Sun Grid Engine (SGE)
Environment setup
To set up your environment you need to execute this on the command line or put in your environment
tcsh/csh
source /nfs/sge/current/default/common/settings.csh
bash
. /nfs/sge/current/default/common/settings.sh
Status of jobs
To check the status of jobs you can visit http://blast.cs.unm.edu/gemonitor/.
Basic commands
qsub
Submits a background job. Example:
qsub -N "jobname" /tools/hw/wrap make test
+ Qsub requires command to be a script
+ Output goes to <jobname>.o<jobnumber>
Please note:
The SGE system will use /bin/csh to execute the shell scripts regardless of
the shell specified at the top. If you are using an alternate shell, use
the -S to specify the shell e.g.
#$ -S /bin/bash
instead of
#!/bin/bash
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:
qstat |
# Checks status of all jobs |
qstat -u user |
# Checks status of user's jobs |
qstat -r |
Show resources being used |
qstat -j jobnum |
Details of 1 job |
qdel
Delete a job. Example:
qdel 2345 # Kills job 2345
qmon
Interactive interface to entire SGE system. Example:
qmon &
Advanced options
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.
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.
- 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)
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=800 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.
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