[CIG-SHORT] Run on cluster using SLURM

[Birendra jha]

Tabrez

Thank you for the tip. However, my problem is to find out the mpirun command, not the script. I have a slurm job script that runs a simple mpi helloworld.c but I still haven't figured out the correct mpirun command to submit a pylith run. I am getting importerror with libpetsc.so. So it's probably a path issue in my mpirun command.

Thanks and regards
Birendra
--------------------------------------------
On Mon, 5/26/14, Tabrez Ali <stali at geology.wisc.edu> wrote:

 Subject: Re: [CIG-SHORT] Run on cluster using SLURM
 To: cig-short at geodynamics.org
 Date: Monday, May 26, 2014, 4:38 AM
 
 Some machines offer the
 option of running jobs interactively (for 
 testing/debugging etc.). E.g. on our cluster
 (also uses slurm) we can 
 request 2 nodes,
 each having 16 cores using the following command
 
 # salloc -N 2 -n 32 bash
 
 and then we can just run any
 MPI program normally, e.g.,
 
 # mpiexec -n 32 ./a.out
 
 or alternatively
 
 # salloc -N 2 -n 32 mpiexec -n 32 ./a.out
 
 You can investigate if
 interactive jobs are allowed your cluster.
 
 T
 
 On
 05/25/2014 01:56 PM, Birendra jha wrote:
 > I tried this as follows but it does not
 work:
 >
 > 1. Get the
 mpirun command from a cluster that uses PBS (and pylith
 works there) by
 > pylith test.cfg
 --scheduler.dry
 >
 > 2.
 Create a bash script e.g. slurm.sh that has the mpirun
 command from PBS cluster except the following parts:
 > -np ${nodes} -machinefile
 ${PBS_NODEFILE}
 > --scheduler.dry
 --nodes=1 --macros.nodes=1 --macros.job.name=
 --macros.job.id=None
 >
 > Here is my slurm.sh:
 >
 > #!/bin/bash
 > #SBATCH --job-name=testjob
 > #SBATCH --workdir=/home2/bjha/test
 > #SBATCH --output=test.out
 > #SBATCH --error=test.err
 > #SBATCH --nodes=2
 >
 #SBATCH --ntasks-per-node=4
 >
 > mpirun /home2/bjha/pylith/bin/mpinemesis
 --pyre-start
 >   /home2/bjha/pylith/bin:/home2/bjha/pylith/lib/python2.7/site-packages/pythia-0.8.1.16-py2.7.egg:/home2/bjha/pylith/lib/python2.7/site-packages:/home2/bjha/pylith/lib64/python2.7/site-packages:/home2/bjha/test:/usr/lib/python2.7:/usr/lib/python2.7/plat-linux2:/usr/lib/python2.7/lib-tk:/usr/lib/python2.7/lib-old:/usr/lib/python2.7/lib-dynload:/usr/local/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages:/usr/lib/python2.7/dist-packages/PIL:/usr/lib/python2.7/dist-packages/gst-0.10:/usr/lib/python2.7/dist-packages/gtk-2.0:/usr/lib/pymodules/python2.7:/usr/lib/python2.7/dist-packages/ubuntu-sso-client:/usr/lib/python2.7/dist-packages/ubuntuone-client:/usr/lib/python2.7/dist-packages/ubuntuone-control-panel:/usr/lib/python2.7/dist-packages/ubuntuone-couch:/usr/lib/python2.7/dist-packages/ubuntuone-installer:/usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol:/home2/bjha/pylith/lib64/python2.7/site-packages
 pythia mpi:mpistart
 >   pylith.apps.PyLithApp:PyLithApp
 test.cfg
 >
 > 3.
 Submit
 > sbatch slurm.sh
 >
 > Question: if
 Pylith/Pyre does not support SLURM--like it does PBS, SGE,
 LSF---how can I extract the mpirun command that I can submit
 to a SLURM cluster?
 >
 > Thanks and regards
 >
 Birendra
 >
 >
 --------------------------------------------
 > On Sun, 5/25/14, Birendra jha<bjha7333 at yahoo.com> 
 wrote:
 >
 >   Subject: Run on cluster using
 SLURM
 >   To: cig-short at geodynamics.org
 >   Date: Sunday, May 25, 2014,
 10:21 PM
 >
 >   Hi
 >
 >   Is it possible to submit a
 pylith run to a
 >   cluster
 that uses SLURM, just like in case of PBS or SGE?
 >
 >
 >   Thanks and regards
 >   Birendra
 >
 >
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 > CIG-SHORT mailing list
 > CIG-SHORT at geodynamics.org
 > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-short
 
 
 -- 
 No one trusts a model except the one who wrote
 it; Everyone trusts an observation except the one who made
 it- Harlow Shapley
 
 
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