Merge branch 'v2.10'

.github/workflows/linuxWF.yml

@@ -212,8 +212,7 @@ jobs:
       if: contains( matrix.variant, '-pycv-' )
       working-directory: ./plugins/pycv/
       run: |
-            pip install --user -r requirements.txt
             source ../../sourceme.sh
             ln -s $(realpath ../../regtest/scripts) ./regtest/scripts
-            ./prepareMakeForDevelop.sh
             make check
+            

docker/fedora39-pycv

@@ -2,10 +2,22 @@ FROM plumed:fedora39
 
 RUN source /etc/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 -r requirements.txt \
+ && ./configurePyCV.sh \
  && ln -s $(realpath ../../regtest/scripts) ./regtest/scripts \
- && python_bin=python3 ./prepareMakeForDevelop.sh \
- && make check
+ && make check_standalone
+# To whom is reading: python > 3.10 gives some problems when using pycv
+# from plumed whithin python. SO please remember to chante  "check_standalone"
+#into "check" to verify that the problem is fixed

docker/rocky8-pycv

@@ -1,11 +1,20 @@
 FROM plumed:rocky8
 
-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

plugins/pycv/.gitignore

@@ -1,4 +1,7 @@
 /Makefile.conf
 *.o
 *.so
-env
+/env*/
+/build*/
+/dist*/
+*.whl

plugins/pycv/CMakeLists.txt

@@ -0,0 +1,75 @@
+cmake_minimum_required(VERSION 3.15...3.27)
+project(
+  ${SKBUILD_PROJECT_NAME}
+  VERSION ${SKBUILD_PROJECT_VERSION}
+  LANGUAGES CXX)
+set(CMAKE_CXX_STANDARD 17)
+
+message(
+  STATUS
+    "Everithing should work fine if you are in the same environment in which you have compiled plumed"
+)
+# FinPlumed is here:
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}")
+# Finding necessary packages
+find_package(Python REQUIRED COMPONENTS Interpreter Development)
+find_package(pybind11 CONFIG REQUIRED)
+find_package(Plumed REQUIRED)
+
+# Finding optionals things
+if(Plumed_HAS_MPI)
+  find_package(MPI REQUIRED)
+endif()
+if(MPI_CXX_FOUND)
+  list(APPEND extraLibs MPI::MPI_CXX)
+endif()
+
+if(Plumed_HAS_OPENMP)
+  find_package(OpenMP REQUIRED)
+endif()
+if(OpenMP_CXX_FOUND)
+  list(APPEND extraLibs OpenMP::OpenMP_CXX)
+endif()
+
+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()
+
+# plumed_STATIC_LDFLAGS_OTHER:INTERNAL=-rdynamic;-Wl,-Bsymbolic;-fopenmp
+# -rdynamic is automatically set by cmake, and also -fPIC
+
+################################################################################
+################################the pycv library################################
+################################################################################
+
+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 "")
+
+install(TARGETS PythonCVInterface DESTINATION pycv)
+
+################################################################################
+###########################The pvCV companion module############################
+################################################################################
+
+pybind11_add_module(plumedCommunications src/PlumedPythonEmbeddedModule.cpp)
+target_link_libraries(plumedCommunications PRIVATE pybind11::headers)
+target_link_libraries(plumedCommunications PUBLIC PythonCVInterface)
+
+# The install directory is the output (wheel) directory
+install(TARGETS plumedCommunications DESTINATION .)

plugins/pycv/FindPlumed.cmake

@@ -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()
+
+  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")
+
+    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")
+
+      message(STATUS "Configuring plumed from executable")
+      execute_process(
+        COMMAND plumed --no-mpi info --include-dir
+        OUTPUT_VARIABLE Plumed_INCLUDEDIR
+        OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+      set(Plumed_INCLUDEDIR
+          ${Plumed_INCLUDEDIR}
+          CACHE INTERNAL "plumed include dir")
+      execute_process(
+        COMMAND plumed --no-mpi info --configuration
+        OUTPUT_VARIABLE Plumed_CONFIG
+        OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+      set(Plumed_CPP_FLAGS "")
+
+      string(REPLACE "\n" ";" ProcessFile_LINES "${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")
+
+      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()
+
+    else()
+      if(Plumed_FIND_REQUIRED)
+        message(FATAL_ERROR "plumed not found")
+      endif()
+    endif()
+  endif()
+endif()

plugins/pycv/Makefile

@@ -1,53 +1,28 @@
-# include the machine dependent configuration
-ifneq ($(MAKECMDGOALS),clean)
-  -include ../../Makefile.conf
-	ifndef canPyCV
-  	include ./Makefile.conf
-	endif
-endif
 
-.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
 
-ifeq ($(SOEXT),dylib)
-  SONAME_OPTION:=-Wl,-install_name
-else
-  SONAME_OPTION:=-Wl,-soname
-endif
+all: pycv_here
 
-all: PythonCVInterface.$(SOEXT)
-
-#-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
-
-%.o: %.cpp $(DEPDIR)/%.d | $(DEPDIR)
-	@echo Compiling object $@
-	@$(CXX) -c $(DEPFLAGS) $(CPPFLAGS) $(PYBIND11FLAG) $(ADDCPPFLAGS) $(CXXFLAGS) $< -o $@
-
-
-$(DEPDIR): ; @mkdir -p $@
-
-DEPFILES := $(OBJS:%.o=$(DEPDIR)/%.d)
-$(DEPFILES):
-include $(wildcard $(DEPFILES))
-
-#-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 $@
 
 clean:
-	rm -f $(OBJS) PythonCVInterface.$(SOEXT)
+	@$(PYTHON) -m  pip uninstall pycv -y
+	@rm -fv pycv_here
 
-check: all
+check_standalone: pycv_here
 	$(MAKE) -C regtest testclean
 	$(MAKE) -C regtest checkfail
+
+#just in case  pytest is still not installed we install it before the tests
+check_python: pycv_here
+	@$(PYTHON) -m pip install pytest
+	@$(PYTHON) -m pytest -v
+
+check: check_standalone check_python