Running OGS in a container

With Singularity

Prerequisites

• Linux or macOS (you may run Singularity with Vagrant on Windows as well)
• A running installation of Singularity 3.0 or higher

Get a container image

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 page.

Option: Create custom image with ogs-container-maker

Build images with ogs-container-maker on Jenkins (login required, ask Lars Bilke for access):

It will build all combinations of format, openmpi_versions and pm. When the build finishes you can download the container (*.sif files) at the jobs page under Build Artifacts.

Run OGS inside a Container (called from outside)

singularity exec --app ogs ogs-6.2.2-serial.sif 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. Everything works as expected and is transparent to the user. When ogs finishes the container stops and you returns to the host system.

The --app ogs selects a pre-defined execution environment in the container (i.e. setting the PATH to /scif/apps/ogs/bin in which all the executables are located). You could also run without the --app-parameter but then you had to specify the full executable path in the container:

singularity exec ogs-6.2.2-serial.sif /scif/apps/ogs/bin/ogs ...

Running a benchmark:

# Create output directories
mkdir -p _out _out_mpi
# Run serial benchmark
singularity exec --app ogs ogs-6.2.2-serial.sif ogs -o _out [ogs-sources]/Tests/Data/Mechanics/Linear/disc_with_hole.prj
# Run serial benchmark with output validation (via vtkdiff)
singularity exec --app ogs ogs-6.2.2-serial.sif 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 singularity exec --app ogs ogs-6.2.2-openmpi-2.1.2.sif 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:

singularity exec --app ogs ogs-6.2.2-serial.sif vtkdiff --help

You can interactively explore the container with singularity shell (you can see that you are in the container because of the Singularity [container image file]:...> prefix of the shell):

# Shell into container
singularity shell ogs-6.2.2-serial.sif
# List files in the container
Singularity ogs-6.2.2-serial.sif:...> ls /scif/apps/ogs/bin
... ogs tetgen vtkdiff
# Exit the container and get back to your hosts shell
Singularity ogs-6.2.2-serial.sif:...> exit