ogscm 2.4.11

OGS Container Maker

OGS Container Maker

General usage

Installation

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

If you build images with Docker (--build-parameter, see below) you need to make sure that you have setup Docker to be runnable without sudo!

Apple ARM specific:

export DOCKER_BUILDKIT=1
docker buildx create --use --name=qemu
docker buildx inspect --bootstrap

Generate container definition

OGS Container Maker has builtin recipes. You need to specify the recipes to use as command arguments. Each of recipes adds options to the tool. Typically you want to start with a compiler. Add the compiler.py recipe and the --help-flag to get more options:

$ ogscm compiler.py --help
...
compiler.py:
  --compiler COMPILER   The compiler to use. Possible options: off, gcc,
                        clang (default: gcc)
  --compiler_version COMPILER_VERSION
                        Compiler version. (default: )
  --iwyy                Install include-what-you-use (requires clang
                        compiler) (default: False)

After specifying the compiler recipe (and optionally setting a non-default compiler and version) you may want to add the ogs.py recipe:

$ ogscm compiler.py ogs.py --help
...
ogs.py:
  --pm {system,off}
                        Package manager to install third-party dependencies
                        (default: conan)
  --ogs OGS             OGS repo on gitlab.opengeosys.org 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 sources OR 'off'
                        to disable OGS building OR 'clean' to disable OGS
                        and all its dev dependencies (default:
                        ogs/ogs@master)
  --cmake_args CMAKE_ARGS
                        CMake argument set has to be quoted and **must**
                        start with a space. e.g. --cmake_args '
                        -DFIRST=TRUE -DFOO=BAR' (default: )
...

Please note that the order of the recipes given on the command line is important. The typical order for the current builtin recipes is compiler.py mpi.py ogs.py ogs_jupyter.py.

To generate a Dockerfile with the default parameters:

$ ogscm compiler.py ogs.py
Evaluating compiler.py
Evaluating ogs.py
Created definition _out/docker/gcc/default/ogs-d18c786e/conan/Dockerfile

With some options (and the mpi.py-recipe):

$ ogscm compiler.py mpi.py ogs.py --ompi 4.0.5 --cmake_args ' -DOGS_BUILD_PROCESSES=LiquidFlow'
Evaluating compiler.py
Evaluating mpi.py
Evaluating ogs.py
Created definition _out/docker/gcc/10/openmpi/4.0.5/ogs-d18c786e/conan/cmake-702517b3/Dockerfile

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

All options

All options for current builtin recipes:

$ ogscm compiler.py mpi.py ogs.py --help
Evaluating compiler.py
Evaluating mpi.py
Evaluating ogs.py
usage: ogscm [-h] [--version] [--out OUT] [--file FILE] [--print] [--format {docker,singularity}] [--base_image BASE_IMAGE] [--runtime_base_image RUNTIME_BASE_IMAGE]
             [--cpu-target {a64fx,aarch64,arm,broadwell,bulldozer,cannonlake,cascadelake,core2,excavator,haswell,i686,icelake,ivybridge,k10,mic_knl,nehalem,nocona,pentium2,pentium3,pentium4,piledriver,power7,power8,power8le,power9,power9le,ppc,ppc64,ppc64le,ppcle,prescott,sandybridge,skylake,skylake_avx512,sparc,sparc64,steamroller,thunderx2,westmere,x86,x86_64,zen,zen2}]
             [--build] [--build_args BUILD_ARGS] [--upload] [--registry REGISTRY] [--tag TAG] [--convert] [--sif_file SIF_FILE] [--convert-enroot] [--enroot-bundle] [--enroot_file ENROOT_FILE] [--force]
             [--runtime-only] [--clean] [--deploy [DEPLOY]] [--pip [package ...]] [--packages [packages ...]] [--compiler COMPILER] [--compiler_version COMPILER_VERSION] [--fortran] [--iwyy] [--ompi OMPI]
             [--mpi_benchmarks] [--mpi_no_entrypoint] [--pm {system,off}] [--ogs OGS] [--cmake_args CMAKE_ARGS] [--cmake_preset CMAKE_PRESET] [--cmake_preset_file CMAKE_PRESET_FILE] [--ccache]
             [--cpmcache] [--parallel PARALLEL] [--gui] [--docs] [--cvode] [--cppcheck] [--gcovr] [--mfront] [--insitu] [--dev] [--mkl] [--petsc_configure_args PETSC_CONFIGURE_ARGS]
             [--version_file VERSION_FILE] [--boost-sourceforge] [--keep-ogs-source] [--keep-ogs-build] [--run-ctest]
             recipe [recipe ...]

positional arguments:
  recipe

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)

General image config:
  --format {docker,singularity}
  --base_image BASE_IMAGE
                        The base image. (default: ubuntu:20.04)
  --runtime_base_image RUNTIME_BASE_IMAGE
                        The runtime base image. (default: )
  --cpu-target {a64fx,aarch64,arm,broadwell,bulldozer,cannonlake,cascadelake,core2,excavator,haswell,i686,icelake,ivybridge,k10,mic_knl,nehalem,nocona,pentium2,pentium3,pentium4,piledriver,power7,power8,power8le,power9,power9le,ppc,ppc64,ppc64le,ppcle,prescott,sandybridge,skylake,skylake_avx512,sparc,sparc64,steamroller,thunderx2,westmere,x86,x86_64,zen,zen2}
                        The CPU microarchitecture to optimize for (archspec). (default: ivybridge)

Image build options:
  --build, -B           Build the images from the definition files (default: False)
  --build_args BUILD_ARGS
                        Arguments to the build command. Have to be quoted and **must** start with a space. E.g. --build_args ' --no-cache' (default: )
  --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)
  --tag TAG             The full docker image tag. Overwrites --registry. (default: )
  --convert, -C         Convert Docker image to Singularity image (default: False)
  --sif_file SIF_FILE   Overwrite output singularity image file name (default: )
  --convert-enroot, -E  Convert Docker image to enroot image (default: False)
  --enroot-bundle       Convert enroot image to enroot bundle (default: False)
  --enroot_file ENROOT_FILE
                        Overwrite output enroot image file name (default: )
  --force               Forces overwriting of image files! (default: False)
  --runtime-only, -R    Generate multi-stage Dockerfiles for small runtime images (default: False)

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: )

Packages to install:
  --pip [package ...]   Install additional Python packages (default: [])
  --packages [packages ...]
                        Install additional OS packages (default: [])

compiler.py:
  --compiler COMPILER   The compiler to use. Possible options: off, gcc, clang (default: gcc)
  --compiler_version COMPILER_VERSION
                        Compiler version. (default: )
  --fortran             Install fortran compiler. (default: False)
  --iwyy                Install include-what-you-use (requires clang compiler) (default: False)

mpi.py:
  --ompi OMPI           OpenMPI version, e.g. 2.1.1, 2.1.5, 3.0.1, 3.1.2 (default: 4.0.6)
  --mpi_benchmarks      Installs OSU MPI benchmarks and mpi_bw, mpi_ring, mpi_hello (default: False)
  --mpi_no_entrypoint   Disables mpi entrypoint. (Use with ogs_jupyter.py recipe) (default: False)

ogs.py:
  --pm {system,off}     Package manager to install third-party dependencies (default: system)
  --ogs OGS             OGS repo on gitlab.opengeosys.org 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
                        sources OR 'off' to disable OGS building OR 'clean' to disable OGS and all its dev dependencies (default: ogs/ogs@master)
  --cmake_args CMAKE_ARGS
                        CMake argument set has to be quoted and **must** start with a space. e.g. --cmake_args ' -DFIRST=TRUE -DFOO=BAR' (default: )
  --cmake_preset CMAKE_PRESET
                        A CMake configuration preset to use. (default: release)
  --cmake_preset_file CMAKE_PRESET_FILE
                        A CMake (user) presets file as a local file path. (default: None)
  --ccache              Enables ccache build caching. (Docker-only) (default: False)
  --cpmcache            Enables CPM source caching. (Docker-only) (default: False)
  --parallel PARALLEL, -j PARALLEL
                        The number of cores to use for compilation. (default: 8)
  --gui                 Builds the GUI (Data Explorer) (default: False)
  --docs                Setup documentation requirements (Doxygen) (default: False)
  --cvode               Install and configure with cvode (default: False)
  --cppcheck            Install cppcheck (default: False)
  --gcovr               Install gcovr (default: False)
  --mfront              Install tfel and build OGS with -DOGS_USE_MFRONT=ON (default: False)
  --insitu              Builds with insitu capabilities (default: False)
  --dev                 Installs development tools (vim, gdb) (default: False)
  --mkl                 Use MKL. By setting this option, you agree to the [Intel End User License Agreement](https://software.intel.com/en-us/articles/end-user-license-agreement). (default: False)
  --petsc_configure_args PETSC_CONFIGURE_ARGS
                        PETSc configuration arguments; has to be quoted. (default: --with-fc=0)
  --version_file VERSION_FILE
                        OGS versions.json file (default: None)
  --boost-sourceforge   Boolean flag to specify whether Boost should be downloaded from SourceForge rather than the current Boost repository. (default: False)
  --keep-ogs-source     Boolean flag to specify whether the OGS source directory should be preserved. (default: False)
  --keep-ogs-build      Boolean flag to specify whether the OGS build directory should be preserved. (default: False)
  --run-ctest           Boolean flag to specify whether to run the OGS ctest-target. (default: False)

Advanced usage

Build OGS from local git repo

You can use the ogs-container-maker to build a container image from your current source code on your host machine:

virtualenv .venv
source .venv/bin/activate
pip install ogscm
ogscm compiler.py ogs.py -B -C -R --ogs [path to ogs sources]

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

• Bump version in pyproject.py and run poetry install
• Create tag
• Push to GitLab (git push --tags)