Re: amber-developers: Testing Parallel

From: Scott Brozell <>
Date: Mon, 14 Apr 2008 13:04:41 -0700 (PDT)


On Mon, 14 Apr 2008, Lachele Foley wrote:

> More fun with parallel tests: mostly FYI, but with questions. And apologies in advance for whatever I forgot to notice or check...
> Another issue for parallel testing with us is that the tests are run like so:
> =====start abbreviated pseudo-script=======
> set up some environment stuff and check sanity
> run the parallel job
> check the output for differences
> =====end abbreviated pseudo-script=======
> On our system, jobs go away to the scheduler by default (like running in the background). So, the tests frequently check for output that hasn't happened yet -- or, in the noesy case, delete the input file before the job runs. I can get the scheduler to run "in the foreground" (or "wait" or "block" -- choose your favorite terminology). But, I seem to be having a quote-character issue. Can someone who knows the shell better than me suggest a fix (SHELL is tcsh)?
> This works:
> [lachele.keats noesy]$ /opt/scali/bin/scasub -qsparams "-W block=true" -mpimon -network gm0,smp -np 2 -npn 2 $sander -O -i mdin -c -o noesy.out
> 44368.keats
> This doesn't:
> [lachele.keats noesy]$ echo $DO_PARALLEL
> /opt/scali/bin/scasub -qsparams "-W block=true" -mpimon -network gm0,smp -np 2 -npn 2
> [lachele.keats noesy]$ $DO_PARALLEL $sander -O -i mdin -c -o noesy.out
> qsub: script file:: No such file or directory
> I don't think using plain qsub is a good idea, either, but if someone wants to explore that option, say so. Brief reasons: qsub seems to want a separate script file (=rewrite tests) and scaMPI complains if not using scasub. Possibly can work around both, and happy to accept suggestions.

Your machine's queue situation seems odd.
Anyway, try
set echo
set verbose
then your two command invocations to see the differences.
My guess is that "-W block=true" -> '-W block=true'
might work and wont hurt.

Received on Fri Apr 18 2008 - 21:19:19 PDT
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