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setting up a way for calling pycv wit the python module
Now pycv works with pip Reordering the installation procedure added a sort of "FIND PLUMED" that does not work setting up a second run option, adding an helper removed the self-import gor getting the path of pycv adding an example Better CMakefiles now it shoudl work with plumed from pkg-config or not installed (just needs the plumed executable in the path) Restored the Makefile restoring the standalone tests adding some extra tests updating the WF Now pycv appears to load correcly set up aslo a few basic tests for pyfunc updated the docker recipes with the new installation method of pycv using pip3 in the makefile sourcing the correct bashrc in rocky8 Now the tests are compatible with with GNUsed and BSDsed
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,20 @@ | ||
| FROM plumed:rocky8 | ||
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| RUN source ./.bashrc \ | ||
| RUN . ./.bashrc \ | ||
| && module load mpi \ | ||
| && export OMPI_MCA_btl_base_warn_component_unused=0 \ | ||
| && export OMPI_MCA_btl_base_verbose=0 \ | ||
| && export OMPI_MCA_plm=isolated \ | ||
| && export OMPI_MCA_btl_vader_single_copy_mechanism=none \ | ||
| && export OMPI_MCA_rmaps_base_oversubscribe=yes \ | ||
| && export PATH=$HOME/opt/bin:$PATH \ | ||
| && export CPATH=$HOME/opt/include:$CPATH \ | ||
| && export INCLUDE=$HOME/opt/include:$INCLUDE \ | ||
| && export LIBRARY_PATH=$HOME/opt/lib:$LIBRARY_PATH \ | ||
| && export LD_LIBRARY_PATH=$HOME/opt/lib:$LD_LIBRARY_PATH \ | ||
| && cd plumed2 \ | ||
| && source ./sourceme.sh \ | ||
| && cd plugins/pycv \ | ||
| && pip3 install --user -r requirements.txt \ | ||
| && ./configurePyCV.sh \ | ||
| && ln -s $(realpath ../../regtest/scripts) ./regtest/scripts \ | ||
| && python_bin=python3 ./prepareMakeForDevelop.sh \ | ||
| && make check |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,7 @@ | ||
| /Makefile.conf | ||
| *.o | ||
| *.so | ||
| env | ||
| /env*/ | ||
| /build*/ | ||
| /dist*/ | ||
| *.whl |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,75 @@ | ||
| cmake_minimum_required(VERSION 3.15...3.27) | ||
| project( | ||
| ${SKBUILD_PROJECT_NAME} | ||
| VERSION ${SKBUILD_PROJECT_VERSION} | ||
| LANGUAGES CXX) | ||
| set(CMAKE_CXX_STANDARD 17) | ||
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|
||
| message( | ||
| STATUS | ||
| "Everithing should work fine if you are in the same environment in which you have compiled plumed" | ||
| ) | ||
| # FinPlumed is here: | ||
| list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}") | ||
| # Finding necessary packages | ||
| find_package(Python REQUIRED COMPONENTS Interpreter Development) | ||
| find_package(pybind11 CONFIG REQUIRED) | ||
| find_package(Plumed REQUIRED) | ||
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| # Finding optionals things | ||
| if(Plumed_HAS_MPI) | ||
| find_package(MPI REQUIRED) | ||
| endif() | ||
| if(MPI_CXX_FOUND) | ||
| list(APPEND extraLibs MPI::MPI_CXX) | ||
| endif() | ||
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| if(Plumed_HAS_OPENMP) | ||
| find_package(OpenMP REQUIRED) | ||
| endif() | ||
| if(OpenMP_CXX_FOUND) | ||
| list(APPEND extraLibs OpenMP::OpenMP_CXX) | ||
| endif() | ||
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| include(CheckCXXCompilerFlag) | ||
| check_cxx_compiler_flag(-fno-gnu-unique USE_NO_GNU_UNIQUE) | ||
| if(USE_NO_GNU_UNIQUE) | ||
| set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-gnu-unique") | ||
| endif() | ||
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| # plumed_STATIC_LDFLAGS_OTHER:INTERNAL=-rdynamic;-Wl,-Bsymbolic;-fopenmp | ||
| # -rdynamic is automatically set by cmake, and also -fPIC | ||
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| ################################################################################ | ||
| ################################the pycv library################################ | ||
| ################################################################################ | ||
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| add_library( | ||
| PythonCVInterface SHARED src/ActionWithPython.cpp src/PythonCVInterface.cpp | ||
| src/PythonFunction.cpp) | ||
| # public, so they trickle down to the python module | ||
| target_compile_definitions(PythonCVInterface PUBLIC ${Plumed_CFLAGS}) | ||
| target_include_directories(PythonCVInterface PUBLIC src ${Plumed_INCLUDEDIR}) | ||
| # #################################################################### | ||
| # uncommenting this brings problems since some symbols here are needed | ||
| # by the python module even if it should be the correct setting... | ||
| # https://gcc.gnu.org/wiki/Visibility could be a starting point | ||
| ####################################################################### | ||
| # target_compile_options(PythonCVInterface PRIVATE -fvisibility=hidden) | ||
| target_link_libraries(PythonCVInterface PRIVATE pybind11::embed) | ||
| target_link_libraries(PythonCVInterface PUBLIC plumedKernel ${extraLibs}) | ||
| # this removes the "lib" prefix | ||
| set_target_properties(PythonCVInterface PROPERTIES PREFIX "") | ||
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| install(TARGETS PythonCVInterface DESTINATION pycv) | ||
|
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| ################################################################################ | ||
| ###########################The pvCV companion module############################ | ||
| ################################################################################ | ||
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| pybind11_add_module(plumedCommunications src/PlumedPythonEmbeddedModule.cpp) | ||
| target_link_libraries(plumedCommunications PRIVATE pybind11::headers) | ||
| target_link_libraries(plumedCommunications PUBLIC PythonCVInterface) | ||
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| # The install directory is the output (wheel) directory | ||
| install(TARGETS plumedCommunications DESTINATION .) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| if(NOT Plumed_FOUND) | ||
| find_package(PkgConfig) | ||
| if(Plumed_FIND_QUIETLY) | ||
| function(message) | ||
| # THIS completely shuts down messages | ||
| endfunction() | ||
| pkg_check_modules(PLUMED QUIET plumedInternals) | ||
| else() | ||
| pkg_check_modules(PLUMED plumedInternals) | ||
| endif() | ||
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| if(Plumed_FOUND) | ||
| if("-D__PLUMED_HAS_MPI=1" IN_LIST Plumed_CFLAGS) | ||
| set(Plumed_HAS_MPI | ||
| 1 | ||
| CACHE INTERNAL "plumed has MPI") | ||
| endif() | ||
| if("-fopenmp" IN_LIST Plumed_STATIC_LDFLAGS_OTHER) | ||
| set(Plumed_HAS_OPENMP | ||
| 1 | ||
| CACHE INTERNAL "plumed has OpenMP") | ||
| endif() | ||
| else() | ||
| message(STATUS "plumed not found via pkgconfig, trying executable") | ||
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| execute_process( | ||
| COMMAND plumed --no-mpi info --include-dir | ||
| RESULT_VARIABLE PLUMED_EXECUTABLE | ||
| OUTPUT_QUIET ERROR_QUIET) | ||
| if(PLUMED_EXECUTABLE EQUAL 0) | ||
| set(Plumed_FOUND | ||
| 1 | ||
| CACHE INTERNAL "plumed found") | ||
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| message(STATUS "Configuring plumed from executable") | ||
| execute_process( | ||
| COMMAND plumed --no-mpi info --include-dir | ||
| OUTPUT_VARIABLE Plumed_INCLUDEDIR | ||
| OUTPUT_STRIP_TRAILING_WHITESPACE) | ||
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| set(Plumed_INCLUDEDIR | ||
| ${Plumed_INCLUDEDIR} | ||
| CACHE INTERNAL "plumed include dir") | ||
| execute_process( | ||
| COMMAND plumed --no-mpi info --configuration | ||
| OUTPUT_VARIABLE Plumed_CONFIG | ||
| OUTPUT_STRIP_TRAILING_WHITESPACE) | ||
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| set(Plumed_CPP_FLAGS "") | ||
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| string(REPLACE "\n" ";" ProcessFile_LINES "${Plumed_CONFIG}") | ||
| foreach(_line ${ProcessFile_LINES}) | ||
| if(${_line} MATCHES "CPPFLAGS=.*") | ||
| set(Plumed_CPP_FLAGS ${_line}) | ||
| string(REGEX REPLACE "CPPFLAGS= *" "" Plumed_CPP_FLAGS | ||
| ${Plumed_CPP_FLAGS}) | ||
| string(REPLACE "\\" "" Plumed_CPP_FLAGS ${Plumed_CPP_FLAGS}) | ||
| string(REPLACE "-D" ";" Plumed_CPP_FLAGS ${Plumed_CPP_FLAGS}) | ||
| # message(STATUS "Found PLUMED CPP_FLAGS: \"${Plumed_CPP_FLAGS}\"") | ||
| # message(STATUS "Found PLUMED CPP_FLAGS:") foreach(_flag | ||
| # ${Plumed_CPP_FLAGS}) message(STATUS " \"${_flag}\"") endforeach() | ||
| endif() | ||
| if(${_line} MATCHES ".*-fopenmp.*") | ||
| set(Plumed_HAS_MPI | ||
| 1 | ||
| CACHE INTERNAL "plumed has MPI") | ||
| endif() | ||
| endforeach() | ||
| set(Plumed_CFLAGS | ||
| ${Plumed_CPP_FLAGS} | ||
| CACHE INTERNAL "plumed Definitions flags") | ||
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| execute_process(COMMAND plumed --no-mpi config -q has mpi | ||
| RESULT_VARIABLE Plumed_WITH_MPI) | ||
| if(Plumed_WITH_MPI EQUAL 0) | ||
| set(Plumed_HAS_MPI | ||
| 1 | ||
| CACHE INTERNAL "plumed has MPI") | ||
| endif() | ||
|
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| else() | ||
| if(Plumed_FIND_REQUIRED) | ||
| message(FATAL_ERROR "plumed not found") | ||
| endif() | ||
| endif() | ||
| endif() | ||
| endif() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,53 +1,28 @@ | ||
| # include the machine dependent configuration | ||
| ifneq ($(MAKECMDGOALS),clean) | ||
| -include ../../Makefile.conf | ||
| ifndef canPyCV | ||
| include ./Makefile.conf | ||
| endif | ||
| endif | ||
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| .PHONY: clean check all | ||
| #Dependency tracking based on https://make.mad-scientist.net/papers/advanced-auto-dependency-generation/#tldr | ||
| #this assumes gcc | ||
| DEPDIR := .deps | ||
| DEPFLAGS = -MT $@ -MMD -MP -MF $(DEPDIR)/$*.d | ||
| PYBIND11FLAG = | ||
| ADDCPPFLAGS:=$(python_cf_embedded) $(pybind11_cflags) $(ADDCPPFLAGS) | ||
| ADDCLDFLAGS:=$(ADDCLDFLAGS) $(python_ld_embedded) | ||
| OBJS = ActionWithPython.o PythonCVInterface.o PythonFunction.o PlumedPythonEmbeddedModule.o | ||
| PYTHON=python | ||
| #optional, just in case you want to override python with ./configurePyCV.sh | ||
| -include Makefile.conf | ||
| #this makefiles assume that pip and pytest are installed | ||
| .PHONY: clean check check_standalone check_python all | ||
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| ifeq ($(SOEXT),dylib) | ||
| SONAME_OPTION:=-Wl,-install_name | ||
| else | ||
| SONAME_OPTION:=-Wl,-soname | ||
| endif | ||
| all: pycv_here | ||
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| all: PythonCVInterface.$(SOEXT) | ||
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| #-fvisibility=hidden is needed for pybind11 (to not conflict with different pybind11 versions) | ||
| #I think I enforced this nearly everywhere I set up a flag for the compiler | ||
| ActionWithPython.o PythonCVInterface.o PythonFunction.o PlumedPythonEmbeddedModule.o: PYBIND11FLAG= -fvisibility=hidden | ||
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| %.o: %.cpp $(DEPDIR)/%.d | $(DEPDIR) | ||
| @echo Compiling object $@ | ||
| @$(CXX) -c $(DEPFLAGS) $(CPPFLAGS) $(PYBIND11FLAG) $(ADDCPPFLAGS) $(CXXFLAGS) $< -o $@ | ||
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| $(DEPDIR): ; @mkdir -p $@ | ||
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| DEPFILES := $(OBJS:%.o=$(DEPDIR)/%.d) | ||
| $(DEPFILES): | ||
| include $(wildcard $(DEPFILES)) | ||
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| #-Wl,--no-as-needed forces the python library to be linked, without this in a WSL does not work | ||
| #TODO: seems that $PLUMED_KERNEL is not needed, check | ||
| PythonCVInterface.$(SOEXT): $(OBJS) | ||
| @echo Linking $@ | ||
| $(LDSHARED) $(SONAME_OPTION),"$(notdir $@)" $(DYNAMIC_LIBS) $(PLUMED_KERNEL) $(ADDCLDFLAGS) $^ -o $@ | ||
| pycv_here: src/*.cpp src/*.h src/pycv/*.py | ||
| @echo installing pycv | ||
| $(PYTHON) -m pip install . | ||
| @touch $@ | ||
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| clean: | ||
| rm -f $(OBJS) PythonCVInterface.$(SOEXT) | ||
| @$(PYTHON) -m pip uninstall pycv -y | ||
| @rm -fv pycv_here | ||
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| check: all | ||
| check_standalone: pycv_here | ||
| $(MAKE) -C regtest testclean | ||
| $(MAKE) -C regtest checkfail | ||
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| #just in case pytest is still not installed we install it before the tests | ||
| check_python: pycv_here | ||
| @$(PYTHON) -m pip install pytest | ||
| @$(PYTHON) -m pytest -v | ||
|
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| check: check_standalone check_python |
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