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Subject: [OMPI users] ompi + bash + GE + modules
From: Mark Suhovecky (suhovecky_at_[hidden])
Date: 2012-01-11 12:42:22


Hi-

We run OpenMPI 1.4.3 on RHEL5 in a cluster environment.
We use Univa Grid Engine 8.0.1 (an SGE spinoff) for job submission.
We've just recently begun supporting the bash shell for submitted jobs,
and are seeing a problem with submitted MPI jobs.

Our software environment is manged with Modules package (version 3.2.8),
so a typical job submission looks something like this

#!/bin/bash
#$ <some GE directives>

module load ompi

mpiexec

when the mpiexec is run, we'll see the following errors

bash: module: line 1: syntax error: unexpected end of file
bash: error importing function definition for `module'

The module int file contains this function, which is what I'm assuming all the fuss is about:

module() { eval `/opt/crc/Modules/$MODULE_VERSION/bin/modulecmd bash $*`; }
export -f module

There will be multiple instances of the error generated- for example, if I'm
running a 48 core mpi-12 job spread across 4 machines,
I'll see these errors printed 3 times. I don't see these errors
on single-machine submitted jobs.

I've found posts for this error on bash, modules, and SGE lists, and have
tried a number of suggested workarounds that all involve changing how I
source modules (in /etc/profile.d, .bash_profile, via BASH_ENV), but
none have gotten rid of this error.

Since we only see this problem with MPI, I figured it couldn't hurt to post
here and see if any of you have had this symptom, and what your solution was.

I should mention that running a submitted MPI job under csh works just fine.

Thanks for any help,

Mark

Mark Suhovecky
HPC System Administrator
Center for Research Computing
University of Notre Dame
suhovecky at nd.edu