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diff --git a/python-ogscm.spec b/python-ogscm.spec new file mode 100644 index 0000000..c9cfab5 --- /dev/null +++ b/python-ogscm.spec @@ -0,0 +1,811 @@ +%global _empty_manifest_terminate_build 0 +Name: python-ogscm +Version: 2.4.8 +Release: 1 +Summary: OGS Container Maker +License: BSD 3-clause +URL: https://gitlab.opengeosys.org/ogs/container-maker +Source0: https://mirrors.aliyun.com/pypi/web/packages/53/56/7cee3027248869be7e3563f2c406dde92c13ff8c61619cc1cbd6f76c1744/ogscm-2.4.8.tar.gz +BuildArch: noarch + +Requires: python3-hpccm +Requires: python3-requests +Requires: python3-PyYAML +Requires: python3-packaging + +%description +# OGS Container Maker + +[](https://badge.fury.io/py/ogscm) + +## General usage + +### Installation + +```bash +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`](https://docs.docker.com/engine/install/linux-postinstall/#manage-docker-as-a-non-root-user)! + + +Apple ARM specific: + +```bash +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: + +```bash +$ 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: + +```bash +$ 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: + +```bash +$ 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): + +```bash +$ 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 + +```bash +docker run --it --rm ogs-ompi-2.1.3 +# in container: +ogs --version +``` + +```bash +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 --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.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`) + + +%package -n python3-ogscm +Summary: OGS Container Maker +Provides: python-ogscm +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-ogscm +# OGS Container Maker + +[](https://badge.fury.io/py/ogscm) + +## General usage + +### Installation + +```bash +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`](https://docs.docker.com/engine/install/linux-postinstall/#manage-docker-as-a-non-root-user)! + + +Apple ARM specific: + +```bash +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: + +```bash +$ 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: + +```bash +$ 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: + +```bash +$ 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): + +```bash +$ 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 + +```bash +docker run --it --rm ogs-ompi-2.1.3 +# in container: +ogs --version +``` + +```bash +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 --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.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`) + + +%package help +Summary: Development documents and examples for ogscm +Provides: python3-ogscm-doc +%description help +# OGS Container Maker + +[](https://badge.fury.io/py/ogscm) + +## General usage + +### Installation + +```bash +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`](https://docs.docker.com/engine/install/linux-postinstall/#manage-docker-as-a-non-root-user)! + + +Apple ARM specific: + +```bash +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: + +```bash +$ 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: + +```bash +$ 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: + +```bash +$ 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): + +```bash +$ 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 + +```bash +docker run --it --rm ogs-ompi-2.1.3 +# in container: +ogs --version +``` + +```bash +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 --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.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`) + + +%prep +%autosetup -n ogscm-2.4.8 + +%build +%py3_build + +%install +%py3_install +install -d -m755 %{buildroot}/%{_pkgdocdir} +if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi +if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi +if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi +if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi +pushd %{buildroot} +if [ -d usr/lib ]; then + find usr/lib -type f -printf "\"/%h/%f\"\n" >> filelist.lst +fi +if [ -d usr/lib64 ]; then + find usr/lib64 -type f -printf "\"/%h/%f\"\n" >> filelist.lst +fi +if [ -d usr/bin ]; then + find usr/bin -type f -printf "\"/%h/%f\"\n" >> filelist.lst +fi +if [ -d usr/sbin ]; then + find usr/sbin -type f -printf "\"/%h/%f\"\n" >> filelist.lst +fi +touch doclist.lst +if [ -d usr/share/man ]; then + find usr/share/man -type f -printf "\"/%h/%f.gz\"\n" >> doclist.lst +fi +popd +mv %{buildroot}/filelist.lst . +mv %{buildroot}/doclist.lst . + +%files -n python3-ogscm -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 2.4.8-1 +- Package Spec generated |