NMODL integration in CoreNeuron nrnivmodl-core workflow (#193)

This PR is to allow us use NMODL with CoreNEURON using nrnivmodl-core workflow:
 * nmodl support for nrnivmodl-core
 * Added support for ispc workflow.
 * Fixed ispc support for halfgap.mod
 * Fixes nrnivmodl-core not correctly setting the OPTMODS_OUTPUTS variable in the Makefile when running on a clean run

Author: st4rl3ss

CMakeLists.txt

@@ -117,7 +117,7 @@ if (ENABLE_NMODL)
     find_package(nmodl REQUIRED)
     set(MOD2C "${nmodl_BINARY}")
     set(NMODL_EXTRA_FLAGS "" CACHE STRING "Extra NMODL options such as passes")
-    separate_arguments(NMODL_EXTRA_FLAGS UNIX_COMMAND "${NMODL_EXTRA_FLAGS}")
+    separate_arguments(NMODL_EXTRA_FLAGS_LIST UNIX_COMMAND "${NMODL_EXTRA_FLAGS}")
     include_directories(${nmodl_INCLUDE})
     if("$ENV{PYTHONPATH}" STREQUAL "")
         set(ENV{PYTHONPATH} "${nmodl_PYTHONPATH}")

coreneuron/CMakeLists.txt

@@ -113,11 +113,12 @@ macro(mod2c_target)
         unset(mod2c_wrapper_outname_)
     endif()
     list(APPEND MOD2C_${mod2c_KEY}_MODS "${mod2c_modname_}")
-    if(${NMODL_FOUND})
+    if(ENABLE_NMODL AND NMODL_FOUND)
         add_custom_command(OUTPUT "${mod2c_output_}" "${mod2c_wrapper_output_}"
                 DEPENDS ${mod2c_MODFILE} ${MOD2C_BINARY}
                 COMMAND ${CMAKE_COMMAND} -E copy "${mod2c_source_}" "${CMAKE_CURRENT_BINARY_DIR}"
-                COMMAND ${MOD2C} "${mod2c_modname_}" -o "${CMAKE_CURRENT_BINARY_DIR}" host ${nmodl_modearg} ${NMODL_EXTRA_FLAGS}
+                COMMAND ${MOD2C} "${mod2c_modname_}" -o "${CMAKE_CURRENT_BINARY_DIR}" host ${nmodl_modearg}
+                    ${NMODL_EXTRA_FLAGS_LIST}
                 WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
     else()
         add_custom_command(OUTPUT "${mod2c_output_}"
@@ -211,7 +212,7 @@ macro(mod2c_from_file name modlist searchpath)
         message(WARNING "Note: halfgap.mod is found in specified mechanism search directory!")
     else()
         set(GAPMOD "${PROJECT_SOURCE_DIR}/tests/integration/ring_gap/mod/halfgap.mod")
-            mod2c_target(KEY ${name} MODFILE "${GAPMOD}" TARGET ${M2C_TARGET})
+        mod2c_target(KEY ${name} MODFILE "${GAPMOD}" TARGET ${M2C_TARGET})
         list(APPEND MOD_PATHS ${GAPMOD})
         message(STATUS "Adding halfgap.mod mod file for tests!")
     endif()
@@ -403,6 +404,12 @@ set(CORENRN_LINK_LIBS "${CORENRN_LINK_LIBS}" PARENT_SCOPE)
 # Share built-in OPTIONAL MODS also with rest of project
 set(CORENRN_OPTMECH_MODS "${MOD2C_OPTMECH_MODS}" PARENT_SCOPE)
 
+foreach(MOD ${MOD2C_OPTMECH_OUTPUTS})
+    get_filename_component(OPTMECH_NAME ${MOD} NAME)
+    list(APPEND OPTMECH_OUTPUTS_LIST ${OPTMECH_NAME})
+endforeach()
+
+set(CORENRN_OPTMECH_OUTPUTS "${OPTMECH_OUTPUTS_LIST}" PARENT_SCOPE)
 
 # The scopmath lib - should not contain dimplic
 add_library(scopmath STATIC ${coreneuron_all_headers} ${scopmath_c_files})
@@ -443,7 +450,7 @@ install(FILES ${MOD2C_UNITS}
 if(ENABLE_HEADER_INSTALL)
     install(DIRECTORY .
             DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/coreneuron
-            FILES_MATCHING PATTERN "*.h*" PATTERN "*.ipp")
+            FILES_MATCHING PATTERN "*.h*" PATTERN "*.ipp" PATTERN "*.ispc")
 
     install(FILES ${KINDERIV_PY} ${MOD_FUNC_C_PL} ${DIMPLIC_C} ${ENGINEMECH_C}
             DESTINATION ${CMAKE_INSTALL_DATADIR}/coreneuron)

coreneuron/nrniv/nrn_setup.cpp

@@ -812,8 +812,8 @@ void nrn_setup(const char* filesdat,
     delete[] file_reader;
 
     model_size();
-    delete [] gidgroups;
-    delete [] imult;
+    delete[] gidgroups;
+    delete[] imult;
 
     if (nrnmpi_myid == 0) {
         printf(" Setup Done   : %.2lf seconds \n", nrn_wtime() - time);
@@ -1011,7 +1011,7 @@ void nrn_cleanup(bool clean_ion_global_map) {
 
     // clean nrnthread_chkpnt
     if (nrnthread_chkpnt) {
-        delete [] nrnthread_chkpnt;
+        delete[] nrnthread_chkpnt;
         nrnthread_chkpnt = nullptr;
     }
 

coreneuron/nrniv/output_spikes.cpp

@@ -98,10 +98,10 @@ void local_spikevec_sort(std::vector<double>& isvect,
 void sort_spikes(std::vector<double>& spikevec_time, std::vector<int>& spikevec_gid) {
     double lmin_time = std::numeric_limits<double>::max();
     double lmax_time = std::numeric_limits<double>::min();
-    if(!spikevec_time.empty()) {
+    if (!spikevec_time.empty()) {
         lmin_time = *(std::min_element(spikevec_time.begin(), spikevec_time.end()));
         lmax_time = *(std::max_element(spikevec_time.begin(), spikevec_time.end()));
-    }	
+    }
     double min_time = nrnmpi_dbl_allmin(lmin_time);
     double max_time = nrnmpi_dbl_allmax(lmax_time);
 

extra/CMakeLists.txt

@@ -26,6 +26,7 @@ endforeach()
 
 # Additional mods
 string(REPLACE ";" " " CORENRN_OPTMODS "${CORENRN_OPTMECH_MODS}")
+string(REPLACE ";" " " CORENRN_OPTMODS_OUTPUTS "${CORENRN_OPTMECH_OUTPUTS}")
 
 # PGI add --c++11;-A option for c++11 flag
 string(REPLACE ";" " " CXX11_STANDARD_COMPILE_OPTION "${CMAKE_CXX11_STANDARD_COMPILE_OPTION}")
@@ -41,6 +42,15 @@ set(BUILD_TYPE_C_FLAGS "${CMAKE_C_FLAGS_${_BUILD_TYPE}}")
 set(BUILD_TYPE_CXX_FLAGS "${CMAKE_CXX_FLAGS_${_BUILD_TYPE}}")
 message("CXX Compile Flags from BUILD_TYPE: ${BUILD_TYPE_CXX_FLAGS}")
 
+if(ENABLE_NMODL)
+    set(nmodl_arguments_c "host --c ${NMODL_EXTRA_FLAGS}")
+    set(nmodl_arguments_ispc "host --ispc ${NMODL_EXTRA_FLAGS}")
+    set(mod2c_install_bin "${nmodl_BINARY}")
+else ()
+    set(nmodl_arguments_c "")
+    set(nmodl_arguments_ispc "")
+    set(mod2c_install_bin "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}/mod2c_core")
+endif ()
 
 configure_file(${nmodl_makefile}.in ${nmodl_makefile} @ONLY)
 

extra/nrnivmodl-core

@@ -8,7 +8,7 @@ set -e
 APP_NAME=$(basename $0)
 _PARENT="$(dirname $BASH_SOURCE)/.."
 ROOTDIR=$(perl -e "use Cwd 'abs_path'; print abs_path('$_PARENT')")
-MAKE_OPTIONS="MECH_NAME MECH_VERSION OUTPUT INCFLAGS LINKFLAGS MODS_PATH OPTMODS VERBOSE"
+MAKE_OPTIONS="MECH_NAME MECH_VERSION OUTPUT INCFLAGS LINKFLAGS MODS_PATH OPTMODS OPTMODS_OUTPUTS VERBOSE"
 PARALLELISM=4
 
 while getopts "n:v:o:i:l:p:chV" OPT; do
@@ -24,7 +24,8 @@ while getopts "n:v:o:i:l:p:chV" OPT; do
     l)
         params_LINKFLAGS="$OPTARG";;
     c)
-        params_OPTMODS="";;
+        params_OPTMODS=""
+        params_OPTMODS_OUTPUTS="";;
     V)
         params_VERBOSE=1;;
     p)

extra/nrnivmodl_core_makefile.in

@@ -9,6 +9,7 @@ MECH_VERSION = 0.0
 MODS_PATH = .
 OUTPUT = @CMAKE_HOST_SYSTEM_PROCESSOR@
 OPTMODS = @CORENRN_OPTMODS@
+OPTMODS_OUTPUTS = @CORENRN_OPTMODS_OUTPUTS@
 DESTDIR =
 
 # Coreneuron dirs
@@ -18,6 +19,9 @@ incdir := @CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_INCLUDEDIR@
 datadir:= @CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_DATADIR@/coreneuron
 datadir_mod2c := @CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_DATADIR@/mod2c
 
+# Binary of MOD2C/NMODL depending on what was activated
+mod2c_install_bin := @mod2c_install_bin@
+
 # Additional variables set in CMAKE usable here
 # - @CORENRN_COMPILE_DEFS
 # - @CORENRN_LINK_DEFS
@@ -41,13 +45,45 @@ CXXCOMPILE = $(CXX) $(CXXFLAGS) @CORENRN_COMPILE_DEFS@ $(INCLUDES)
 CXX_LINK_EXE = $(CXX) $(CXXFLAGS) @CMAKE_EXE_LINKER_FLAGS@
 CXX_LINK_SHARED = $(CXX) $(CXXFLAGS) @CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS@ @CMAKE_SHARED_LIBRARY_CXX_FLAGS@ @CMAKE_SHARED_LINKER_FLAGS@
 
+ISPC = @CMAKE_ISPC_COMPILER@
+ISPC_FLAGS = @CMAKE_ISPC_FLAGS@
+ISPC_COMPILE = $(ISPC) $(ISPC_FLAGS) -I$(incdir) -I@nmodl_INCLUDE@
+
+# Variables used in the "ARTIFICIAL_CELL" detection
+mod_c_srcs_path =
+mod_ispc_srcs_path =
+mod_c_srcs_names =
+mod_ispc_srcs_names =
+define check_file
+	ifeq (@ENABLE_ISPC_TARGET@, ON)
+		ifeq ($(shell grep -q $(2) $(1); echo $$?), 0)
+			mod_c_srcs_path += $(MODC_DIR)/$(notdir $(1))
+			mod_c_srcs_names += $(notdir $(1))
+		else
+			mod_ispc_srcs_path += $(MODC_DIR)/$(notdir $(1))
+			mod_ispc_srcs_names += $(notdir $(1))
+		endif
+	else
+		mod_c_srcs_path += $(MODC_DIR)/$(notdir $(1))
+		mod_c_srcs_names += $(notdir $(1))
+	endif
+endef
+
 # File path config (internal)
 MODC_DIR = $(OUTPUT)/core/mod2c
 OBJS_DIR = $(OUTPUT)/core/build
 mod_files = $(sort $(notdir $(wildcard $(MODS_PATH)/*.mod)))
+mod_paths = $(sort $(wildcard $(MODS_PATH)/*.mod))
 mod_names = $(mod_files:.mod=) $(OPTMODS:.mod=)
-modc_files = $(addprefix $(MODC_DIR)/,$(addsuffix .cpp,$(mod_names)))
-mod_objs   = $(addprefix $(OBJS_DIR)/,$(addsuffix .o,$(mod_names)))
+mod_all_cpp_files = $(addprefix $(MODC_DIR)/,$(addsuffix .cpp,$(mod_names)))
+mod_c_objs = $(addprefix $(OBJS_DIR)/,$(addsuffix .o,$(basename $(mod_c_srcs_names)))) $(addprefix $(OBJS_DIR)/,$(addsuffix .o,$(basename $(filter %.cpp, $(OPTMODS_OUTPUTS)))))
+mod_ispc_objs = $(addprefix $(OBJS_DIR)/,$(addsuffix .obj,$(basename $(mod_ispc_srcs_names)))) $(addprefix $(OBJS_DIR)/,$(addsuffix .obj,$(basename $(filter %.ispc, $(OPTMODS_OUTPUTS)))))
+
+$(foreach ittxtfile, $(mod_paths), $(eval $(call check_file, $(ittxtfile), ARTIFICIAL_CELL)))
+
+mod_c_files = $(patsubst %.mod,%.cpp,$(mod_c_srcs_path))
+mod_ispc_files = $(patsubst %.mod,%.ispc,$(mod_ispc_srcs_path))
+mod_ispc_c_files = $(patsubst %.mod,%.cpp,$(mod_ispc_srcs_path))
 
 kinderiv_h = $(MODC_DIR)/_kinderiv.h
 mod_func_o = $(OBJS_DIR)/_mod_func.o
@@ -80,27 +116,42 @@ $(special): $(coremech_lib)
 	  -L $(OUTPUT) -l$(coremech_libname) $(CORENRNLIB_FLAGS) -Wl,-rpath,'$(DESTDIR_RPATH)' -Wl,-rpath,$(libdir) $(LDFLAGS)
 
 
-$(coremech_lib): $(mod_func_o) $(dimplic_o) $(mod_objs) build_always
+$(coremech_lib): $(mod_func_o) $(dimplic_o) $(mod_c_objs) $(mod_ispc_objs) build_always
 	@printf " => $(C_GREEN)LINKING$(C_RESET) library $(coremech_lib) Mod files: $(mod_files) (+ $(OPTMODS))\n"
 	$(CXX_LINK_SHARED) -I $(incdir) -DADDITIONAL_MECHS $(datadir)/enginemech.cpp -o ${coremech_lib} ${_SONAME} \
-	  $(mod_func_o) $(dimplic_o) $(mod_objs) $(datadir)/libscopmath.a $(CORENRNLIB_FLAGS) -Wl,-rpath,$(libdir) $(LDFLAGS)
+	  $(mod_func_o) $(dimplic_o) $(mod_c_objs) $(mod_ispc_objs) $(datadir)/libscopmath.a $(CORENRNLIB_FLAGS) -Wl,-rpath,$(libdir) $(LDFLAGS)
 
 
-# Generic build cpp->o. Need PIC for shared lib
+# Generic build cpp->.o Need PIC for shared lib
 $(OBJS_DIR)/%.o: $(MODC_DIR)/%.cpp $(kinderiv_h) | $(OBJS_DIR)
 	@printf " -> $(C_GREEN)Compiling$(C_RESET) $<\n"
 	$(CXXCOMPILE) @CMAKE_CXX_COMPILE_OPTIONS_PIC@ -c $< -o $@
 
+# Generic build ispc->.obj Need PIC for shared lib
+$(OBJS_DIR)/%.obj: $(MODC_DIR)/%.ispc | $(OBJS_DIR)
+	@printf " -> $(C_GREEN)Compiling with ISPC$(C_RESET) $<\n"
+	$(ISPC_COMPILE) @CMAKE_ISPC_COMPILE_OPTIONS_PIC@ $< -o $@
 
-# Build cpp files with mod2c
-$(MODC_DIR)/%.cpp: $(MODS_PATH)/%.mod | $(MODC_DIR)
+# Build ispc files with mod2c/nmodl
+$(mod_ispc_files): $(MODC_DIR)/%.ispc: $(MODS_PATH)/%.mod | $(MODC_DIR)
 	@printf " -> $(C_GREEN)MOD2C$(C_RESET) $<\n"
 	MODLUNIT=$(datadir_mod2c)/nrnunits.lib \
-	  $(bindir)/mod2c_core $< -o $(MODC_DIR)/
+	  $(mod2c_install_bin) $< -o $(MODC_DIR)/ @nmodl_arguments_ispc@
+
+# Static pattern to set up the dependencies for the previous recipe.
+$(mod_ispc_c_files): $(MODC_DIR)/%.cpp: $(MODC_DIR)/%.ispc
+
+# Build cpp files with mod2c/nmodl
+$(mod_c_files): $(MODC_DIR)/%.cpp: $(MODS_PATH)/%.mod | $(MODC_DIR)
+	@printf " -> $(C_GREEN)MOD2C$(C_RESET) $<\n"
+	MODLUNIT=$(datadir_mod2c)/nrnunits.lib \
+	  $(mod2c_install_bin) $< -o $(MODC_DIR)/ @nmodl_arguments_c@
 
 # If .mod doesnt exist attempt from previously built opt mods in shared/
 $(MODC_DIR)/%.cpp: $(datadir_mod2c)/%.cpp | $(MODC_DIR)
 	ln -s $< $@
+$(MODC_DIR)/%.ispc: $(datadir_mod2c)/%.ispc | $(MODC_DIR)
+	ln -s $< $@
 
 
 # Mod registration. Compiled by generic rule. Dont overwrite if not changed
@@ -112,10 +163,10 @@ $(mod_func_c): build_always | $(MODC_DIR)
 
 # Header to avoid function callbacks using function pointers
 # Move all mods to temp and bring back only those required
-$(kinderiv_h): $(modc_files) build_always | $(MODC_DIR)
+$(kinderiv_h): $(mod_all_cpp_files) build_always | $(MODC_DIR)
 	@printf " -> $(C_GREEN)Generating$(C_RESET) $(kinderiv_h)\n"
 	cd $(MODC_DIR) && mkdir -p _tmp &&	mv [^_]*.cpp _tmp/ && \
-	  mv $(addprefix _tmp/,$(notdir $(modc_files))) ./ || true
+	  mv $(addprefix _tmp/,$(notdir $(mod_all_cpp_files))) ./ || true
 	rm -rf $(MODC_DIR)/_tmp
 	cd $(MODC_DIR) && python $(datadir)/kinderiv.py