forked from lijiext/lammps
update build system to make it auto-adapt to include python support or not into MLIAP
This commit is contained in:
Axel Kohlmeyer
parent
3ed41295cd
commit
3f5a896aab
|
|
@ -194,7 +194,6 @@ endif()
|
|||
# "hard" dependencies between packages resulting
|
||||
# in an error instead of skipping over files
|
||||
pkg_depends(MLIAP SNAP)
|
||||
pkg_depends(MLIAP PYTHON)
|
||||
pkg_depends(MPIIO MPI)
|
||||
pkg_depends(USER-ATC MANYBODY)
|
||||
pkg_depends(USER-LB MPI)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,30 @@
|
|||
# Find the Cythonize tool.
|
||||
#
|
||||
# This code sets the following variables:
|
||||
#
|
||||
# Cythonize_EXECUTABLE
|
||||
#
|
||||
# adapted from https://github.com/cmarshall108/cython-cmake-example/blob/master/cmake/FindCython.cmake
|
||||
#=============================================================================
|
||||
|
||||
if(CMAKE_VERSION VERSION_LESS 3.12)
|
||||
find_package(PythonInterp 3.6 QUIET) # Deprecated since version 3.12
|
||||
if(PYTHONINTERP_FOUND)
|
||||
set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
|
||||
endif()
|
||||
else()
|
||||
find_package(Python3 3.6 COMPONENTS Interpreter QUIET)
|
||||
endif()
|
||||
|
||||
# Use the Cython executable that lives next to the Python executable
|
||||
# if it is a local installation.
|
||||
if(Python3_EXECUTABLE)
|
||||
get_filename_component(_python_path ${Python3_EXECUTABLE} PATH)
|
||||
find_program(Cythonize_EXECUTABLE
|
||||
NAMES cythonize3 cythonize cythonize.bat
|
||||
HINTS ${_python_path})
|
||||
endif()
|
||||
|
||||
include(FindPackageHandleStandardArgs)
|
||||
FIND_PACKAGE_HANDLE_STANDARD_ARGS(Cythonize REQUIRED_VARS Cythonize_EXECUTABLE)
|
||||
mark_as_advanced(Cythonize_EXECUTABLE)
|
||||
|
|
@ -50,6 +50,7 @@ function(check_for_autogen_files source_dir)
|
|||
file(GLOB SRC_AUTOGEN_FILES ${source_dir}/style_*.h)
|
||||
file(GLOB SRC_AUTOGEN_PACKAGES ${source_dir}/packages_*.h)
|
||||
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
|
||||
list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/MLIAP/mliap_model_python_couple ${source_dir}/MLIAP/mliap_model_python_couple.cpp)
|
||||
foreach(_SRC ${SRC_AUTOGEN_FILES})
|
||||
get_filename_component(FILENAME "${_SRC}" NAME)
|
||||
if(EXISTS ${source_dir}/${FILENAME})
|
||||
|
|
|
|||
|
|
@ -1,3 +1,29 @@
|
|||
execute_process(COMMAND cythonize mliap_model_python_couple.pyx WORKING_DIRECTORY ../src/MLIAP)
|
||||
# if PYTHON package is included we may also include Python support in MLIAP
|
||||
set(ENABLE_MLIAP_PYTHON_DEFAULT OFF)
|
||||
if(PKG_PYTHON)
|
||||
find_package(Cythonize)
|
||||
if(Cythonize_FOUND)
|
||||
set(ENABLE_MLIAP_PYTHON_DEFAULT ON)
|
||||
endif()
|
||||
endif()
|
||||
|
||||
target_compile_definitions(lammps PRIVATE -DLMP_MLIAPPY)
|
||||
option(ENABLE_MLIAP_PYTHON "Build MLIAP package with Python support" ${ENABLE_MLIAP_PYTHON_DEFAULT})
|
||||
|
||||
if(ENABLE_MLIAP_PYTHON)
|
||||
find_package(Cythonize REQUIRED)
|
||||
if(NOT_PKG_PYTHON)
|
||||
message(FATAL_ERROR "Must install PYTHON package for MLIAP_PYTHON")
|
||||
endif()
|
||||
|
||||
set(MLIAP_CYTHON_DIR ${CMAKE_BINARY_DIR}/cython)
|
||||
file(MAKE_DIRECTORY ${MLIAP_CYTHON_DIR})
|
||||
add_custom_command(OUTPUT ${MLIAP_CYTHON_DIR}/mliap_model_python_couple.cpp ${MLIAP_CYTHON_DIR}/mliap_model_python_couple.h
|
||||
COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_SOURCE_DIR}/MLIAP/mliap_model_python_couple.pyx ${MLIAP_CYTHON_DIR}/mliap_model_python_couple.pyx
|
||||
COMMAND ${Cythonize_EXECUTABLE} ${MLIAP_CYTHON_DIR}/mliap_model_python_couple.pyx -3
|
||||
WORKING_DIRECTORY ${MLIAP_CYTHON_DIR}
|
||||
MAIN_DEPENDENCY ${LAMMPS_SOURCE_DIR}/MLIAP/mliap_model_python_couple.pyx
|
||||
COMMENT "Generating C++ sources with cythonize...")
|
||||
target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
|
||||
target_sources(lammps PRIVATE ${MLIAP_CYTHON_DIR}/mliap_model_python_couple.cpp)
|
||||
target_include_directories(lammps PRIVATE ${MLIAP_CYTHON_DIR})
|
||||
endif()
|
||||
|
|
|
|||
|
|
@ -666,10 +666,10 @@ A general interface for machine-learning interatomic potentials, including PyTor
|
|||
|
||||
**Install:**
|
||||
|
||||
To use this package, also the :ref:`SNAP package <PKG-SNAP>`
|
||||
package needs to be installed. If building the *mliappy* model,
|
||||
use -DLMP_MLIAPPY and the :ref:`PYTHON package <PKG-PYTHON>`
|
||||
package needs to be installed. The version of python must be >3.5.
|
||||
To use this package, also the :ref:`SNAP package <PKG-SNAP>` package needs
|
||||
to be installed. To make the *mliappy* model available, also the
|
||||
:ref:`PYTHON package <PKG-PYTHON>` package needs to be installed and the version of
|
||||
python must be 3.5 or later.
|
||||
|
||||
**Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
|
||||
|
||||
|
|
@ -681,8 +681,8 @@ package needs to be installed. The version of python must be >3.5.
|
|||
* :doc:`compute_style mliap <compute_mliap>`
|
||||
* examples/mliap (see README)
|
||||
|
||||
When built with the *mliappy* model using -DLMP_MLIAPPY, this package
|
||||
includes an extension for coupling with python models, including PyTorch.
|
||||
When built with the *mliappy* model this package includes an extension for
|
||||
coupling with python models, including PyTorch.
|
||||
In this case, the python interpreter linked to LAMMPS will need cython and numpy installed.
|
||||
The examples build models with PyTorch, which would thus need to be installed.
|
||||
|
||||
|
|
|
|||
|
|
@ -2,6 +2,6 @@
|
|||
# See the README file for more explanation
|
||||
|
||||
python_SYSINC = $(shell which python-config > /dev/null 2>&1 && python-config --includes || :)
|
||||
python_SYSLIB = $(shell which python-config > /dev/null 2>&1 && python-config --ldflags || :)
|
||||
python_SYSLIB = -lpython3 $(shell which python-config > /dev/null 2>&1 && python-config --ldflags || :)
|
||||
python_SYSPATH =
|
||||
PYTHON=python
|
||||
|
|
|
|||
|
|
@ -0,0 +1,3 @@
|
|||
|
||||
../mliap_model_python_couple.cpp: ../mliap_model_python_couple.pyx
|
||||
cythonize -3 ../mliap_model_python_couple.cpp
|
||||
|
|
@ -106,6 +106,10 @@ if (test $1 = "PERI") then
|
|||
depend USER-OMP
|
||||
fi
|
||||
|
||||
if (test $1 = "PYTHON") then
|
||||
depend MLIAP
|
||||
fi
|
||||
|
||||
if (test $1 = "RIGID") then
|
||||
depend KOKKOS
|
||||
depend USER-OMP
|
||||
|
|
@ -114,6 +118,7 @@ fi
|
|||
|
||||
if (test $1 = "SNAP") then
|
||||
depend KOKKOS
|
||||
depend MLIAP
|
||||
fi
|
||||
|
||||
if (test $1 = "USER-CGSDK") then
|
||||
|
|
|
|||
|
|
@ -26,24 +26,42 @@ action () {
|
|||
fi
|
||||
}
|
||||
|
||||
# enforce package dependency
|
||||
if (test $1 = 1 || test $1 = 2) then
|
||||
if (test ! -e ../sna.h) then
|
||||
echo "Must install SNAP package to use MLIAP package"
|
||||
exit 1
|
||||
fi
|
||||
fi
|
||||
|
||||
# all package files with no dependencies
|
||||
|
||||
for file in *.cpp *.h; do
|
||||
for file in *.cpp *.h *.pyx; do
|
||||
test -f ${file} && action $file
|
||||
done
|
||||
|
||||
# edit 2 Makefile.package files to include/exclude package info
|
||||
|
||||
if (test $1 = 1) then
|
||||
|
||||
if (test -e ../Makefile.package) then
|
||||
sed -i -e 's|^PKG_INC =[ \t]*|&-DLMP_MLIAPPY |' ../Makefile.package
|
||||
if (test "$(type cythonize 2> /dev/null)" != "" && test -e ../python_impl.cpp) then
|
||||
if (test -e ../Makefile.package) then
|
||||
sed -i -e 's|^PKG_INC =[ \t]*|&-DMLIAP_PYTHON |' ../Makefile.package
|
||||
fi
|
||||
if (test -e ../Makefile.package.settings) then
|
||||
sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings
|
||||
# multiline form needed for BSD sed on Macs
|
||||
sed -i -e '4 i \
|
||||
include ..\/..\/lib\/python\/Makefile.mliap_python
|
||||
' ../Makefile.package.settings
|
||||
fi
|
||||
cythonize -3 ../mliap_model_python_couple.pyx
|
||||
fi
|
||||
|
||||
elif (test $1 = 0) then
|
||||
|
||||
if (test -e ../Makefile.package) then
|
||||
sed -i -e 's/[^ \t]*-DLMP_MLIAPPY[^ \t]* //g' ../Makefile.package
|
||||
sed -i -e 's/[^ \t]*-DMLIAP_PYTHON[^ \t]* //g' ../Makefile.package
|
||||
fi
|
||||
|
||||
rm -f ../mliap_model_python_couple.cpp ../mliap_model_python_couple.h
|
||||
sed -i -e '/^include.*python.*mliap_python.*$/d' ../Makefile.package.settings
|
||||
fi
|
||||
|
|
|
|||
|
|
@ -21,7 +21,7 @@
|
|||
#include "mliap_model_linear.h"
|
||||
#include "mliap_model_quadratic.h"
|
||||
#include "mliap_descriptor_snap.h"
|
||||
#ifdef LMP_MLIAPPY
|
||||
#ifdef MLIAP_PYTHON
|
||||
#include "mliap_model_python.h"
|
||||
#endif
|
||||
|
||||
|
|
@ -74,12 +74,12 @@ ComputeMLIAP::ComputeMLIAP(LAMMPS *lmp, int narg, char **arg) :
|
|||
model = new MLIAPModelQuadratic(lmp);
|
||||
iarg += 2;
|
||||
}
|
||||
#ifdef LMP_MLIAPPY
|
||||
#ifdef MLIAP_PYTHON
|
||||
else if (strcmp(arg[iarg+1],"mliappy") == 0) {
|
||||
model = new MLIAPModelPython(lmp);
|
||||
iarg += 2;
|
||||
}
|
||||
#endif
|
||||
#endif
|
||||
else error->all(FLERR,"Illegal compute mliap command");
|
||||
modelflag = 1;
|
||||
} else if (strcmp(arg[iarg],"descriptor") == 0) {
|
||||
|
|
|
|||
|
|
@ -21,7 +21,7 @@
|
|||
#include "mliap_model_linear.h"
|
||||
#include "mliap_model_quadratic.h"
|
||||
#include "mliap_descriptor_snap.h"
|
||||
#ifdef LMP_MLIAPPY
|
||||
#ifdef MLIAP_PYTHON
|
||||
#include "mliap_model_python.h"
|
||||
#endif
|
||||
|
||||
|
|
@ -128,7 +128,7 @@ void PairMLIAP::allocate()
|
|||
|
||||
void PairMLIAP::settings(int narg, char ** arg)
|
||||
{
|
||||
|
||||
|
||||
if (narg < 4)
|
||||
error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
|
|
@ -152,12 +152,12 @@ void PairMLIAP::settings(int narg, char ** arg)
|
|||
if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command");
|
||||
model = new MLIAPModelQuadratic(lmp,arg[iarg+2]);
|
||||
iarg += 3;
|
||||
#ifdef LMP_MLIAPPY
|
||||
#ifdef MLIAP_PYTHON
|
||||
} else if (strcmp(arg[iarg+1],"mliappy") == 0) {
|
||||
if (iarg+3 > narg) error->all(FLERR,"Illegal pair_style mliap command");
|
||||
model = new MLIAPModelPython(lmp,arg[iarg+2]);
|
||||
iarg += 3;
|
||||
#endif
|
||||
#endif
|
||||
} else error->all(FLERR,"Illegal pair_style mliap command");
|
||||
modelflag = 1;
|
||||
} else if (strcmp(arg[iarg],"descriptor") == 0) {
|
||||
|
|
|
|||
|
|
@ -26,7 +26,7 @@
|
|||
#include <cstring>
|
||||
#include <Python.h> // IWYU pragma: export
|
||||
|
||||
#ifdef LMP_MLIAPPY
|
||||
#ifdef MLIAP_PYTHON
|
||||
#include "mliap_model_python.h"
|
||||
// The above should somehow really be included in the next file.
|
||||
// We could get around this with cython --capi-reexport-cincludes
|
||||
|
|
@ -58,14 +58,14 @@ PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)
|
|||
// one-time initialization of Python interpreter
|
||||
// pyMain stores pointer to main module
|
||||
external_interpreter = Py_IsInitialized();
|
||||
|
||||
#ifdef LMP_MLIAPPY
|
||||
|
||||
#ifdef MLIAP_PYTHON
|
||||
// Inform python intialization scheme of the mliappy module.
|
||||
// This -must- happen before python is initialized.
|
||||
int err = PyImport_AppendInittab("mliap_model_python_couple", PyInit_mliap_model_python_couple);
|
||||
if (err) error->all(FLERR,"Could not register MLIAPPY embedded python module.");
|
||||
#endif
|
||||
|
||||
#endif
|
||||
|
||||
Py_Initialize();
|
||||
PyEval_InitThreads();
|
||||
|
||||
|
|
|
|||
|
|
@ -49,6 +49,8 @@ packages_ntopo.h
|
|||
# other auto-generated files
|
||||
lmpinstalledpkgs.h
|
||||
lmpgitversion.h
|
||||
mliap_model_python_couple.cpp
|
||||
mliap_model_python_couple.h
|
||||
# removed on 9 Sep 2020
|
||||
mergesort.h
|
||||
# renamed on 8 May 2020
|
||||
|
|
|
|||
Loading…
Reference in New Issue