VMD-L Mailing List

From: Florian Haberl (Florian.Haberl_at_chemie.uni-erlangen.de)
Date: Wed Jan 19 2005 - 02:56:39 CST

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
 -------------------------------------------------------------------------------
-- 
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 Florian Haberl                            Universitaet Erlangen/
 Computer-Chemie-Centrum    Nuernberg
                                                      Naegelsbachstr. 25
                                                      D-91052 Erlangen
  Mailto: florian.haberl AT chemie.uni-erlangen.de
 -------------------------------------------------------------------------------