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
