neuronsimulator · alexsavulescu · Aug 20, 2022 · Aug 20, 2022 · Dec 11, 2022 · Dec 11, 2022
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -503,6 +503,24 @@ endif()
 # initialize CLI11 submodule
 cpp_cc_git_submodule(CLI11 BUILD PACKAGE CLI11 REQUIRED)
 
+# =============================================================================
+# 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
 # =============================================================================

diff --git a/cmake/ConfigFileSetting.cmake b/cmake/ConfigFileSetting.cmake
@@ -158,8 +158,6 @@ 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)
 file(COPY ${PROJECT_SOURCE_DIR}/share/lib/nrnunits.lib

diff --git a/cmake/NeuronFileLists.cmake b/cmake/NeuronFileLists.cmake
@@ -267,45 +267,6 @@ 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
@@ -447,9 +408,7 @@ 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

diff --git a/cmake/modules/FindSUNDIALS.cmake b/cmake/modules/FindSUNDIALS.cmake
@@ -0,0 +1,58 @@
+# =============================================================================
+# Sundials
+# =============================================================================
+
+include(ExternalProject)
+set(SUNDIALS_PREFIX "${THIRD_PARTY_DIRECTORY}/sundials")
+set(SUNDIALS_INCLUDE_DIR "${SUNDIALS_PREFIX}/include")
+set(SUNDIALS_LIB_DIR "${SUNDIALS_PREFIX}/lib")
+make_directory(${SUNDIALS_INCLUDE_DIR})
+
+set(SUNDIALS_C_FLAGS ${CMAKE_C_FLAGS})
+list(REMOVE_ITEM SUNDIALS_C_FLAGS "-tp=haswell")
+set(SUNDIALS_CXX_FLAGS ${CMAKE_CXX_FLAGS})
+list(REMOVE_ITEM SUNDIALS_CXX_FLAGS "-tp=haswell")
+include(ExternalProject)
+ExternalProject_Add(
+  sundials-external
+  PREFIX "${SUNDIALS_PREFIX}"
+  # cmake-format: off
+  # GIT_REPOSITORY https://github.com/LLNL/sundials.git
+  # Forked to following, to allow RPowerR to use hoc_pow
+  GIT_REPOSITORY https://github.com/neuronsimulator/sundials.git
+  # GIT_TAG e2f29c34f324829302037a1492db480be8828084   6.2.0 -> CVodeMem no longer "visible" GIT_TAG
+  # c09e732080a214694b209032ec627c93fed45340  4
+  #GIT_TAG 811234254d37652954daff0ccdb7af9813736846 # 3.2.1
+  GIT_TAG 71b3daec18ce66a7c011be9501a31567aa5c09b6 # 3.2.1 hines/hoc_pow
+  # GIT_TAG 7ed895fd102226dbc52225e6b2c6e26ef1cafa0e  #2.7.0
+  # cmake-format: on
+  GIT_SHALLOW ON
+  GIT_PROGRESS ON
+  # UPDATE_COMMAND ""
+  CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+             -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+             -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+             -DCMAKE_C_FLAGS=${SUNDIALS_C_FLAGS}
+             -DCMAKE_CXX_FLAGS=${SUNDIALS_CXX_FLAGS}
+             -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+             -DEXAMPLES_INSTALL=OFF
+             -DBUILD_ARKODE=OFF
+             -DBUILD_CVODES=OFF
+             -DBUILD_IDAS=OFF
+             -DBUILD_KINSOL=OFF
+             -DEXAMPLES_ENABLE_C=OFF
+             -DMPI_ENABLE=OFF
+             -DPTHREAD_ENABLE=ON
+             -DSUNDIALS_PRECISION=double
+             -DUSE_GENERIC_MATH=ON
+             -DCMAKE_POSITION_INDEPENDENT_CODE=ON
+             -DBUILD_SHARED_LIBS=OFF
+             -DMPI_C_COMPILER=${MPI_C_COMPILER}
+             -DCMAKE_INSTALL_LIBDIR=${SUNDIALS_LIB_DIR}
+  BUILD_BYPRODUCTS
+    <INSTALL_DIR>/lib/libsundials_ida.a <INSTALL_DIR>/lib/libsundials_cvode.a
+    <INSTALL_DIR>/lib/libsundials_nvecserial.a <INSTALL_DIR>/lib/libsundials_nvecpthreads.a
+    <INSTALL_DIR>/lib/libsundials_nvecparallel.a)
+
+add_library(SUNDIALS INTERFACE IMPORTED)
+add_dependencies(SUNDIALS sundials-external)
diff --git a/cmake_nrnconf.h.in b/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@
 

diff --git a/docs/install/debug.md b/docs/install/debug.md
@@ -211,6 +211,27 @@ explicitly: `-DNRN_SANITIZERS=undefined` will not compile NMODL code with UBSan
 enabled, you must additionally pass `-DNMODL_SANITIZERS=undefined` to enable
 instrumentation of NMODL code.
 
+#### 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
 --------------------------------------
 

diff --git a/docs/python/simctrl/cvode.rst b/docs/python/simctrl/cvode.rst
@@ -140,6 +140,21 @@ CVode
 
 
 
+.. method:: CVode.version
+
+
+    Syntax:
+        ``"major.minor.patch" = cvode.version()``
+
+
+    Description:
+        Returns the version string. Eg. "3.2.1"
+
+
+----
+
+
+
 .. method:: CVode.spike_stat