fewer steps.

First we start a job that provides a pvserver:

qsub -I -l select=1:node_type=skl:ncpus=1:mem=16gb,walltime=02:00:00 -q smp

In the interactive shell we then run the pvserver and tell it to listen on a dedicated port XXXXX, use the number from your username for this to have unique port:

module load vis/paraview/5.11.0-MPI-Linux-osmesa
pvserver --server-port=XXXXX

The pvserver then gives us the info on how to connect to it, like this:

Connection URL: cs://<nodename>:XXXXX
Accepting connection(s): <nodename>:XXXXX

In order to connect a local Paraview to the pvserver on that node, an SSH tunnel needs to be created according to the following scheme on the local computer:

ssh -N -L 11111:<nodename>:XXXXX <user>@training.hlrs.de

This shell must now remain open in the background while the Paraview is running.

Then we can start the Paraview on our own computer and with that connect to the pvserver over the tunnel. On the command line this works with:

paraview -url=cs://localhost:11111

ssh -L 11111:localhost:XXXXX <user>@training.hlrs.de /opt/hlrs/non-spack/vis/paraview/ParaView-5.11.0-osmesa-MPI-Linux-Python3.9-x86_64/bin/pvserver --server-port=XXXXX

paraview -url=cs://localhost:11111

ssh -R XXXXX:localhost:XXXXX <user>@training.hlrs.de /opt/hlrs/non-spack/vis/paraview/ParaView-5.11.0-osmesa-MPI-Linux-Python3.9-x86_64/bin/pvserver --reverse-connection --client-host=localhost --server-port=XXXXX