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I guess this is not OpenMPI related anymore. I can repeat the essential problem interactively:
% echo $SHELL
% echo $SHLVL
% cat hello
% /bin/bash hello
% /bin/csh hello
% . hello
/bin/.: Permission denied
I think I need to hope the administrator can fix it. Sorry for the bother...
From: users [mailto:users-bounces_at_[hidden]] On Behalf Of Reuti
Sent: Monday, April 07, 2014 3:27 PM
To: Open MPI Users
Subject: EXTERNAL: Re: [OMPI users] Problem with shell when launching jobs with OpenMPI 1.6.5 rsh
Am 07.04.2014 um 22:04 schrieb Blosch, Edwin L:
> I am submitting a job for execution under SGE. My default shell is /bin/csh.
Where - in SGE or on the interactive command line you get?
> 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.
This looks really like csh is trying to interpret bash commands. In case SGE's queue is set up to have "shell_start_mode posix_compliant" set, the first line of the script is not treated in a special way. You can change the shell only by "-S /bin/bash" then (or redefine the queue to have "shell_start_mode unix_behavior" set and get the expected behavior when starting a script [side effect: the shell is not started as login shell any longer. See also `man sge_conf` => "login_shells" for details]).
BTW: you don't want a tight integration by intention?
> 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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