This is may be what's messing you up:
export PATH=/ansys_inc/v170/ansys
This sets your path to that directory exclusively, which means all sorts of
things aren't going to work. You probably want this instead:
export PATH=/ansys_inc/v170/ansys:$PATH
However, since you're not using ANSYS, you probably don't even need that line
in there.
Furthermore, your MPIRUN wrapper ($MPI_HOME/mpi/myrinet/sge_mpirun) may not
exist.
There are a bunch of other lesser oddities with your file. Do you have a local
systems administrator or expert with whom you can consult?
--
Gary Jackson, Ph.D.
ITSD/ISS
Johns Hopkins University Applied Physics Laboratory
(240) 228-9952
On 7/26/16, 2:13 PM, "sge-discuss-boun...@liverpool.ac.uk on behalf of
zist...@u.washington.edu" wrote:
>Hello,
>
>I am trying to start an LS-DYNA job through SGE but have no experience writing
>scripts and submitting jobs to a cluster. I have the basic structure figured
>out from looking at examples online, but am not able to successfully execute
>my script. Most likely something is wrong in the way I am calling mpirun and
>the LD_LIBRARY_PATH. Any suggestions on how to correct my script?
>
>Thanks!
>Jessica
>
>Command line: $ qsub -pe mpi 16 script.sh
>
>Here's my script:
>#!/bin/bash
>#$ -S /bin/bash
>#$ -cwd
>#$ -V
>#$ -N lsdyna_test5
>#$ -j y
>#$ -o lsdyna-test5.out
>
>export MPI_HOME=/opt/gridengine
>export PATH=$MPI_HOME/bin:$PATH
>export LD_LIBRARY_PATH=#$MPI_HOME/lib/linux-x64:$LD_LIBRARY_PATH
>export MPIRUN=$MPI_HOME/mpi/myrinet/sge_mpirun
>#
>export LSDYNA=/ansys_inc/v170/ansys/bin/lsdyna170
>export LSTC_LICENSE=NETWORK
>export LSTC_LICENSE_SERVER=swlic01.s.uw.edu
>export LSTC_MEMORY=auto
>export PATH=/ansys_inc/v170/ansys
>#
>$MPIRUN -TCP -np $NSLOTS -hostfile $TMPDIR/machines $LSDYNA i=LSDYNAexport.k
>echo "Program ended"
>
>Here's my output file:
>/opt/gridengine/edfault/spool/compute-2-0/active_jobs/28.1/pe_hostfile
>compute-2-0
>compute-2-0
>compute-2-0
>compute-2-0
>compute-2-0
>compute-2-0
>compute-2-0
>compute-2-0
>compute-2-12
>compute-2-12
>compute-2-12
>compute-2-12
>compute-2-12
>compute-2-12
>compute-2-12
>compute-2-12
>/opt/gridengine/edfault/spool/compute-2-0/job_scripts/28: line 23:
>opt/gridengine/mpi/myrinet/sge_mpirun
>: No such file or directory
>Program ended
>rm: cannot remove `/tmp/28.1.all.q/rsh': No such file or directory
>
>
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