[gmx-users] chaining jobs in queuing systems
Dallas B. Warren
Dallas.Warren at vcp.monash.edu.au
Fri Dec 2 02:47:25 CET 2005
I pass the following command to submit a job ...
qsub -v NJOBS=##,NJOB=## script.tcsh
And the script contains the following code (plus some other stuff which
is standard anyway). Adjust to suit your particular situation,
simulation, computer etc. If you use a computing center, then those
that run it will be able to provide you with advice etc. The one I use
actually wrote this script for me.
#!/bin/tcsh
#PBS -v NJOBS,NJOB
#
# check to ensure NJOB and NJOBS is defined
#
if (! $?NJOBS ) then
$ECHO "\nNJOBS (total number of jobs in sequence) is not set -
defaulting to 1\n"
setenv NJOBS 1
endif
if (! $?NJOB) then
$ECHO "\nNJOB (current job number in sequence) is not set -
defaulting to 1\n"
setenv NJOB 1
endif
#
# determine number for last job
#
@ lastnjob = $NJOB
@ lastnjob--
setenv LASTNJOB $lastnjob
#
# do correct preprocessing if first simulation block
#
if ( $NJOB < 1 ) then
grompp -f md -c md_$LASTNJOB -t md_$LASTNJOB -p topology -e
md_$LASNJOB -o md_$NJOB -np ##
else
tpbconv -s md_$LASTNJOB.tpr -f md_$LASTNJOB.trr -o md_$NJOB.tpr
-extend #####
endif
#
# perform the simulation
#
sleep 5
mpirun mdrun -deffnm md_$NJOB
#
# Check exit status
#
set errstat=$?
if ($errstat != 0) then
sleep 5
$ECHO "\nJob number $NJOB returned an error status $errstat -
stopping job.\n"
exit $errstat
endif
#
# Now increment NJOB and submit subsequent jobs
#
if ( $NJOB < $NJOBS ) then
@ njob=$NJOB
@ njob++
setenv NJOB $njob
$ECHO "\nSubmitting job number $NJOB in sequence of $NJOBS jobs\n"
qsub $PBS_JOBNAME
else
$ECHO "\nFinished last job in sequence of $NJOBS jobs\n"
endif
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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