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Merge pull request #3689 from rbberger/cmake_optional_python_install

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cmake: remove pip install from install target
This commit is contained in:
Axel Kohlmeyer
2023-03-16 10:46:15 -04:00
committed by GitHub
parent 730e5d2e64 4940bda15f
commit 45a3e30f6c
2 changed files with 2 additions and 168 deletions
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29
cmake/CMakeLists.txt
View File

@ -856,35 +856,6 @@ else()
${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
endif()
###############################################################################
# Add LAMMPS python module to "install" target. This is taylored for building
# LAMMPS for package managers and with different prefix settings.
# This requires either a shared library or that the PYTHON package is included.
###############################################################################
if(BUILD_SHARED_LIBS OR PKG_PYTHON)
if(CMAKE_VERSION VERSION_LESS 3.12)
# adjust so we find Python 3 versions before Python 2 on old systems with old CMake
set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
find_package(PythonInterp) # Deprecated since version 3.12
if(PYTHONINTERP_FOUND)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
else()
# backward compatibility
if(PYTHON_EXECUTABLE)
set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
endif()
find_package(Python COMPONENTS Interpreter)
endif()
if(Python_EXECUTABLE)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/lib)
file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/src)
file(COPY ${LAMMPS_SOURCE_DIR}/version.h DESTINATION ${CMAKE_BINARY_DIR}/python/src)
file(COPY ${LAMMPS_PYTHON_DIR}/README ${LAMMPS_PYTHON_DIR}/pyproject.toml ${LAMMPS_PYTHON_DIR}/setup.py ${LAMMPS_PYTHON_DIR}/lammps DESTINATION ${CMAKE_BINARY_DIR}/python/lib)
install(CODE "if(\"\$ENV{DESTDIR}\" STREQUAL \"\")\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX})\n else()\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR})\n endif()")
endif()
endif()
include(Testing)
include(CodeCoverage)
include(CodingStandard)

141
doc/src/Python_install.rst
View File

@ -27,124 +27,19 @@ interpreter can find it and installing the LAMMPS shared library into a
folder that the dynamic loader searches or inside of the installed
``lammps`` package folder. There are multiple ways to achieve this.
#. Do a full LAMMPS installation of libraries, executables, selected
headers, documentation (if enabled), and supporting files (only
available via CMake), which can also be either system-wide or into
user specific folders.
#. Install both components into a Python ``site-packages`` folder, either
system-wide or in the corresponding user-specific folder. This way no
additional environment variables need to be set, but the shared
library is otherwise not accessible.
#. Do an installation into a virtual environment. This can either be an
installation of the Python package only or a full installation of LAMMPS.
#. Do an installation into a virtual environment.
#. Leave the files where they are in the source/development tree and
adjust some environment variables.
.. tabs::
.. tab:: Full install (CMake-only)
:ref:`Build the LAMMPS executable and library <library>` with
``-DBUILD_SHARED_LIBS=on``, ``-DLAMMPS_EXCEPTIONS=on`` and
``-DPKG_PYTHON=on`` (The first option is required, the other two
are optional by recommended). The exact file name of the shared
library depends on the platform (Unix/Linux, macOS, Windows) and
the build configuration being used. The installation base folder
is already set by default to the ``$HOME/.local`` directory, but
it can be changed to a custom location defined by the
``CMAKE_INSTALL_PREFIX`` CMake variable. This uses a folder
called ``build`` to store files generated during compilation.
.. code-block:: bash
# create build folder
mkdir build
cd build
# configure LAMMPS compilation
cmake -C ../cmake/presets/basic.cmake -D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on ../cmake
# compile LAMMPS
cmake --build .
# install LAMMPS into $HOME/.local
cmake --install .
This leads to an installation to the following locations:
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=================================================================+=============================================================+
| LAMMPS Python package | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$HOME/.local/lib/`` (32bit) | Set shared loader environment variable to this path |
| | * ``$HOME/.local/lib64/`` (64bit) | (see below for more info on this) |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS executable | * ``$HOME/.local/bin/`` | |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS potential files | * ``$HOME/.local/share/lammps/potentials/`` | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
+------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
For a system-wide installation you need to set
``CMAKE_INSTALL_PREFIX`` to a system folder like ``/usr`` (or
``/usr/local``); the default is ``${HOME}/.local``. The
installation step for a system folder installation (**not** the
configuration/compilation) needs to be done with superuser
privilege, e.g. by using ``sudo cmake --install .``. The
installation folders will then be changed to (assuming ``/usr`` as
prefix):
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+=========================================================+=============================================================+
| LAMMPS Python package | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit) | ``X.Y`` depends on the installed Python version |
| | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``/usr/lib/`` (32bit) | |
| | * ``/usr/lib64/`` (64bit) | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS executable | * ``/usr/bin/`` | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS potential files | * ``/usr/share/lammps/potentials/`` | |
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
To be able to use the "user" installation you have to ensure that
the folder containing the LAMMPS shared library is either included
in a path searched by the shared linker (e.g. like
``/usr/lib64/``) or part of the ``LD_LIBRARY_PATH`` environment
variable (or ``DYLD_LIBRARY_PATH`` on macOS). Otherwise you will
get an error when trying to create a LAMMPS object through the
Python module.
.. code-block:: bash
# Unix/Linux
export LD_LIBRARY_PATH=$HOME/.local/lib:$LD_LIBRARY_PATH
# macOS
export DYLD_LIBRARY_PATH=$HOME/.local/lib:$DYLD_LIBRARY_PATH
If you plan to use the LAMMPS executable (e.g., ``lmp``), you may
also need to adjust the ``PATH`` environment variable (but many
newer Linux distributions already have ``$HOME/.local/bin``
included). Example:
.. code-block:: bash
export PATH=$HOME/.local/bin:$PATH
To make those changes permanent, you can add the commands to your
``$HOME/.bashrc`` file. For a system-wide installation is is not
necessary due to files installed in system folders that are loaded
automatically when a login shell is started.
.. tab:: Python package only
.. tab:: Python package
Compile LAMMPS with either :doc:`CMake <Build_cmake>` or the
:doc:`traditional make <Build_make>` procedure in :ref:`shared
@ -272,38 +167,6 @@ folder that the dynamic loader searches or inside of the installed
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
If you do a full installation (CMake only) with "install", this
leads to the following installation locations:
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |
+========================+========================================================+=============================================================+
| LAMMPS Python Module | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` | ``X.Y`` depends on the installed Python version |
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS shared library | * ``$VIRTUAL_ENV/lib/`` (32bit) | Set shared loader environment variable to this path |
| | * ``$VIRTUAL_ENV/lib64/`` (64bit) | (see below for more info on this) |
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS executable | * ``$VIRTUAL_ENV/bin/`` | |
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
| LAMMPS potential files | * ``$VIRTUAL_ENV/share/lammps/potentials/`` | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
+------------------------+--------------------------------------------------------+-------------------------------------------------------------+
In that case you need to modify the ``$HOME/myenv/bin/activate``
script in a similar fashion you need to update your
``$HOME/.bashrc`` file to include the shared library and
executable locations in ``LD_LIBRARY_PATH`` (or
``DYLD_LIBRARY_PATH`` on macOS) and ``PATH``, respectively.
For example with:
.. code-block:: bash
# Unix/Linux
echo 'export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
# macOS
echo 'export DYLD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$DYLD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
.. tab:: In place usage
You can also :doc:`compile LAMMPS <Build>` as usual in