Basic usage

LAMMPS resources:

Version 16Mar2018

submission script:

#!/bin/bash

#SBATCH --job-name=<job-name>

#SBATCH --output LAMMPS_%j.out

#SBATCH --error LAMMPS-%j.err

##SBATCH --mail-type=ALL

#SBATCH --qos=<queue>

#SBATCH --mail-user=<mail-user>

#SBATCH --ntasks=<# of MPI processes>              # Number of MPI processes (CPUs)

#SBATCH --mem-per-cpu=2G                           # Per processor memory request

#SBATCH --time=96:00:00                            # Walltime in hh:mm:ss or d-hh:mm:ss

########################Optional Part####################################

# These codes aim to make subfolders ./data and ./sav if they don't exist

if [ ! -d "./data" ]; then

   mkdir ./data

    # Will enter here if $DIRECTORY exists, even if it contains spaces

fi

if [ ! -d "./sav" ]; then

   mkdir ./sav

    # Will enter here if $DIRECTORY exists, even if it contains spaces

fi

##########################################################################

module purge

module load intel/2018  openmpi/3.0.0 lammps/13Mar18

mpiexec lmp_ufhpc -in in.* > job.log

Version 11Aug2017

submission script:

#!/bin/bash

# For lammps: must have in in.* within the directory

#!/bin/bash

#$ -N <job_name>

#$ -cwd

#$ -pe mpi <no._of_processors> (ie 8, 16)

#$ -S /bin/bash

#$ -q <queue_name> (eg. all.q or single.q)

#$ -e lammps.err

#$ -o lammps.out

module load compilers/intel_2018

LAMMPS=/share/apps/lammps/lammps-16Mar18/src/lmp_intel_cpu_intelmpi

MPIRUN=mpiexec.hydra

$MPIRUN $LAMMPS < in.*

Version 11Aug2017

submission script:

#!/bin/bash

# For lammps: must have in in.* within the directory

#!/bin/bash

#$ -N <job_name>

#$ -cwd

#$ -pe mpi <no._of_processors> (ie 8, 16)

#$ -S /bin/bash

#$ -q <queue_name> (eg. all.q or single.q)

#$ -e lammps.err

#$ -o lammps.out

module load compilers/intel_16.0.3

export LAMMPS=/share/apps/lammps/lammps-11Aug17/src/lmp_mpi

MPIRUN=mpiexec.hydra

$MPIRUN $LAMMPS < in.*

LAMMPS Kokkos version submission script

#!/bin/bash

#SBATCH --job-name=3000k_10mol_100ps_NVT_oxygen_gas

#SBATCH --output=LAMMPS_%j.out

#SBATCH --error LAMMPS-%j.err

#SBATCH --account=michael.tonks

#SBATCH --qos=michael.tonks

#SBATCH --mail-type=END,FAIL

#SBATCH --mail-user=sly1993@ufl.edu

#SBATCH --ntasks=128

#SBATCH --cpus-per-task=1

#SBATCH --distribution=cyclic:cyclic

#SBATCH --mem-per-cpu=2048mb

#SBATCH --time=15-00:00:00

#SBATCH --partition=hpg2-compute

#SBATCH --nodes=6

########################Optional Part####################################

# These codes aim to make subfolders ./data and ./sav if they don't exist

if [ ! -d "./data" ]; then

  mkdir ./data

    Will enter here if $DIRECTORY exists, even if it contains spaces

fi

if [ ! -d "./sav" ]; then

  mkdir ./sav

    Will enter here if $DIRECTORY exists, even if it contains spaces

fi

##########################################################################

export OMP_PROC_BIND=spread

module purge

#module load intel/2018 openmpi/3.1.0

module load intel/2019.1.144 openmpi/4.0.0 cmake/3.6.3

#module load python

LAMMPS=/home/sly1993/bin/lmp_12_Dec_kk_mpi

# LAMMPS=lmp_intel_cpu_intelmpi_Aug22_18_2016CHO

#LAMMPS=/home/sly1993/bin/lmp_intel_cpu_openmpi

#LAMMPS=$HPC_LAMMPS_BIN/lmp_ufhpc

#LAMMPS=/home/sly1993/lmp_ufhpc

# LAMMPS=/home/sly1993/lmp_mpi

srun --mpi=pmix_v2 $LAMMPS -k on -sf kk -pk kokkos newton on neigh half comm no -in in.relax > job.log

You must install LAMMPS on Hermes

2) Create a software folder in your home directory (ie. ‘mkdir ~/soft’)

3) Upload the tarball to the ‘soft’ directory using WinSCP (https://winscp.net/eng/download.php) or MobaXterm (http://mobaxterm.mobatek.net/)

4) Untar the lammps tarball (ie. ‘tar -xvf lammps-stable.tar.gz’)

5) Go to the lammps src folder (ie. ‘cd lammps-*/src’)

6) Compile lammps (ie. make mpi)

7) Create a bin folder in your home directory (ie. ‘mkdir ~/bin’)

8) Copy the lammps executable to the bin folder (ie. ‘cp lmp_mpi ~/bin)

9) In your working directory have your lammps input files (ie. ‘in.lammps’)

10) Create a file ‘qlammps’ in your working directory

11) Inside the qlammps enter the following –

Submission script:

#!/bin/sh

# For lammps must have in in.* within the directory

#$ -S /bin/bash

#$ -q <queue_name> (eg. all2.q, all.q, eight.q or single.q)

#$ -pe mpi <no._of_processors> (ie 8, 24 etc)

#$ -cwd

#$ -e err.lammps

#$ -N <job_name>

export LAMMPS=/home/<username>/bin/lmp_mpi

export MPIRUN=/opt/intel/openmpi-1.4.4/bin/mpirun

$MPIRUN -machinefile $TMPDIR/machines -np $NSLOTS $LAMMPS < in.*

12) To run simply enter ‘qsub qlammps’

13) To check if your job is running use ‘qstat -u <username>’

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