CoreNEURON GPU build integration improvements (#707)

* CoreNEURON GPU build integration improvements
 - For GPU we need to build CoreNEURON statically. Those libraries
   needs to be linked to special directly (dlopen is not supported)
 - CoreNEURON now prepares necessary link library flag for NEURON
 - If user specify -coreneuron as an argument to nrnivmodl then
   necessary coreneuron libraries are linked to special directly.
* If -coreneuron is provided to nrnivmodl then nrnivmodl-core is
automatically called
* Test now use nrnivmodl -coreneuron flag
* Enable binary special if CoreNEURON is enabled
* Emit error if -coreneuron is used without enabling it
* Address review comments, update coreneuron submodule

Author: pramodk

CMakeLists.txt

@@ -289,6 +289,8 @@ if(NRN_ENABLE_CORENEURON)
     add_external_project(coreneuron)
     set(CORENEURON_DIR ${PROJECT_SOURCE_DIR}/external/coreneuron)
   endif()
+  get_property (CORENEURON_LIB_LINK_FLAGS GLOBAL PROPERTY CORENEURON_LIB_LINK_FLAGS)
+  set(NRN_ENABLE_BINARY_SPECIAL ON)
 endif()
 
 # =============================================================================
@@ -506,6 +508,8 @@ if(cmake_generator_tolower MATCHES "makefile")
   message(STATUS "--------------+--------------------------------------------------------------")
   message(STATUS " Build option | Status")
   message(STATUS "--------------+--------------------------------------------------------------")
+  message(STATUS "C COMPILER    | ${CMAKE_C_COMPILER}")
+  message(STATUS "CXX COMPILER  | ${CMAKE_CXX_COMPILER}")
   message(STATUS "BUILD_TYPE    | ${CMAKE_BUILD_TYPE} (allowed: ${allowableBuildTypes})")
   message(STATUS "COMPILE FLAGS | ${COMPILER_FLAGS}")
   message(STATUS "Shared        | ${NRN_ENABLE_SHARED}")
@@ -574,6 +578,7 @@ if(cmake_generator_tolower MATCHES "makefile")
   message(STATUS "CoreNEURON    | ${NRN_ENABLE_CORENEURON}")
   if(NRN_ENABLE_CORENEURON)
     message(STATUS "  PATH        | ${CORENEURON_DIR}")
+    message(STATUS "  LINK FLAGS  | ${CORENEURON_LIB_LINK_FLAGS}")
   endif()
   message(STATUS "--------------+--------------------------------------------------------------")
   message(STATUS " See documentation : https://www.neuron.yale.edu/neuron/")

bin/nrnivmodl.in

@@ -3,6 +3,7 @@ set -e
 
 ARCH=@host_cpu@
 MODSUBDIR=@modsubdir@
+USER_PWD=`pwd`
 
 if test "x${NRNHOME}" = x ; then
 	prefix=@prefix@
@@ -43,6 +44,12 @@ if which xcrun; then
     fi
 fi
 
+LinkCoreNEURON=false
+if [ "$1" = "-coreneuron" ] ; then
+      LinkCoreNEURON=true
+      shift
+fi
+
 UserINCFLAGS=""
 if [ "$1" = "-incflags" ] ; then
       UserINCFLAGS="$2"
@@ -162,7 +169,19 @@ if test -n "$cfiles" ; then
 	COBJS=`echo "$cfiles" | sed 's/\.c/.o/g'`
 fi
 
-@NRN_BINARY_SPECIAL_TRUE@@USING_CMAKE_TRUE@make -j 4 -f "${MAKEFILEDIR}/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "COBJFILES=$COBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" special &&
+# call nrnivmodl-core if CoreNEURON is enabled and requested via CLI
+if [ "$LinkCoreNEURON" = true ] ; then
+  :
+  @USING_CMAKE_FALSE@ printf "ERROR : CoreNEURON is not compatible with autotools, build with CMake build system!\n"
+  @USING_CMAKE_FALSE@ exit 1
+  @USING_CMAKE_TRUE@@CORENEURON_ENABLED_FALSE@ printf "ERROR : CoreNEURON support is not enabled!\n"
+  @USING_CMAKE_TRUE@@CORENEURON_ENABLED_FALSE@ exit 1
+  @USING_CMAKE_TRUE@@CORENEURON_ENABLED_TRUE@ cd $USER_PWD
+  @USING_CMAKE_TRUE@@CORENEURON_ENABLED_TRUE@ $bindir/nrnivmodl-core $MODSUBDIR
+  @USING_CMAKE_TRUE@@CORENEURON_ENABLED_TRUE@ cd $MODSUBDIR
+fi
+
+@NRN_BINARY_SPECIAL_TRUE@@USING_CMAKE_TRUE@make -j 4 -f "${MAKEFILEDIR}/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "COBJFILES=$COBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" "LinkCoreNEURON=$LinkCoreNEURON" special &&
 @NRN_BINARY_SPECIAL_TRUE@@USING_CMAKE_FALSE@make -j 4 -f "${MAKEFILEDIR}/nrniv_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "COBJFILES=$COBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" special &&
 @NRN_BINARY_SPECIAL_TRUE@  echo "Successfully created $MODSUBDIR/special"
 
@@ -172,7 +191,7 @@ fi
 @NRN_BINARY_SPECIAL_FALSE@  mdir='${NRNHOME}'/share/nrn/demo/release/${MODSUBDIR}
 @NRN_BINARY_SPECIAL_FALSE@fi
 @NRN_BINARY_SPECIAL_FALSE@@USING_CMAKE_FALSE@make -j 4 -f "$MAKEFILEDIR/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODLO" "COBJFILES=$CLO" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" libnrnmech.la
-@NRN_BINARY_SPECIAL_FALSE@@USING_CMAKE_TRUE@make -j 4 -f "$MAKEFILEDIR/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "COBJFILES=$COBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" libnrnmech.la VERBOSE=1
+@NRN_BINARY_SPECIAL_FALSE@@USING_CMAKE_TRUE@make -j 4 -f "$MAKEFILEDIR/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS" "COBJFILES=$COBJS" "UserLDFLAGS=$UserLDFLAGS" "UserINCFLAGS=$UserINCFLAGS" "LinkCoreNEURON=$LinkCoreNEURON" libnrnmech.la VERBOSE=1
 @NRN_BINARY_SPECIAL_FALSE@  echo '#!/bin/sh
 @NRN_BINARY_SPECIAL_FALSE@if test "x${NRNHOME}" = "x" ; then
 @NRN_BINARY_SPECIAL_FALSE@    NRNHOME='"\"${prefix}\""'

bin/nrnivmodl_makefile_cmake.in

@@ -66,6 +66,11 @@ else
     extra_lib_link = $(NRNLIB_FLAGS)
 endif
 
+# add coreneuron flags
+ifeq ($(LinkCoreNEURON), true)
+    EXTRA_LDFLAGS = @CORENEURON_LIB_LINK_FLAGS@
+endif
+
 # If no DESTDIR (we are probably just building) we use $ORIGIN (@loader_path in OSX)
 _ORIGIN := $(if $(filter Darwin,$(OS_NAME)),@loader_path,$$ORIGIN)
 _SONAME := -Wl,$(if $(filter Darwin,$(OS_NAME)),-install_name${_cm}@rpath/,-soname${_cm})$(notdir ${mech_lib})
@@ -82,7 +87,7 @@ C_GREEN := \033[32m
 special: $(mech_lib)
 	@printf " => $(C_GREEN)LINKING$(C_RESET) executable $(special) LDFLAGS are: $(LDFLAGS)\n"
 	(cd .. ;  $(CXX_LINK_EXE) -I $(incdir) -I $(incdir)/nrncvode -DAUTO_DLOPEN_NRNMECH=0 $(datadir)/nrnmain.cpp -o $(special) \
-	  -L $(OBJS_DIR) -l$(mech_libname) $(NRNLIB_FLAGS) -l$(mech_libname) $(extra_lib_link) -Wl,-rpath,'$(DESTDIR_RPATH)' -Wl,-rpath,$(libdir) $(LDFLAGS))
+	  -L $(OBJS_DIR) -l$(mech_libname) $(NRNLIB_FLAGS) -l$(mech_libname) $(extra_lib_link) -Wl,-rpath,'$(DESTDIR_RPATH)' -Wl,-rpath,$(libdir) $(LDFLAGS) $(EXTRA_LDFLAGS))
 
 $(mech_lib): $(mech_lib_type)
 

cmake/ConfigFileSetting.cmake

@@ -47,6 +47,14 @@ set(libdir \${exec_prefix}/lib)
 set(USING_CMAKE_FALSE "#")
 set(USING_CMAKE_TRUE "")
 
+if(NRN_ENABLE_CORENEURON)
+  set(CORENEURON_ENABLED_TRUE "")
+  set(CORENEURON_ENABLED_FALSE "#")
+else()
+  set(CORENEURON_ENABLED_TRUE "#")
+  set(CORENEURON_ENABLED_FALSE "")
+endif()
+
 # ~~~
 # A variable that doesn't start out as #undef but as #define needs an
 # explicit @...@ replacement in the .h.in files.

external/coreneuron

@@ -110,9 +110,7 @@ if(NRN_ENABLE_PYTHON AND PYTEST_FOUND)
     add_custom_target(
       coreneuron_mod ALL
       COMMAND
-        ${CMAKE_COMMAND} -E env ${TEST_ENV} $ENV{SHELL} ${CMAKE_BINARY_DIR}/bin/nrnivmodl .
-      COMMAND
-        ${CMAKE_COMMAND} -E env ${TEST_ENV} $ENV{SHELL} ${CMAKE_BINARY_DIR}/bin/nrnivmodl-core .
+        ${CMAKE_COMMAND} -E env ${TEST_ENV} $ENV{SHELL} ${CMAKE_BINARY_DIR}/bin/nrnivmodl -coreneuron .
        WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/test/mod)
     add_dependencies(coreneuron_mod nrniv nrniv-core)