.. _dev_quick_start: Quick Start for Developers ========================== .. _dev_shell: Unix Shell ---------- Currently, compass only supports ``bash`` and related unix shells (such as ``ksh`` on the Mac). We do not support ``csh``, ``tcsh`` or other variants of ``csh``. An activation script for those shells will not be created. If you normally use ``csh``, ``tcsh`` or similar, you will need to temporarily switch to bash by calling ``/bin/bash`` each time you want to use compass. .. _dev_compass_repo: Set up a compass repository: for beginners ------------------------------------------ To begin, obtain the main branch of the `compass repository `_ with: .. code-block:: bash git clone git@github.com:MPAS-Dev/compass.git cd compass git submodule update --init --recursive The E3SM repository and a clone of E3SM for MALI development are submodules of the compass repository. .. _dev_conda_env: compass pixi and Spack environments, compilers and system modules ----------------------------------------------------------------- As a developer, you will need your own deployment environment with the latest dependencies for compass and a development installation of ``compass`` from the branch you're working on. Compass now uses ``mache.deploy`` for deployment. In this repository, the entry point is ``./deploy.py``. You will typically rerun ``./deploy.py`` each time you check out a new branch or create a new worktree with ``git``. In most cases, you do not need to rerun deployment while you are editing existing files in the ``compass`` package because ``compass`` is installed in editable mode. .. note:: ``./deploy.py`` expects ``pixi`` to be available either on ``PATH`` or at ``~/.pixi/bin/pixi``. If your ``pixi`` executable lives somewhere else, pass it explicitly with ``--pixi ``. Supported machines ~~~~~~~~~~~~~~~~~~ If you are on one of the :ref:`dev_supported_machines`, run: .. code-block:: bash ./deploy.py [--machine ] [--compiler ...] \ [--mpi ...] [--deploy-spack] [--no-spack] \ [--prefix ] [--recreate] [--with-albany] If you are on a login node, machine detection typically works automatically. You can pass ``--machine `` explicitly if needed. By default, Compass will reuse existing machine-specific Spack environments when the current deployment needs them. On supported machines, this now means per-toolchain library environments together with a shared software environment for tool binaries such as ESMF and MOAB. Use ``--deploy-spack`` when you want to build or update those Spack environments. Use ``--no-spack`` for a pixi-only deployment. Environments with Albany ~~~~~~~~~~~~~~~~~~~~~~~~ If you are working with MALI, use ``--with-albany`` so the Albany and Trilinos libraries are included in the deployed Spack library environment. Albany is currently only supported for some machine/compiler/MPI combinations, most commonly ``gnu`` builds on supported machines. Unknown machines ~~~~~~~~~~~~~~~~ If a machine is not known to ``mache``, add machine support first (see :ref:`dev_add_supported_machine`). For workflows that need custom machine config files, see :ref:`config_files`. What the script does ~~~~~~~~~~~~~~~~~~~~ ``./deploy.py`` can: * create or update a local pixi deployment prefix (``pixi-env`` by default) * install `Jigsaw `_ and `Jigsaw-Python `_ from the ``jigsaw-python`` submodule when needed * install the ``compass`` package from the local branch in editable mode so changes you make to the repo are reflected immediately * optionally deploy or reuse Spack library environments for selected compiler/MPI toolchains, plus a shared Spack software environment for supporting binaries * generate activation scripts (``load_*.sh``) Useful flags ~~~~~~~~~~~~ ``--machine`` Set the machine explicitly instead of relying on automatic detection ``--prefix`` Choose the deployment prefix for the pixi environment ``--compiler``, ``--mpi`` Select compiler/MPI combinations, primarily for Spack deployment ``--deploy-spack`` Deploy supported Spack library/software environments instead of only reusing existing ones ``--no-spack`` Disable all Spack use for this run and rely on pixi dependencies instead ``--spack-path`` Set the Spack checkout path used for deployment ``--recreate`` Recreate deployment artifacts if they already exist ``--bootstrap-only`` Update only the bootstrap pixi environment used internally by deployment ``--mache-fork``, ``--mache-branch``, ``--mache-version`` Test deployment against a specific mache fork, branch or version Activating the environment ~~~~~~~~~~~~~~~~~~~~~~~~~~ Each time you want to work with compass, source one of the generated load scripts: .. code-block:: bash source ./load_*.sh This activates the deployment environment, loads machine modules when appropriate, and sets environment variables needed by ``compass`` and MPAS components. When you are working inside a suite or test-case work directory, source ``load_compass_env.sh`` instead. This is a symlink to the load script you used while setting up the work directory. When a generated load script is sourced from the root of the compass repository, it reinstalls the version of ``compass`` from that location into the active deployment environment. This is what lets one deployment prefix be shared across several branches or worktrees, as long as you re-source the load script in the repo you want to work from. The active load script path is exported in ``COMPASS_LOAD_SCRIPT``. Compass still accepts ``LOAD_COMPASS_ENV`` as a legacy fallback while the migration is in progress. If you wish to work with another compiler or MPI library, rerun ``./deploy.py`` with the desired options so the corresponding load script is generated or refreshed. Make sure you build MPAS with the same compiler and MPI combination as the load script you plan to use. Switching between different compass environments ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Many developers are switching between different ``compass`` branches. We have 2 main workflows for doing this: checking out different branches in the same directory (with ``git checkout``) or creating new directories for each branch (with ``git worktree``). Either way, you need to be careful that the version of the ``compass`` package that is installed in the environment you are using is the one you want. But how to handle it differs slightly between these workflows. If you are developing or using multiple ``compass`` branches in the same directory (switching between them using ``git checkout``), you will need to make sure you update your environment after changing branches. If dependencies are unchanged, you can usually just re-source a load script in the branch root: ``source ./load_*.sh`` Similarly, if you are developing or using multiple ``compass`` branches but you use a different directory for each (creating the directories with ``git worktree``), you will need to make sure the version of the ``compass`` package in your active environment is the one you want. If your branches use the same ``compass`` version (so the dependencies are the same), you can use the same deployment prefix for all of them. You will tell the environment which branch to use by running ``source ./load_*.sh`` from the *root of the directory (worktree) you want to work with* before proceeding. In both of these workflows, you can modify the ``compass`` code and the environment will notice the changes as you make them. However, if you have added or removed any files during your development, you need to source the load script again: ``source ./load_*.sh`` in the root of the repo or worktree so that the added or removed files will be accounted for in the environment. If you know that ``compass`` has different dependencies in a branch or worktree you are working on compared to a previous branch you have worked with (or if you aren't sure), it is safest to not just reinstall the ``compass`` package but also to check the dependencies by re-running ``./deploy.py`` with the same arguments as above. This will also reinstall the ``compass`` package from the current directory. The activation script includes a check to see if the version of compass used to produce the load script is the same as the version of compass in the current branch. If the two don't match, an error like the following results and the environment is not activated: .. code-block:: $ source load_compass_test_morpheus_gnu_openmpi.sh This load script is for a different version of compass: __version__ = '1.2.0-alpha.6' Your code is version: __version__ = '1.2.0-alpha.7' You need to run ./deploy.py to update your environment and load script. If you need more than one environment (e.g. because you are testing multiple branches at the same time), use different deployment prefixes with ``./deploy.py --prefix ``. .. note:: If you switch branches and *do not* remember to recreate the environment (``./deploy.py``) or at least source the activation script (``load_*.sh``), you are likely to end up with an incorrect and possibly unusable ``compass`` package in your environment. In general, if one wishes to switch between environments created for different compass branches or applications, the best practice is to end the current terminal session and start a new session with a clean environment before executing the other compass load script. Similarly, if you want to run a job script that itself sources the load script, it's best to start a new terminal without having sourced a load script at all. .. note:: With the environment activated, you can switch branches and update just the ``compass`` package with: .. code-block:: bash python -m pip install --no-deps --no-build-isolation -e . The activation script will do this automatically when you source it in the root directory of your compass branch. The activation script will also check if the current compass version matches the one used to create the activation script, thus catching situations where the dependencies are out of date and ``./deploy.py`` needs to be rerun. Troubleshooting ~~~~~~~~~~~~~~~ If you run into trouble with the environment or just want a clean start, you can run: .. code-block:: bash ./deploy.py [--machine ] [--compiler ...] \ [--mpi ...] [--deploy-spack] [--no-spack] --recreate The ``--recreate`` flag will delete the deployment artifacts and create them from scratch. This takes just a little extra time. .. _dev_creating_only_env: Creating/updating only the compass environment ---------------------------------------------- For some workflows, you may only want to create the pixi environment and not build or reuse Spack environments. In such cases, run: .. code-block:: bash ./deploy.py --no-spack When ``--no-spack`` is not used, omitting ``--deploy-spack`` still means Compass will try to reuse any required pre-existing Spack environments. To update only the bootstrap environment used internally by deployment, run: .. code-block:: bash ./deploy.py --bootstrap-only Each time you want to work with compass, source the generated load script: .. code-block:: bash source ./load_*.sh This will load the appropriate deployment environment for ``compass``. It will also set an environment variable ``COMPASS_LOAD_SCRIPT`` that points to the activation script. ``compass`` uses this to make a symlink to the activation script called ``load_compass_env.sh`` in the work directory. If you switch to another branch, you will need to rerun: .. code-block:: bash ./deploy.py to make sure dependencies are up to date and the ``compass`` package points to the current directory. .. note:: With the environment activated, you can switch branches and update just the ``compass`` package with: .. code-block:: bash python -m pip install --no-deps --no-build-isolation -e . This will be substantially faster than rerunning ``./deploy.py ...`` but at the risk that dependencies are not up to date. Since dependencies change fairly rarely, this will usually be safe. .. _dev_build_mpas: Building MPAS components ------------------------ The MPAS repository is a submodule of the compass repository. For example, to compile MPAS-Ocean: .. code-block:: bash source ./load_*.sh cd E3SM-Project/components/mpas-ocean/ make MALI can be compiled with or without the Albany library that contains the first-order velocity solver. The Albany first-order velocity solver is the only velocity option that is scientifically validated, but the Albany library is not available for every compiler yet. Therefore, in some situations it is desirable to compile without Albany to run basic tests on platforms where Albany is not available. This basic mode of MALI can be compiled similarly to MPAS-Ocean, i.e.: .. code-block:: bash source ./load_*.sh cd MALI-Dev/components/mpas-albany-landice make Compiling MALI with Albany has not yet been standardized. Some information is available at `https://github.com/MALI-Dev/E3SM/wiki `_, and complete instructions will be added here in the future. See the last column of the table in :ref:`dev_supported_machines` for the right ```` command for each machine and compiler. .. _dev_working_with_compass: Running compass from the repo ----------------------------- If you follow the procedure above, you can run compass with the ``compass`` command-line tool exactly like described in the User's Guide :ref:`quick_start` and as detailed in :ref:`dev_command_line`. To list test cases you need to run: .. code-block:: bash compass list The results will be the same as described in :ref:`setup_overview`, but the test cases will come from the local ``compass`` directory. To set up a test case, you will run something like: .. code-block:: bash compass setup -t ocean/global_ocean/QU240/mesh -m $MACHINE -w $WORKDIR -p $MPAS where ``$MACHINE`` is an ES3M machine, ``$WORKDIR`` is the location where compass test cases will be set up and ``$MPAS`` is the directory where the MPAS model executable has been compiled. See :ref:`dev_compass_setup` for details. To list available test suites, you would run: .. code-block:: bash compass list --suites And you would set up a suite as follows: .. code-block:: bash compass suite -s -c ocean -t nightly -m $MACHINE -w $WORKDIR -p $MPAS When you want to run the code, go to the work directory (for the suite or test case), log onto a compute node (if on an HPC machine) and run: .. code-block:: bash source load_compass_env.sh compass run The first command will source the same activation script that you used to set up the suite or test case (``load_compass_env.sh`` is just a symlink to the load script you sourced before setting up the suite or test case). .. _dev_compass_style: Code style for compass ---------------------- ``compass`` complies with the coding conventions of `PEP8 `_. Rather than memorize all the guidelines, the easiest way to stay in compliance as a developer writing new code or modifying existing code is to use a PEP8 style checker. One option is to use an IDE with a PEP8 style checker built in, such as `PyCharm `_. See `this tutorial `_ for some tips on checking code style in PyCharm. Here's the manual way to check for PEP8 compliance. `Flake8 `_ is a PEP8 checker that is included in the ``compass`` development environment. For each of the files you have modified, you can run the Flake8 checker to see a list of all instances of non-compliance in that file. .. code-block:: bash $flake8 example.py example.py:77:1: E302 expected 2 blank lines, found 1 For this example, we would just add an additional blank line after line 77 and run the checker again to make sure we've resolved the issue. Once you open a pull request for your feature, there is an additional PEP8 style checker at this stage. .. _dev_compass_repo_advanced: Set up a compass repository with worktrees: for advanced users -------------------------------------------------------------- This section uses ``git worktree``, which provides more flexibility but is more complicated. See the beginner section above for the simpler version. In the worktree version, you will have many unix directories, and each corresponds to a git branch. It is easier to keep track of, and easier to work with many branches at once. Begin where you keep your repositories: .. code-block:: bash mkdir compass cd compass git clone git@github.com:MPAS-Dev/compass.git main cd main The ``MPAS-Dev/compass`` repo is now ``origin``. You can add more remotes. For example: .. code-block:: bash git remote add mark-petersen git@github.com:mark-petersen/compass.git git fetch mark-petersen To view all your remotes: .. code-block:: bash git remote -v To view all available branches, both local and remote: .. code-block:: bash git branch -a We will use the git worktree command to create a new local branch in its own unix directory: .. code-block:: bash cd compass/main git worktree add -b new_branch_name ../new_branch_name origin/main cd ../new_branch_name In this example, we branched off ``origin/main``, but you could start from any branch, which is specified by the last ``git worktree`` argument. There are two ways to build the MPAS executable: 1. Compass submodule (easier): This guarantees that the MPAS commit matches compass. It is also the default location for finding the MPAS model so you don't need to specify the ``-p`` flag at the command line or put the MPAS model path in your config file (if you even need a config file at all): .. code-block:: bash git submodule update --init --recursive cd E3SM-Project/components/mpas-ocean/ # load modules make gfortran For the "load modules" step, see :ref:`machines` for specific instructions. 2. Other E3SM directory (advanced): Create your own clone of the ``E3SM-Project/E3SM`` or ``MALI-Dev/E3SM`` repository elsewhere on disk. Either make an ``ocean.cfg`` or ``landice.cfg`` that specifies the absolute path to the path where the ``ocean_model`` or ``landice_model`` executable is found, or specify this path on the command line with ``-p``. You are responsible for knowing if this particular version of MPAS component's code is compatible with the version of ``compass`` that you are using. The simplest way to set up a new repo for MALI development in a new directory is: .. code-block:: bash git clone git@github.com:MALI-Dev/E3SM.git your_new_branch cd your_new_branch git checkout -b your_new_branch origin/develop The equivalent for MPAS-Ocean development would be: .. code-block:: bash git clone git@github.com:E3SM-Project/E3SM.git your_new_branch cd your_new_branch git checkout -b your_new_branch origin/main