Test-software-page

Category

Chemistry

Program On

Sapelo2

Version

3Mar2020

Author / Distributor

Please see http://lammps.sandia.gov/authors.html

Description

From http://lammps.sandia.gov/ : "LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. "

Running Program

Also refer to Running Jobs on Sapelo2.

For more information on Environment Modules on Sapelo2 please see the Lmod page.

Version 3Mar2020

• Using the foss/2019b toolchain

This version was compiled with the foss/2019b toolchain (GNU 8.3.0 compilers and OpenMPI 3.1.4) and it is installed in /apps/eb/LAMMPS/3Mar2020-foss-2019b-Python-3.7.4-kokkos/

The binary is called lmp and it was compiled with the following packages:

   'ASPHERE', 'BODY', 'CLASS2', 'COLLOID', 'COMPRESS', 'CORESHELL', 'DIPOLE',
   'GRANULAR', 'KIM', 'KSPACE', 'MANYBODY', 'MC', 'MESSAGE', 'MISC',
   'MOLECULE', 'MPIIO', 'PERI', 'POEMS', 'PYTHON', 'QEQ', 'REPLICA', 'RIGID',
   'SHOCK', 'SNAP', 'SPIN', 'SRD', 'VORONOI',
   'ATC', 'BOCS', 'CGDNA', 'CGSDK', 'COLVARS', 'DIFFRACTION', 'DPD', 'DRUDE',
   'EFF', 'FEP', 'H5MD', 'LB', 'MANIFOLD', 'MEAMC', 'MESO', 'MGPT', 'MISC',
   'MOFFF', 'MOLFILE', 'NETCDF', 'PHONON', 'PLUMED', 'PTM', 'QTB', 'REAXC',
   'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF'

To use this version of Lammps, first load the modules with

ml LAMMPS/3Mar2020-foss-2019b-Python-3.7.4-kokkos

The name of the binary is lmp and it does not work on the AMD Opteron processors. To exclude these processors, please add the following line in your job submission script:

#SBATCH --constraint=EDR

• Using the intel/2019b toolchain

This version was compiled with the intel/2019b toolchain (Intel 2019.5.281 compilers, GNU 8.3.0, and the Intel MPI) and it is installed in /apps/eb/LAMMPS/3Mar2020-intel-2019b-Python-3.7.4-kokkos/

The binary is called lmp and it was compiled with the following packages: 'ASPHERE', 'BODY', 'CLASS2', 'COLLOID', 'COMPRESS', 'CORESHELL', 'DIPOLE',

   'GRANULAR', 'KIM', 'KSPACE', 'MANYBODY', 'MC', 'MESSAGE', 'MISC',
   'MOLECULE', 'MPIIO', 'PERI', 'POEMS', 'PYTHON', 'QEQ', 'REPLICA', 'RIGID',
   'SHOCK', 'SNAP', 'SPIN', 'SRD', 'VORONOI',
   'ATC', 'BOCS', 'CGDNA', 'CGSDK', 'COLVARS', 'DIFFRACTION', 'DPD', 'DRUDE',
   'EFF', 'FEP', 'H5MD', 'LB', 'MANIFOLD', 'MEAMC', 'MESO', 'MGPT', 'MISC',
   'MOFFF', 'MOLFILE', 'NETCDF', 'PHONON', 'PLUMED', 'PTM', 'QTB', 'REAXC',
   'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF'

To use this version of Lammps, first load the modules with

ml LAMMPS/3Mar2020-intel-2019b-Python-3.7.4-kokkos

The name of the binary is lmp and it does not work on the AMD Opteron processors. To exclude these processors, please add the following line in your job submission script:

#SBATCH --constraint=EDR

File:Matlab test3.pdf

Example of shell scripts to run LAMMPS on the batch queue:

To use version 3Mar2020 with foss/2019b toolchain

To run lmp version 3Mar2020 as a parallel job, using e.g. 1 node and 16 cores per node (sub.sh)

#!/bin/bash
#SBATCH --job-name=lammpsjob          # Job name
#SBATCH --partition=batch             # Partition (queue) name
#SBATCH --constraint=EDR              # node feature
#SBATCH --nodes=1                     # Number of nodes
#SBATCH --ntasks=16                   # Number of MPI ranks
#SBATCH --ntasks-per-node=16          # How many tasks on each node
#SBATCH --cpus-per-task=1             # Number of cores per MPI rank 
#SBATCH --mem-per-cpu=600mb           # Memory per processor
#SBATCH --time=02:00:00               # Time limit hrs:min:sec
#SBATCH --output=%x.%j.out            # Standard output log
#SBATCH --error=%x.%j.err             # Standard error log
#SBATCH --mail-type=END,FAIL          # Mail events (NONE, BEGIN, END, FAIL, ALL)
#SBATCH --mail-user=username@uga.edu  # Where to send mail

cd $SLURM_SUBMIT_DIR

ml LAMMPS/3Mar2020-foss-2019b-Python-3.7.4-kokkos

mpirun lmp < file.in > file.out

Note: Here file.in and file.out are only sample filenames for the input parameters and the output file. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the email address need to be modified appropriately as well.

Documentation

Please see links from http://lammps.sandia.gov/

A user manual is available at http://lammps.sandia.gov/doc/Manual.html

Installation

Source code downloaded from https://www.lammps.org/download.html

System

64-bit Linux