Compile NEURON mechanisms as C++ (#1597)

* Make embedded .mod files C++ compatible. * Generate C++ code from nocmodl instead of C. * Require C++14, drop references to C++98/C++11. * Retain C linkage for variables that are still referred to from C code, or which are loaded with dlopen(). * Fix deprecation warnings from compatibility wrappers in NEURON build. * Add C++ mechanism documentation. * nrnmingwenv: keep GCC toolchain for RxD reactions. * Update CMake/semantic version to 9.0.0, update CoreNEURON submodule to have the same version. * Update .gitignore. Co-authored-by: Pramod S Kumbhar <[email protected]> Co-authored-by: Alexandru Săvulescu <[email protected]> Co-authored-by: Michael Hines <[email protected]>
neuronsimulator · Jun 20, 2022 · f242cc8 · f242cc8
1 parent 2c3a21d
commit f242cc8
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diff --git a/.clang-format.changes b/.clang-format.changes
@@ -1,3 +1,3 @@
 SortIncludes: false
-Standard: c++11
-StatementMacros: [MKDLL, MKDLLdec, MKDLLif, MKDLLvp, MKDLLvpf]
+Standard: c++14
+StatementMacros: [MKDLL, MKDLLdec, MKDLLif, MKDLLvp, MKDLLvpf]
diff --git a/.gitignore b/.gitignore
@@ -1,7 +1,9 @@
 .clang-format
 .cmake-format.yaml
+external/tests/
 nmodlconf.h.in
 nrnconf.h.in
+test/ringtest/*.dat
 build
 .DS_Store
 .eggs/
@@ -21,25 +23,25 @@ virtualenv
 # These files are generated at build time
 # It would be a good idea to create them in the
 # build directory in the future.
-src/nrnoc/apcount.c
-src/nrnoc/exp2syn.c
-src/nrnoc/expsyn.c
-src/nrnoc/feature.c
-src/nrnoc/hh.c
+src/nrnoc/apcount.cpp
+src/nrnoc/exp2syn.cpp
+src/nrnoc/expsyn.cpp
+src/nrnoc/feature.cpp
+src/nrnoc/hh.cpp
 src/nrnoc/hh.mod.orig
 src/nrnoc/hocusr.h
-src/nrnoc/intfire1.c
-src/nrnoc/intfire2.c
-src/nrnoc/intfire4.c
-src/nrnoc/netstim.c
+src/nrnoc/intfire1.cpp
+src/nrnoc/intfire2.cpp
+src/nrnoc/intfire4.cpp
+src/nrnoc/netstim.cpp
 src/nrnoc/nrnversion.
 src/nrnoc/nrnversion.h
-src/nrnoc/oclmp.c
-src/nrnoc/passive.c
-src/nrnoc/pattern.c
-src/nrnoc/ppmark.c
-src/nrnoc/stim.c
-src/nrnoc/svclmp.c
-src/nrnoc/syn.c
-src/nrnoc/vclmp.c
+src/nrnoc/oclmp.cpp
+src/nrnoc/passive.cpp
+src/nrnoc/pattern.cpp
+src/nrnoc/ppmark.cpp
+src/nrnoc/stim.cpp
+src/nrnoc/svclmp.cpp
+src/nrnoc/syn.cpp
+src/nrnoc/vclmp.cpp
 share/lib/python/neuron/help_data.dat
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -17,14 +17,14 @@ if(DEFINED ENV{CRAYPE_VERSION})
 endif()
 project(
   NEURON
-  VERSION 8.2.0
+  VERSION 9.0.0
   LANGUAGES C CXX
   HOMEPAGE_URL "https://www.neuron.yale.edu/neuron/")
 
 # =============================================================================
 # CMake common project settings
 # =============================================================================
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 

diff --git a/bin/nrnivmodl.in b/bin/nrnivmodl.in
@@ -151,13 +151,13 @@ for i in "${files[@]}" ; do
   dir_name="$(dirname "$f")"
   # Note: indentation for shell lines in make rules must be a tab
   echo "\
-./${base_name// /\\ }.c: ${f// /\\ }.mod
+./${base_name// /\\ }.cpp: ${f// /\\ }.mod
 	@printf \" -> \$(C_GREEN)NMODL\$(C_RESET) \$<\\\n\"
 	(cd \"$dir_name\"; @NRN_NOCMODL_SANITIZER_ENVIRONMENT_STRING@ MODLUNIT=\$(NRNUNITS) \$(NOCMODL) \"$base_name.mod\" -o \"$mdir\")
 
-./${base_name// /\\ }.o: ./${base_name// /\\ }.c
+./${base_name// /\\ }.o: ./${base_name// /\\ }.cpp
 	@printf \" -> \$(C_GREEN)Compiling\$(C_RESET) \$<\\\n\"
-	\$(COMPILE) -I\"$dir_name\" \$(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c \$< -o \$@
+	\$(CXXCOMPILE) -I\"$dir_name\" \$(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c \$< -o \$@
 " >> "$MODMAKE"
 done
 

diff --git a/bin/nrnivmodl_makefile_cmake.in b/bin/nrnivmodl_makefile_cmake.in
@@ -61,15 +61,11 @@ ifeq (@NRN_INCLUDE_MPI_HEADERS@, ON)
   INCLUDES += $(if @MPI_C_INCLUDE_PATH@, -I$(subst ;, -I,@MPI_C_INCLUDE_PATH@),)
 endif
 
-# CC/CXX are always defined. If the definition comes from default change it
-ifeq ($(origin CC), default)
-    CC = @CMAKE_C_COMPILER@
+# CXX is always defined. If the definition comes from default change it
+ifeq ($(origin CXX), default)
     CXX = @CMAKE_CXX_COMPILER@
 endif
-CFLAGS = @BUILD_TYPE_C_FLAGS@ @CMAKE_C_FLAGS@
-CXXFLAGS = @BUILD_TYPE_CXX_FLAGS@ @CMAKE_CXX_FLAGS@ @CXX11_STANDARD_COMPILE_OPTION@
-
-COMPILE = $(CC) $(CFLAGS) @NRN_COMPILE_DEFS_STRING@ @NRN_COMPILE_FLAGS_STRING@
+CXXFLAGS = @BUILD_TYPE_CXX_FLAGS@ @CMAKE_CXX_FLAGS@ @CMAKE_CXX14_STANDARD_COMPILE_OPTION@
 CXXCOMPILE = $(CXX) $(CXXFLAGS) @NRN_COMPILE_DEFS_STRING@ @NRN_COMPILE_FLAGS_STRING@
 CXX_LINK_EXE = $(CXX) $(CXXFLAGS) @CMAKE_EXE_LINKER_FLAGS@ @NRN_LINK_FLAGS_STRING@
 CXX_LINK_SHARED = $(CXX) $(CXXFLAGS) @CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS@ @CMAKE_SHARED_LIBRARY_CXX_FLAGS@ @CMAKE_SHARED_LINKER_FLAGS@
@@ -139,12 +135,12 @@ mech_lib_static: mod_func.o $(mod_objs) $(nrn_lib) build_always
 
 mod_func.o: mod_func.cpp
 	@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\n"
-	$(COMPILE) $(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c $< -o $@
+	$(CXXCOMPILE) $(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c $< -o $@
 
 # Generic build c->o. Need PIC for shared lib
 $(OBJS_DIR)/%.o: $(MODC_DIR)/%.c | $(OBJS_DIR)
 	@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\n"
-	$(COMPILE) $(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c $< -o $@
+	$(CXXCOMPILE) $(INCLUDES) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c $< -o $@
 
 
 include makemod2c_inc

diff --git a/cmake/CMakeListsNrnMech.cmake b/cmake/CMakeListsNrnMech.cmake
@@ -66,9 +66,6 @@ foreach(link_lib ${NRN_LINK_LIBS})
   string(APPEND NRN_LINK_DEFS " ${link_flag}")
 endforeach()
 
-# PGI add --c++11;-A option for c++11 flag
-string(REPLACE ";" " " CXX11_STANDARD_COMPILE_OPTION "${CMAKE_CXX11_STANDARD_COMPILE_OPTION}")
-
 # Compiler flags depending on cmake build type from BUILD_TYPE_<LANG>_FLAGS
 string(TOUPPER "${CMAKE_BUILD_TYPE}" _BUILD_TYPE)
 set(BUILD_TYPE_C_FLAGS "${CMAKE_C_FLAGS_${_BUILD_TYPE}}")

diff --git a/cmake/CompilerHelper.cmake b/cmake/CompilerHelper.cmake
@@ -58,7 +58,5 @@ endif()
 if(CMAKE_CXX_COMPILER_ID MATCHES "PGI")
   # CMake adds strict standard complaint PGI flag "-A" which breaks compilation of old codes (e.g.
   # spdlog, fmt)
-  set(CMAKE_CXX98_STANDARD_COMPILE_OPTION "")
-  set(CMAKE_CXX11_STANDARD_COMPILE_OPTION --c++11)
   set(CMAKE_CXX14_STANDARD_COMPILE_OPTION --c++14)
 endif()
diff --git a/cmake/ConfigFileSetting.cmake b/cmake/ConfigFileSetting.cmake
@@ -293,7 +293,7 @@ if(MINGW)
   nrn_configure_file(nrnsetupmingw.nsi src/mswin)
   nrn_configure_file(pre_setup_exe.sh src/mswin)
   # Just name and not path since setup.exe user chooses location of install.
-  set(CC x86_64-w64-mingw32-gcc.exe)
+  set(CXX x86_64-w64-mingw32-g++.exe)
   set(BUILD_MINGW_TRUE "")
   set(BUILD_MINGW_FALSE "#")
   set(nrnskip_rebase "#")

diff --git a/cmake/MacroHelper.cmake b/cmake/MacroHelper.cmake
@@ -234,14 +234,14 @@ endmacro()
 # =============================================================================
 # Run nocmodl to convert NMODL to C
 # =============================================================================
-macro(nocmodl_mod_to_c modfile_basename)
+macro(nocmodl_mod_to_cpp modfile_basename)
   add_custom_command(
-    OUTPUT ${modfile_basename}.c
+    OUTPUT ${modfile_basename}.cpp
     COMMAND
       ${CMAKE_COMMAND} -E env "MODLUNIT=${PROJECT_BINARY_DIR}/share/nrn/lib/nrnunits.lib"
       ${NRN_NOCMODL_SANITIZER_ENVIRONMENT} ${PROJECT_BINARY_DIR}/bin/nocmodl ${modfile_basename}.mod
-    COMMAND sed "'s/_reg()/_reg_()/'" ${modfile_basename}.c > ${modfile_basename}.c.tmp
-    COMMAND mv ${modfile_basename}.c.tmp ${modfile_basename}.c
+    COMMAND sed "'s/_reg()/_reg_()/'" ${modfile_basename}.cpp > ${modfile_basename}.cpp.tmp
+    COMMAND mv ${modfile_basename}.cpp.tmp ${modfile_basename}.cpp
     DEPENDS nocmodl ${modfile_basename}.mod
     WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/src/nrniv)
 endmacro()

diff --git a/cmake/NeuronFileLists.cmake b/cmake/NeuronFileLists.cmake
@@ -2,6 +2,7 @@
 # Lists of header files to install
 # =============================================================================
 set(HEADER_FILES_TO_INSTALL
+    bbsavestate.h
     cabvars.h
     cspmatrix.h
     cspredef.h
@@ -46,7 +47,8 @@ set(HEADER_FILES_TO_INSTALL
     scoplib.h
     section.h
     spconfig.h
-    spmatrix.h)
+    spmatrix.h
+    treeset.h)
 
 # =============================================================================
 # Lists of headers populated using check_include_files

diff --git a/docs/guide/how_to_get_started.rst b/docs/guide/how_to_get_started.rst
@@ -31,3 +31,12 @@ Using NMODL to add new mechanisms to NEURON
 * NEURON comes with a bunch of mod files that can serve as starting points for "programming by example." Under MSWin the default mechanisms (hh, pas, expsyn etc.) are in `github.com/neuronsimulator/nrn/tree/master/src/nrnoc <https://github.com/neuronsimulator/nrn/tree/master/src/nrnoc>`_. A large collection of mod files is at `github.com/neuronsimulator/nrn/tree/master/share/examples/nrniv/nmodl <https://github.com/neuronsimulator/nrn/tree/master/share/examples/nrniv/nmodl>`_.
 * You may also find useful examples in `ModelDB <https://modeldb.yale.edu>`_.
 
+.. include:: ../rst_substitutions.txt
+
+.. note::
+  Starting in |neuron_with_cpp_mechanisms|, NMODL is translated into C++ code
+  instead of C.
+  This change is not fully backwards compatible, and you may find that older
+  NMODL code needs to be updated to work with |neuron_with_cpp_mechanisms|.
+  This is principally an issue for MOD files that include ``VERBATIM`` blocks.
+  For more information, see :ref:`porting-mechanisms-to-cpp`.
diff --git a/docs/guide/index.rst b/docs/guide/index.rst
@@ -13,4 +13,5 @@ Guides
    import3d
    optimization
    randomness
+   porting_mechanisms_to_cpp
    faq