ExternalProject SUNDIALS 3.2.1

.gitmodules

@@ -37,3 +37,7 @@
 [submodule "external/spdlog"]
 	path = external/spdlog
 	url = https://github.com/gabime/spdlog.git
+[submodule "external/sundials"]
+	path = external/sundials
+	url = https://github.com/neuronsimulator/sundials.git
+	branch = hines/hoc_pow

CMakeLists.txt

@@ -596,6 +596,24 @@ cpp_cc_git_submodule(CLI11 BUILD PACKAGE CLI11 REQUIRED)
 
 # coreneuron targets will get propagated down from the subdirectory
 
+# =============================================================================
+# Enable NRN_DIGEST
+# =============================================================================
+if(NRN_ENABLE_DIGEST)
+  set(NRN_DIGEST 1)
+else()
+  set(NRN_DIGEST 0)
+endif()
+
+# =============================================================================
+# Enable NRN_ARCH_INDEP_EXP_POW
+# =============================================================================
+if(NRN_ENABLE_ARCH_INDEP_EXP_POW)
+  set(NRN_ARCH_INDEP_EXP_POW 1)
+else()
+  set(NRN_ARCH_INDEP_EXP_POW 0)
+endif()
+
 # =============================================================================
 # Enable NMODL code-generator support
 # =============================================================================
@@ -949,21 +967,42 @@ add_custom_target(
   COMMAND ${PROJECT_SOURCE_DIR}/external/coding-conventions/bin/format
   WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
 
-# Prepare a shell script to format only files modified with respect to master branch
+# Prepare a shell script to format only files modified with respect to master/main branch that still
+# exist on disk (filters out deleted files).
 file(
   WRITE ${CMAKE_CURRENT_BINARY_DIR}/format-pr.sh
-  "\
-#!bash\n\
-set -e\n\
-cmd='cd ${PROJECT_SOURCE_DIR} && external/coding-conventions/bin/format `git diff --name-only master`'\n\
-echo $cmd\n\
-cd ${PROJECT_SOURCE_DIR} && external/coding-conventions/bin/format `git diff --name-only master`\n\
+  "#!/bin/bash
+set -euo pipefail
+
+# Try 'main' first, then fall back to 'master'
+for base in main master; do
+    if git rev-parse --verify \"\$base\" >/dev/null 2>&1; then
+        BASE_BRANCH=\"\$base\"
+        break
+    fi
+done
+
+if [ -z \"\${BASE_BRANCH:-}\" ]; then
+    echo \"Error: Neither 'main' nor 'master' branch found.\" >&2
+    exit 1
+fi
+
+echo \"Formatting changes vs '\$BASE_BRANCH' (existing files only)...\" >&2
+
+# Get changed files, but only pass files that still exist
+git diff --name-only \"\$BASE_BRANCH\" | \\
+while read -r file; do
+    if [ -e \"\$file\" ]; then
+        printf '%s\\n' \"\$file\"
+    fi
+done | \\
+xargs --no-run-if-empty external/coding-conventions/bin/format \"\$@\"
 ")
 
 add_custom_target(
   format-pr
   COMMAND bash ${CMAKE_CURRENT_BINARY_DIR}/format-pr.sh
-  COMMENT "Format only files modified with respect to master branch."
+  COMMENT "Format only files modified with respect to main/master (existing files only)"
   WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
 
 # =============================================================================

cmake/ConfigFileSetting.cmake

@@ -156,8 +156,6 @@ configure_file("${PROJECT_SOURCE_DIR}/src/nrnoc/nrnconfigargs.h.in"
                "${PROJECT_BINARY_DIR}/src/nrnoc/nrnconfigargs.h" @ONLY)
 configure_file("${PROJECT_SOURCE_DIR}/src/nrncvode/nrnneosm.h.in"
                "${PROJECT_BINARY_DIR}/src/nrncvode/nrnneosm.h" @ONLY)
-configure_file("${PROJECT_SOURCE_DIR}/src/sundials/sundials_config.h.in"
-               "${PROJECT_BINARY_DIR}/src/sundials/sundials_config.h" @ONLY)
 configure_file("${PROJECT_SOURCE_DIR}/share/lib/nrn.defaults.in"
                "${PROJECT_BINARY_DIR}/share/nrn/lib/nrn.defaults" @ONLY)
 

cmake/NeuronFileLists.cmake

@@ -266,45 +266,6 @@ set(NRNCVODE_FILE_LIST
     occvode.cpp
     tqueue.cpp)
 
-# =============================================================================
-# Files in sundials directory
-# =============================================================================
-nrn_create_file_list(
-  SUNDIALS_CVODES
-  "${PROJECT_SOURCE_DIR}/src/sundials/cvodes"
-  cvband.c
-  cvbandpre.c
-  cvbbdpre.c
-  cvdense.c
-  cvdiag.c
-  cvodea.c
-  cvodes.c
-  cvodesio.c
-  cvspgmr.c)
-
-nrn_create_file_list(
-  SUNDIALS_IDA
-  "${PROJECT_SOURCE_DIR}/src/sundials/ida"
-  idaband.c
-  idabbdpre.c
-  ida.c
-  idadense.c
-  idaic.c
-  idaio.c
-  idaspgmr.c)
-nrn_create_file_list(
-  SUNDIALS_SHARED
-  "${PROJECT_SOURCE_DIR}/src/sundials/shared"
-  band.c
-  dense.c
-  iterative.c
-  nvector.c
-  nvector_serial.c
-  smalldense.c
-  spgmr.c
-  sundialsmath.c)
-set(NRN_SUNDIALS_SRC_FILES ${SUNDIALS_CVODES} ${SUNDIALS_IDA} ${SUNDIALS_SHARED})
-
 set(SPARSE_FILES_LIST bksub.cpp getelm.cpp lineq.cpp prmat.cpp subrows.cpp)
 
 # scopmath sources
@@ -446,9 +407,7 @@ nrn_create_file_list(NRN_NRNIV_SRC_FILES ${NRN_NRNIV_SRC_DIR} ${NRNIV_FILE_LIST}
 nrn_create_file_list(NRN_PARALLEL_SRC_FILES ${NRN_PARALLEL_SRC_DIR} ${NRN_PARALLEL_FILES_LIST})
 if(NRN_ENABLE_MPI)
   nrn_create_file_list(NRN_PARALLEL_SRC_FILES ${PROJECT_SOURCE_DIR}/src/nrniv
-                       nvector_nrnparallel_ld.cpp)
-  nrn_create_file_list(NRN_PARALLEL_SRC_FILES ${PROJECT_SOURCE_DIR}/src/sundials/shared
-                       nvector_parallel.c)
+                       nvector_nrnparallel_ld.cpp nvector_parallel.cpp)
 endif()
 nrn_create_file_list(NRN_SPARSE_SRC_FILES ${PROJECT_SOURCE_DIR}/src/sparse ${SPARSE_FILES_LIST})
 nrn_create_file_list(NRN_SCOPMATH_SRC_FILES ${PROJECT_SOURCE_DIR}/src/scopmath

cmake/modules/FindSUNDIALS.cmake

@@ -0,0 +1,54 @@
+# cmake/modules/FindSUNDIALS.cmake
+
+set(SUNDIALS_SOURCE_DIR "${PROJECT_SOURCE_DIR}/external/sundials")
+
+# Use the same pattern as other submodules in NEURON
+if(NOT EXISTS "${SUNDIALS_SOURCE_DIR}/CMakeLists.txt")
+  message(STATUS "SUNDIALS submodule not found.")
+  include(${PROJECT_SOURCE_DIR}/cmake/ExternalProjectHelper.cmake)
+  nrn_initialize_submodule(external/sundials)
+endif()
+
+if(NOT EXISTS "${SUNDIALS_SOURCE_DIR}/CMakeLists.txt")
+  message(FATAL_ERROR "Failed to initialize SUNDIALS submodule")
+endif()
+
+set(SUNDIALS_PREFIX "${CMAKE_BINARY_DIR}/external/sundials")
+set(SUNDIALS_INCLUDE_DIR "${SUNDIALS_PREFIX}/include")
+set(SUNDIALS_LIB_DIR "${SUNDIALS_PREFIX}/lib")
+
+include(ExternalProject)
+ExternalProject_Add(
+  sundials
+  SOURCE_DIR "${SUNDIALS_SOURCE_DIR}"
+  PREFIX "${SUNDIALS_PREFIX}"
+  CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+             -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+             -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+             -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+             -DCMAKE_POSITION_INDEPENDENT_CODE=ON
+             -DBUILD_SHARED_LIBS=OFF
+             -DEXAMPLES_ENABLE_C=OFF
+             -DEXAMPLES_INSTALL=OFF
+             -DBUILD_ARKODE=OFF
+             -DBUILD_CVODES=OFF
+             -DBUILD_IDAS=OFF
+             -DBUILD_KINSOL=OFF
+             -DMPI_ENABLE=OFF
+             -DPTHREAD_ENABLE=ON
+             -DSUNDIALS_PRECISION=double
+             -DUSE_GENERIC_MATH=ON
+  BUILD_BYPRODUCTS
+    <INSTALL_DIR>/lib/libsundials_cvode.a <INSTALL_DIR>/lib/libsundials_ida.a
+    <INSTALL_DIR>/lib/libsundials_nvecserial.a <INSTALL_DIR>/lib/libsundials_nvecpthreads.a
+  INSTALL_DIR "${SUNDIALS_PREFIX}")
+
+add_library(SUNDIALS INTERFACE IMPORTED)
+add_dependencies(SUNDIALS sundials)
+
+set(SUNDIALS_INCLUDE_DIR
+    "${SUNDIALS_INCLUDE_DIR}"
+    PARENT_SCOPE)
+set(SUNDIALS_LIB_DIR
+    "${SUNDIALS_LIB_DIR}"
+    PARENT_SCOPE)

cmake_nrnconf.h.in

@@ -88,12 +88,6 @@
 /* Define to the version of this package. */
 #cmakedefine PACKAGE_VERSION @PACKAGE_VERSION@
 
-/* Define SUNDIALS data type 'realtype' as 'long double' */
-#cmakedefine SUNDIALS_DOUBLE_PRECISION @SUNDIALS_DOUBLE_PRECISION@
-
-/* Use generic math functions */
-#cmakedefine SUNDIALS_USE_GENERIC_MATH @SUNDIALS_USE_GENERIC_MATH@
-
 /* Version number of package */
 #cmakedefine VERSION @VERSION@
 

docs/install/debug.md

@@ -241,6 +241,27 @@ NMODL supports the sanitizers in a similar way, but this has to be enabled
 explicitly: `-DNRN_SANITIZERS=undefined` will also compile NMODL code with UBSan
 enabled.
 
+#### Updating rxd test data for new versions of CVode
+
+Updates to new versions of SUNDIALS integrators produce different,
+but presumably as accurate, results. These differences can cause CI failures.
+A method to update rxd test data is, from the top level nrn folder:
+```
+nrnivmodl test/rxd/*.mod
+PYTHONPATH=./test/rxd:$PYTHONPATH pytest -s ./test/rxd/ --save ./test/rxd/testdata/tests
+python share/lib/python/neuron/rxdtests/run_all.py
+cp -r ./share/lib/python/neuron/rxdtests/test_data/* ./test/rxd/testdata/rxdtests/
+cp -r ./test/rxd/testdata/tests/* ./test/rxd/testdata/test
+rm -r -f ./test/rxd/testdata/tests
+(cd share/lib/python/neuron/tests; python test_rxd.py --save test_rxd.json)
+```
+When everything is working again, cd to test/rxd/testdata, start a new branch,
+commit, and push to ``https://github.com/neuronsimulator/rxdtestdata``.
+Individual rxd tests can be run, e.g., by
+```
+PYTHONPATH=./test/rxd:$PYTHONPATH pytest -s ./test/rxd/3d/test_ics_currents.py
+```
+
 Profiling and performance benchmarking
 --------------------------------------
 

docs/progref/simctrl/cvode.rst

@@ -273,6 +273,34 @@ CVode
 
 
 
+.. method:: CVode.version
+
+    .. tab:: Python
+
+
+        Syntax:
+            ``"major.minor.patch" = cvode.version()``
+
+
+        Description:
+            Returns the version string. Eg. "3.2.1"
+
+
+    .. tab:: HOC
+
+
+        Syntax:
+            ``"major.minor.patch" = cvode.version()``
+
+
+        Description:
+            Returns the version string. Eg. "3.2.1"
+
+
+----
+
+
+
 .. method:: CVode.spike_stat
 
     .. tab:: Python

share/lib/python/neuron/rxdtests/tests/hybrid/bistable_hybrid.py

@@ -28,10 +28,12 @@
 ca = rxd.Species(
     r,
     d=diff_constant,
-    initial=lambda node: 1
-    if (0.8 < node.x and node.segment in dend1)
-    or (node.x < 0.2 and node.segment in dend2)
-    else 0,
+    initial=lambda node: (
+        1
+        if (0.8 < node.x and node.segment in dend1)
+        or (node.x < 0.2 and node.segment in dend2)
+        else 0
+    ),
 )
 bistable_reaction = rxd.Rate(ca, -ca * (1 - ca) * (0.01 - ca))
 h.finitialize()

share/lib/python/neuron/rxdtests/tests/hybrid/bistable_hybrid_change_nthread.py

@@ -28,10 +28,12 @@
 ca = rxd.Species(
     r,
     d=diff_constant,
-    initial=lambda node: 1
-    if (0.8 < node.x and node.segment in dend1)
-    or (node.x < 0.2 and node.segment in dend2)
-    else 0,
+    initial=lambda node: (
+        1
+        if (0.8 < node.x and node.segment in dend1)
+        or (node.x < 0.2 and node.segment in dend2)
+        else 0
+    ),
 )
 bistable_reaction = rxd.Rate(ca, -ca * (1 - ca) * (0.01 - ca))
 h.finitialize()

share/lib/python/neuron/rxdtests/tests/hybrid/bistable_hybrid_cvode.py

@@ -28,10 +28,12 @@
     r,
     d=diff_constant,
     atolscale=0.1,
-    initial=lambda node: 1
-    if (0.8 < node.x and node.segment in dend1)
-    or (node.x < 0.2 and node.segment in dend2)
-    else 0,
+    initial=lambda node: (
+        1
+        if (0.8 < node.x and node.segment in dend1)
+        or (node.x < 0.2 and node.segment in dend2)
+        else 0
+    ),
 )
 bistable_reaction = rxd.Rate(ca, -ca * (1 - ca) * (0.01 - ca))
 h.finitialize()

share/lib/python/neuron/rxdtests/tests/hybrid/bistable_hybrid_cvode_change_nthread.py

@@ -28,10 +28,12 @@
     r,
     d=diff_constant,
     atolscale=0.1,
-    initial=lambda node: 1
-    if (0.8 < node.x and node.segment in dend1)
-    or (node.x < 0.2 and node.segment in dend2)
-    else 0,
+    initial=lambda node: (
+        1
+        if (0.8 < node.x and node.segment in dend1)
+        or (node.x < 0.2 and node.segment in dend2)
+        else 0
+    ),
 )
 bistable_reaction = rxd.Rate(ca, -ca * (1 - ca) * (0.01 - ca))
 h.finitialize()

share/lib/python/neuron/rxdtests/tests/hybrid/pure_diffusion_hybrid.py

@@ -34,10 +34,12 @@
 ca = rxd.Species(
     r,
     d=diff_constant,
-    initial=lambda node: 1
-    if (0.8 < node.x and node.segment in dend1)
-    or (node.x < 0.2 and node.segment in dend2)
-    else 0,
+    initial=lambda node: (
+        1
+        if (0.8 < node.x and node.segment in dend1)
+        or (node.x < 0.2 and node.segment in dend2)
+        else 0
+    ),
 )
 h.finitialize()
 initial_amount = (

share/lib/python/neuron/rxdtests/tests/hybrid/pure_diffusion_hybrid_cvode.py

@@ -34,10 +34,12 @@
 ca = rxd.Species(
     r,
     d=diff_constant,
-    initial=lambda node: 1
-    if (0.8 < node.x and node.segment in dend1)
-    or (node.x < 0.2 and node.segment in dend2)
-    else 0,
+    initial=lambda node: (
+        1
+        if (0.8 < node.x and node.segment in dend1)
+        or (node.x < 0.2 and node.segment in dend2)
+        else 0
+    ),
 )
 h.finitialize()
 initial_amount = (

share/lib/python/neuron/tests/test_all.py

@@ -4,7 +4,6 @@
 $Id$
 """
 
-
 # import your specific test here
 # and add it to the "suite" function below
 from neuron.tests import test_vector, test_neuron