Merge branch 'master' into leite/balanced_files2

neuronsimulator · Nov 6, 2024 · c72d108 · c72d108
2 parents 342e8f8 + 2abbd25
commit c72d108
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Showing 33 changed files with 280 additions and 434 deletions.
diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
@@ -45,7 +45,7 @@ jobs:
 
     strategy:
       matrix:
-        os: [ macOS-12, ubuntu-20.04]
+        os: [macOS-13, ubuntu-20.04]
         config:
           - { matrix_eval : "CC=gcc-9 CXX=g++-9",   build_mode: "setuptools"}
           - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", music: ON}

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -71,6 +71,7 @@ option(NRN_ENABLE_THREADS "Allow use of multithreading" ${NRN_ENABLE_THREADS_DEF
 option(NRN_ENABLE_MPI "Enable MPI support" ${NRN_ENABLE_MPI_DEFAULT})
 option(NRN_ENABLE_MUSIC "Enable MUSIC support" ${NRN_ENABLE_MUSIC_DEFAULT})
 option(NRN_ENABLE_RX3D "Enable rx3d support" ${NRN_ENABLE_RX3D_DEFAULT})
+option(NRN_ENABLE_NMODL "Enable NMODL code-generator support" ${NRN_ENABLE_NMODL_DEFAULT})
 option(NRN_ENABLE_CORENEURON "Enable CoreNEURON support" ${NRN_ENABLE_CORENEURON_DEFAULT})
 option(NRN_ENABLE_BACKTRACE "Enable pretty-printed backtraces" ${NRN_ENABLE_BACKTRACE_DEFAULT})
 option(NRN_ENABLE_TESTS "Enable unit tests" ${NRN_ENABLE_TESTS_DEFAULT})
@@ -502,6 +503,49 @@ endif()
 # initialize CLI11 submodule
 cpp_cc_git_submodule(CLI11 BUILD PACKAGE CLI11 REQUIRED)
 
+# =============================================================================
+# Enable NMODL code-generator support
+# =============================================================================
+if(NRN_ENABLE_NMODL OR NRN_ENABLE_CORENEURON)
+
+  set(NMODL_ENABLE_PYTHON_BINDINGS
+      OFF
+      CACHE BOOL "Enable NMODL python bindings")
+  nrn_add_external_project(nmodl)
+  set(CORENRN_NMODL_BINARY ${CMAKE_BINARY_DIR}/bin/nmodl${CMAKE_EXECUTABLE_SUFFIX})
+  set(NMODL_TARGET_TO_DEPEND nmodl)
+  set(NMODL_PROJECT_BINARY_DIR ${CMAKE_BINARY_DIR}/external/nmodl)
+  # install nrnunits.lib and libpywrapper.so from external/nmodl
+  install(
+    FILES ${NMODL_PROJECT_BINARY_DIR}/lib/libpywrapper${CMAKE_SHARED_LIBRARY_SUFFIX}
+    DESTINATION lib
+    COMPONENT pywrapper
+    OPTIONAL)
+  install(
+    FILES ${NMODL_PROJECT_BINARY_DIR}/share/nmodl/nrnunits.lib
+    DESTINATION share/nmodl
+    COMPONENT nrnunits)
+
+  # set correct arguments for nmodl for cpu/gpu target
+  set(CORENRN_NMODL_FLAGS
+      ""
+      CACHE STRING "Extra NMODL options such as passes")
+
+endif()
+
+# =============================================================================
+# Flags for using NOCMODL/NMODL
+# =============================================================================
+if(NRN_ENABLE_NMODL)
+  set(NRN_NMODL_--neuron "--neuron")
+  set(NRN_CODEGENERATOR_NAME "nmodl")
+  set(NRN_CODEGENERATOR_TARGET nmodl)
+else()
+  set(NRN_NMODL_--neuron "")
+  set(NRN_CODEGENERATOR_NAME "nocmodl")
+  set(NRN_CODEGENERATOR_TARGET nocmodl)
+endif()
+
 # =============================================================================
 # Enable CoreNEURON support
 # =============================================================================
@@ -536,7 +580,7 @@ if(NRN_ENABLE_CORENEURON)
   get_property(CORENRN_LIB_LINK_FLAGS GLOBAL PROPERTY CORENRN_LIB_LINK_FLAGS)
   get_property(CORENRN_NEURON_LINK_FLAGS GLOBAL PROPERTY CORENRN_NEURON_LINK_FLAGS)
   get_property(CORENRN_ENABLE_SHARED GLOBAL PROPERTY CORENRN_ENABLE_SHARED)
-  get_property(CORENRN_NMODL_BINARY GLOBAL PROPERTY CORENRN_NMODL_BINARY)
+
   # NEURON tests that link against CoreNEURON need to depend on it.
   set(CORENEURON_TARGET_TO_DEPEND coreneuron-for-tests)
 
@@ -1047,6 +1091,7 @@ if(NRN_ENABLE_CORENEURON)
   message(STATUS "  PATH        | ${CORENEURON_DIR}")
   message(STATUS "  LINK FLAGS  | ${CORENRN_LIB_LINK_FLAGS}")
 endif()
+message(STATUS "NMODL codegen   | ${NRN_ENABLE_NMODL}")
 if(NRN_UNIVERSAL2_BUILD)
   message(STATUS "CMAKE_OSX_ARCH| ${CMAKE_OSX_ARCHITECTURES}")
 endif()

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -85,7 +85,7 @@ stages:
     - job: 'MacOSWheels'
       timeoutInMinutes: 60
       pool:
-        vmImage: 'macOS-12'
+        vmImage: 'macOS-13'
       strategy:
         matrix:
           Python38:

diff --git a/bin/nrnivmodl.in b/bin/nrnivmodl.in
@@ -187,7 +187,7 @@ for i in "${files[@]}" ; do
   echo "\
 ${base_name// /\\ }.cpp: ${f}.mod \$(NOCMODL)
 	@printf \" -> \$(C_GREEN)NMODL\$(C_RESET) \$<\\\n\"
-	(cd \"$dir_name\"; @NRN_NOCMODL_SANITIZER_ENVIRONMENT_STRING@ MODLUNIT=\$(NRNUNITS) \$(NOCMODL) \"$base_name.mod\" -o \"$mdir\" $UserNMODLFLAGS)
+	(cd \"$dir_name\"; @NRN_NOCMODL_SANITIZER_ENVIRONMENT_STRING@ MODLUNIT=\$(NRNUNITS) \$(NOCMODL) \"$base_name.mod\" @NRN_NMODL_--neuron@ -o \"$mdir\" $UserNMODLFLAGS)
 
 ./${base_name// /\\ }.o: ${base_name// /\\ }.cpp
 	@printf \" -> \$(C_GREEN)Compiling\$(C_RESET) ${PWD}/\$<\\\n\"

diff --git a/bin/nrnivmodl_core_makefile.in b/bin/nrnivmodl_core_makefile.in
@@ -16,8 +16,10 @@ DESTDIR =
 TARGET_LIB_TYPE = $(BUILD_TYPE)
 
 # required for OSX to execute nrnivmodl-core
-ifeq ($(origin SDKROOT), undefined)
-  export SDKROOT := $(shell xcrun --sdk macosx --show-sdk-path)
+ifeq ($(OS_NAME), Darwin)
+  ifeq ($(origin SDKROOT), undefined)
+    export SDKROOT := $(shell xcrun --sdk macosx --show-sdk-path)
+  endif
 endif
 
 # CoreNEURON installation directories

diff --git a/bin/nrnivmodl_makefile_cmake.in b/bin/nrnivmodl_makefile_cmake.in
@@ -71,7 +71,7 @@ CXX_LINK_EXE = $(CXX) $(CXXFLAGS) @CMAKE_EXE_LINKER_FLAGS@ @NRN_LINK_FLAGS_STRIN
 CXX_LINK_SHARED = $(CXX) $(CXXFLAGS) @CMAKE_SHARED_LIBRARY_CREATE_CXX_FLAGS@ @CMAKE_SHARED_LIBRARY_CXX_FLAGS@ @CMAKE_SHARED_LINKER_FLAGS@ @NRN_LINK_FLAGS_STRING@
 
 ifeq ($(UserNMODLBIN), )
-NOCMODL = $(bindir)/nocmodl
+NOCMODL = $(bindir)/@NRN_CODEGENERATOR_NAME@
 else
 NOCMODL = $(UserNMODLBIN)
 endif

diff --git a/cmake/BuildOptionDefaults.cmake b/cmake/BuildOptionDefaults.cmake
@@ -14,6 +14,7 @@ set(NRN_ENABLE_THREADS_DEFAULT ON)
 set(NRN_ENABLE_MPI_DEFAULT ON)
 set(NRN_ENABLE_MUSIC_DEFAULT OFF)
 set(NRN_ENABLE_RX3D_DEFAULT ON)
+set(NRN_ENABLE_NMODL_DEFAULT OFF)
 set(NRN_ENABLE_CORENEURON_DEFAULT OFF)
 set(NRN_ENABLE_BACKTRACE_DEFAULT OFF)
 set(NRN_ENABLE_TESTS_DEFAULT OFF)

diff --git a/cmake/Coverage.cmake b/cmake/Coverage.cmake
@@ -34,7 +34,7 @@ if(NRN_ENABLE_COVERAGE)
   if(NOT BUILD_TYPE_UPPER STREQUAL "DEBUG")
     message(WARNING "Using CMAKE_BUILD_TYPE=Debug is recommended with NRN_ENABLE_COVERAGE")
   endif()
-  set(NRN_COVERAGE_FLAGS_UNQUOTED --coverage -fno-inline)
+  set(NRN_COVERAGE_FLAGS_UNQUOTED --coverage -fno-inline -fprofile-update=atomic)
   string(JOIN " " NRN_COVERAGE_FLAGS ${NRN_COVERAGE_FLAGS_UNQUOTED})
   set(NRN_COVERAGE_LINK_FLAGS --coverage)
 

diff --git a/cmake/MacroHelper.cmake b/cmake/MacroHelper.cmake
@@ -153,17 +153,18 @@ macro(nocmodl_mod_to_cpp modfile_basename)
   if(CMAKE_VERSION VERSION_LESS "3.17")
     set(REMOVE_CMAKE_COMMAND "remove")
   endif()
+  get_filename_component(modfile_output_dir ${PROJECT_SOURCE_DIR}/${modfile_basename}.mod DIRECTORY)
   add_custom_command(
     OUTPUT ${PROJECT_BINARY_DIR}/${modfile_basename}.cpp
     COMMAND
       ${CMAKE_COMMAND} -E env "MODLUNIT=${PROJECT_BINARY_DIR}/share/nrn/lib/nrnunits.lib"
-      ${NRN_NOCMODL_SANITIZER_ENVIRONMENT} $<TARGET_FILE:nocmodl>
-      ${PROJECT_SOURCE_DIR}/${modfile_basename}.mod
+      ${NRN_NOCMODL_SANITIZER_ENVIRONMENT} $<TARGET_FILE:${NRN_CODEGENERATOR_TARGET}>
+      ${PROJECT_SOURCE_DIR}/${modfile_basename}.mod ${NRN_NMODL_--neuron} -o ${modfile_output_dir}
     COMMAND sed ${NOCMODL_SED_EXPR} ${PROJECT_SOURCE_DIR}/${modfile_basename}.cpp >
             ${PROJECT_BINARY_DIR}/${modfile_basename}.cpp
     COMMAND ${CMAKE_COMMAND} -E ${REMOVE_CMAKE_COMMAND}
             ${PROJECT_SOURCE_DIR}/${modfile_basename}.cpp
-    DEPENDS nocmodl ${PROJECT_SOURCE_DIR}/${modfile_basename}.mod
+    DEPENDS ${NRN_CODEGENERATOR_TARGET} ${PROJECT_SOURCE_DIR}/${modfile_basename}.mod
             ${PROJECT_BINARY_DIR}/share/nrn/lib/nrnunits.lib
     WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/src/nrniv)
 endmacro()

diff --git a/cmake/coreneuron/packages/Findnmodl.cmake b/cmake/coreneuron/packages/Findnmodl.cmake
diff --git a/docs/install/mac_pkg.md b/docs/install/mac_pkg.md
@@ -162,7 +162,7 @@ generally only for the architecture indicated by ```uname -m```. That is
 ok for openmpi but since the various python libraries are linked against
 during build to create the version specific neuron modules, those python
 installers also have to be universal. Fortunately, universal python versions
-can be found at [python.org](http://python.org/Downloads/macOS) at least for
+can be found at [python.org](https://www.python.org/downloads/macos) at least for
 (as of 2022-01-01) python3.8, python3.9, and python3.10.
 
 - ```xcode-select --install```:

diff --git a/docs/nmodl/NMODL_language.ipynb b/docs/nmodl/NMODL_language.ipynb
@@ -444,56 +444,6 @@
     "### LOCAL"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "### DISCRETE\n",
-    "\n",
-    "Short description"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "#### Example mod file"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!cat mod/disc.mod"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "#### Functionality example"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "!cat python_scripts/disc.py"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%run python_scripts/disc.py"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/docs/nmodl/mod/disc.mod b/docs/nmodl/mod/disc.mod
diff --git a/docs/nmodl/python_scripts/disc.py b/docs/nmodl/python_scripts/disc.py
diff --git a/external/nmodl b/external/nmodl
diff --git a/share/examples/nrniv/nmodl/cadifusl.mod b/share/examples/nrniv/nmodl/cadifusl.mod
@@ -66,7 +66,7 @@ INITIAL {
 	}
 }
 
-LOCAL frat[NANN] 	: gets extra cm when multiplied by diam
+LOCAL frat[NANN]	: gets extra cm when multiplied by diam
 
 PROCEDURE coord() {
 	LOCAL r, dr2

diff --git a/share/examples/nrniv/nmodl/cagkftab.py b/share/examples/nrniv/nmodl/cagkftab.py
@@ -121,6 +121,10 @@ def test_1d():
 test_1d_vecs = test_1d()  # keep in existence in case of later use
 
 
+def assert_isclose(a, b, abs_tol):
+    assert isclose(a, b, abs_tol=abs_tol), f"{a = } {b = } delta = {a - b} {abs_tol = }"
+
+
 def setup_tables():
     ln_ca_range = (-18, 4, 0.1)  # about 1e-9 to 1e2 in steps of 0.1 log unit
     v_range = (-80, 50, 1)  # -80mV to 50mV in 1mV steps
@@ -132,8 +136,8 @@ def setup_tables():
         for j, lnca in enumerate(casteps):
             malp.x[i][j] = alp(v, lnca)
             mbet.x[i][j] = bet(v, lnca)
-            assert isclose(malp.x[i][j], h.alp_cagk(v, exp(lnca)), abs_tol=1e-9)
-            assert isclose(mbet.x[i][j], h.bet_cagk(v, exp(lnca)), abs_tol=1e-9)
+            assert_isclose(malp.x[i][j], h.alp_cagk(v, exp(lnca)), abs_tol=1e-9)
+            assert_isclose(mbet.x[i][j], h.bet_cagk(v, exp(lnca)), abs_tol=1e-9)
 
     # dimensions specified in size, min, max format
     h.table_alp_cagkftab(

diff --git a/share/examples/nrniv/nmodl/nonlin.py b/share/examples/nrniv/nmodl/nonlin.py
@@ -17,7 +17,8 @@
 
 def dif(tol):
     for cell in cells:
-        assert cell.dif() < tol
+        residual = cell.dif()
+        assert residual < tol, f"{residual = }, {tol = }"
 
 
 def solve(a, b, c):

diff --git a/share/examples/nrniv/nmodl/synpre.mod b/share/examples/nrniv/nmodl/synpre.mod
@@ -81,8 +81,4 @@ PROCEDURE getonset() {
 	if (vpre > vprethresh && t > onset + deadtime) {
 		onset = t
 	}
-
-	VERBATIM
-	return 0;
-	ENDVERBATIM
 }