On Tue, 27 Apr 2010, Frederik Himpe wrote:
OpenMPI is installed in its own prefix
(/shared/apps/openmpi/gcc-4.4/1.4.1), and can be loaded by the
environment module (http://modules.sourceforge.net/) openmpi.
Now I can successfully run this pe job:
#!/bin/bash
#$ -N test
#$ -q all.q
#$ -pe openmpi 20
#$ -cwd
. /etc/profile.d/modules.sh
module add sge gmp mpfr gcc openmpi/gcc-4.4
mpirun -np $NSLOTS hostname
This script results in empty test.p[oe]* files and a test.o* file with
different node hostnames, but test.e* contains these errors:
bash: module: line 1: syntax error: unexpected end of file
bash: error importing function definition for `module'
bash: module: line 1: syntax error: unexpected end of file
bash: error importing function definition for `module'
It seems somehow the module environment tools are called in a wrong way,
but I cannot figure out how this happens. These errors are triggered by
the mpirun command (commenting out mpirun and just leaving the rest of
the script intact, does not result in these errors.). I cannot reproduce
these errors with any other kind of job, nor do they happen when I login
to any node with ssh or when running the bash command.
So, what exactly does mpirun call which might trigger this error?
This seems to be a known problem for gridengine...
http://gridengine.sunsource.net/ds/viewMessage.do?dsForumId=38&dsMessageId=238562
--
Edmund Sumbar
AICT Research Support Group
esum...@ualberta.ca
780.492.9360
