Sun Grid Engine Command-Dump

Here in the institute we have a Sun Grid Engine available. It is a tool to post computing-jobs on other workspaces (we have I think up to 60 available). There are certain commands and things that I do regularly which I tend to forget after half a year, or which might be useful for orthes.

  • Show all jobs that are running on the grid
    qstat -u \* or alternativly for a single user qstat -u behinger

  • exclude a single computer/host from running a job
    qsub -l mem=5G,h=!computername.domain script.sh
    to exclude multiple hosts: h=!h4&!h5 or h=!(h4|h5) Source
    of course mem=5G is an arbitrary other requirement.

  • Run a gridjob on a single R-File
    add #!/usr/bin/Rscript in the beginning of the file, then you can simply run qsub Rscript_name.R. I had problems using qsub Rscript -e "Rscript_name.R" due to the many quotes that would need escaping (I use to call the grid using system() command in matlab/R).

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