Lammps Installation For Parallel Run in Linux

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code.“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, mesoscale, or continuum scale.”

Pre Installation Steps:-These installation steps are for Ubuntu/kubuntu. Change it according to your Linux operating system wherever it is required.

  • Check installed compilers
dpkg --list | grep compiler
  • Install all necessary gcc and fortran compilers
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install build-essential
gcc -v
make -v
sudo apt-get install gfortran
  • Install python, zlib.h etc.

Check if python is already installed

python --version

If it is not installed in your system, then go for these commands:-

sudo apt-get install build-essential checkinstall
sudo apt-get install libreadline-gplv2-dev libncursesw5-dev libssl-dev libsqlite3-dev tk-dev libgdbm-dev libc6-dev libbz2-dev
./configure
make
sudo checkinstall

or

sudo add-apt-repository ppa:fkrull/deadsnakes
sudo apt-get update
sudo apt-get install python2.7 #for python 2.7#

or

sudo apt-get install make build-essential zlib1g-dev libbz2-dev libreadline-dev
sudo apt-get update
sudo apt-get install sqlite3 libsqlite3-dev
sudo apt-get install libssl-dev
  • For the installation of zlib and png

for libpng use this command in your terminal:

sudo apt-get install libpng-dev
sudo apt-get install zlib1g-dev

After these installations two important installations are required,
install FFTW libraries:-

sudo apt-get install libfftw3-dev
  • Installation of openmpi

Before installation of Openmpi, you have to install some dependencies manually, please go through these steps for installation

Step – 1 : Install the basic dependency packages

sudo apt-get install libibnetdisc-dev

Step – 2 : Download the latest openmpi package from here ;

https://www.open-mpi.org/software/ompi/v4.0/

Step – 3: Extract the openmpi package and open the directory ; if you have problem in extraction, then go through this link;

https://askubuntu.com/questions/191390/how-to-use-sudo-command-to-install-tar-gz

Or use these commands for extraction:-

tar -xzf archive-name.tar.gz
cd archive-name

Step – 4: Configure the installation file, after entering the package folder by using:-

cd openmpi #if your archive-name is openmpi#
./configure --prefix="/home/$sandeep/.openmpi" #sandeep is my username, change it accordingly#
make && sudo make install

Step –5: Setup environment path and test mpirun

export PATH="$PATH:/home/user/.openmpi/bin"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"
mpirun

If everything goes fine, then you should see the following message on running the command mpirun in the terminal :

mpirun could not find anything to do
  • Addition of path manually for Openmpi (Parallel Run)

To install gedit (Text editor):-

GEDIT is a popular text editor which may be required for editing the text files inside LAMMPS libraries. Install it by using this command in the terminal;

sudo apt-get install gedit

Open home/filesyetem/etc and open terminal using:-

sudo gedit bash.bashrc

add the two path in the end:-

export PATH="$PATH:/home/user/.openmpi/bin"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"
sudo gedit profile

Add these two paths in the end:

export PATH="$PATH:/home/user/.openmpi/bin"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/user/.openmpi/lib/"

*for python related errors, you can go through these commands

sudo apt-get install python
sudo apt-get install python-dev
sudo apt-get install python-lxml
sudo apt-get install libxml2-dev
sudo apt-get install libxslt-dev
  • Lammps Installation Steps:-

Step 1. Download LAMMPS tarball from the website:-

https://lammps.sandia.gov/doc/Install_tarball.html
or clone it from github by using this command in the terminal:

git clone -b stable https://github.com/lammps/lammps.git mylammps 

This command will clone stable version of Lammps in the mylammps directory

Step 2. Extract all the files at the same place using same command which is used for extraction in pre-installation process for openmpi and fftw installation.
Step 3. Open terminal over src

make yes-std
make yes-USER-REAXC
make yes-REAX
make yes-MEAM

But sometimes make yes-std creates a problem for installation all the standard package as a bulk. So it is advised that don’t install it initially as a bulk. If it is working properly, then it is ok. Unfortunately, if it is not working properly then go through this command in src folder, and try to install all the packages manually:-

make no-std

Step 4. Enter lib in LAMMPS directory by using these commands in the terminal:-

cd mylammps
cd lib

Step 5. Enter reax and open terminal inside it and type

make -f Makefile.gfortran 

Step 6. Enter poems folder in the terminal:-

cd ..
cd poems
make -f Makefile.g++Enter
 

In meam folder,open terminal from there and type:-

make -f Makefile.gfortran

For installation of the software change working directory to src and do the following for finalizing the installation:-

make no-kokkos
make no-kim
make no-voronoi
make no-gpu
make no-mpiio
make mpi

   After make mpi command, sit relax and Lammps will install in some time for the parallel run in the system.

Running Lammps Parallel:-
Use following command for running Lammps parallelly in your system:

  mpirun -np 45 lmp_mpi -in in.lj 

Here in.lj is your input script and 45 is number of processors for parallel run. lmp_mpi executive should be in the same folder in which you are giving lammps run.
or , use this command for the default location:-

mpirun -np 45 ~/softwares/mylammps/src/lmp_mpi -in in.lj

References:-
1. Lammps Installation http:// http://lammps.sandia.gov/
2. Open Mpi Installation https://www.open-mpi.org/

Leave a Reply