This page describes how to run OGS with the help of a Linux container (for users). To build OGS with the help of a container go to the Developer Guide (for developers).
envinf2(UFZ), Juwels (SC Jülich), Taurus (TU Dresden).
On the EVE cluster system (UFZ) you can use prebuilt images which can be used for PETSc-based cluster jobs.
Simply download an image from the releases page.
Simply download an image from the latest master-branch build page.
# Linux only: singularity exec ogs-6.x.x-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. 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: singularity exec ogs-6.x.x-serial.sif /usr/local/ogs/bin/ogs ...
Running a benchmark:
# Create output directories mkdir -p _out _out_mpi # Run serial benchmark singularity exec ogs-6.x.x-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 ogs-6.x.x-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 ogs ogs-6.x.x-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.
singularity exec ogs-6.x.x-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.x.x-serial.sif # List files in the container Singularity ogs-6.x.x-serial.sif:...> ls /scif/apps/ogs/bin ... ogs tetgen vtkdiff # Exit the container and get back to your hosts shell Singularity ogs-6.x.x-serial.sif:...> exit
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 singularity shell my-container.sif # 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: singularity exec my-container.sif bash -c 'source .venv/bin/activate && ogs ...'
-guiin its name)
singularity exec ogs-xxx-gui-xxx.sif DataExplorer
You may use this container on e.g.
envinf1 with X11 forwarding (
ssh -XY envinf1).
Although Singularity is the preferred container runtime you can use Docker too.
docker pull registry.opengeosys.org/ogs/ogs/ogs-serial
docker run --rm -it registry.opengeosys.org/ogs/ogs/ogs-serial
You will notice that the interactive session in your container is isolated from your host, i.e. you do not have access to files on your host. You need to explicitly mount them on
mkdir ~/ogs_out docker run --rm -it -v $HOME/code/ogs6/ogs/Tests/Data:/tmp/data:ro -v $HOME/ogs_out:/tmp/out registry.opengeosys.org/ogs/ogs/ogs-serial /usr/local/ogs/bin/ogs -o /tmp/out /tmp/data/Elliptic/cube_1x1x1_SteadyStateDiffusion/cube_1e4.prj exit ls ~/ogs_out # [shows ogs generated output files]