[GE users] Anyone running Schrodinger chem/modeling apps under SGE6?

Chris Dagdigian 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
PGP KeyID: 83D4310E iChat/AIM: bioteamdag  Web: http://bioteam.net

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