Enable nmodl as submodule to CoreNEURON (#208)

  - can use following command to enable submodule:
    cmake .. -DCORENRN_ENABLE_NMODL=ON -DCORENRN_ENABLE_ISPC=OFF
    cmake .. -DCORENRN_ENABLE_NMODL=ON  -DCORENRN_ENABLE_ISPC=ON
  - Option -DCORENRN_ENABLE_NMODL=OFF (default) should use old mod2c
  - One can set -DCORENRN_NMODL_DIR=<nmodl_install_prefix> to use pre-compiled NMODL
  - Update nmodl submodule to latest master

Author: pramodk

.gitmodules

@@ -2,3 +2,6 @@
 	path = external/mod2c
   url = https://github.com/BlueBrain/mod2c
   branch = master
+[submodule "external/nmodl"]
+	path = external/nmodl
+	url = https://github.com/BlueBrain/nmodl

CMake/AddNmodlSubmodule.cmake

@@ -0,0 +1,26 @@
+# =============================================================================
+# Copyright (C) 2016-2019 Blue Brain Project
+#
+# See top-level LICENSE file for details.
+# =============================================================================
+
+include(FindPkgConfig)
+
+find_path(NMODL_PROJ NAMES CMakeLists.txt PATHS "${CORENEURON_PROJECT_SOURCE_DIR}/external/nmodl")
+find_package_handle_standard_args(NMODL REQUIRED_VARS NMODL_PROJ)
+
+if(NOT NMODL_FOUND)
+  find_package(Git 1.8.3 QUIET)
+  if(NOT ${GIT_FOUND})
+    message(FATAL_ERROR "git not found, clone repository with --recursive")
+  endif()
+  message(STATUS "Sub-module nmodl missing : running git submodule update --init --recursive")
+  execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init --recursive --
+                          ${CORENEURON_PROJECT_SOURCE_DIR}/external/nmodl
+                  WORKING_DIRECTORY ${CORENEURON_PROJECT_SOURCE_DIR})
+else()
+  message(STATUS "Using nmodl submodule from ${NMODL_PROJ}")
+endif()
+
+add_subdirectory(${CORENEURON_PROJECT_SOURCE_DIR}/external/nmodl)
+

CMake/packages/Findlikwid.cmake

@@ -14,7 +14,7 @@
 # Using likwid:
 #
 # ::
-#   set(LIKWID_ROOT "" CACHE PATH "Path likwid performance monitoring and benchmarking suite")
+#   set(LIKWID_DIR "" CACHE PATH "Path likwid performance monitoring and benchmarking suite")
 #   find_package(likwid REQUIRED)
 #   include_directories(${likwid_INCLUDE_DIRS})
 #   target_link_libraries(foo ${likwid_LIBRARIES})
@@ -27,8 +27,8 @@
 #   likwid_INCLUDE   - list of required include directories
 #   likwid_LIBRARIES - list of required library directories
 
-find_path(likwid_INCLUDE_DIRS "likwid.h" HINTS "${LIKWID_ROOT}/include")
-find_library(likwid_LIBRARIES likwid HINTS "${LIKWID_ROOT}/lib")
+find_path(likwid_INCLUDE_DIRS "likwid.h" HINTS "${LIKWID_DIR}/include")
+find_library(likwid_LIBRARIES likwid HINTS "${LIKWID_DIR}/lib")
 
 # Checks 'REQUIRED', 'QUIET' and versions.
 include(FindPackageHandleStandardArgs)

CMake/packages/Findnmodl.cmake

@@ -14,7 +14,7 @@
 # Using nmodl:
 #
 # ::
-#   set(CORENRN_NMODL_ROOT "" CACHE PATH "Path nmodl source-to-source compiler root")
+#   set(CORENRN_NMODL_DIR "" CACHE PATH "Path to nmodl source-to-source compiler installation")
 #   find_package(nmodl REQUIRED)
 #   include_directories(${nmodl_INCLUDE_DIRS})
 #   target_link_libraries(foo ${nmodl_LIBRARIES})
@@ -29,16 +29,16 @@
 
 
 # UNIX paths are standard, no need to write.
-find_program(nmodl_BINARY NAMES nmodl
-        HINTS "${CORENRN_NMODL_ROOT}/bin" QUIET)
+find_program(nmodl_BINARY NAMES nmodl${CMAKE_EXECUTABLE_SUFFIX}
+        HINTS "${CORENRN_NMODL_DIR}/bin" QUIET)
 
-find_path(nmodl_INCLUDE "nmodl/fast_math.ispc" HINTS "${CORENRN_NMODL_ROOT}/include")
-find_path(nmodl_PYTHONPATH "nmodl/__init__.py" HINTS "${CORENRN_NMODL_ROOT}/lib/python")
+find_path(nmodl_INCLUDE "nmodl/fast_math.ispc" HINTS "${CORENRN_NMODL_DIR}/include")
+find_path(nmodl_PYTHONPATH "nmodl/__init__.py" HINTS "${CORENRN_NMODL_DIR}/lib/python")
 
 # Checks 'REQUIRED', 'QUIET' and versions.
 include(FindPackageHandleStandardArgs)
 
 find_package_handle_standard_args(nmodl
   FOUND_VAR nmodl_FOUND
   REQUIRED_VARS nmodl_BINARY nmodl_INCLUDE nmodl_PYTHONPATH)
-  
+

CMakeLists.txt

@@ -63,8 +63,8 @@ option(CORENRN_ENABLE_CUDA_UNIFIED_MEMORY "Enable CUDA unified memory support" O
 option(CORENRN_ENABLE_UNIT_TESTS "Enable unit tests execution" ON)
 option(CORENRN_ENABLE_GPU "Enable GPU support using OpenACC" OFF)
 
-set(CORENRN_NMODL_ROOT "" CACHE PATH "Path nmodl source-to-source compiler root")
-set(LIKWID_ROOT "" CACHE PATH "Path to likwid performance analysis suite")
+set(CORENRN_NMODL_DIR "" CACHE PATH "Path to nmodl source-to-source compiler installation")
+set(LIKWID_DIR "" CACHE PATH "Path to likwid performance analysis suite")
 
 set(CORENRN_FRONTEND_C_COMPILER gcc CACHE FILEPATH "C compiler for building mod2c [frontend]")
 set(CORENRN_FRONTEND_CXX_COMPILER g++ CACHE FILEPATH "C++ compiler for building mod2c [frontend]")
@@ -152,23 +152,25 @@ endif()
 # NMODL specific options
 # =============================================================================
 if(CORENRN_ENABLE_NMODL)
-  find_package(nmodl REQUIRED)
-  include_directories(${nmodl_INCLUDE})
-
-  # copy to make nrnivmodl-core work from build as well instal directory
-  set(CORENRN_NMODL_BINARY ${CMAKE_BINARY_DIR}/bin/nmodl${CMAKE_EXECUTABLE_SUFFIX})
-  configure_file(${nmodl_BINARY} ${CORENRN_NMODL_BINARY} COPYONLY)
-
-  # path to python interface
-  set(ENV{PYTHONPATH} "${nmodl_PYTHONPATH}:$ENV{PYTHONPATH}")
-  set(CORENRN_NMODL_PYTHONPATH $ENV{PYTHONPATH})
-
+  find_package(nmodl)
+  if (nmodl_FOUND)
+    set(CORENRN_NMODL_BINARY ${nmodl_BINARY})
+    set(CORENRN_NMODL_INCLUDE ${nmodl_INCLUDE})
+    # path to python interface
+    set(ENV{PYTHONPATH} "${nmodl_PYTHONPATH}:$ENV{PYTHONPATH}")
+    set(CORENRN_NMODL_PYTHONPATH $ENV{PYTHONPATH})
+  else()
+    include(AddNmodlSubmodule)
+    set(CORENRN_NMODL_BINARY ${CMAKE_BINARY_DIR}/bin/nmodl${CMAKE_EXECUTABLE_SUFFIX})
+    set(CORENRN_NMODL_INCLUDE ${CMAKE_BINARY_DIR}/include)
+  endif()
+  include_directories(${CORENRN_NMODL_INCLUDE})
   set(CORENRN_NMODL_FLAGS "" CACHE STRING "Extra NMODL options such as passes")
   separate_arguments(NMODL_EXTRA_FLAGS_LIST UNIX_COMMAND "${CORENRN_NMODL_FLAGS}")
 else()
-  # use mod2c if nmodl not enabled
   include(AddMod2cSubmodule)
   set(CORENRN_NMODL_BINARY ${CMAKE_BINARY_DIR}/bin/mod2c_core${CMAKE_EXECUTABLE_SUFFIX})
+  set(CORENRN_NMODL_INCLUDE ${CMAKE_BINARY_DIR}/include)
 endif()
 
 
@@ -230,7 +232,7 @@ if(cmake_generator_tolower MATCHES "makefile")
   message(STATUS "OpenMP              | ${CORENRN_ENABLE_OPENMP}")
   message(STATUS "NMODL               | ${CORENRN_ENABLE_NMODL}")
   if(CORENRN_ENABLE_NMODL)
-    message(STATUS "  PATH              | ${nmodl_BINARY}")
+    message(STATUS "  PATH              | ${CORENRN_NMODL_BINARY}")
     message(STATUS "  ISPC              | ${CORENRN_ENABLE_ISPC}")
   else()
     message(STATUS "MOD2C               | ${MOD2C_PROJ}")

coreneuron/CMakeLists.txt

@@ -184,7 +184,8 @@ set_target_properties(coreneuron corenrnmech scopmath
 add_custom_command(TARGET coreneuron
                    POST_BUILD
                    COMMAND ${CMAKE_BINARY_DIR}/bin/nrnivmodl-core -i
-                           -I${CORENEURON_PROJECT_SOURCE_DIR}
+                           "-I${CORENEURON_PROJECT_SOURCE_DIR} -I${CORENRN_NMODL_INCLUDE}"
+                           -n ${CORENRN_NMODL_BINARY}
                            ${CORENEURON_PROJECT_SOURCE_DIR}/tests/integration/ring_gap/mod
                    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/bin
                    BYPRODUCTS ${CMAKE_BINARY_DIR}/bin/${CMAKE_SYSTEM_PROCESSOR}/special-core

coreneuron/utils/file_utils.cpp

@@ -33,7 +33,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include <errno.h>
 
 #if defined(MINGW)
-    #define mkdir(dir_name, permission) _mkdir(dir_name)
+#define mkdir(dir_name, permission) _mkdir(dir_name)
 #endif
 
 /* adapted from : gist@jonathonreinhart/mkdir_p.c */

external/nmodl

@@ -8,13 +8,13 @@ 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 VERBOSE"
+MAKE_OPTIONS="NMODL_BINARY MECH_VERSION OUTPUT INCFLAGS LINKFLAGS MODS_PATH VERBOSE"
 PARALLELISM=4
 
 while getopts "n:v:o:i:l:p:hV" OPT; do
     case "$OPT" in
     n)
-        params_MECH_NAME="$OPTARG";;
+        params_NMODL_BINARY="$OPTARG";;
     v)
         params_MECH_VERSION="$OPTARG";;
     o)
@@ -30,7 +30,7 @@ while getopts "n:v:o:i:l:p:hV" OPT; do
     h)
         echo "$APP_NAME [options, ...] [mods_path]"
         echo "Options:"
-        echo "  -n <name>       Optionally add mech name to library, as suffix"
+        echo "  -n <binary>     NMODL code generation compiler path"
         echo "  -v <version>    Set libcorenrnmech version (default: 0.0)"
         echo "  -o <output_dir> Set the output dir (default: <arch>-core)"
         echo "  -i <incl_flags> Definitions passed to the compiler, typically '-I dir..'"

extra/nrnivmodl-core

@@ -4,12 +4,12 @@
 # Mod files are looked up in the cwd, unless MODS_PATH is set
 
 # Mechanisms version are by default 0.0, but should be overriden
-MECH_NAME =
+
 MECH_VERSION = 0.0
 MODS_PATH = .
 OUTPUT = @CMAKE_HOST_SYSTEM_PROCESSOR@
 DESTDIR =
-
+NMODL_BINARY =
 # Coreneuron dirs
 bindir := $(ROOT)/bin
 libdir := $(ROOT)/lib
@@ -18,7 +18,7 @@ datadir:= $(ROOT)/share/coreneuron
 datadir_mod2c := $(ROOT)/share/mod2c
 
 # Binary of MOD2C/NMODL depending on what was activated
-nmodl_binary_path := $(bindir)/@nmodl_binary_name@
+nmodl_binary_path = $(if $(NMODL_BINARY),$(NMODL_BINARY), $(bindir)/@nmodl_binary_name@)
 
 # Additional variables set in CMAKE usable here
 # - @CORENRN_COMPILE_DEFS
@@ -45,7 +45,7 @@ CXX_LINK_SHARED = $(CXX) $(CXXFLAGS) @CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS@ @CM
 
 ISPC = @CMAKE_ISPC_COMPILER@
 ISPC_FLAGS = @CMAKE_ISPC_FLAGS@
-ISPC_COMPILE = $(ISPC) $(ISPC_FLAGS) -I$(incdir) -I@nmodl_INCLUDE@
+ISPC_COMPILE = $(ISPC) $(ISPC_FLAGS) -I$(incdir)
 
 # Variables used in the "ARTIFICIAL_CELL" detection
 mod_c_srcs_path =
@@ -91,8 +91,7 @@ dimplic_c  = $(MODC_DIR)/_dimplic.cpp
 dimplic_o  = $(OBJS_DIR)/_dimplic.o
 
 special  = $(OUTPUT)/special-core
-LIB_SUFFIX_ = $(if $(MECH_NAME),_$(MECH_NAME),)
-coremech_libname = corenrnmech$(LIB_SUFFIX_).$(MECH_VERSION)
+coremech_libname = corenrnmech.$(MECH_VERSION)
 coremech_lib = $(OUTPUT)/lib$(coremech_libname)@CMAKE_SHARED_LIBRARY_SUFFIX@
 
 # If no DESTDIR (we are probably just building) we use $ORIGIN (@loader_path in OSX)