LAMMPS-Sapelo2
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: KSPACE, MISC, MOLECULE, REPLICA, RIGID, USER-MISC, USER-REAXC, REAX, MC, SRD, MEAM, USER-AWPMD, USER-COLVARS, USER-DIFFRACTION, USER-DPD, USER-DRUDE, USER-EFF, USER-FEP, USER-OMP, USER-PHONON, USER-SMD, USER-SPH, USER-TALLY, ASPHERE, PERI, and fluid membrane code.
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: KSPACE, MISC, MOLECULE, REPLICA, RIGID, USER-MISC, USER-REAXC, REAX, MC, SRD, MEAM, USER-AWPMD, USER-COLVARS, USER-DIFFRACTION, USER-DPD, USER-DRUDE, USER-EFF, USER-FEP, USER-OMP, USER-PHONON, USER-SMD, USER-SPH, USER-TALLY, ASPHERE, PERI, and fluid membrane code.
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
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://github.com/lammps/lammps/archive
System
64-bit Linux