The image you downloaded is a relocatable and renamable file we recommend putting in a dedicated directory to easily find it. While it can be any directory, in this tutorial we will assume you put it in $HOME/apptainer-images :

mkdir -p $HOME/apptainer-images
mv lammps.sif $HOME/apptainer-images/lammps.sif

To illustrate the various commands, a set of LAMMPS input files is available in the form of an archive via this link. The archive contains the necessary files to perform molecular dynamics calculations for a Silicon/Carbon hybrid system, where atom interactions are modeled using a Modified Embedded Atom Method (MEAM) potential. The files included are as follows:

• data.meam is a file containing the positions of Silicon and Carbon atoms, as well as the definition of the simulation box.
• in.file is the main LAMMPS input script. It defines the variables required by LAMMPS and provides the necessary instructions to perform molecular dynamics calculations.
• library.meam is a file of generic parameters used by the MEAM potential to represent default interactions between a wide variety of chemical elements.
• SiC.meam is also a file defining MEAM interaction parameters. Unlike the previous file, it specifically defines interactions between Silicon and Carbon atoms.

In this tutorial, we will assume that the input files contained in this archive are in the current directory:

tar -xzf DIAMOND-tutorial.tar.gz # Extracts the content of the archive, creates ./tutorial
cd ./tutorial

One liner command#

For impatient folks, here is how to launch a parallel LAMMPS computation using the container image (previously downloaded and stored in $HOME/apptainer-images/lammps.sif). In the case where the current directory contains all mandatory LAMMPS input files :

apptainer exec $HOME/apptainer-images/lammps.sif mpirun -np <N> lmp_mpi -in <input.lammps>

Detailed usage for the LAMMPS container#

This section presents different ways to use the LAMMPS image. For more details about Apptainer commands, please look at this tutorial.

Using the LAMMPS container for sequential runs#

To run LAMMPS sequentially (ie. without parallelization) without any container, one would use the following command :

lmp_mpi -in in.file

where all LAMMPS input files (including in.file, the main input) are stored in the current directory.

To do the same inside a container, we can run three equivalent commands. In each case, we suppose the Apptainer image lammps.sif can be found at $HOME/apptainer-images/lammps.sif.

• One can use apptainer exec to execute a specific command in the container.

apptainer exec $HOME/apptainer-images/lammps.sif lmp_mpi -in in.file

• One can use apptainer run to call the container’s default command, namely the lmp_mpi executable. We also append instructions at the end of the command allowing to locate LAMMPS input file.

apptainer run $HOME/apptainer-images/lammps.sif -in in.file # "lmp_mpi" is implicitly called by "run"

• One can eventually execute the image as a binary, which is strictly identical to using apptainer run.

$HOME/apptainer-images/lammps.sif -in in.file

Using the LAMMPS container for parallel runs#

The $HOME/apptainer-images/lammps.sif image embedds a parallelized (through OpenMP and MPI) version of LAMMPS.

In the case where no containerization would be used, the typical LAMMPS call would look like :

OMP_NUM_THREADS=2 mpirun -np 4 lmp_mpi -in in.file

Using the container, the same command becomes

apptainer exec --env OMP_NUM_THREADS=2 $HOME/apptainer-images/lammps.sif mpirun -np 4 lmp_mpi -in in.file

Remark

Without any specification, LAMMPS uses by default a single OpenMP thread ($OMP_NUM_THREADS=1) and splitts MPI processes over all available cores.

Display help#

To display the container’s help message (supposing the image is stored at $HOME/apptainer-images/lammps.sif) :

apptainer run-help $HOME/apptainer-images/lammps.sif

To display the container’s meta-data (code owner, version, image author, …) :

apptainer inspect $HOME/apptainer-images/lammps.sif

To run the help command specific to the LAMMPS executable in the container (lmp_mpi) :

apptainer exec $HOME/apptainer-images/lammps.sif lmp_mpi -h

or

apptainer run $HOME/apptainer-images/lammps.sif -h

or

$HOME/apptainer-images/lammps.sif -h

Partial or total isolation#

By default, Apptainer does not fully isolate the container from the host system. One can either have partial or total isolation using respectively the flags --no-mount or --no-home and --contain-all (see this link for more information).

Whenever --containall is activated, the directory on the host machine containing LAMMPS input-files cannot be accessed from the container !

apptainer run --containall $HOME/apptainer-images/lammps.sif -in in.file # in.file not found !

It is then required to manually mount the current directory ($PWD) to the one where we are located by default in the container ($HOME) using the --bind flag. For instance :

apptainer run --containall --bind $PWD:$HOME \ # Mounting the current directory to $HOME in the container.
  $HOME/apptainer-images/lammps.sif -in in.file

in the case where LAMMPS input files are in the current directory ($PWD).

Interatomic potentials#

In LAMMPS, atom interactions are modeled using force fields (or interatomic potentials), and their parameters are specified within formatted files. The type of interaction to apply (i.e., the type of file to look for) in each case is explicitly stated in the main LAMMPS input file.

For example, in our case, the in.file input file instructs LAMMPS to model Silicon/Carbon interactions using the parameters found in SiC.meam.

During execution, the code searches for files describing the interactions in the following order:

• First, it looks for a file corresponding (location, potential type, name, …) to what’s defined in the main input (in.file). If nothing is found at the specified path in the main input file (`in.file``), for example, if the file has been inadvertently renamed:

mv SiC.meam old.meam # inadvertent renaming

then the code searches in the directory designated by the environment variable $LAMMPS_POTENTIALS.

For this specific container image, the $LAMMPS_POTENTIALS variable points inside the container to /usr/share/lammps/potentials. This directory contains the default potenital files included with the version LAMMPS present in the container.

In the (quite rare) case where one has another set of potential they wish to use by default (in $HOME/Documents/softs/lammps/potentials/ for example), it is however possible to alter this behaviour. This is achievable in two ways :

• On one hand, we can overwite the content of /usr/share/lammps/potentials by mounting another directory from the host machine to this very path (using --bind). In such cases, $LAMMPS_POTENTIALS still points towards /usr/share/lammps/potentials but the content of this directory is overwritten.

# We overwrite /usr/share/lammps/potentials in the container.
apptainer run --bind $HOME/Documents/softs/lammps/potentials/:/usr/share/lammps/potentials \
  $HOME/apptainer-images/lammps.sif -in in.file

• On the other hand, one can also redefine $LAMMPS_POTENTIALS (using --env) to make it point to another path from the host machine . Here, $LAMMPS_POTENTIALS is modified and the code looks for potentials in the newly defined path.

# If no isolation option is used, $HOME/Documents/softs/lammps/potentials/
# is shared with the container.
apptainer run --env LAMMPS_POTENTIALS=$HOME/Documents/softs/lammps/potentials/\
  $HOME/apptainer-images/lammps.sif -in in.file

• However, make sure to ensure that this new directory is also accessible within the container. For example:

# By default, /opt/lammps-potentials is not shared between the host and the container
# We have to mount this directory with --bind.
apptainer run --env LAMMPS_POTENTIALS=/opt/lammps-potentials \ # redefining $LAMMPS_POTENTIALS
  --bind /opt/lammps-potentials:/opt/lammps-potentials       \ # mount the directory in the container
  $HOME/apptainer-images/lammps.sif -in in.file

Exercices#

First exercice#

How to use the container image to run a sequential LAMMPS computation ?

Data

• The image is located at : $HOME/apptainer-images/lammps.sif
• Input files (including the main input file in.file) are located in the current directory : $PWD

Possible answers :

• apptainer run $HOME/apptainer-images/lammps.sif -in in.file
• or apptainer exec $HOME/apptainer-images/lammps.sif lmp_mpi -in in.file
• or $HOME/apptainer-images/lammps.sif -in in.file
• or

apptainer exec \
  --env OMP_NUM_THREADS=1 \
  $HOME/apptainer-images/lammps.sif \
  mpirun -np 1 lmp_mpi -in in.file

Second exercice#

How to use the container image to run a LAMMPS computation (1 OpenMP thread and 16 MPI cores) ?

Data

• The image is located at : $HOME/apptainer-images/lammps.sif
• Input files (including the main input file in.file) are located in the current directory : $PWD

Example of a possible answer :

apptainer exec \
  $HOME/apptainer-images/lammps.sif \
  mpirun -np 16 lmp_mpi -in in.file

where --env OMP_NUM_THREADS=1 is implicit and use by default by the container.

Third exercice#

How to use the container image to run a LAMMPS computation (2 OpenMP threads and 8 MPI cores) which is fully isolated from the host system ?

Data

• The image is located at : $HOME/apptainer-images/lammps.sif
• Input files (including the main input file in.file) are located at : $HOME/lammps-examples/exercice/

Example of a possible answer :

apptainer exec \
  --containall \
  --env OMP_NUM_THREADS=2 \
  --bind $HOME/lammps-examples/exercice/=$HOME \
  $HOME/apptainer-images/lammps.sif \
  mpirun -np 8 lmp_mpi -in in.file