Kim Lab

SunGridEngine

Sun Grid Engine is deprecated and not currently available on the cluster

• Sun Documentation: http://gridengine.sunsource.net/howto/howto.html

• Basic Commands - see man pages for details:
  • qsub <shell script> : submit a script for execution
  • qsub -b y <binary> : submit a binary for execution
  • qlogin : request an unloaded node for interactive use
    • also see http://c1.genomics.upenn.edu/wiki/index.php/HPC:Using_qlogin
    • this command is comparable to using ssh to switch to a node
  • qstat -j <jobid> : show the status of a job
  • qdel <jobid> : cancel a job
  • qstat -f : display all of your jobs queued or running
  • qhost -j : display which jobs are on which host
  • qstat -u <user> : display jobs queued or running for a single user
  • qstat -f -u '*' : to see all jobs
  • qsub -l mem_free=4G <shell script> : request that there are at least 4GB RAM free on the node where your script will run
  • qsub -q all.q -p -100 -cwd job1.sh : submit job1.sh from current working directory to queue named "all.q" with low priority -100 (default priority is 0)

• Tips and Tricks
  • To export all environment variables to the SGE environment use qsub -V
  • To export a specific environment variable, use qsub -v <ENVNAME>
• More SGE docs
  • http://www.cis.upenn.edu/acg/sge.html