Hi,
> Am 29.04.2015 um 14:43 schrieb Marlies Hankel <[email protected]>:
>
> Dear all,
>
> I found a problem with openMPI jobs when I set the $TMP/$TMPDIR to an nfs
> mounted storage. OpenMPI (version 1.8.4 with intel) writes out an error
> message that it will create some files there which might slow things down.
> And this is exactly what happens. I actually have the executables in a D
> state instead of R and things are ridiculously slow.
>
> The problem does not happen when I use qlogin and I found that $TMP/$TMPDIR
> are not set and so I assume openMPI is using local /tmp instead? Also, all is
> fine when I run directly on the nodes. Also, things wehre fien before I
> switched SGE temp to the nfs file system.
>
> I need the SGE temp directory to be the nfs mounted file system, so I cannot
> change that. But does somebody know how I can tell openMPI to use local /tmp?
>
> Out of curiosity, why does a jobs via qsub set $TMPDIR and qlogin does not?
> What is the difference between the two? I have been using the qlogin for
> testing when things have gone wrong via qsub assuming that the environment
> set up would be the same.
With `qlogin` you get a fresh shell without any set environment. You can get
all the variables there when you source in .profile resp. .bash_profile or
.bash_login:
***
MYPARENT=`ps -p $$ -o ppid --no-header`
#MYPARENT=`ps -p $MYPARENT -o ppid --no-header`
#MYPARENT=`ps -p $MYPARENT -o ppid --no-header`
MYSTARTUP=`ps -p $MYPARENT -o command --no-header`
if [ "${MYSTARTUP:0:13}" = "sge_shepherd-" ]; then
echo "Running inside SGE"
MYJOBID=${MYSTARTUP:13}
MYJOBID=${MYJOBID% -bg}
echo "Job $MYJOBID"
set -a
while read LINE; do export $LINE; done <
/var/spool/sge/${HOSTNAME%%.*}/active_jobs/$MYJOBID.1/environment
unset HISTFILE
fi
***
The number of calls to set "MYPARENT" depend on the startup ("builtin" vs.
"ssh").
-- Reuti
> Best wishes and thank you in advance for your help
>
> Marlies
>
> --
>
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> Dr. Marlies Hankel
> Research Fellow
> High Performance Computing, Quantum Dynamics& Nanotechnology
> Theory and Computational Molecular Sciences Group
> Room 229 Australian Institute for Bioengineering and Nanotechnology (75)
> The University of Queensland
> Qld 4072, Brisbane
> Australia
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> Email: [email protected]
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>
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