Sample Jobs
Last update: Apr 23, 2024

Introduction
Sample input and jobscript are also available for each installed application. Those samples can also be used as a template
file for your jobs. In this page, we will show you procedures how to run those sample jobs using GAMESS and Gromacs
examples. As for Gaussian, please check the special way using g16sub/g09sub first.

List of Installed Applications
There are several ways to know which applications are installed.

1. at web page
You can see the application list in this page.

2. module avail"module avail" command will give you a (long) list of applications. Applications which should be submitted as jobs would
be listed in "/apl/modules/apl" category, which is colored with red in the box below.
[user@ccfep3 ~]$ module avail---------------------------- /apl/modules/defaults ----------------------------2022----------------------------- /apl/modules/oneapi -----------------------------compiler-rt/2022.0.2 intelmpi/2021.7.1

mkl/2022.0.2 tbb/2021.7.1

compiler-rt/2022.2.1 intelpython/2022.0.0 mkl/2022.2.1
...
(中略)
...
------------------------------- /apl/modules/apl ------------------------------amber/20u13

gromacs/2021.4-CUDA

amber/22u1

gromacs/2021.6

cp2k/9.1

gromacs/2021.6-CUDA

openmolcas/v21.10

cp2k/9.1-impi

gromacs/2022.4

crystal/17-1.0.2

gromacs/2022.4-CUDA

gamess/2021R1

GRRM/14-g09

nwchem/6.8

nwchem/7.0.2
openmolcas/v22.10
orca/4.2.1
orca/5.0.3

gamess/2022R2GRRM/17-g09

qe/6.8gaussian/09e01

GRRM/17-g16

qe/6.8-gpu

gaussian/16b01

lammps/2021-Sep29

gaussian/16c01

lammps/2021-Sep29-CUDA siesta/4.1.5-mpi

gaussian/16c02
genesis/2.0.3

lammps/2022-Jun23

reactionplus/1.0
siesta/4.1.5-omp

lammps/2022-Jun23-CUDA turbomole/7.6-mpi

genesis/2.0.3-CUDA namd/2.14
gromacs/2021.4

turbomole/7.6-serial

namd/2.14-CUDA

turbomole/7.6-smp

Key:loaded directory/ auto-loaded default-version modulepath[user@ccfep3 ~]$(Press "q" key or scroll to the bottom to quit "module avail" command.")

3. see /apl directly
Non-OS standard applications and libraries are installed under /apl. You can directly check the list there.
[user@ccfep3 /apl]$ ls
amber crystal gaussian hpc-x

mvapich nwchem

orca reactionplus

aocc cuda

genesis lammps namd

aocl diracgromacs modules nbo

cp2k gamess GRRM

oneapipbs siesta

openmolcas psi4 turbomole

molpro nvhpc

openmpi

qevmdtest[user@ccfep3 /apl]$ ls /apl/amber
20u13 22u1
[user@ccfep3 /apl]$ ls /apl/amber/20u13
amber.csh build

configure lib64

READMEamber.shdat

recipe_at update_ambercmakelogs

AmberTools CMakeLists.txt doc

Makefile samples

benchmarks cmake-packaging includebin

config.hlib

updateutils

miniconda sharewget-log

miniforge src[user@ccfep3 /apl]$

Location of Sample Files
Sample input for a certain application is generally available under /apl/(application name)/(version/revision)/samples
directory.
Example: check sample directory of gromacs 2021.6.
[user@ccfep3 /apl]$ ls /aplamber crystal gaussian hpc-x

mvapich nwchem

aocc cuda

genesis lammps namd

aocl diracgromacs modules nbo

cp2k gamess GRRM

oneapiorca reactionplus
pbs siesta

openmolcas psi4 turbomole

molpro nvhpc

openmpi

qevmd[user@ccfep3 /apl]$ ls /apl/gromacs/
2021.4 2021.4-CUDA 2021.6 2021.6-CUDA 2022.4 2022.4-CUDA[user@ccfep3 /apl]$ ls /apl/gromacs/2021.6
bin include lib64 samples share[user@ccfep3 /apl]$ ls /apl/gromacs/2021.6/samples/
conf.grosample-mpi.csh sample-threadmpi.csh topol.top

grompp.mdp sample-mpi.sh sample-threadmpi.sh(package name with "-CUDA" is GPU-enabled version.)

Files in Sample Directory
In a sample directory, there is only one input data set in principle.However, there can be several job scripts in a sample
directory (same input but using different shell, hardware, setting method).
Examples:sample.sh => /bin/sh sample script
sample.csh => /bin/csh sample script
sample-gpu.sh => /bin/sh sample script using GPU
Reading and comparing those files might be helpful to you.

Example: gamess 2022R2
There are three scripts (sample.csh, sample-module.sh, sample.sh) for GAMESS 2022R2.
[user@ccfep4 ~]$ ls /apl/gamess/2022R2/samples/
exam01.inp sample.csh sample-module.sh sample.sh

Example: gromacs 2021.6
There are four different scripts for Gromacs 2021.6.
[user@ccfep4 samples]$ ls
conf.grosample-mpi.csh sample-threadmpi.csh topol.top

grompp.mdp sample-mpi.sh sample-threadmpi.sh-mpi => parallel version with Open MPI (HPC-X); multinode parallel possible.
-threadmpi => thread MPI parallel version (multinode parallel not available).

Run Sample: Basics
copy files to your directory.
"cd" to the directory, where the copied files exist
submit a job (e.g. jsub sample.sh)(Usually, you can run samples on the login servers (e.g. sh ./sample.sh))
The way of # of CPUs specification might be different between "jsub" and "sh" cases.
GPU runs are not possible on ccfep. Please login to ccgpu from ccfep (ssh ccgpu).
Ccgpu is equipped with two GPU cards. MPI-parallel tests are also possible.

Example 1: gamess2022R2
We here assume your test directory is ~/gamess2022R2_test.
[user@ccfep4 ~]$ mkdir -p ~/gamess2022R2_test[user@ccfep4 ~]$ cd ~/gamess2022R2_test[user@ccfep4 gamess2022R2_test]$ cp /apl/gamess2022R2/samples/* .
[user@ccfep4 gamess2022R2_test]$ ls
exam01.inp sample-module.sh sample.csh sample.sh[user@ccfep4 gamess2022R2_test]$ jsub sample.sh
4008689.cccms1

Status of submitted job can be checked with "jobinfo -c".
[user@ccfep4 gamess2022R2_test]$ jobinfo -c-------------------------------------------------------------------------------Queue Job ID Name

Status CPUs User/Grp

Elaps Node/(Reason)-------------------------------------------------------------------------------H

4008689 sample.shRun

4 user/----- ccc001-------------------------------------------------------------------------------[user@ccfep4 gamess2022R2_test]$

If the system is not terribly crowded, the job will soon finish and you can get the result.
[user@ccfep4 gamess2022R2_test]$ ls ~/gamess2022R2_test
exam01.dat exam01.log sample-module.sh sample.sh.e4008689
exam01.inp sample.csh sample.shsample.sh.o4008689[user@ccfep4 gamess2022R2_test]$

Reference: sample.csh (Explanations colored with blue do not exist in the original file.)#!/bin/sh#PBS -l select=1:ncpus=4:mpiprocs=4:ompthreads=1 # <= 4-core job (in a vnode)#PBS -l walltime=24:00:00 # <= time limit of this jobs is 24 hours
if [ ! -z "${PBS_O_WORKDIR}" ]; thencd ${PBS_O_WORKDIR} # <= cd to directory where you submit job (standard action for PBS jobs)
NCPUS=$(wc -l < ${PBS_NODEFILE})
else
NCPUS=4 # <= these two lines are setting for non-queuing system run
export OMP_NUM_THREADS=1
fi
module -s purge
module -s load intelmpi/2021.7.1# <= load required packages; depend on application

module -s load compiler-rt/2022.2.1# processes per node; equal to mpiprocs value
PPN=4 # <= PPN = process per node; set to the mpiprocs value defined in the beginning
VERSION=2022R2
RUNGMS=/apl/gamess/${VERSION}/rungms
INPUT=exam01.inp

${RUNGMS} ${INPUT:r} 00 $NCPUS $PPN >& ${INPUT%.*}.log # <= run GAMESS here

Example 2: gromacs 2021.6
We here assume your test directory is ~/gromacs2021.6_test.
[user@ccfep4 ~]$ mkdir -p ~/gromacs2021.6_test[user@ccfep4 ~]$ cd ~/gromacs2021.6_test[user@ccfep4 gromacs2021.6_test]$ cp /apl/gromacs/2021.6/samples/* .
[user@ccfep4 gromacs2021.6_test]$ ls
conf.grosample-mpi.csh sample-threadmpi.csh topol.top

grompp.mdp sample-mpi.sh sample-threadmpi.sh[user@ccfep4 gromacs2021.6_test]$ jsub sample-mpi.sh
4008695.ccpbs1

Status of submitted job can be checked with "jobinfo -c".
[user@ccfep3 gromacs2021.6_test]$ jobinfo -c-------------------------------------------------------------------------------Queue Job ID Name

Status CPUs User/GrpElaps Node/(Reason)-------------------------------------------------------------------------------H

4008695 sample-mpi.sh Run

6 user/----- ccc001--------------------------------------------------------------------------------

If the system is not terribly crowded, the job will soon finish and you can get the result.
[user@ccfep4 gromacs2021.6_test]$ ls ~/gromacs2021.6_test
conf.gromd.logsample-mpi.sh.e4008695 topol.top

confout.gro mdout.mdp
ener.edr

mdrun.out

sample-mpi.sh.o4008695 topol.tpr
sample-threadmpi.csh

grompp.mdp sample-mpi.csh sample-threadmpi.sh
grompp.out sample-mpi.shstate.cpt[user@ccfep4 gromacs2021.6_test]$

Reference: sample-mpi.sh (Explanation colored with blue do not exist in the original file.)#!/bin/sh#PBS -l select=1:ncpus=6:mpiprocs=6:ompthreads=1 # <= 6 core jobs (6 MPI processes)#PBS -l walltime=00:30:00 # <= time limit is 30 minutes
if [ ! -z "${PBS_O_WORKDIR}" ]; then
cd "${PBS_O_WORKDIR}"fi# non-module version. /apl/hpc-x/2.13.1/hpcx-rebuild-gcc11.sh # <= load Open MPI (HPC-X) environment
hpcx_load
export LD_LIBRARY_PATH="/apl/pbs/22.05.11/lib:${LD_LIBRARY_PATH}". /apl/gromacs/2021.6/bin/GMXRC # <= load Gromacs related setting## module version#module -s purge#module -s load --auto gromacs/2021.6 # <= setting above is also defined in this module##############################################################################
N_MPI=6
N_OMP=1
gmx grompp -f grompp.mdp >& grompp.out
mpirun -v -n ${N_MPI} gmx_mpi mdrun -ntomp ${N_OMP} -s topol >& mdrun.out

Tips about job scripts
You can found some examples of job header lines in this page.