Full installation instructions¶
Installation instructions for the gmxapi Python package,
built on GROMACS.
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.
Contents
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).
Overview¶
Typically, setting up the gmxapi Python package follows these three steps. If this overview is sufficient for your computing environment, you may disregard the rest of this document.
Install GROMACS¶
Locate your GROMACS installation, or build and install GROMACS 2020 or higher.
See also
The following assumes GROMACS is installed to /path/to/gromacs
Set up a Python virtual environment¶
python3 -m venv $HOME/myvenv
. $HOME/myvenv/bin/activate
python -m ensurepip --default-pip
pip install --upgrade pip setuptools
pip install --upgrade scikit-build
See also
Background¶
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
GROMACS requirements¶
The Python package requires a GROMACS installation. Locate an existing GROMACS installation, or build and install GROMACS before proceeding.
Note
Note that gmxapi requires that GROMACS is configured with GMXAPI=ON and BUILD_SHARED_LIBS=ON.
These are enabled by default in most cases. If these options were overridden
for your GROMACS installation, you will see CMake errors when trying to build
and install the gmxapi Python package or other client software.
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.
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).
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.
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
If you have a different MPI C compiler wrapper, substitute it for mpicc above.
Installing the Python package¶
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,
though 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.
Recommended installation¶
The instructions in this section assume that pip is able to download files from the internet. Alternatively, refer to Offline install.
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).
The following instructions use the venv module.
Alternative virtual environments, such as Conda <https://docs.conda.io/en/latest/>,
should work fine, but are beyond the scope of this document.
(We welcome contributed recipes!)
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.
Create a Python 3 virtual environment:
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 $HOME/myvenv/bin/activate
(myvenv)$
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.)
Activating the virtual environment may change your shell prompt to indicate the environment is active. The prompt is omitted from the remaining examples, but the remaining examples assume the virtual environment 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
See also
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 :py:mod`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.
This will first build the gmxapi Python package and install it to a temporary
location in the build tree. Sphinx can then import the package to automatically
extract Python docstrings.
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\`
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(orGROMACS_DIR) is not a path containing directories likebinandshare.
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 the 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.