Nov 17, 2017

Cluster Documentation

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Connect



Please use a Secure Shell Client to connect to cluster.mathstat.dal.ca.

Interactive queue

The Interactive queue is useful to run software with a graphical user interface or programs not suitable for the Batch queues. Please type qrsh to get an ssh session to the least loaded Compute Node. The X-Server for windows is available for download from the Department servers and X11 tunneling can be used for starting graphical applications over ssh. For faster graphics, please export the DISPLAY variable to that of the local X-server after connecting to the cluster using ssh, as encryption of X11 traffic slows down graphics performance when using X11 tunneling.

Batch queue

The Batch queues can be used the following way. Please note that this is a simple example. The Grid Engine User's manual has detailed information on the available options for Batch queue use. Create a submit script in the following format -

#!/bin/sh
#$ -S /bin/sh
. /etc/profile
#$ -o job_output
#$ -M <your email address>
#$ -m be
cd <path to the job>
<The job to be submitted starts here>

Useful commands

  • To submit a Batch job - qsub <submit.sh>
  • To see the status of jobs and/or queues - qstat -u <username> or qstat -f
  • To terminate a job : qdel <job-id>
  • To get an interactive session with new compute nodes - qrsh -q 2009
  • To get an interactive session with the compute nodes that have 32GB ram - qrsh -q 32G
  • To submit a Batch job to the new compute nodes - qsub -q 2009-batch <submit.sh>
  • To submit a Batch job to compute nodes that have 32GB ram - qsub -q 32G-batch <submit.sh>
  • To get an interactive session with the compute nodes that have 512GB ram - qrsh -q 512G
  • To submit a Batch job to compute nodes that have 512GB ram - qsub -q 512G-batch <submit.sh>
  • To get an interactive session with the compute nodes that have 192GB ram - qrsh -q 192G
  • To submit a Batch job to compute nodes that have 192GB ram - qsub -q 192G-batch <submit.sh>

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