OGS Container Maker
General usage
Installation
virtualenv ~/.venv/ogs-container-maker
source ~/.venv/ogs-container-maker/bin/activate
pip install ogscmIf 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 --bootstrapGenerate 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/DockerfileWith 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/DockerfileBuild 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 --versionsingularity 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.prjAll 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 --download-f2cblaslapack=1)
--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.ymltoconfig/deploy_hosts.yml -
hosthas to be a SSH host to which you have passwordless access - Deploy to the host with
... -D myhost
PyPi Publication
- Bump version in
pyproject.pyand runpoetry install - Create tag
- Push to GitLab (
git push --tags)