Using Sun Grid Engine (SGE) @ CS

Using Sun Grid Engine @ CS

To set up your environment you need to execute this on the command line

source /nfs/sge/current/default/common/settings.csh (if you are using csh/tcsh)\

. /nfs/sge/current/default/common/settings.sh (bash)

To check the status of jobs you can visit http://blast.cs.unm.edu/gemonitor/.

qsub - submit background job. Example:

qsub -N "jobname" /tools/hw/wrap make test

qbsub - submit a binary background job. This is a wrapper script to qsub that does away with the necessity to use scripts. Example:

qbsub make OPT=1234 my_target

qrsh - submit foreground job. Example:

qrsh make test

qstat - check status of jobs. Examples:

qdel - Delete a job. Example:

qdel 2345 # Kills job 2345

qmon - Interactive interface to entire SGE system. Example:

qmon &

1. If you need to pass your environment to the Queuing system use the -V flag ie.

qsub -V ./job.sh

For example if you set a specific LD_LIBRARY_PATH that you want passed to your scripts -V is the way to go.

2. If you need to put the .o and .e files somewhere else other than your home directory add -e and -o flags ie.

qbsub -o $PWD -e $PWD mystuff

This will put both .o and .e files in whatever the present working directory is.

3. To send a job to a particular machine use the -q flag ie.

qsub -q shelby.q,io.q,rhea.q script.pl

Will dispatch the job only to shelby, io or rhea (in that particular order)

4. Request a particular resource ie. machine job needs to run on has to have at least 800 MB of memory use the -l flag ie.

qsub -l mem_total=800M script.pl

or if you need to run a job on MacOS X only do

qsub -l arch=darwin

You could also use glinux for x86 version of Linux and lx24-amd64 for AMD64 architecture ie. AMD Opteron or Athlon64.