CMake

CMake Example: Serial LAMMPS Build

Note

This is a minimal example using the command line version of CMake to build LAMMPS with no customization.

1. To allocate an interactive job on compute node type:

   srun -p short --pty -N 1 -n 28 /bin/bash
   

2. Download the source code to LAMMPS:

   cd ~
   wget https://github.com/lammps/lammps/archive/refs/tags/stable_29Aug2024.tar.gz
   tar -xvf stable_29Aug2024.tar.gz 
   

3. Load the following modules required for building LAMMPS:

   module load gcc/11.1.0
   module load cmake/3.23.2
   

4. For LAMMPS, you will need to create and use the build directory with the following command:

   cd lammps-stable_29Aug2024
   mkdir -p build
   cd build/
   

5. Load the CMake module and use CMake to generate a build environment in a new directory.

   cmake -C ../cmake/presets/most.cmake ../cmake
   

6. Next, you will work on the compilation and linking of all objects, libraries, and executables using the selected build tool.

   cmake --build .
   make install
   

7. The cmake --build command will launch the compilation, which, if successful, will ultimately generate an executable lmpinside thebuildfolder. Now you can start running LAMMPS using ./lmp. To use the LAMMPS build, you will need to setup your environment so the binaries are in your PATH. This can be completed by including the following export statement in your sbatch script or have it as a script that you can source in your job script:

   #!/bin/bash
   #SBATCH -N 1
   #SBATCH -n 1
   #SBATCH -p short
   
   module load gcc/11.1.0
   
   export PATH=/home/$USER/lammps-stable_29Aug2024/build:$PATH
   
   cd ~
   lmp -in /home/$USER/lammps-stable_29Aug2024/examples/melt/in.melt
   

   or create the following script in your $HOME called lammps_env.sh

   #!/bin/bash
   module load gcc/11.1.0
   
   export PATH=/home/$USER/lammps-stable_29Aug2024/build:$PATH
   

   and modify your sbatch job script to source this environment file that will setup your environment for your job:

   #!/bin/bash
   #SBATCH -N 1
   #SBATCH -n 1
   #SBATCH -p short
   
   source /home/$USER/lammps_env.sh
   
   cd ~
   lmp -in /home/$USER/lammps-stable_29Aug2024/examples/melt/in.melt
   

CMake Example: Parallel LAMMPS Build

See also

Makefile Example: Installing LAMMPS

The following instructions to build LAMMPS using cmake.

1. Running LAMMPS in parallel is possible using a domain decomposition parallelization. In order to build the MPI version, first allocate an interactive job on compute node by typing:

   srun -N 1 -n 28 --constraint=ib --pty /bin/bash
   

2. Download the source code to LAMMPS:

   cd ~
   wget https://github.com/lammps/lammps/archive/refs/tags/stable_29Aug2024.tar.gz
   tar -xvf stable_29Aug2024.tar.gz 
   

3. Load the required modules required for building LAMMPS:

   module load gcc/11.1.0
   module openmpi/4.1.2-gcc11.1
   module load cmake/3.23.2
   

4. For LAMMPS, you will need to create and use the build directory with the following command:

   cd lammps-stable_29Aug2024
   mkdir -p build
   cd build/
   

5. In the build directory, run the following commands with DBUILD_MPI=yes to build the MPI version :

   cmake -C ../cmake/presets/most.cmake ../cmake -DBUILD_MPI=yes
   cmake --build .
   make install
   

6. The instructions above will create a lmp inside the build directory that is MPI compliant. To use the LAMMPS build, you will need to setup your environment so the binaries are in your PATH. This can be completed by including the following export statement in your sbatch script or have it as a script that you can source in your job script:

   #!/bin/bash
   #SBATCH -N 1
   #SBATCH -n 8
   #SBATCH -p short
   
   module load gcc/11.1.0
   module openmpi/4.1.2-gcc11.1
   
   export PATH=/home/$USER/lammps-stable_29Aug2024/build:$PATH
   
   cd ~
   mpirun -n 8 lmp_mpi -in /home/$USER/lammps-stable_29Aug2024/examples/melt/in.melt
   

   or create the following script in your $HOME called lammps_env.sh

   #!/bin/bash
   module load gcc/11.1.0
   module openmpi/4.1.2-gcc11.1
   
   export PATH=/home/$USER/lammps-stable_29Aug2024/build:$PATH
   

   and modify your sbatch job script to source this environment file that will setup your environment for your job:

   #!/bin/bash
   #SBATCH -N 1
   #SBATCH -n 8
   #SBATCH -p short
   
   source /home/$USER/lammps_env.sh
   
   cd ~
   mpirun -n 8 lmp_mpi -in /home/$USER/lammps-stable_29Aug2024/examples/melt/in.melt
   

Note

When compiled with MPI, the binaries expect mpirun or mpiexec with the number of tasks to run.

Now, you can start running LAMMPS using mpirun -n 1 ./lmp -h.