Am 27.04.2010 um 16:57 schrieb Edmund Sumbar:
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
In the thread of the mentioned list I posted these workarounds:
http://www.beowulf.org/pipermail/beowulf/2010-January/027273.html
-- Reuti
--
Edmund Sumbar
AICT Research Support Group
esum...@ualberta.ca
780.492.9360
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