ARCHER logo ARCHER banner

The ARCHER Service is now closed and has been superseded by ARCHER2.

  • ARCHER homepage
  • About ARCHER
    • About ARCHER
    • News & Events
    • Calendar
    • Blog Articles
    • Hardware
    • Software
    • Service Policies
    • Service Reports
    • Partners
    • People
    • Media Gallery
  • Get Access
    • Getting Access
    • TA Form and Notes
    • kAU Calculator
    • Cost of Access
  • User Support
    • User Support
    • Helpdesk
    • Frequently Asked Questions
    • ARCHER App
  • Documentation
    • User Guides & Documentation
    • Essential Skills
    • Quick Start Guide
    • ARCHER User Guide
    • ARCHER Best Practice Guide
    • Scientific Software Packages
    • UK Research Data Facility Guide
    • Knights Landing Guide
    • Data Management Guide
    • SAFE User Guide
    • ARCHER Troubleshooting Guide
    • ARCHER White Papers
    • Screencast Videos
  • Service Status
    • Detailed Service Status
    • Maintenance
  • Training
    • Upcoming Courses
    • Online Training
    • Driving Test
    • Course Registration
    • Course Descriptions
    • Virtual Tutorials and Webinars
    • Locations
    • Training personnel
    • Past Course Materials Repository
    • Feedback
  • Community
    • ARCHER Community
    • ARCHER Benchmarks
    • ARCHER KNL Performance Reports
    • Cray CoE for ARCHER
    • Embedded CSE
    • ARCHER Champions
    • ARCHER Scientific Consortia
    • HPC Scientific Advisory Committee
    • ARCHER for Early Career Researchers
  • Industry
    • Information for Industry
  • Outreach
    • Outreach (on EPCC Website)

You are here:

  • ARCHER
  • User Guides & Documentation
  • Essential Skills
  • Quick Start Guide
  • ARCHER User Guide
  • ARCHER Best Practice Guide
  • Scientific Software Packages
  • UK Research Data Facility Guide
  • Knights Landing Guide
  • Data Management Guide
  • SAFE User Guide
  • ARCHER Troubleshooting Guide
  • ARCHER White Papers
  • Screencast Videos

Contact Us

support@archer.ac.uk

Twitter Feed

Tweets by @ARCHER_HPC

ISO 9001 Certified

ISO 27001 Certified

LAMMPS

Useful links

LAMMPS Web page
LAMMPS Documentation

Access

LAMMPS is open source software distributed under the GNU GPL. All ARCHER users have access to the LAMMPS binaries.

Running

To run LAMMPS you need to add the correct module to your environment:

module add lammps

will add the executable lmp_xc30 into your path.

By default the 17th Nov 2016 version of LAMMPS is loaded. Older versions of LAMMPS are also installed on ARCHER. The input file format changed in 2014 and therefore we have left the older versions installed so as not to impact any users running these version. We recommend you use the default version but if you need an older version, you can lost which versions of LAMMPS are installed with the following command:

module avail lammps

An example job submission script is shown below.

#!/bin/bash --login
#PBS -N lammps

# Select 128 nodes (maximum of 3072 cores)
#PBS -l select=128

#PBS -l walltime=00:05:00

# Replace this with your budget code
#PBS -A budget

# Move to directory that script was submitted from
export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)
cd $PBS_O_WORKDIR

module load lammps

# Run LAMMPS
aprun -n 3072 lmp_xc30 -in in.rhodo > rhodopsin.out

More recent versions

More recent versions than the default 17 Nov 2016 (the latest being 11 May 2018) have been compiled with the Intel compiler. As LAMMPS comes with a large number of optional packages, we encourage users to download and compile LAMMPS themselves. This section provides a brief overview of the process on ARCHER.

Download the latest stable version using git, and select the optional package you want, e.g.:

$ git clone https://github.com/lammps/lammps.git
$ cd lammps/src
$ make yes-asphere yes-granular

Take a copy of the XC30 Makefile from the centrally installed version:

$ cp /usr/local/packages/lammps/lammps-11May18/lammps/src/MAKE/MACHINES/Makefile.xc30 \
  MAKE/MACHINES

Ensure you are using the appropiate programming environment, and compile:

$ module swap PrgEnv-cray/5.2.82 PrgEnv-intel
$ module swap intel intel/17.0.3.191 
$ module load fftw
$ make xc30

Contact the helpdesk if you need assistance compiing your own version.

Default Version

The defualt version of LAMMPS (17 Nov 2016) and older version were compiled using the Gnu compiler.

Full compilation instructions for compiling can be found on ARCHER at:

/usr/local/packages/lammps/install_instructions/lammps_install_archer_17Nov2016_withshared.txt

The above file gives compilation instructions for the 17th Nov 2016 installation which includes the LAMMPS shared library. If you want to build a version without the shared library then the installation instructions for doing so can be found at:

/usr/local/packages/lammps/install_instructions/lammps_install_archer_7Dec2015.txt

Please note that as of March 2016 the default version of gcc on ARCHER became version 5.1.0. LAMMPS has been found to be unstable when built with this version and will often fail with a segmentation violation. The solution is to use an older version of gcc when building LAMMPS e.g. version 4.9.3.

module swap gcc gcc/4.9.3 

will swap from the default version of gcc to version 4.9.3

Optional packages compiled

A list of optional packages compiled:

Installed YES: package ASPHERE
Installed YES: package BODY
Installed YES: package CLASS2
Installed YES: package COLLOID
Installed YES: package COMPRESS
Installed YES: package CORESHELL
Installed YES: package DIPOLE
Installed YES: package GRANULAR
Installed YES: package KSPACE
Installed YES: package MANYBODY
Installed YES: package MC
Installed YES: package MISC
Installed YES: package MOLECULE
Installed YES: package OPT
Installed YES: package PERI
Installed YES: package QEQ
Installed YES: package REPLICA
Installed YES: package RIGID
Installed YES: package SHOCK
Installed YES: package SNAP
Installed YES: package SRD

Copyright © Design and Content 2013-2019 EPCC. All rights reserved.

EPSRC NERC EPCC