MPI support for PBS

At the moment PBS does not supports mpi jobs, but we can add this feature, if you can help us. We do not have access to PBS resource, which supports mpi jobs.

Will it work, if we add to the PBS start script the line:
#PBS -l nodes=xx

and we start the executable with:
mpirun -np xx ./execute.bin

?
Thanks

Hi,

This is what I did to the source code:

LinuxWrapperForGrids w = null;
try {
w = new LinuxWrapperForGrids(path);

    if (!"".equals(pJob.getConfiguredResource().getResource().trim())) {
        w.writeln("#PBS -q " +

pJob.getConfiguredResource().getResource() + " \n"); //// in this case
resource is job queue
}
w.writeln("#PBS -W stagein=localinputs" + pJob.getId() + ".tgz@" +
host + ":$HOME/" + SSHDIR + pJob.getId() + "/localinputs.tgz \n"
+ "#PBS -W stageout=" + pJob.getId() + "@" + host +
":$HOME/" + SSHDIR + " \n"
//+ "stderr.log." + pJob.getId() + "@" + host + ":$HOME/" +
SSHDIR + pJob.getId() + "/stderr.log,"
//+ "stdout.log." + pJob.getId() + "@" + host + ":$HOME/" +
SSHDIR + pJob.getId() + "/stdout.log \n"
+ "#PBS -e stderr.log." + pJob.getId() + " \n"
+ "#PBS -o stdout.log." + pJob.getId() + " \n");
if (BinaryHandler.isMPI(jsdl)){
int nodenumber =0;
try {
nodenumber =
(int)jsdl.getJobDescription().getResources().getTotalCPUCount().getUpperBoundedRange().getValue();
} catch (Exception e) {
e.printStackTrace();
}
w.writeln("#PBS -l ncpus="+nodenumber+" \n");
}

I tested it works properly.

I do not call/add the function below:

w.runMPI(binname, params, stdOut, stdErr, "" + nodenumber);

The reason is to give flexibility to the workflow developer to code their
script with the cluster environment.

Regards

On Tue, Sep 10, 2013 at 5:08 PM, imi i-mi@users.sf.net wrote:

At the moment PBS does not supports mpi jobs, but we can add this feature,
if you can help us. We do not have access to PBS resource, which supports
mpi jobs.

Will it work, if we add to the PBS start script the line:
PBS -l nodes=xx

and we start the executable with:
mpirun -np xx ./execute.bin

?
Thanks

---

• [feature-requests:#56]http://sourceforge.net/p/guse/feature-requests/56/MPI support for PBS
  *

Status: open
Created: Mon Sep 09, 2013 05:52 PM UTC by Muhammad Farhan Sjaugi
Last Updated: Mon Sep 09, 2013 05:52 PM UTC
Owner: nobody

Hi,

I'm wondering whether PBS plugins supports MPI application?

Regards

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/guse/feature-requests/56/

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--
Muhammad Farhan Sjaugi, S.Kom. M.Sc
email: fhn@cbcommunity.or.id

Thank You!

The next version will contain "#PBS -l ncpus=", but not the mpirun .

I agree. I think ncpus is more appropriate since the job scheduler can
easily assign the cpus across the cluster.

Somemore, since the introduction of multicore processors, one node is not
longer identical with one cpu, hence number

of cpus is more correct.

Regards

On Tue, Sep 10, 2013 at 6:58 PM, imi i-mi@users.sf.net wrote:

Thank You!

The next version will contain "#PBS -l ncpus=", but not the mpirun .

• [feature-requests:#56]http://sourceforge.net/p/guse/feature-requests/56/MPI support for PBS
  *

Status: open
Created: Mon Sep 09, 2013 05:52 PM UTC by Muhammad Farhan Sjaugi
Last Updated: Tue Sep 10, 2013 09:08 AM UTC
Owner: nobody

Hi,

I'm wondering whether PBS plugins supports MPI application?

Regards

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/guse/feature-requests/56/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/

--
Muhammad Farhan Sjaugi, S.Kom. M.Sc
email: fhn@cbcommunity.or.id

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