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container.md 3.43 KiB 
date = "2018-11-14T15:00:13+01`:00"
title = "Running OGS in a container"
author = "Lars Bilke"
weight = 10

[menu]
  [menu.userguide]
    parent = "basics"

With Singularity

Prerequisites

  • Linux or macOS
    • Note: You can run Singularity on Windows inside a virtual machine using WSL 2 or with Vagrant
  • A running installation of Singularity 3.0 or higher
    • Available on Eve (UFZ), envinf1 (UFZ), Juwels (SC Jülich), Taurus (TU Dresden)

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.

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

Run the DataExplorer inside a Container

  • Get a Singularity container with the DataExplorer (has -gui in its name)
  • singularity exec --app ogs ogs-xxx-gui-xxx.sif DataExplorer

You may use this container on e.g. envinf1 with X11 forwarding (ssh -XY envinf1).