Re: [Starcluster] Multiple MPI jobs on SunGrid Engine with StarCluster

From: Damian Eads <no email>
Date: Mon, 21 Jun 2010 17:14:52 -0700

Hi Justin,

Please see the attached image. It shows the output of top when I try
to start a 20 process OpenMPI job using qsub. Notice that it doesn't
spread the processes across the cluster.

root_at_domU-12-31-39-0E-29-81:/data/tesla# start-large.sh birds-1.cfg

root_at_domU-12-31-39-0E-29-81:/data/tesla# cat
../teslaconf/scripts/start-large.sh
#!/bin/bash

NP=20


for i in $*
do
  JOBNAME=`echo $i | sed 's/\.cfg//g' | sed 's/^.*\///g'`
  OUTFILE=/tmp/az-${JOBNAME}.out
  ERRFILE=/tmp/az-${JOBNAME}.err
  export PATH=/data/teslaconf/scripts:/data/tesla:$PATH
  CMD="qsub -N ${JOBNAME} -pe orte ${NP} -o ${OUTFILE} -e ${ERRFILE}
-wd /data/tesla -V ../teslaconf/scripts/tesla-train.sh ${NP} $i"
  echo Running $CMD
  $CMD
done

root_at_domU-12-31-39-0E-29-81:/data/tesla# cat
../teslaconf/scripts/tesla-train.sh
#!/bin/bash

PYTHON_VERSION=python2.6
PYTHONPATH=/data/prefix/python2.6/site-packages

mpirun -hostfile /data/teslaconf/machines -wd /data/tesla \
       -n $1 -x PYTHONPATH=/data/prefix/lib/python2.6/site-packages
./tesla-train --config $2

Ideas?

Thanks,

Damian

On Mon, Jun 21, 2010 at 10:02 AM, Damian Eads <eads_at_soe.ucsc.edu> wrote:
> Hi Justin,
>
> Thank you for your explanation on MPI/SGE integration. A few quick questions:
>
> On Mon, Jun 21, 2010 at 9:46 AM, Justin Riley <jtriley_at_mit.edu> wrote:
>> So the above explains the parallel environment setup within SGE. It
>> turns out that if you're using a parallel environment with OpenMPI, you
>> do not have to specify --byslot/--bynodes/-np/-host/etc options to
>> mpirun given that SGE will handle the round_robin/fill_up modes for you
>> and automatically assign hosts and number of processors to be used by
>> OpenMPI.
>>
>> So, for your use case I would change the commands as follows:
>> - -----------------------------------------------------------------
>>    qsub -pe orte 24 ./myjobscript.sh experiment-1
>>    qsub -pe orte 24 ./myjobscript.sh experiment-2
>>    qsub -pe orte 24 ./myjobscript.sh experiment-3
>>    ...
>>    qsub -pe orte 24 ./myjobscript.sh experiment-100
>>
>> where ./myjobscript.sh calls mpirun as follows
>>
>>    mpirun -x PYTHONPATH=/data/prefix/lib/python2.6/site-packages
>>                 -wd /data/experiments ./myprogram $1
>
> So I don't need to specify the number of slots to use in mpirun? The
> Sun GridEngine will somehow pass this information to mpirun? Is the
> mpirun argument -n 1 by default?
>
>> - -----------------------------------------------------------------
>> NOTE: You can also pass -wd to the qsub command instead of mpirun and
>> along the same lines I believe you can pass -v option to qsub rather
>> than -x to mpirun. Neither of these should make a difference, just
>> shifts where the -x/-wd concern is (from MPI to SGE).
>
> Good idea. This will clean things up a bit. Thanks for suggesting it.
>
>> I will add a section to the docs about using SGE/OpenMPI integration on
>> StarCluster based on this email.
>>
>>> Perhaps if carefully
>>> used, this will ensure that there is a root MPI process running on the
>>> master node for every MPI job that's simultaneously running.
>>
>> Is this a requirement for you to have a root MPI process on the master
>> node for every MPI job? If you're worried about oversubscribing the
>> master node with MPI processes, then this SGE/OpenMPI integration should
>> relieve those concerns. If not, what's the reason for needing a 'root
>> MPI process' running on the master node for every MPI job?
>
> It's not a requirement but reflects some ignorance on my part. <aybe
> I'm confused about why the first node is called master. I was assuming
> it had that name because it was performing some kind of special
> coordination.
>
> Do I still need to provide the -hostfile option? Or is this automatic now?
>
> Thanks a lot!
>
> Damian
>
> -----------------------------------------------------
> Damian Eads                           Ph.D. Candidate
> University of California             Computer Science
> 1156 High Street         Machine Learning Lab, E2-489
> Santa Cruz, CA 95064    http://www.soe.ucsc.edu/~eads
>

-- 
-----------------------------------------------------
Damian Eads                           Ph.D. Candidate
University of California             Computer Science
1156 High Street         Machine Learning Lab, E2-489
Santa Cruz, CA 95064    http://www.soe.ucsc.edu/~eads

Received on Mon Jun 21 2010 - 20:14:53 EDT