Quick Start for Developers

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.

Set up a compass repository: for beginners

To begin, obtain the main branch of the compass repository with:

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.

compass conda environment, compilers and system modules

As a developer, you will need your own environment with the latest dependencies for compass and a development installation of compass from the branch you’re working on.

The conda directory in the repository has a tool configure_compass_env.py that can get you started.

You will need to run ./conda/configure_compass_env.py each time you check out a new branch or create a new worktree with git. Typically, you will not need to run this command when you make changes to files within the compass python package. These will automatically be recognized because compass is installed into the conda environment in “editable” mode. You will need to run the command if you add new code files or data files to the package because these don’t get added automatically.

Whether you are on one of the Supported Machines or an “unknown” machine, you will need to specify a path where Miniforge3 either has already been installed or an empty directory where the script can install it. You must have write permission in the base environment (if it exists).

Note

We have found that an existing Miniconda3 installation does not always work well for compass, so please start with Miniforge3 instead.

Note

It is very important that you not use a shared installation of Miniforge3 or Miniconda3 such as the base environment for E3SM-Unified for compass development. Most developers will not have write access to shared environments, meaning that you will get write-permission errors when you try to update the base environment or create the compass development environment.

For anyone who does have write permission to a shared environment, you would be creating your compass development environment in a shared space, which could cause confusion.

Please use your own personal installation of Miniforge3 for development, letting configure_compass_env.py download and install Miniforge3 for you if you don’t already have it installed.

Supported machines

If you are on one of the Supported Machines, run:

./conda/configure_compass_env.py --conda <base_path_to_install_or_update_conda> \
    -c <compiler> [--mpi <mpi>] [-m <machine>] [--with_albany] \
    [--with_petsc]

The <base_path_to_install_or_update_conda> is typically ~/miniforge3. This is the location where you would like to install Miniforge3 or where it is already installed. If you have limited space in your home directory, you may want to give another path. If you already have it installed, that path will be used to add (or update) the compass test environment.

See the machine under Supported Machines for a list of available compilers to pass to -c. If you don’t supply a compiler, you will get the default one for that machine (usually Intel). Typically, you will want the default MPI flavor that compass has defined for each compiler, so you should not need to specify which MPI version to use but you may do so with --mpi if you need to.

If you are on a login node, the script should automatically recognize what machine you are on. You can supply the machine name with -m <machine> if you run into trouble with the automatic recognition (e.g. if you’re setting up the environment on a compute node, which is not recommended).

Environments with Albany

If you are working with MALI, you should specify --with_albany. This will ensure that the Albany and Trilinos libraries are included among those built with system compilers and MPI libraries, a requirement for many MAlI test cases. Currently, only Albany is only supported with gnu compilers.

It is safe to add the --with_albany flag for MPAS-Ocean but it is not recommended unless a user wants to be able to run both models with the same conda/spack environment. The main downside is simply that unneeded libraries will be linked in to MPAS-Ocean.

Environments with PETSc and Netlib-LAPACK

If you are working with MPAS-Ocean test cases that need PETSc and Netlib-LAPACK, you should specify --with_petsc to point to Spack environments where these libraries are included. Appropriate environment variables for pointing to these libraries will be build into the resulting load script (see below).

Unknown machines

If your are on an “unknown” machine, typically a Mac or Linux laptop or workstation, you will need to specify which flavor of MPI you want to use (mpich or openmpi):

./conda/configure_compass_env.py --conda <conda_path> --mpi <mpi>

Again, the <conda_path> is typically ~/miniforge3, and is the location where you would like to install Miniforge3 or where it is already installed. If you already have it installed, that path will be used to add (or update) the compass test environment.

We only support one set of compilers for Mac and Linux (gnu for Linux and clang with gfortran for Mac), so there is no need to specify them. See Other Machines for more details.

In addition, unknown machines require a config file to be specified when setting up the compass test environment. A config file can be specified using -f <filename>, where <filename> is an absolute or relative path to the file. More information, including example config files, can be found in Config Files.

Note

Currently, there is not a good way to build Albany for an unknown machine as part of the compass deployment process, meaning MALI will be limited to the shallow-ice approximation (SIA) solver.

To get started on HPC systems that aren’t supported by Compass, get in touch with the developers.

What the script does

In addition to installing Miniforge3 and creating the conda environment for you, this script will also:

  • install Jigsaw and Jigsaw-Python from source from the jigsaw-python submodule. These tools are used to create many of the meshes used in Compass.

  • install the compass package from the local branch in “development” mode so changes you make to the repo are immediately reflected in the conda environment.

  • with the --update_spack flag on supported machines, installs or reinstalls a spack environment with various system libraries. The --spack flag can be used to point to a location for the spack repo to be checked out. Without this flag, a default location is used. Spack is used to build several libraries with system compilers and MPI library, including: ParallelIO (parallel i/o in NetCDF format) ESMF (making mapping files in parallel), Trilinos, Albany, Netlib-LAPACK and PETSc. Please uses these flags with caution, as they can affect shared environments! See Deploying a new spack environment.

  • with the --with_albany flag, creates or uses an existing Spack environment that includes Albany and Trilinos.

  • with the --with_petsc flag, creates or uses an existing Spack environment that includes PETSc and Netlib-LAPACK.

  • make an activation script called load_*.sh, where the details of the name encode the conda environment name, the machine, compilers, MPI libraries, and optional libraries, e.g. load_dev_compass_<version>_<machine>_<compiler>_<mpi>.sh (<version> is the compass version, <machine> is the name of the machine, <compiler> is the compiler name, and mpi is the MPI flavor).

  • optionally (with the --check flag), run some tests to make sure some of the expected packages are available.

Optional flags

--check

Check to make sure expected commands are present

--python

Select a particular python version (the default is currently 3.8)

--env_name

Set the name of the environment (and the prefix for the activation script) to something other than the default (dev_compass_<version> or dev_compass_<version>_<mpi>).

--update_jigsaw

Used to reinstall Jigsaw and Jigsaw-Python into the conda environment if you have made changes to the Jigsaw (c++) code in the jigsaw-python submodule. You should not need to reinstall Jigsaw-Python if you have made changes only to the python code in jigsaw-python, as the python package is installed in edit mode.

Activating the environment

Each time you want to work with compass, you will need to run:

source ./load_dev_compass_<version>_<machine>_<compiler>_<mpi>.sh

This will load the appropriate conda environment, load system modules for compilers, MPI and libraries needed to build and run MPAS components, and set environment variables needed for MPAS or compass. It will also set an environment variable LOAD_COMPASS_ENV that points to the activation script. compass uses this to make an symlink to the activation script called load_compass_env.sh in the work directory. When the load script is executed from the base of the compass repository (i.e., as source ./load_dev_compass_<version>_<machine>_<compiler>_<mpi>.sh), it will install the version of the compass package from that location into the associated conda environment. When the load script is executed from the work directory through the symlink, it will activate the associated conda environment, but does not install the compass package into the conda environment; it is assumed that is already up to date from when the conda environment was created or last updated.

It is generally recommended to activate the compass environment (from either the compass repo or via the workdir symlink) from a clean environment. Unexpected behavior may occur if activating a different compass environment after having one already activated.

Once you have sourced the activation script, you can run compass commands anywhere, and it always refers to that branch. To find out which branch you are actually running compass from, you should run:

echo $LOAD_COMPASS_ENV

This will give you the path to the load script, which will also tell you where the branch is. If you do not use the worktree approach, you will also need to check what branch you are currently on with git log, git branch or a similar command.

If you wish to work with another compiler, simply rerun the configure script with a new compiler name and an activation script will be produced. You can then source either activation script to get the same conda environment but with different compilers and related modules. Make sure you are careful to set up compass by pointing to a version of the MPAS model that was compiled with the correct compiler.

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 conda 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 compass environment after changing branches. Often the branches you’re developing will make use of the same conda environment, because they are using the same compass version (so the dependencies aren’t changing). The same conda environment (e.g. dev_compass_<version>) can safely be used with multiple branches if you explicitly reinstall the compass package you want to use into the conda environment after moving to a new branch. You can do this by simply re-executing source ./load_dev_compass_<version>_<machine>_<compiler>_<mpi>.sh from the root of the repo before proceeding.

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 conda 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 conda environment (e.g. dev_compass_<version>) for all of them. But you will only be able to test one of them at a time. You will tell the conda environment which branch to use by running source ./load_dev_compass_<version>_<machine>_<compiler>_<mpi>.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 conda 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_dev_compass_<version>_<machine>_<compiler>_<mpi>.sh in the root of the repo or worktree so that the added or removed files will be accounted for in the conda 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: ./conda/configure_compass_env.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:

$ 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 ./conda/configure_compass_env.py to update your conda
environment and load script.

If you need more than one conda environment (e.g. because you are testing multiple branches at the same time), you can choose your own name for the conda environment. Typically, this might be something related to the name of the branch you are developing. This can be done with the --env-name argument to ./conda/configure_compass_env.py. You can reuse the same custom-named environment across multiple branches if that is useful. Just remember to reinstall compass each time you switch branches.

Note

If you switch branches and do not remember to recreate the conda environment (./conda/configure_compass_env.py) or at least source the activation script (load_dev_compass*.sh), you are likely to end up with an incorrect and possibly unusable compass package in your conda 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 conda environment activated, you can switch branches and update just the compass package with:

python -m pip install -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 the configure script needs to be rerun.

Troubleshooting

If you run into trouble with the environment or just want a clean start, you can run:

./conda/configure_compass_env.py --conda <conda_path> -c <compiler> --recreate

The --recreate flag will delete the conda environment and create it from scratch. This takes just a little extra time.

Creating/updating only the compass environment

For some workflows (e.g. for MALI development with the Albany library when the MALI build environment has been created outside of compass, for example, on an unsupported machine), you may only want to create the conda environment and not build PIO, ESMF or other packages with system compilers, or include any system modules or environment variables in your activation script. In such cases, run with the --env_only flag:

./conda/configure_compass_env.py --conda <conda_path> --env_only

Each time you want to work with compass, you will need to run:

source ./load_dev_compass_<version>.sh

This will load the appropriate conda environment for compass. It will also set an environment variable LOAD_COMPASS_ENV 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:

./conda/configure_compass_env.py --conda <conda_path> --env_only

to make sure dependencies are up to date and the compass package points to the current directory.

Note

With the conda environment activated, you can switch branches and update just the compass package with:

python -m pip install -e .

This will be substantially faster than rerunning ./conda/configure_compass_env.py ... but at the risk that dependencies are not up-to-date. Since dependencies change fairly rarely, this will usually be safe.

Building MPAS components

The MPAS repository is a submodule of the compass repository. For example, to compile MPAS-Ocean:

source ./load_dev_compass_<version>_<machine>_<compiler>_<mpi>.sh
cd E3SM-Project/components/mpas-ocean/
make <mpas_make_target>

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.:

source ./load_dev_compass_<version>_<machine>_<compiler>_<mpi>.sh
cd MALI-Dev/components/mpas-albany-landice
make <mpas_make_target>

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 Supported Machines for the right <mpas_make_target> command for each machine and compiler.

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 Quick Start for Users and as detailed in Command-line interface.

To list test cases you need to run:

compass list

The results will be the same as described in Setting up test cases, but the test cases will come from the local compass directory.

To set up a test case, you will run something like:

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 compass setup for details.

To list available test suites, you would run:

compass list --suites

And you would set up a suite as follows:

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:

source load_compass_env.sh
compass run

The first command will source the same activation script (load_dev_compass_<version>_<machine>_<compiler>_<mpi>.sh) that you used to set up the suite or test case (load_compass_env.sh is just a symlink to that activation script you sourced before setting up the suite or test case).

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 conda 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.

$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.

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:

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:

git remote add mark-petersen git@github.com:mark-petersen/compass.git
git fetch mark-petersen

To view all your remotes:

git remote -v

To view all available branches, both local and remote:

git branch -a

We will use the git worktree command to create a new local branch in its own unix directory:

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):

    git submodule update --init --recursive
cd E3SM-Project/components/mpas-ocean/
# load modules
make gfortran

    For the “load modules” step, see 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:

    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:

    git clone git@github.com:E3SM-Project/E3SM.git your_new_branch
cd your_new_branch
git checkout -b your_new_branch origin/main