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and Reefs","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"# pygetm\n\nThis is a rewrite of the [General Estuarine Transport Model (GETM)](https://getm.eu).\nIt is mostly written in Python; only performance-critical sections of the code are\nimplemented in Fortran.\n\n## Installing\n\nFirst, ensure you have [Anaconda](https://docs.anaconda.com/free/anaconda/):\n   - Linux/Mac: execute `conda --version` in a terminal\n   - Windows: look for \"Anaconda prompt\" in the start menu\n\nOn some systems (notably, HPC clusters), you may need to load an anaconda module first:\ntry `module load anaconda` or `module load anaconda3`\n\nIf you do *not* have Anaconda, install [Miniconda](https://docs.anaconda.com/miniconda/).\n\nFrom here on, we will be working in a terminal window. On Windows, open a terminal by choosing \"Anaconda prompt\" in the start menu.\n\n### Install a prebuilt version from conda-forge\n\nTo install or update pygetm:\n\n```\nconda install -c conda-forge pygetm\n```\n\n### Manual build and install\n\nIf you need a customized version of pygetm, for instance, built with specific compiler\noptions, or with specific biogeochemical models that are not part of the standard\n[FABM](https://fabm.net) distribution, you can manually obtain the pygetm source code,\nbuild it, and then install it.\n\nTo obtain the repository with setups and scripts, first set up and activate a conda\nenvironment with all necessary build tools:\n\n```\ngit clone --recursive https://github.com/BoldingBruggeman/getm-rewrite.git\ncd getm-rewrite\nconda env create -f environment.yml\nconda activate pygetm\n```\n\nIf you are installing on an system that already has a Fortran\ncompiler and MPI libraries that you would like to use, replace `environment.yml` with\n`environment-min.yml` in the above.\n\nThe above requires that you already have [Git](https://git-scm.com/) installed.\nIf you do not, you can install this with `conda install -c conda-forge git`.\n\nFinally, to build on Linux/Mac, execute\n\n```\nsource ./install\n```\n\nIf you are using a different shell than bash, you may need to replace `source` by `bash`.\n\nOn Windows, you build pygetm with\n\n```\ninstall.bat\n```\n\nYou can customize the build step as follows:\n* To set the Fortran compiler, set environment variable `FC` to your desired Fortran\n  compiler executable. For instance, in a bash shell: `export FC=ifort`. This can be done\n  in your terminal before running the install script, or by adding it to the install\n  script itself.\n* To set compilation flags, set environment variable `FFLAGS` to your desired flags.\n  For instance, in a bash shell: `export FFLAGS=-fcheck=all`. This can be done in your\n  terminal before running the install script, or by adding it to the install script\n  itself.\n* To set cmake options used to compile FABM, such as `-DFABM_EXTRA_INSTITUTES` or\n  `-DFABM_\u003cINSTITUTE\u003e_BASE`, add `cmake_opts=\u003cCMAKE_OPTIONS\u003e` to [`python/setup.cfg`](https://github.com/BoldingBruggeman/getm-rewrite/blob/devel/python/setup.cfg)\n\n#### Staying up to date\n\nTo update this repository including its submodules (GOTM, FABM, etc.), make sure you are\nin the getm-rewrite directory and execute:\n\n```\ngit pull\ngit submodule update --init --recursive\nconda env update -f \u003cENVIRONMENT_YML\u003e\nconda activate pygetm\n```\n\nIn the above, replace `\u003cENVIRONMENT_YML\u003e` with the name of the environment file you used\npreviously: `environment.yml` for stand-alone conda environments, or `environment-min.yml`\nfor a setup that uses the local MPI implementation and Fortran compiler.\n\nFinally, rebuild by executing `source ./install` on Linux/Mac, or `install.bat` on Windows.\n\n## Using pygetm\n\nYou should always activate the correct Python environment before you use the model with\n`conda activate pygetm`. This needs to be done any time you start a new shell.\n\n### Jupyter Notebooks\n\nThe best place to start is the [`python/examples`](https://github.com/BoldingBruggeman/getm-rewrite/tree/devel/python/examples)\ndirectory with Jupyter Notebooks that demonstrate the functionality of the model:\n\n```\ncd python/examples\npython -m jupyterlab\n```\n\n### Simulations\n\nSome of the original GETM test cases have been ported to pygetm:\n\n* [north_sea](https://github.com/BoldingBruggeman/getm-rewrite/blob/devel/python/examples/north_sea_legacy.py)\n  - including [an extended version](https://github.com/BoldingBruggeman/getm-rewrite/blob/devel/python/examples/north_sea.py)\n  that shows new pygetm features such as command-line configurability.\n* [box_spherical](https://github.com/BoldingBruggeman/getm-rewrite/blob/devel/python/examples/box_spherical.py)\n* [seamount](https://github.com/BoldingBruggeman/getm-rewrite/blob/devel/python/examples/seamount.py)\n\nTo run a simulation:\n\n```\npython \u003cRUNSCRIPT.py\u003e [OPTIONS]\n```\n\nTo run in parallel:\n\n```\nmpiexec -n \u003cNCPUS\u003e python \u003cRUNSCRIPT.py\u003e [OPTIONS]\n```\n\n## Contributing\n\nHow to contribute to the development:\n\n  1. [Make a fork](https://github.com/BoldingBruggeman/getm-rewrite/fork) of the\n     repository under your private GitHub account(\\*)\n  2. Commit your changes to your forked repository\n  3. Make a [pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests)\n\nNote that all communication in relation to development of GETM is done via\nGitHub using [issues](https://github.com/BoldingBruggeman/tickets/issues).\n\n\n(\\*) If you use a service other than GitHub for your daily work - please have a\nlook [here](https://stackoverflow.com/questions/37672694/can-i-submit-a-pull-request-from-gitlab-com-to-github)\n\nhttps://yarchive.net/comp/linux/collective_work_copyright.html\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["biogeochemical-models","coupling","hydrodynamic-modeling"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/95602","html_url":"https://ost.ecosyste.ms/projects/95602"}