1 ==============================
2 Full installation instructions
3 ==============================
7 Installation instructions for the :py:mod:`gmxapi` Python package,
10 Command line examples assume the `bash <https://www.gnu.org/software/bash/>`_ shell.
12 .. note:: Regarding multiple GROMACS installations:
13 Many GROMACS users switch between multiple GROMACS installations on the same
14 computer using an HPC module system and/or a :ref:`GMXRC <getting access to |Gromacs|>` configuration script.
15 For the equivalent sort of environment switching with the :py:mod:`gmxapi` Python package,
16 we recommend installing it in a different
17 `Python virtual environment <https://www.google.com/search?q=python+virtual+environment>`_
18 for each GROMACS installation.
19 Once built, a particular copy of the :py:mod:`gmxapi` Python package always refers to the
20 same GROMACS installation.
22 .. contents:: Contents
28 The following documentation contains frequent references to the pip_ tool
29 for installing Python packages. In some cases, an unprivileged user should
30 use the ``--user`` command line flag to tell pip_ to install packages
31 into the user site-packages directory rather than the default site-packages
32 directory for the Python installation. This flag is not appropriate when
33 running :command:`pip` in a virtual environment (as recommended) and is omitted in
34 this documentation. If you need the ``--user`` flag, you should modify the
35 example commands to look something like :command:`pip install --upgrade somepackage --user`
39 These instructions use the executable names :command:`python` and :command:`pip`
40 instead of :command:`python3` or :command:`pip3`. Some Python installations require the ``3``
41 suffix, but it is usually not necessary if you have already activated a Python
42 virtual environment (recommended).
47 Typically, setting up the *gmxapi* Python package follows these three steps.
48 If this overview is sufficient for your computing environment,
49 you may disregard the rest of this document.
54 Locate your GROMACS installation, or build and install GROMACS 2020 or higher.
56 .. seealso:: `GROMACS installation <http://manual.gromacs.org/documentation/current/install-guide/index.html>`_
58 The following assumes GROMACS is installed to :file:`/path/to/gromacs`
60 Set up a Python virtual environment
61 -----------------------------------
65 python3 -m venv $HOME/myvenv
66 . $HOME/myvenv/bin/activate
67 python -m ensurepip --default-pip
68 pip install --upgrade pip setuptools
69 pip install --upgrade cmake scikit-build
71 .. seealso:: :ref:`gmxapi venv`
73 Install the gmxapi Python package
74 ---------------------------------
78 . /path/to/gromacs/bin/GMXRC
81 .. seealso:: :ref:`installation`
86 *gmxapi* comes in three parts:
88 * GROMACS gmxapi library for C++.
89 * This Python package, supporting Python 3.6 and higher
90 * MD restraint plugins and sample gmxapi client code
95 The Python package requires a GROMACS installation.
96 Locate an existing GROMACS installation, or
97 `build and install GROMACS <http://manual.gromacs.org/documentation/current/install-guide/index.html>`_
102 Note that gmxapi requires that GROMACS is configured with ``GMXAPI=ON`` and ``BUILD_SHARED_LIBS=ON``.
103 These are enabled by default in most cases. If these options were overridden
104 for your GROMACS installation, you will see CMake errors when trying to build
105 and install the gmxapi Python package or other client software.
107 Then, "source" the :file:`GMXRC` file from the GROMACS installation
108 :ref:`as you normally would <getting access to |Gromacs|>`
109 before using GROMACS, or note its installation location so that you can pass it
110 to the build configuration.
112 Build system requirements
113 -------------------------
115 gmxapi can be built for Python 3.6 and higher.
117 You will need a C++ 14 compatible compiler and a reasonably up-to-date version
119 Full gmxapi functionality may also require an MPI compiler (e.g. :command:`mpicc`).
121 Important: To build a module that can be imported by Python, you need a Python
122 installation that includes the Python headers. Unfortunately, it is not always
123 obvious whether these headers are present or where to find them. The simplest
124 answer is to just try to build the Python package using these instructions, and
125 if gmxapi is unable to find the Python tools it needs, try a different Python
126 installation or install the additional development packages.
128 On a Linux system, this may require installing packages such as ``python-dev``
129 and/or ``python3-dev``.
130 If you are building Python, either from scratch or with a tool like
131 :command:`pyenv install` (see
132 `wiki entry <https://github.com/pyenv/pyenv/wiki#how-to-build-cpython-with---enable-shared>`_
134 be sure to enable installation of the Python C library with the
135 ``--enable-shared`` flag.
136 Alternatively, various Python distributions provide a
137 sufficient build environment while only requiring installation into a user
138 home directory. (Some examples below.)
140 If you are using an HPC system with software available through modules you may
141 be able to just :command:`module load` a different Python installation and find one
144 Python environment requirements
145 -------------------------------
147 gmxapi requires Python 3.6 or higher. Check your version with
148 :command:`python3 --version` or :command:`python --version`.
152 The following documentation assumes you do not need to use a trailing '3' to
153 access a Python 3 interpreter on your system.
154 The default Python interpreter on your system may use :command:`python3` and :command:`pip3`
155 instead of :command:`python` and :command:`pip`. You can check the version with
156 :command:`python3 --version` or :command:`python --version` and :command:`pip --version`.
158 To build and install, you need the Python packages for
159 cmake_, networkx_, scikit-build_, and setuptools_
160 (all available from `PyPI with pip <https://pip.pypa.io/en/stable/>`_).
162 For full functionality, you should also have mpi4py_ and numpy_.
163 These requirements and version numbers are listed in :file:`requirements.txt`.
165 The easiest way to make sure you have the requirements installed, first update
166 pip_, then use the :file:`requirements.txt` file provided with the repository.
167 File paths in this section are relative to the root directory of your local copy
168 of the GROMACS source.
170 Confirm that pip_ is available, install pip_ if it is missing, or get
171 instructions on how to install pip_::
173 python -m ensurepip --default-pip
175 Install or upgrade required components::
177 python -m pip install --upgrade pip
178 pip install --upgrade setuptools
180 "requirements" files in GROMACS source tree
181 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
183 If you are building from source code in a local copy of the GROMACS source
184 repository, some helpful files allow you to preinstall the Python requirements
185 before installing the :py:mod:`gmxapi` package.
187 pip install -r python_packaging/src/requirements.txt
189 If building documentation or running tests,
190 :command:`pip install -r python_packaging/requirements-docs.txt` or
191 :command:`pip install -r python_packaging/requirements-test.txt`,
192 respectively, or see below.
194 Documentation build requirements
195 --------------------------------
197 See :ref:`gmxapi_package_documentation`
199 .. _testing_requirements:
204 Testing is performed with `pytest <https://docs.pytest.org/en/latest/>`_.
205 Tests also require numpy_.
206 You can probably install both with pip_::
208 pip install pytest numpy
210 To test the full functionality also requires an MPI parallel environment.
211 You will need the mpi4py_ Python package and an MPI launcher
212 (such as :command:`mpiexec`, :command:`mpirun`, a launcher provided by your HPC queuing system,
213 or whatever is provided by your favorite MPI package for your operating system).
215 .. _mpi_requirements:
220 For the ensemble simulations features, you will need an MPI installation.
221 On an HPC system, this means you will probably have to use :command:`module load`
222 to load a compatible set of MPI tools and compilers.
223 Check your HPC documentation or try :command:`module avail` to look for an
224 ``openmpi``, ``mpich``, or ``mvapich`` module and matching compiler module.
225 This may be as simple as::
230 Note that the compilers loaded might not be the first compilers discovered
231 automatically by the build tools we will use below,
232 so you may have to specify compilers on the command line for consistency.
233 It may be necessary to require that GROMACS, gmxapi,
234 and the sample code are built with the same compiler(s).
236 Note that strange errors have been known to occur when mpi4py_ is built with
237 different a different tool set than has been used to build Python and gmxapi.
238 If the default compilers on your system are not sufficient for GROMACS or gmxapi,
239 you may need to build, e.g., OpenMPI or MPICH, and/or build mpi4py_ with a
240 specific MPI compiler wrapper. This can complicate building in environments such
243 Set the MPICC environment variable to the MPI compiler wrapper and forcibly
246 export MPICC=`which mpicc`
247 pip install --no-cache-dir --upgrade --no-binary ":all:" --force-reinstall mpi4py
249 If you have a different MPI C compiler wrapper, substitute it for :command:`mpicc` above.
253 Installing the Python package
254 =============================
256 We recommend using Python's `pip <https://pip.pypa.io/en/stable/>`_
257 package installer to automatically download, build, and install the latest
258 version of the gmxapi package into a Python
259 `virtual environment <https://docs.python.org/3/tutorial/venv.html>`_,
260 though it is also possible to install without a virtual environment.
261 If installing without a virtual environment as an un-privileged user,
262 you may need to set the CMake variable ``GMXAPI_USER_INSTALL``
263 (``-DGMXAPI_USER_INSTALL=ON`` on the :command:`cmake` command line)
264 and / or use the ``--user`` option with :command:`pip install`.
266 Recommended installation
267 ------------------------
269 The instructions in this section assume that *pip* is able to download files
270 from the internet. Alternatively, refer to :ref:`gmxapi offline install`.
272 Locate or install GROMACS
273 ^^^^^^^^^^^^^^^^^^^^^^^^^
275 You need a GROMACS installation that includes the gmxapi headers and library.
276 If GROMACS 2020 or higher is already installed,
277 *and* was configured with ``GMXAPI=ON`` at build time,
278 you can just source the :ref:`GMXRC <getting access to |Gromacs|>`
279 (so that the Python package knows where to find GROMACS)
280 and skip to the next section.
282 Otherwise, install a supported version of GROMACS.
283 When building GROMACS from source, be sure to configure cmake with the flag
284 ``-DGMXAPI=ON`` (default).
286 Set the environment variables for the GROMACS installation so that the gmxapi
287 headers and library can be found when building the Python package.
288 If you installed to a :file:`gromacs-gmxapi` directory in your home directory as
289 above and you use the :command:`bash` shell, do::
291 source $HOME/gromacs-gmxapi/bin/GMXRC
295 Set up a Python virtual environment
296 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
298 We recommend installing the Python package in a virtual environment.
299 If not installing in a virtual environment, you may not be able to install
300 necessary prerequisites (e.g. if you are not an administrator of the system you are on).
302 The following instructions use the :py:mod:`venv` module.
303 Alternative virtual environments, such as Conda_,
304 should work fine, but are beyond the scope of this document.
305 (We welcome contributed recipes!)
307 Depending on your computing environment, the Python 3 interpreter may be accessed
308 with the command :command:`python` or :command:`python3`. Use :command:`python --version` and
309 :command:`python3 --version` to figure out which you need to use. The following assumes
310 the Python 3 interpreter is accessed with :command:`python3`.
312 Create a Python 3 virtual environment::
314 python3 -m venv $HOME/myvenv
316 Activate the virtual environment. Your shell prompt will probably be updated with the name of the environment you
317 created to make it more obvious.
321 $ source $HOME/myvenv/bin/activate
326 After activating the *venv*, :command:`python` and :command:`pip` are sufficient.
327 (The '3' suffix will no longer be necessary and will be omitted in the rest
330 Activating the virtual environment may change your shell prompt to indicate the
331 environment is active. The prompt is omitted from the remaining examples, but
332 the remaining examples assume the virtual environment is still active.
333 (Don't do it now, but you can deactivate the environment by running :command:`deactivate`.)
338 It is always a good idea to update pip_ and setuptools_ before installing
339 new Python packages::
341 pip install --upgrade pip setuptools
343 The gmxapi installer requires a few additional packages. It is best to make sure
344 they are installed and up to date before proceeding.
348 pip install --upgrade cmake scikit-build
350 For MPI, we use mpi4py_.
351 Make sure it is using the same MPI installation that we are building
352 GROMACS against and building with compatible compilers.
356 python -m pip install --upgrade pip setuptools
357 MPICC=`which mpicc` pip install --upgrade mpi4py
359 .. seealso:: :ref:`mpi_requirements`
361 Install the latest version of gmxapi
362 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
364 Fetch and install the latest official version of gmxapi from the Python Packaging Index::
366 # Get the latest official release.
369 The `PyPI repository <https://pypi.org/project/gmxapi/#history>`_
370 may include pre-release versions,
371 but :command:`pip` will ignore them unless you use the ``--pre`` flag::
373 # Get the latest version, including pre-release versions.
374 pip install --pre gmxapi
376 If :command:`pip` does not find your GROMACS installation, use one of the following
377 environment variables to provide a hint.
382 If you have a single GROMACS installation at :file:`/path/to/gromacs`, it is usually
383 sufficient to provide this location to :command:`pip` through the :envvar:`gmxapi_DIR`
384 environment variable.
388 gmxapi_DIR=/path/to/gromacs pip install gmxapi
393 If you have multiple builds of GROMACS distinguished by suffixes
394 (e.g. *_d*, *_mpi*, etcetera), or if you need to provide extra hints to :command:`pip`
395 about the software tools that were used to build GROMACS, you can specify a
396 directory in which the installer can find a CMake "tool chain".
398 In the following example, ``${SUFFIX}`` is the suffix that distinguishes the
399 particular build of GROMACS you want to target (refer to GROMACS installation
400 instructions for more information.) ``${SUFFIX}`` may simply be empty, or ``''``.
404 GMXTOOLCHAINDIR=/path/to/gromacs/share/cmake/gromacs${SUFFIX} pip install gmxapi
409 You can also install the :py:mod:`gmxapi` Python package from within a local copy of
410 the GROMACS source repository. Assuming you have already obtained the GROMACS
411 source code and you are in the root directory of the source tree, you will find
412 the :py:mod:`gmxapi` Python package sources in the :file:`python_packaging/src` directory.
416 cd python_packaging/src
417 pip install -r requirements.txt
420 .. _gmxapi offline install:
425 If the required dependencies are already installed, you can do a quick installation
426 without internet access, either from the source directory or from a source archive.
428 For example, the last line of the previous example could be replaced with::
430 pip install --no-cache-dir --no-deps --no-index --no-build-isolation .
432 Refer to pip_ documentation for descriptions of these options.
434 If you have built or downloaded a source distribution archive, you can provide
435 the archive file to :command:`pip` instead of the ``.`` argument::
437 pip install gmxapi-0.1.0.tar.gz
439 In this example, the archive file name is as was downloaded from
440 `PyPI <https://pypi.org/project/gmxapi/#history>`_ or as built locally,
441 according to the following instructions.
443 Building a source archive
444 -------------------------
446 A source archive for the gmxapi python package can be built from the GROMACS
447 source repository using Python ``setuptools`` and ``scikit-build``.
451 pip install --upgrade setuptools scikit-build
452 cd python_packaging/src
453 python setup.py sdist
455 This command will create a ``dist`` directory containing a source distribution
456 archive file. The file name has the form *gmxapi-<version>.<suffix>*, where
457 *<version>* is the version from the ``setup.py`` file, and *<suffix>* is
458 determined by the local environment or by additional arguments to ``setup.py``.
462 Python documentation for
463 `creating a source distribution
464 <https://docs.python.org/3/distutils/sourcedist.html#creating-a-source-distribution>`_
466 Package maintainers may update the online respository by uploading a freshly
467 built ``sdist`` with ``python -m twine upload dist/*``
469 .. _gmxapi_package_documentation:
471 Accessing gmxapi documentation
472 ==============================
474 Documentation for the Python classes and functions in the gmx module can
475 be accessed in the usual ways, using ``pydoc`` from the command line or
476 ``help()`` in an interactive Python session.
478 The complete documentation (which you are currently reading)
479 can be browsed `online <http://manual.gromacs.org/current/gmxapi/>`__
480 or built from a copy of the GROMACS source repository.
482 Documentation is built from a combination of Python module documentation and
483 static content, and requires a local copy of the GROMACS source repository.
488 To build the full gmxapi documentation with GROMACS, configure GROMACS with
489 ``-DGMX_PYTHON_PACKAGE=ON`` and build the GROMACS documentation normally.
490 This will first build the *gmxapi* Python package and install it to a temporary
491 location in the build tree. Sphinx can then import the package to automatically
492 extract Python docstrings.
494 Sometimes the build environment can choose a different Python interpreter than
495 the one you intended.
496 You can set the ``Python3_ROOT`` or ``CMAKE_PREFIX_PATH`` CMake variable to
497 explicitly choose the Python installation or *venv* directory.
499 If you use pyenv or pyenv-virtualenv to dynamically manage your Python version,
500 you can help identify a particular version with ``pyenv version-name`` and the
501 directory with ``pyenv prefix {version}``. For example::
503 -DPython3_ROOT=$(pyenv prefix $(pyenv version-name))
508 Alternatively, build the ``docs`` Docker image from ``python_packaging/docker/docs.dockerfile``
509 or pull a prebuilt image from DockerHub. Refer to the dockerfile or to
510 https://hub.docker.com/r/gmxapi/docs for more information.
514 Document sample_restraint package. Reference issue
515 `3027 <https://gitlab.com/gromacs/gromacs/-/issues/3027>`_
517 .. _gmxapi install troubleshooting:
522 AttributeError: module 'enum' has no attribute 'IntFlag'
523 --------------------------------------------------------
525 If you had older versions of some of the dependencies installed,
526 you might have picked up a transitive dependency on the ``enum34`` package.
529 pip uninstall -y enum34
531 and see if that fixes the problem. If not, try a fresh virtual environment
532 (see above) to help narrow down the problem before you
533 `open an issue <https://gitlab.com/gromacs/gromacs/-/issues/>`_.
535 Couldn't find the ``gmxapi`` support library?
536 ---------------------------------------------
538 If you don't want to "source" your :ref:`GMXRC <getting access to |Gromacs|>` file, you
539 can tell the package where to find a gmxapi compatible GROMACS installation with
540 ``gmxapi_DIR``. E.g. ``gmxapi_DIR=/path/to/gromacs pip install .``
542 Before updating the ``gmxapi`` package it is generally a good idea to remove the
543 previous installation and to start with a fresh build directory. You should be
544 able to just ``pip uninstall gmxapi``.
546 Do you see something like the following?
550 CMake Error at gmx/core/CMakeLists.txt:45 (find_package):
551 Could not find a package configuration file provided by "gmxapi" with any
552 of the following names:
557 Add the installation prefix of "gmxapi" to CMAKE_PREFIX_PATH or set
558 "gmxapi_DIR" to a directory containing one of the above files. If "gmxapi"
559 provides a separate development package or SDK, be sure it has been
562 This could be because
564 * GROMACS is not already installed
565 * GROMACS was built without the CMake variable ``GMXAPI=ON``
566 * or if ``gmxapi_DIR`` (or ``GROMACS_DIR``) is not a path containing directories
567 like ``bin`` and ``share``.
569 If you are not a system administrator you are encouraged to install in a Python
570 virtual environment, created with virtualenv or Conda_.
571 Otherwise, you will need to specify the ``--user`` flag to ``pip``.
573 Two of the easiest problems to run into are incompatible compilers and
574 incompatible Python. Try to make sure that you use the same C and C++
575 compilers for GROMACS, for the Python package, and for the sample
576 plugin. These compilers should also correspond to the :command:`mpicc` compiler
577 wrapper used to compile mpi4py_. In order to build the Python
578 package, you will need the Python headers or development installation,
579 which might not already be installed on the machine you are using. (If
580 not, then you will get an error about missing :file:`Python.h` at some
581 point.) If you have multiple Python installations (or modules available
582 on an HPC system), you could try one of the other Python installations,
583 or you or a system administrator could install an appropriate Python dev
584 package. Alternatively, you might try installing your own Anaconda or
585 MiniConda in your home directory.
587 If an attempted installation fails with CMake errors about missing
588 “gmxapi”, make sure that Gromacs is installed and can be found during
589 installation. For instance,
593 gmxapi_DIR=/Users/eric/gromacs python setup.py install --verbose
595 Pip and related Python package management tools can be a little too
596 flexible and ambiguous sometimes. If things get really messed up, try
597 explicitly uninstalling the :py:mod:`gmxapi` module and its dependencies, then do
598 it again and repeat until :command:`pip` can no longer find any version of any
607 Successfully running the test suite is not essential to having a working
608 :py:mod:`gmxapi` package. We are working to make the testing more robust, but
609 right now the test suite is a bit delicate and may not work right, even
610 though you have a successfully built the :py:mod:`gmxapi` package. If you want to
611 troubleshoot, though, the main problems seem to be that automatic
612 installation of required python packages may not work (requiring manual
613 installations, such as with :command:`pip install somepackage`) and ambiguities
614 between python versions.
616 If you are working in a development branch of the repository, note that
617 the upstream branch may be reset to ``master`` after a new release is
618 tagged. In general, but particularly on the ``devel`` branch, when you
619 do a :command:`git pull`, you should use the ``--rebase`` flag.
621 If you fetch this repository and then see a git status like this::
625 Your branch and 'origin/devel' have diverged,
626 and have 31 and 29 different commits each, respectively.
628 then :py:mod:`gmxapi` has probably entered a new development cycle. You can
629 do :command:`git pull --rebase` to update to the latest development branch.
631 If you do a :command:`git pull` while in ``devel`` and get a bunch of unexpected
632 merge conflicts, do :command:`git merge --abort; git pull --rebase` and you should
635 If you are developing code for gmxapi, this should be an indication to
636 rebase your feature branches for the new development cycle.
638 .. _cmake: https://pypi.org/project/cmake/
640 .. _Conda: https://docs.conda.io/en/latest/
642 .. _mpi4py: https://pypi.org/project/mpi4py/
644 .. _networkx: https://pypi.org/project/networkx/
646 .. _numpy: https://www.numpy.org/
648 .. _pip: https://pip.pypa.io/en/stable/
650 .. _scikit-build: https://pypi.org/project/scikit-build/
652 .. _setuptools: https://pypi.org/project/setuptools/