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help > Setting up Linux stand alone (SSHing into a SLURM system)

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Setting up Linux stand alone (SSHing into a SLURM system)

Hi I am trying to set up the CONN stand alone and I've got it to the point where the GUI shows up, but then it errors out.

I attached an image of the error and below is the text from my bashrc

export PATH=/home/elamy1/software/conn18b_glnxa64/:$PATH
export MCRROOT=/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/mcr/R2018b/v95
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/runtime/glnxa64;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/opengl/lib/glnxa64;
export XAPPLRESDIR=${MCRROOT}/X11/app-defaults;
export LD_LIBRARY_PATH;

Attachment: Screen Shot 2020-06-28 at 3.37.24 AM.png

RE: Setting up Linux stand alone (SSHing into a SLURM system)

Hi Adam,

Not sure about this error, but it looks perhaps like a problem with X11 forwarding during your SSH session. Are you able to launch other GUI-based software from your SLURM server without a problem?

In general I would probably recommend connecting to your SLURM server using VNC (or, if your institution allows it some web-based portal like openondemand.org). In my experience that should be considerably faster and less error-prone than attempting to use X11 forwarding over ssh. If that is not possible, and connecting remotely to your SLURM system with a workable graphical-interface is out of the question, then perhaps consider running your analyses using CONN batch-commands, which do not require any GUI so they can be run entirely over a terminal ssh session.

Hope this helps
Alfonso
Originally posted by Adam Elamy: