Looks to me like the problem is here:

/bin/.: Permission denied.

Appears you don't have permission to exec bash??


On Apr 7, 2014, at 1:04 PM, Blosch, Edwin L <edwin.l.blosch@lmco.com> wrote:

I am submitting a job for execution under SGE.  My default shell is /bin/csh.  The script that is submitted has #!/bin/bash at the top.  The script runs on the 1st node allocated to the job.  The script runs a Python wrapper that ultimately issues the following mpirun command:
 
/apps/local/test/openmpi/bin/mpirun --machinefile mpihosts.914 -np 48 -x LD_LIBRARY_PATH -x MPI_ENVIRONMENT=1 --mca btl ^tcp --mca shmem_mmap_relocate_backing_file -1 --bind-to-core --bycore --mca orte_rsh_agent /usr/bin/rsh --mca plm_rsh_disable_qrsh 1 /apps/local/test/solver/bin/solver_openmpi -cycles 50 -ri restart.0 -i flow.inp >& output
 
Just so there’s no confusion, OpenMPI is built without support for SGE.  It should be using rsh to launch.
 
There are 4 nodes involved (each 12 cores, 48 processes total).  In the output file, I see 3 sets of messages as shown below.  I assume I am seeing 1 set of messages for each of the 3 remote nodes where processes need to be launched:
 
/bin/.: Permission denied.
OPAL_PREFIX=/apps/local/falcon2014/openmpi: Command not found.
export: Command not found.
PATH=/apps/local/test/openmpi/bin:/bin:/usr/bin:/usr/ccs/bin:/usr/local/bin:/usr/openwin/bin:/usr/local/etc:/home/bloscel/bin:/usr/ucb:/usr/bsd: Command not found.
export: Command not found.
LD_LIBRARY_PATH: Undefined variable.
 
These look like errors you get when csh is trying to parse commands intended for bash. 
 
Does anyone know what may be going on here?
 
Thanks,
 
Ed
 
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