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Subject: Re: [OMPI users] EXTERNAL: Re: Problem with shell when launching jobs with OpenMPI 1.6.5 rsh
From: Blosch, Edwin L (edwin.l.blosch_at_[hidden])
Date: 2014-04-07 16:14:01

If I create a program called hello which just contains the line "echo hello", then I do

"/bin/. hello" then I get permission denied.

Is that what you mean?

I might be lost in esoteric corners of Linux. What is "." under /bin ? There is no program there by that name. I've heard of "." as a shell built-in, but I haven't seen it prefixed by /bin before.

From: users [mailto:users-bounces_at_[hidden]] On Behalf Of Ralph Castain
Sent: Monday, April 07, 2014 3:10 PM
To: Open MPI Users
Subject: EXTERNAL: Re: [OMPI users] Problem with shell when launching jobs with OpenMPI 1.6.5 rsh

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_at_[hidden]<mailto:edwin.l.blosch_at_[hidden]>> 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?



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