VMD-L Mailing List
From: Florian Haberl (Florian.Haberl_at_chemie.uni-erlangen.de)
Date: Wed Jan 19 2005 - 02:56:39 CST
- Next message: Justin Gullingsrud: "Re: Rotating and translating molecules .."
- Previous message: Sichun Yang: "how to display PDB with MODEL card"
- Maybe in reply to: Brian Bennion: "Re: PBS script for LINUX cluster"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Hi,
you can easily write some skript, i^ve done this here csh based:
It^s not for namd but can easily be changed:
"man csh" should help you for questions.
#!/bin/csh
echo "Running GROMACS3-MD "
echo "g3md topol[.tpr] machine"
if ( $2 == mekong ) then
set jobtype = parallel
setenv MDRUN "/home/haberl/mekong/gromacs/x86_64-unknown-linux-gnu/bin/
mdrun"
setenv MPIRUN "/opt/mpich/ch-p4/bin/mpirun -machinefile "\$PBS_NODEFILE"
-np 2"
echo running on mekong
endif
# producing submit file
cat > _$reqnam <<EOF
#!/bin/csh
cd $cwd
$MPIRUN $MDRUN -nice 4 -s $1 -o $1 -c $1_after_md
/bin/rm $cwd/_$reqnam
EOF
# Queuing with pbs
echo $queue
if ( $jobtype == parallel ) then
/opt/pbs/bin/qsub -q batch_at_server -j oe -k oe -r n -m n -N GMX$reqnam -l
nodes=1:ppn=2:$queue _$reqnam
echo "Job $1 wurde als GMX$reqnam in parallele Queue $queue geschickt..."
else
/opt/pbs/bin/qsub -q batch_at_server -j oe -k oe -r n -m n -N GMX$reqnam -l
nodes=1:$queue _$reqnam
echo "Job $1 wurde als GMX$reqnam in serielle Queue $queue geschickt..."
endif
exit
Hope this helps, you can also make your submit skript with perl or other
languages.
Greetings,
Florian
-- ------------------------------------------------------------------------------- Florian Haberl Universitaet Erlangen/ Computer-Chemie-Centrum Nuernberg Naegelsbachstr. 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- -- ------------------------------------------------------------------------------- Florian Haberl Universitaet Erlangen/ Computer-Chemie-Centrum Nuernberg Naegelsbachstr. 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de -------------------------------------------------------------------------------
- Next message: Justin Gullingsrud: "Re: Rotating and translating molecules .."
- Previous message: Sichun Yang: "how to display PDB with MODEL card"
- Maybe in reply to: Brian Bennion: "Re: PBS script for LINUX cluster"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]