[GE users] parallel jobs submission help

Wheeler, Dr M.D. mdw10 at leicester.ac.uk
Thu Nov 25 20:49:48 GMT 2004


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OK I think that I have gone some way to sorting my problem out
 
I have 3 compute nodes set up on my system, however sge only appears to submit jobs to the first node
 
if i run a script with the line
 
> qsub -pe mpich 2 molpro.sh
 
where molpro.sh is 
 
#!/bin/bash
#
#$ -cwd
#$ -j y
#$ -S /bin/bash
molpro -n2 test.com
 
everything runs ok (on two procs)
 
now if I submit another job
 
> qsub -pe mpich 2 molpro1.sh
 
where molpro1.sh
 
#!/bin/bash
#
#$ -cwd
#$ -j y
#$ -S /bin/bash
#molpro -n2 test1.com
 
this second job sits in the queue
 
do I have to tell it which queue to allocate the job to???
 
Cheers
Martyn

 
________________________________

From: Reuti [mailto:reuti at staff.uni-marburg.de]
Sent: Thu 25/11/2004 19:20
To: users at gridengine.sunsource.net
Subject: RE: [GE users] parallel jobs submission help



> Thanks for your response, is it a problem that the version of molpro that I
> have uses tcgmsg rather than mpi?  I don't see a parallel environment for
> tcgmsg....!

No, there are no MPI commands at all in the startmpi.sh ... scripts. It just
prepares all for MPI. You can use the mpi example to set up a parallel
environemnt in SGE, and you can rename it to tcgmsg. The things you have to do
is to set the PBS_NODEFILE as I wrote in your script to point to
$TMPDIR/machines. If PBS_NODEFILE is defined, Molpro will built the necessary
PROCGRP file for the used "parallel" command in tcgmsg on it's own.

> molpro does all of the parallelisation for you, all you have to tell it is
> how many cpus to use

Well, Molpro "tries" to do it in the correct way with LoadLeveler and PBS, but
this is not well documented. I looked into the Molpro source
(utilities/molpro.c) to see the behavior.

Cheers - Reuti

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