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Subject: Re: [OMPI users] OpenMPI & SGE: bash errors at mpirun
From: Reuti (reuti_at_[hidden])
Date: 2010-05-02 16:19:37


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
> esumbar_at_[hidden]
> 780.492.9360
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