LAMMPS

LAMMPS is available on the following servers.

• Large-Scale Parallel Computing Server
• Accelerator Server
• Parallel Computing and Informatics Server
• Virtual Server

Available executables

Create a script file in advance.

#!/bin/sh
#PBS -l select=nodes
#PBS -q queue
#PBS -N jobname

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf  $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

aprun [ -n MPI total tasks ][ -N MPI tasks per node ] -j 1 /work/app/LAMMPS/current/src/lmp_intel_omp  < input file > output file 2> error file

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

(Example)

#!/bin/sh
#PBS -l select=1
#PBS -q P_016
#PBS -N lammps

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf  $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

aprun -n 36 -N 36 -j 1 /work/app/LAMMPS/current/src/lmp_intel_omp < in.ij > lammps.out 2> lammps.err

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

Available executables
*Note: When using 7Aug19 or 3Mar2020 on the accelerator server, switch the module to “CUDA 10.1.243”.
*Note: When using 29Oct20 or 29Sep21 on the accelerator server, switch the module to “CUDA 10.2.89”.
*Note: When using 23Jun22 on the accelerator server, switch the module to “CUDA 10.2.89”, “intel 21.5.0”, and “gcc”.
*Note: When using 2Aug23 on the accelerator server, switch the module to “CUDA 11.6.2”, “intel 22.3.1”, and “gcc”.

Create a script file in advance.

#!/bin/sh
#PBS -l select=nodes
#PBS -q queue
#PBS -N jobname

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

mpirun [ -np MPI total tasks ][ -ppn MPI tasks per node ] -hostfile $PBS_NODEFILE /usr/local/app/LAMMPS/current/src/lmp_gpu -sf gpu -pk gpu GPUs per node < input file > output file 2> error file

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

(Example) Accelerator Server

#!/bin/sh
#PBS -l select=1
#PBS -q A_004
#PBS -N lammps

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

mpirun -np 30 -ppn 30 -hostfile $PBS_NODEFILE /usr/local/app/LAMMPS/current/src/lmp_gpu -sf gpu -pk gpu 10 < in.ij > lammps.out 2> lammps.err

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

(Example) Accelerator Server(7 Aug 19)

#!/bin/sh
#PBS -l select=1
#PBS -q A_004
#PBS -N lammps

module switch cudatoolkit/9.0.176 cudatoolkit/10.1.243

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

mpirun -np 30 -ppn 30 -hostfile $PBS_NODEFILE /usr/local/app/LAMMPS/lammps-7Aug19/src/lmp_gpu -sf gpu -pk gpu 10 < in.ij > lammps.out 2> lammps.err

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

Available executables

Create a script file in advance.

#!/bin/sh
#PBS -l select=nodes
#PBS -q queue
#PBS -N jobname

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf  $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

mpirun [ -np MPI total tasks ] [ -ppn MPI tasks per node ] -hostfile $PBS_NODEFILE /usr/local/app/LAMMPS/current/src/lmp_intel_cpu_intelmpi < input file > output file 2> error file

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

(Example)

#!/bin/sh
#PBS -l select=1
#PBS -q C_002
#PBS -N lammps

DIRNAME=`basename $PBS_O_WORKDIR`
WORKDIR=/work/$USER/$PBS_JOBID
mkdir -p $WORKDIR
cp -raf  $PBS_O_WORKDIR $WORKDIR
cd $WORKDIR/$DIRNAME

mpirun -np 36 -ppn 36 -hostfile $PBS_NODEFILE  /usr/local/app/LAMMPS/current/src/lmp_intel_cpu_intelmpi < in.ij > lammps.out 2> lammps.err

cd; if cp -raf $WORKDIR/$DIRNAME $PBS_O_WORKDIR/.. ; then rm -rf $WORKDIR; fi

Available executables

Execute the commands as follows.

mpirun [ -np MPI total tasks ][ -ppn MPI tasks per node ] -hostfile hostfile /usr/local/app/LAMMPS/current/src/lmp_intel_cpu_intelmpi  < input file > output file

(Example)

mpirun -np 2  -hostfile hostfile /usr/local/app/LAMMPS/current/src/lmp_intel_cpu_intelmpi  < in.ij > lammps.out