Full installation instructions

This document provides detailed documentation about building and installing the gmxapi Python package.

GROMACS is a high performance computational science tool that is optimized for a variety of specialized hardware and parallel computing environments. To make the best use of a computing environment, GROMACS is usually built from source code.

Users of Python based molecular science tools may have various requirements and use a variety of Python distributions, so gmxapi extension code is most useful when built from source code for a specific GROMACS installation and Python environment.

This document has a lot of detail. If you don’t need a lot of reference material, you may just jump ahead to the Recommended installation.

Command line examples assume the bash shell.

Note

Regarding multiple GROMACS installations: Many GROMACS users switch between multiple GROMACS installations on the same computer using an HPC module system and/or a GMXRC configuration script. For the equivalent sort of environment switching with the gmxapi Python package, we recommend installing it in a different Python virtual environment for each GROMACS installation. Once built, a particular copy of the gmxapi Python package always refers to the same GROMACS installation.

Note

The following documentation contains frequent references to the pip tool for installing Python packages. In some cases, an unprivileged user should use the --user command line flag to tell pip to install packages into the user site-packages directory rather than the default site-packages directory for the Python installation. This flag is not appropriate when running pip in a virtual environment (as recommended) and is omitted in this documentation. If you need the --user flag, you should modify the example commands to look something like pip install --upgrade somepackage --user

Note

These instructions use the executable names python and pip instead of python3 or pip3. Some Python installations require the 3 suffix, but it is usually not necessary if you have already activated a Python virtual environment (recommended).

Requirements

gmxapi comes in three parts:

• GROMACS gmxapi library for C++.
• This Python package, supporting Python 3.5 and higher
• MD restraint plugins and sample gmxapi client code

Build system requirements

gmxapi can be built for Python 3.5 and higher.

You will need a C++ 14 compatible compiler and a reasonably up-to-date version of CMake. Full gmxapi functionality may also require an MPI compiler (e.g. mpicc).

The Python package requires a GROMACS installation. Build and install GROMACS before proceeding. Be sure to configure CMake with the GMXAPI=ON option.

Then, “source” the GMXRC file from the GROMACS installation as you normally would before using GROMACS, or note its installation location so that you can pass it to the build configuration.

Note

If you are using a managed computing resource, such as a research HPC cluster, GROMACS may already be installed, but you will need GROMACS 2020 or later, and it must be configured with GMXAPI=ON.

Important: To build a module that can be imported by Python, you need a Python installation that includes the Python headers. Unfortunately, it is not always obvious whether these headers are present or where to find them. The simplest answer is to just try to build the Python package using these instructions, and if gmxapi is unable to find the Python tools it needs, try a different Python installation or install the additional development packages.

On a Linux system, this may require installing packages such as python-dev and/or python3-dev. If you are building Python, either from scratch or with a tool like pyenv install (see wiki entry ), be sure to enable installation of the Python C library with the --enable-shared flag. Alternatively, various Python distributions provide a sufficient build environment while only requiring installation into a user home directory. (Some examples below.)

If you are using an HPC system with software available through modules you may be able to just module load a different Python installation and find one that works.

Python environment requirements

gmxapi requires Python 3.5 or higher. Check your version with python3 --version or python --version.

Note

The following documentation assumes you do not need to use a trailing ‘3’ to access a Python 3 interpreter on your system. The default Python interpreter on your system may use python3 and pip3 instead of python and pip. You can check the version with python3 --version or python --version and pip --version.

To build and install, you also need the packages cmake, setuptools, networkx, and scikit-build.

For full functionality, you should also have mpi4py and numpy. These requirements and version numbers are listed in requirements.txt.

The easiest way to make sure you have the requirements installed, first update pip, then use the requirements.txt file provided with the repository. File paths in this section are relative to the root directory of your local copy of the GROMACS source.

Confirm that pip is available, install pip if it is missing, or get instructions on how to install pip:

python -m ensurepip --default-pip

Install or upgrade required components:

python -m pip install --upgrade pip
pip install --upgrade setuptools

“requirements” files in GROMACS source tree

If you are building from source code in a local copy of the GROMACS source repository, some helpful files allow you to preinstall the Python requirements before installing the gmxapi package.

pip install -r python_packaging/src/requirements.txt

If building documentation or running tests, pip install -r python_packaging/requirements-docs.txt or pip install -r python_packaging/requirements-test.txt, respectively, or see below.

Documentation build requirements

See Accessing gmxapi documentation

Testing requirements

Testing is performed with pytest. Tests also require numpy. You can probably install both with pip:

pip install pytest numpy

To test the full functionality also requires an MPI parallel environment. You will need the mpi4py Python package and an MPI launcher (such as mpiexec, mpirun, a launcher provided by your HPC queuing system, or whatever is provided by your favorite MPI package for your operating system).

MPI requirements

For the ensemble simulations features, you will need an MPI installation. On an HPC system, this means you will probably have to use module load to load a compatible set of MPI tools and compilers. Check your HPC documentation or try module avail to look for an openmpi, mpich, or mvapich module and matching compiler module. This may be as simple as

module load gcc
module load mpicc

Note that the compilers loaded might not be the first compilers discovered automatically by the build tools we will use below, so you may have to specify compilers on the command line for consistency. It may be necessary to require that GROMACS, gmxapi, and the sample code are built with the same compiler(s).

Note that strange errors have been known to occur when mpi4py is built with different a different tool set than has been used to build Python and gmxapi. If the default compilers on your system are not sufficient for GROMACS or gmxapi, you may need to build, e.g., OpenMPI or MPICH, and/or build mpi4py with a specific MPI compiler wrapper. This can complicate building in environments such as Conda.

Set the MPICC environment variable to the MPI compiler wrapper and forcibly reinstall mpi4py.

export MPICC=`which mpicc`
pip install --no-cache-dir --upgrade --no-binary \":all:\" --force-reinstall mpi4py

Installing the Python package

We recommend you install the gmxapi package in a Python virtual environment (virtualenv or venv). There are several ways to do this, and it is also possible to install without a virtual environment. If installing without a virtual environment as an un-privileged user, you may need to set the CMake variable GMXAPI_USER_INSTALL (-DGMXAPI_USER_INSTALL=ON on the cmake command line) and / or use the --user option with pip install.

Sometimes the build environment can choose a different Python interpreter than the one you intended. You can set the PYTHON_EXECUTABLE CMake variable to explicitly choose the Python interpreter for your chosen installation. For example: -DPYTHON_EXECUTABLE=\`which python\`

Recommended installation

We recommend using Python’s pip package installer to automatically download, build, and install the latest version of the gmxapi package into a Python virtual environment. gmxapi requires an existing GROMACS installation.

The instructions in this section assume that pip is able to download files from the internet.

Locate or install GROMACS

You need a GROMACS installation that includes the gmxapi headers and library. If GROMACS 2020 or higher is already installed, and was configured with GMXAPI=ON at build time, you can just source the GMXRC (so that the Python package knows where to find GROMACS) and skip to the next section.

Otherwise, install a supported version of GROMACS. When building GROMACS from source, be sure to configure cmake with the flag -DGMXAPI=ON (default).

Set the environment variables for the GROMACS installation so that the gmxapi headers and library can be found when building the Python package. If you installed to a gromacs-gmxapi directory in your home directory as above and you use the bash shell, do:

source $HOME/gromacs-gmxapi/bin/GMXRC

Set up a Python virtual environment

We recommend installing the Python package in a virtual environment. If not installing in a virtual environment, you may not be able to install necessary prerequisites (e.g. if you are not an administrator of the system you are on).

Create a Python 3 virtual environment.

For Python 3, use the venv module. Depending on your computing environment, the Python 3 interpreter may be accessed with the command python or python3. Use python --version and python3 --version to figure out which you need to use. The following assumes the Python 3 interpreter is accessed with python3.

Note

After activating the venv, python and pip are sufficient. (The ‘3’ suffix will no longer be necessary and will be omitted in the rest of this document.)

python3 -m venv $HOME/myvenv

Activate the virtual environment. Your shell prompt will probably be updated with the name of the environment you created to make it more obvious.

$ source $HOME/myvenv/bin/activate
(myvenv)$

Activating the virtual environment changes your shell prompt to indicate the environment is active. The prompt is omitted from the remainging examples, but the remaining examples assume the virtualenv is still active. (Don’t do it now, but you can deactivate the environment by running deactivate.)

Install dependencies

It is always a good idea to update pip and setuptools before installing new Python packages:

pip install --upgrade pip setuptools

The gmxapi installer requires a few additional packages. It is best to make sure they are installed and up to date before proceeding.

pip install --upgrade cmake scikit-build

For MPI, we use mpi4py. Make sure it is using the same MPI installation that we are building GROMACS against and building with compatible compilers.

python -m pip install --upgrade pip setuptools
MPICC=`which mpicc` pip install --upgrade mpi4py

Install the latest version of gmxapi

Fetch and install the latest version of gmxapi from the Python Packaging Index:

pip install gmxapi

If pip does not find your GROMACS installation, use one of the following environment variables to provide a hint.

gmxapi_DIR

If you have a single GROMACS installation at /path/to/gromacs, it is usually sufficient to provide this location to pip through the gmxapi_DIR environment variable.

Example:

gmxapi_DIR=/path/to/gromacs pip install gmxapi

GMXTOOLCHAINDIR

If you have multiple builds of GROMACS distinguished by suffixes (e.g. _d, _mpi, etcetera), or if you need to provide extra hints to pip about the software tools that were used to build GROMACS, you can specify a directory in which the installer can find a CMake “tool chain”.

In the following example, ${SUFFIX} is the suffix that distinguishes the particular build of GROMACS you want to target (refer to GROMACS installation instructions for more information.) ${SUFFIX} may simply be empty, or ''.

GMXTOOLCHAINDIR=/path/to/gromacs/share/cmake/gromacs${SUFFIX} pip install gmxapi

Install from source

You can also install the gmxapi Python package from within a local copy of the GROMACS source repository. Assuming you have already obtained the GROMACS source code and you are in the root directory of the source tree, you will find the gmxapi Python package sources in the python_packaging/src directory.

cd python_packaging/src
pip install -r requirements.txt
pip install .

Offline install

If the required dependencies are already installed, you can do a quick installation without internet access, either from the source directory or from a source archive.

For example, the last line of the previous example could be replaced with:

pip install --no-cache-dir --no-deps --no-index --no-build-isolation .

Refer to pip documentation for descriptions of these options.

If you have built or downloaded a source distribution archive, you can provide the archive file to pip instead of the . argument:

pip install gmxapi-0.1.0.tar.gz

In this example, the archive file name is as was downloaded from PyPI or as built locally, according to the following instructions.

Building a source archive

A source archive for the gmxapi python package can be built from the GROMACS source repository using Python setuptools and scikit-build.

Example:

pip install --upgrade setuptools scikit-build
cd python_packaging/src
python setup.py sdist

This command will create a dist directory containing a source distribution archive file. The file name has the form gmxapi-<version>.<suffix>, where <version> is the version from the setup.py file, and <suffix> is determined by the local environment or by additional arguments to setup.py.

See also

Python documentation for creating a source distribution

Package maintainers may update the online respository by uploading a freshly built sdist with python -m twine upload dist/*

Accessing gmxapi documentation

Documentation for the Python classes and functions in the gmx module can be accessed in the usual ways, using pydoc from the command line or help() in an interactive Python session.

The complete documentation (which you are currently reading) can be browsed online or built from a copy of the GROMACS source repository.

Documentation is built from a combination of Python module documentation and static content, and requires a local copy of the GROMACS source repository.

Build with GROMACS

To build the full gmxapi documentation with GROMACS, configure GROMACS with -DGMX_PYTHON_PACKAGE=ON and build the GROMACS documentation normally.

Docker web server

Alternatively, build the docs Docker image from python_packaging/docker/docs.dockerfile or pull a prebuilt image from DockerHub. Refer to the dockerfile or to https://hub.docker.com/r/gmxapi/docs for more information.

Troubleshooting

Couldn’t find the gmxapi support library? If you don’t want to “source” your GMXRC file, you can tell the package where to find a gmxapi compatible GROMACS installation with gmxapi_DIR. E.g. gmxapi_DIR=/path/to/gromacs pip install .

Before updating the gmxapi package it is generally a good idea to remove the previous installation and to start with a fresh build directory. You should be able to just pip uninstall gmxapi.

Do you see something like the following?

CMake Error at gmx/core/CMakeLists.txt:45 (find_package):
   Could not find a package configuration file provided by "gmxapi" with any
   of the following names:

     gmxapiConfig.cmake
     gmxapi-config.cmake

   Add the installation prefix of "gmxapi" to CMAKE_PREFIX_PATH or set
   "gmxapi_DIR" to a directory containing one of the above files.  If "gmxapi"
   provides a separate development package or SDK, be sure it has been
   installed.

This could be because

• GROMACS is not already installed
• GROMACS was built without the CMake variable GMXAPI=ON
• or if gmxapi_DIR (or GROMACS_DIR) is not a path containing directories like bin and share.

If you are not a system administrator you are encouraged to install in a Python virtual environment, created with virtualenv or Conda. Otherwise, you will need to specify the --user flag to pip.

Two of the easiest problems to run into are incompatible compilers and incompatible Python. Try to make sure that you use the same C and C++ compilers for GROMACS, for the Python package, and for the sample plugin. These compilers should also correspond to the mpicc compiler wrapper used to compile mpi4py. In order to build the Python package, you will need the Python headers or development installation, which might not already be installed on the machine you are using. (If not, then you will get an error about missing Python.h at some point.) If you have multiple Python installations (or modules available on an HPC system), you could try one of the other Python installations, or you or a system administrator could install an appropriate Python dev package. Alternatively, you might try installing your own Anaconda or MiniConda in your home directory.

If an attempted installation fails with CMake errors about missing “gmxapi”, make sure that Gromacs is installed and can be found during installation. For instance,

gmxapi_DIR=/Users/eric/gromacs python setup.py install --verbose

Pip and related Python package management tools can be a little too flexible and ambiguous sometimes. If things get really messed up, try explicitly uninstalling the gmxapi module and its dependencies, then do it again and repeat until pip can no longer find any version of any of the packages.

pip uninstall gmxapi
pip uninstall cmake
# ...

Successfully running the test suite is not essential to having a working gmxapi package. We are working to make the testing more robust, but right now the test suite is a bit delicate and may not work right, even though you have a successfully built gmxapi package. If you want to troubleshoot, though, the main problems seem to be that automatic installation of required python packages may not work (requiring manual installations, such as with pip install somepackage) and ambiguities between python versions.

If you are working in a development branch of the repository, note that the upstream branch may be reset to master after a new release is tagged. In general, but particularly on the devel branch, when you do a git pull, you should use the --rebase flag.

If you fetch this repository and then see a git status like this:

$ git status
On branch devel
Your branch and 'origin/devel' have diverged,
and have 31 and 29 different commits each, respectively.

then gmxapi has probably entered a new development cycle. You can do git pull --rebase to update to the latest development branch.

If you do a git pull while in devel and get a bunch of unexpected merge conflicts, do git merge --abort; git pull --rebase and you should be back on track.

If you are developing code for gmxapi, this should be an indication to rebase your feature branches for the new development cycle.