Hi Mark I wonder if you need to initialize the module command environment inside your SGE bash submission script:
$MODULESHOME/init/<shell> where <shell> is bash in this case. See 'man module' for more details. This would be before you actually invoke the module command: module load openmpi I am guessing your users' default shell is csh, and they may perhaps have a 'csh' module environment initialized by their .cshrc, but the job submission script is in bash. Anyway, we use Torque, not SGE, so this is just a guess. I hope it helps, Gus Correa On Jan 11, 2012, at 12:42 PM, Mark Suhovecky wrote: > > Hi- > > We run OpenMPI 1.4.3 on RHEL5 in a cluster environment. > We use Univa Grid Engine 8.0.1 (an SGE spinoff) for job submission. > We've just recently begun supporting the bash shell for submitted jobs, > and are seeing a problem with submitted MPI jobs. > > Our software environment is manged with Modules package (version 3.2.8), > so a typical job submission looks something like this > > #!/bin/bash > #$ <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 > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users