The permission denied looks like it is being issued against '/bin/.'
What do you get if you grep your own username from /etc/passwd? That is, % grep Edwin /etc/passwd If your shell is listed as /bin/csh, then you need to use csh's syntax, which would be % source hello (which will also work from bash). The dot command is specific to sh/bash, and csh sees it as you trying to run /bin/., which is the same as tying any directory name as a command. [roo]$ csh [roo]% /bin/. /bin/.: Permission denied. [roo]% . foo.txt /bin/.: Permission denied. [roo]% /bin /bin: Permission denied. Try specifically invoking bash, then try it % bash $ . hello On Mon, Apr 7, 2014 at 4:36 PM, Blosch, Edwin L <edwin.l.blo...@lmco.com> wrote: > I guess this is not OpenMPI related anymore. I can repeat the essential > problem interactively: > > % echo $SHELL > /bin/csh > > % echo $SHLVL > 1 > > % cat hello > echo Hello > > % /bin/bash hello > Hello > > % /bin/csh hello > Hello > > % . hello > /bin/.: Permission denied > > I think I need to hope the administrator can fix it. Sorry for the bother... > > > -----Original Message----- > From: users [mailto:users-boun...@open-mpi.org] 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? > > -- Reuti > > >> 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 >> >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> http://www.open-mpi.org/mailman/listinfo.cgi/users > > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > _______________________________________________ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
