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Apptainer and Environment Modules

On the new platform, environment modules integrate with Apptainer to provide consistent, containerized runtimes for HPC applications. When you module load an application, the module system:

  • Resolves and loads required dependencies (e.g., gcc, mpi)
  • Sets per-application environment variables (e.g., $EXEC_CMD_VASP, $EXEC_CMD_QE)
  • Updates a convenience variable $EXEC_CMD to the most recently loaded application's command
  • Maintains $EXEC_CMDS as a colon-separated list of loaded application exec variables (e.g., EXEC_CMD_VASP:EXEC_CMD_QE)

Example session

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>>>> module load espresso/6.3-gcc-openmpi-openblas
The module gcc/11.2.0 is loaded
The module mpi/ompi-4.1.1 is loaded
The module espresso/6.3-gcc-openmpi-openblas is loaded

Loading espresso/6.3-gcc-openmpi-openblas
  Loading requirement: gcc/11.2.0 mpi/ompi-4.1.1

>>>> echo $EXEC_CMD
apptainer exec --bind /export,/scratch,/dropbox,/cluster-001-share \
  /export/compute/software/applications/espresso/6.3-gcc-openmpi-openblas/image.sif

>>>> echo $EXEC_CMDS
EXEC_CMD_QE

>>>> echo $EXEC_CMD_QE
apptainer exec --bind /export,/scratch,/dropbox,/cluster-001-share \
  /export/compute/software/applications/espresso/6.3-gcc-openmpi-openblas/image.sif

>>>> module load vasp/5.4.4-gcc-openmpi-openblas-fftw-scalapack
The module vasp/5.4.4-gcc-openmpi-openblas-fftw-scalapack is loaded

>>>> echo $EXEC_CMDS
EXEC_CMD_VASP:EXEC_CMD_QE

>>>> echo $EXEC_CMD
apptainer exec --bind /export,/scratch,/dropbox,/cluster-001-share \
  /export/compute/software/applications/vasp/5.4.4-gcc-openmpi-openblas-fftw-scalapack/image.sif

>>>> echo $EXEC_CMD_VASP
apptainer exec --bind /export,/scratch,/dropbox,/cluster-001-share \
  /export/compute/software/applications/vasp/5.4.4-gcc-openmpi-openblas-fftw-scalapack/image.sif

Notes: - The Apptainer command binds common platform directories into the container (e.g., /export, /scratch, /dropbox, and the cluster share such as /cluster-001-share). - $EXEC_CMD always points to the last loaded application's container exec command. - Use per-app variables (e.g., $EXEC_CMD_VASP, $EXEC_CMD_QE) when you need to be explicit in job scripts.

Using in job scripts

See: - Jobs via Command Line - Batch Scripts > General Structure - Batch Scripts > Sample Scripts