Normal Job Run file
com file:
%nproc=8
run File:
#PBS -l nodes=1:ppn=8
#PBS -l mem=400mb
#PBS -q mercury
#PBS -j oe
#PBS -m ea
#PBS -M yourname@youremail.com
#PBS -l walltime=24:00:00
#PBS -r y
#PBS -N yourjobname
cd $PBS_O_WORKDIR
g03 <comfilename>.com
g03_cleanup.csh <comfilename>.log
Job on Herculaneum
com file:
%NProcLinda=2
%NProcShared=4
run file:
#PBS -l nodes=2:ppn=4
#PBS -l mem=400mb
#PBS -q mercury
#PBS -j oe
#PBS -m ea
#PBS -M yourname@youremail.com
#PBS -l walltime=24:00:00
#PBS -r y
#PBS -N mytestjob
if $?PBS_NODEFILE then
foreach node ( `cat $PBS_NODEFILE | sort | uniq` )
if $?GAUSS_LFLAGS then #GAUSS_LFLAGS is required
setenv GAUSS_LFLAGS "${GAUSS_LFLAGS} ${node}"
else
setenv GAUSS_LFLAGS ${node}
endif
end
setenv GAUSS_LFLAGS "-nodelist '${GAUSS_LFLAGS}' -mp 4"
endif
cd $PBS_O_WORKDIR
g03l <comfilename>.com
g03_cleanup.csh <comfilename>.log
#PBS -l nodes=1:ppn=16
#PBS -l mem=400mb
#PBS -l walltime=200:00:00
#PBS -q mercury
#PBS -m ae
#PBS -j oe
#PBS -M yourname@youremail.com
#PBS -r y
#PBS -N mytestjob
cd $PBS_O_WORKDIR
mpiexec -np 16 sander.MPI -O \
-i input.in \
-o output.out \
-p topfile.top \
-c rstfile.rst \
-r rstfile.rst \
-x crdfile.crd \
-ref refrstfile.rst
Amber9 Job on Herculaneum
#PBS -l nodes=4:ppn=4
#PBS -l mem=400mb
#PBS -l walltime=200:00:00
#PBS -q mercury
#PBS -m ae
#PBS -j oe
#PBS -M youraccount@yourdomain.edu
#PBS -r y
#PBS -N mytestjob
cd $PBS_O_WORKDIR
mpiexec -np 16 sander.MPI -O \
-i input.in \
-o output.out \
-p topfile.top \
-c rstfile.rst \
-r rstfile.rst \
-x crdfile.crd \
-ref refrstfile.rst
Amber9 Job on Pompeii
#PBS -l nodes=16:ppn=1
#PBS -l mem=400mb
#PBS -l walltime=200:00:00
#PBS -q mercury
#PBS -m ae
#PBS -j oe
#PBS -M yourname@youremail.com
#PBS -r y
#PBS -N mytestjob
cd $PBS_O_WORKDIR
mpiexec -np 16 sander.MPI -O \
-i input.in \
-o output.out \
-p topfile.top \
-c rstfile.rst \
-r rstfile.rst \
-x crdfile.crd \
-ref refrstfile.rst