[GE users] Anyone running Schrodinger chem/modeling apps under SGE6?
dag at sonsorol.org
Thu Feb 24 15:16:28 GMT 2005
One of the more interesting SGE projects I did last year involved
getting Schrodinger products (glide, impact, etc.) happily integrated
with SGE 5.3EE including flexlm license management and epilog scripts
that catch and resubmit jobs that failed with errors that were machine
Interestingly enough the same techniques used on the SGE 5.3 system are
not working all that well on a new cluster running SGE 6.0u3 - in the
past the Schrodinger job dispatch code easily and trivially exec'ed the
submit script that did all the heavy work of setting ENV vars, calling
qsub and passing back the jobID to Schrodinger so that their workflow
tools knew how to kill or abort running jobs. Pretty basic.
Now on a SGE 6.0u3 cluster, that process seems to hang - the shell
script is invoked and the qsub command it calls hangs forever until
reaching a timeout limit. The only way we can reliably get single,
non-parallel jobs to run is to "fool" Schrodinger into thinking the job
is "remote" in which case it uses passwordless SSH to exec the master
submit script. In this situation everything works perfectly.
Rather than detail the Schrodinger jmonitor and jdispatch functions for
an uninterested list :) I thought I'd ask 2 questions:
(1) This suite has some minimal workflow tools which require it to be
aware of running jobs. This requires passing the SGE job ID back to the
job dispatch process. This is done in their code by opening a pipe to
the "qsub ./master-job-script.sh" command so that the STDOUT can be
parsed in order to grab the jobID value. -- Has anything changed with
qsub in 6.0 vs 5.3 regarding it's use and behavior of STDIN and STDOUT?
Any new arguments need to be passed to qsub?
(2) Are there any current Schrodinger users running SGE 6.0 who are
willing to talk off-list about their integration and experiences?
I'll summarize anything I learn and if I can get permission I'll post
details on Schrodinger/SGE integration specifics once we get things
working as smoothly with 6.0 as it did with 5.3EE
Chris Dagdigian, <dag at sonsorol.org>
BioTeam - Independent life science IT & informatics consulting
Office: 617-665-6088, Mobile: 617-877-5498, Fax: 425-699-0193
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