Running OGS in a container

This page describes how to run OGS with the help of a Linux container (for users) with Apptainer, formerly Singularity.

Prerequisites

• A running installation of Apptainer:
  • Available on Eve (UFZ), all envinfs (UFZ), Juwels (SC Jülich), Taurus (TU Dresden).
  • See the Apptainers Admin guide for install instructions.

Get a container image

Recommended option on EVE: use prebuilt images

On the EVE cluster system (UFZ) you can use prebuilt images which can be used for PETSc-based cluster jobs.

Option: Download a release image (preferred)

Simply download an image from the releases page.

Option: Download image from the latest master-branch build

Simply download an image from the latest master-branch build:

• ogs-serial.squashfs
• ogs-mkl.squashfs (with and MKL Pardiso-support )
• ogs-petsc.squashfs (with PETSC-support)
• ogs-petsc-mkl.squashfs (with PETSC- and MKL Pardiso-support )

Run OGS inside a Container (called from outside)

# Linux only:
apptainer exec ogs-6.x.x-serial.squashfs ogs some/path/project.prj

This starts the container, mounts your home directory inside the container, passes the current working directory and runs the ogs executable (in your home directory which is mounted inside the container) with the passed project file. When using containers, everything stays transparent to the user. When OGS finishes the container stops and returns to the host system.

You can also specify the full executable path in the container:

# Works on macOS too:
apptainer exec ogs-6.x.x-serial.squashfs /usr/local/ogs/bin/ogs ...

Running a benchmark:

# Create output directories
mkdir -p _out _out_mpi
# Run serial benchmark
apptainer exec ogs-6.x.x-serial.squashfs ogs -o _out [ogs-sources]/Tests/Data/Mechanics/Linear/disc_with_hole.prj
# Run serial benchmark with output validation (via vtkdiff)
apptainer exec ogs-6.x.x-serial.squashfs ogs -o _out -r [ogs-sources]/Tests/Data/Mechanics/Linear [ogs-sources]/Tests/Data/Mechanics/Linear/disc_with_hole.prj
# Run parallel benchmark with MPI
mpirun -np 4 apptainer ogs ogs-6.x.x-openmpi-2.1.2.squashfs ogs -o _out_mpi [ogs-sources]/Tests/Data/Mechanics/Linear/disc_with_hole.prj

You can run other contained executables as well, e.g. vtkdiff:

apptainer exec ogs-6.x.x-serial.squashfs vtkdiff --help

You can interactively explore the container with apptainer shell (you can see that you are in the container because of the Apptainer> prefix of the shell):

# Shell into container
apptainer shell ogs-6.x.x-serial.squashfs
# List binaries in the container
Apptainer> ls $PATH
... ogs vtkdiff
# Exit the container and get back to your hosts shell
Apptainer> exit

Custom Python environment for the container

For certain benchmarks or tutorials you may need additional Python packages. You can create a Python virtual environment inside the container (stored on your host) and install packages via pip (inside the container):

mkdir my-working-directory && cd my-working-directory
apptainer shell my-container.squashfs

# Now in the container
virtualenv .venv
source .venv/bin/activate
pip install numpy # or whatever you need
# run ogs
exit

# Now outside the container
# The virtualenv-directory .venv still persists
# If you want to run something in the container with exec, source the venv before:
apptainer exec my-container.squashfs bash -c 'source .venv/bin/activate && ogs ...'