GridEngine
From FarmShare
We're using the Debian packages of "Sun Grid Engine" which isn't quite "Sun" anymore since Oracle bought Sun, and the Debian packages are a bit behind the current forks of Open Grid Engine or Son of Grid Engine or Univa Grid Engine.
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documentation
Start with 'man sge_intro'. Move on to 'man qsub'. Try submitting a simple job with 'echo "sleep 3600" | qsub", then run 'qstat' and 'qdel'.
shell mode
GE can run in "POSIX mode" or "Unix mode". See the "shell_start_mode" section of 'man sge_conf'
# qconf -sconf|grep shell shell_start_mode unix_behavior login_shells bash,sh,ksh,csh,tcsh
So you'll want to explicitly specify your shell with the -S flag to qsub. E.g.
# get rid of spurious messages about tty/terminal types #$ -S /bin/sh
useful commands
- see all hosts: qhost
- see which jobs are on which hosts: qhost -j
- see all jobs: qstat -f -u "*"
- see all host attributes: qstat -f -F -u "*"
queues
Under SGE, a 'queue' is a set of settings that get applied to jobs that are assigned to that queue.
We are using pretty much the default settings. This page should contain a description of all of the settings we've changed away from the defaults along with a reason for doing so.
We created four queues: bigmem.q, long.q, main.q and test.q. Use 'qconf -sql' to list queues, 'qconf -sq queue_name' to see the queue settings.
main.q
Most jobs end up here. Time limit is 48hrs.
bigmem.q
This queue is explicitly tied to the machine with more physical memory. Same settings as main.q
long.q
2week time limit instead of 48hrs
test.q
15min time limit instead of 48hrs
starter method
There is a file /usr/local/libexec/gridengine/job_start.sh which sets up the checkpointing environment if you specified checkpointing for your job.