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OGS Container Maker

General usage

Installation

virtualenv ~/.venv/ogs-container-maker
source ~/.venv/ogs-container-maker/bin/activate
pip install ogscm

Generate container definition

$ ogscm
Creating 1 image definition(s)...
Created definition _out/docker/ubuntu_17.10/ogs-4c7de6a4/serial/conan/cmake-d41d8cd9/Dockerfile

# With user options
$ ogscm --format singularity --ompi 2.1.3 --cmake_args ' -DOGS_BUILD_PROCESSES=GroundwaterFlow'
Creating 1 image definition(s)...
Created definition _out/singularity/ubuntu_17.10/ogs-4c7de6a4/openmpi-2.1.3/conan/cmake-fde09bf7/Singularity.de

Build image

Add the --build-flag.

Convert Docker image to Singularity image:

Add the --convert-flag (requires Singularity 3.x).

Run

docker run --it --rm ogs-ompi-2.1.3
# in container:
ogs --version
singularity shell ogs-ompi-2.1.3.sif
# in container:
ogs --version
# OR directly run from host
singularity exec ogs-ompi-2.1.3.sif ogs local/path/to/square_1e0.prj

Using the combinatorial builder

Creates Docker definition files with different OpenMPI implementations and OpenGeoSys parallel configuration (from the current master), builds the docker images and converts them to Singularity images:

python build.py --ogs ufz/ogs@master --ompi 2.1.2 3.1.2 --build --convert

Check help for more options:

$ ogscm --help
usage: ogscm [-h] [--version] [--out OUT] [--file FILE] [--print]
              [--format [{docker,singularity} [{docker,singularity} ...]]]
              [--pm [{system,conan,spack,off} [{system,conan,spack,off} ...]]]
              [--ompi [OMPI [OMPI ...]]] [--ogs [OGS [OGS ...]]]
              [--cmake_args [CMAKE_ARGS [CMAKE_ARGS ...]]] [--build]
              [--upload] [--registry REGISTRY] [--convert] [--runtime-only]
              [--ccache] [--parallel PARALLEL] [--base_image BASE_IMAGE]
              [--compiler COMPILER] [--compiler_version COMPILER_VERSION]
              [--gui] [--docs] [--jenkins] [--cvode] [--cppcheck] [--iwyy]
              [--gcovr] [--mpi_benchmarks] [--dev] [--insitu]
              [--pip [package [package ...]]] [--clean] [--deploy [DEPLOY]]

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  --out OUT             Output directory (default: _out)
  --file FILE           Overwrite output recipe file name (default: )
  --print, -P           Print the definition to stdout (default: False)

Combinatorial options:
  All combinations of the given options will be generated

  --format [{docker,singularity} [{docker,singularity} ...]]
  --pm [{system,conan,spack,off} [{system,conan,spack,off} ...]]
                        Package manager to install third-party dependencies
                        (default: ['conan'])
  --ompi [OMPI [OMPI ...]]
                        OpenMPI version, e.g. 2.1.1, 2.1.5, 3.0.1, 3.1.2
                        (default: ['off'])
  --ogs [OGS [OGS ...]]
                        OGS GitHub repo in the form 'user/repo@branch' OR
                        'user/repo@@commit' to checkout a specific commit OR a
                        path to a local subdirectory to the git cloned OGS
                        sourcesOR 'off' to disable OGS building (default:
                        ['ufz/ogs@master'])
  --cmake_args [CMAKE_ARGS [CMAKE_ARGS ...]]
                        CMake argument sets have to be quoted and **must**
                        start with a space. e.g. --cmake_args ' -DFIRST=TRUE
                        -DFOO=BAR' ' -DSECOND=TRUE' (default: [''])

Image build options:
  --build, -B           Build the images from the definition files (default:
                        False)
  --upload, -U          Upload Docker image to registry (default: False)
  --registry REGISTRY   The docker registry the image is tagged and uploaded
                        to. (default: registry.opengeosys.org/ogs/ogs)
  --convert, -C         Convert Docker image to Singularity image (default:
                        False)
  --runtime-only, -R    Generate multi-stage Dockerfiles for small runtime
                        images (default: False)
  --ccache              Enables ccache build caching. (default: False)
  --parallel PARALLEL, -j PARALLEL
                        The number of cores to use for compilation. (default:
                        10)

Additional options:
  --base_image BASE_IMAGE
                        The base image. (default: ubuntu:18.04)
  --compiler COMPILER   The compiler to use. Possible options: off, gcc, clang
                        (default: gcc)
  --compiler_version COMPILER_VERSION
                        Compiler version. (default: )
  --gui                 Builds the GUI (Data Explorer) (default: False)
  --docs                Setup documentation requirements (Doxygen) (default:
                        False)
  --jenkins             Setup Jenkins slave (default: False)
  --cvode               Install and configure with cvode (default: False)
  --cppcheck            Install cppcheck (default: False)
  --iwyy                Install include-what-you-use (default: False)
  --gcovr               Install gcovr (default: False)
  --mpi_benchmarks      Installs OSU MPI benchmarks as scif app and mpi_bw,
                        mpi_ring,mpi_hello (default: False)
  --dev                 Installs development tools (vim, gdb) (default: False)
  --insitu              Builds with insitu capabilities (default: False)
  --pip [package [package ...]]
                        Install additional Python packages (default: [''])

Maintenance:
  --clean               Cleans up generated files in default directories.
                        (default: False)

Image deployment:
  --deploy [DEPLOY], -D [DEPLOY]
                        Deploys to all configured hosts (in
                        config/deploy_hosts.yml) with no additional arguments
                        or to the specified host. Implies --build and
                        --convert arguments. (default: )

Advanced usage

Build OGS from local git repo

You can use the ogs-container-maker to build multiple container images from your current source code at once. The following commands will build (-B-parameter) 4 docker container (using one serial and 3 MPI-enabled configurations), convert them to Singularity image files (-C) and strip everything out but the runtime-requirements (-R). You can find the images in _out/images.

cd ogs
git submodule update --init ThirdParty/container-maker
virtualenv .venv
source .venv/bin/activate
pip install -r ThirdParty/container-maker/requirements.txt
export PYTHONPATH="${PYTHONPATH}:${PWD}/ThirdParty/container-maker"
python ThirdParty/container-maker/ogscm/cli.py -B -C -R --ogs . --pm system --cvode --ompi off 2.1.6 3.1.4 4.0.1

Deploy image files

  • Requires rsync
  • Rename the file config/deploy_hosts_example.yml to config/deploy_hosts.yml
  • host has to be a SSH host to which you have passwordless access
  • Deploy to the host with ... -D myhost

PyPi Publication

  • Check if requirements.txt has changed, change setup.py accordingly
  • Bump version in version.py
  • python setup.py sdist
  • twine upload dist/*