I'm using SGE 6.1 and OpenMPI 1.4.1 built with gridengine support. I've got this parallel environment defined in SGE:
pe_name openmpi slots 100 user_lists NONE xuser_lists NONE start_proc_args /bin/true stop_proc_args /bin/true allocation_rule $fill_up control_slaves TRUE job_is_first_task FALSE urgency_slots min OpenMPI is installed in its own prefix (/shared/apps/openmpi/gcc-4.4/1.4.1), and can be loaded by the environment module (http://modules.sourceforge.net/) openmpi. Now I can successfully run this pe job: #!/bin/bash #$ -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? -- Frederik Himpe <fhi...@vub.ac.be>
