To run graphical applications on the palmetto cluster, users will need to “tunnel” or “forward” graphical data from the cluster to their local machines. This requires users to be running an “X-server” on their local machines. Linux systems typically have an X-server pre-installed. Max OS X users and Windows users will typically need to install an X-server program.
The MobaXterm SSH client for Windows comes with an X-server built-in, but Windows users that are using another SSH client will need to install one.
Logging in to Palmetto with X-tunneling enabled
Windows Users (MobaXterm)
Ensure that the X-server is running by hovering your mouse pointer over the X-server button in the MobaXterm GUI. If not, click on the button to start the X-server. Then, log-in as usual.
See below for an example of how to run graphical applications once logged in.
Windows Users (Other SSH client)
Here, we describe the steps for Windows users that are using the SSH Secure Shell Client. Users will need the following software to run graphical applications:
SSH Secure Shell by SSH Communications Security Corporation site license: https://www.ssh.com/ssh/download/.
Xming, Windows-based X-server (http://www.straightrunning.com/XmingNotes and select “Xming” under Public Domain Releases)
When installing Xming, using all of the default settings is recommended, but it is not necessary to install the built-in PuTTY SSH client:
Xming can be launched from the Windows Start menu.
When you launch Xming, it will be running in the background, listening for incoming data. You can see that it’s running by noting the Xming icon in the system tray:
Mac OS X 10.9+ users
Mac OS X users will need to install XQuartz: https://www.xquartz.org/. After installing Xquartz, do not open/launch it. Open a terminal, and enter the following command without logging in to Palmetto:
$ defaults write org.macosforge.xquartz.X11 enable_iglx -bool true
Now, log in to Palmetto from the terminal using the
command, providing the additional
$ ssh -Y email@example.com
You should see that XQuartz is automatically launched. See below for an example of how to run graphical applications once logged in.
No need to install any software. Just log in to Palmetto
from the terminal using the
ssh command, providing the
$ ssh -X firstname.lastname@example.org
Running an Application on Palmetto with a Tunneled GUI (an example)
Once logged-in with X-tunneling enabled, you can quickly test your setup with the following commands; first, start an interactive job:
[username@login001 ~]$ qsub -I -X qsub (Warning): Interactive jobs will be treated as not rerunnable qsub: waiting for job 11678.pbs02 to start qsub: job11678.pbs02 ready
You must include the
-X switch with
qsub -I when using graphical applications
in your interactive job. After the job is started, run the
[username@node0058 ~]$ glxgears
You should see a new Window appear with some graphical output.
As a more complex example,
we’ll launch an interactive job for running COMSOL 4.2a using the
This interactive job can be started using a
qsub command with the
-X option, like this:
qsub -I -X -l select=1:ncpus=4:mpiprocs=4:mem=64gb,walltime=2:00:00
qsub command will launch an interactive job
with X11 tunneling
using one “chunk” of cluster hardware consisting of
4 compute cores,
4 MPI processes,
64 GB RAM,
and this job will run for up to 2 hours.
When this interactive job begins running,
you will be logged-in to one of the compute nodes
where you can begin running the COMSOL GUI.
$ module add comsol/5.2 $ comsol -np4 -tmpdir /local_scratch
Note: you are now running COMSOL on Palmetto, so if you attempt to browse for a file to open, you’ll only be able to look in the filesystems on Palmetto. If you need to open a file on your local workstation, you must first copy that file to Palmetto so you can access it there.
Tunneling X11 is not very fast, so the performance of the GUI will be much slower than that of a program running on your local workstation. It may take approximately 15 seconds for the tunneled GUI to be displayed by your local X-server. Interacting with the tunneled GUI (clicking buttons and using menus, etc.) may be slow, so please consider the amount of data moving back-and-forth between your workstation and Palmetto. The performance may be even worse if you’re tunneling the GUI to an off-campus location.