[Beowulf] Re: Contents of Beowulf digest Vol 17, Issue 12, hybrid (openmp+mpi) job submit (solution)

Ufuk Utku Turuncoglu turuncu at be.itu.edu.tr
Thu Jul 14 04:29:01 EDT 2005


hi,

i found the solition of my problem at the end. The problem is related 
with default shell (/bin/ksh, in NIS).
I change my default shell to tcsh and i edit the .tcshrc file to define 
the OMP_NUM_THREADS as 2.
that is all,

thanks for your help,

ufuk

my previous mail in list,

i try to run a job that is parallelized using openmp and mpi programming
interfaces (hybrid). I need to run mpi jobs in each node as an openmp job.
for this reason, i have to define OMP_NUM_THREADS environment variable for
each one of the node. first i try to put it into .profile file but it is
not sucessful. also i try to write an LSF job script and i fail too. The
LSF script as fallows,

#!/bin/ksh
#BSUB -J MM5_RUN         # job name
#BSUB -n 2               # sum of number of tasks
#BSUB -R "span[ptile=1]" # number of processes per node
#BSUB -m "cn07 cn08"     # run host
#BSUB -o mm5lsf.out      # output file name
#BSUB -q cigq            # queue name
#BSUB -L /bin/bash            #
#BSUB -E "export OMP_NUM_THREADS=2"

. ${PWD}/mm5.deck.par
time mpirun -np 2 -machinefile ../machfile ./mm5.mpp

in this case. job run in each of the specified node as a single processor
mode (except execution host, because it is same machine which is login in
and OMP_NUM_THREADS environment variable comes from .profile file).

how can i run a command (or script) in each node just before runing mpi
executable?

thanks,

Ufuk Utku Turuncoglu
Istanbul Technical University
Informatics Institute


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