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LAMMPS - 22Aug2018

Table of Contents

Basic information

  • Official Website: https://lammps.sandia.gov/
  • License: GNU GENERAL PUBLIC LICENSE (GPL)
  • Installed on: Apolo II <about_apolo-ii> , Cronos <about_cronos>

Tested on (Requirements)

  • OS base: CentOS (x86_64) ≥ 6.6 (Rocks 6.2)
  • Compiler: Intel MPI Library ≥ 17.0.1
  • Math Library: Intel MKL ≥ 17.0.1

Installation

The following procedure will compile LAMMPS as an executable, using the Intel MPI implementation and MKL as the Linear Algebra Library.

  1. Load the necessary modules for compiling LAMMPS

    $ module load impi
$ module load mkl
$ module load python/3.x.x

    Note

    The installation script requires Python ≥ 3.0

  2. Download and compile the desired packages before compiling lammps.

    The flag yes-all activates the compilation of all the packages. However, some lammps packages require external libraries and additional configuration procedures.

    After executing yes-all, these packages that require additional configuration procedures can be disabled executing make no-lib.

    These make options (yes-all, no-lib) are used to reproduce the list of packages present in LAMMPS Ubuntu prebuild version. For more information read1.

    $ git clone -b stable_22Aug2018 https://github.com/lammps/lammps.git
$ cd lammps/src
$ make yes-all     # install all pkgs in src dir
$ make no-lib      # remove all pkgs with libs

  3. To check which packages are going to be installed, execute:

    $ make ps

  4. If you want to install an additional package, read the specific procedure in2.

    After following the procedure described in the page, execute:

    $ make yes-<LIB_NAME>

    Example for USER_COLVARS

    $ make yes-user-colvars

    Verify again executing make ps that you have enabled correctly the installation of the desired packages.

    Warning

    If you have an existing version of LAMMPS and you want to add a new package it's necessary to recompile LAMMPS.

  5. Compile LAMMPS with it's packages. This procedure will compile it using the Intel architecture options defined by default in src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi

    $ make intel_cpu_intelmpi

    Note

    icpc: command line warning #10006: ignoring unknown option '-qopt-zmm-usage=high'

    This message appears when you compile LAMMPS using the intel_cpu_intelmpi architecture but the Intel processor doesn't have the AVX512 instruction set. If this is the case, just ignore the warning message. For more information about the flag qopt-zmm-usage read3.

  6. If you want to install LAMMPS in a specific directory, create the directories and copy the binary as follows:

    $ mkdir -p <INSTALL_DIR>/bin
$ cp lmp_intel_cpu_intelmpi <INSTALL_DIR>/bin/
$ cd <INSTALL_DIR>/bin/
$ ln -s lmp_intel_cpu_intelmpi lammps

    Note

    For more information about the installation process, read the official page4.

  7. Finally, if the program will be used with Environment modules, create the respective module.

Alternative Installation modes

  • If you want to compile LAMMPS as a static library called liblammps_machine.a, then execute:

    $ make mode=lib <machine>

  • If you want to compile LAMMPS as a shared library called liblammps_machine.so, then execute:

    $ make mode=shlib <machine>

Test LAMMPS

After installing LAMMPS, run the benchmarks present in the repository.

$ sbatch example.sh

The following code is an example for running LAMMPS using SLURM:

src/lammps-bench.sh

Modulefile

Apolo II

src/22Aug18_apolo

Cronos

src/22Aug18_cronos

References

Authors

  1. Download an executable for Linux, Pre-built Ubuntu Linux executables -LAMMPS documentation. Retrieved January 17, 2019, from https://lammps.sandia.gov/doc/Install_linux.html#ubuntu↩

  2. Include packages in build - LAMMPS documentation Retrieved June 10, 2019, from https://lammps.sandia.gov/doc/Build_package.html↩

  3. Intel® C++ Compiler 19.0 Developer Guide and Reference, qopt-zmm-usage, Qopt-zmm-usage. Retrieved January 17, 2019, from https://software.intel.com/en-us/cpp-compiler-developer-guide-and-reference-qopt-zmm-usage-qopt-zmm-usage↩

  4. Download source via Git - LAMMPS documentation. Retrieved January 17, 2019, from https://lammps.sandia.gov/doc/Install_git.html↩