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Job Examples

Gaussian Job Examples

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


Amber Job Examples
Amber9 Job on Olympus
#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