Merge remote-tracking branch 'origin/develop' into feature/fortran-32…

…index-build

.clang-format

@@ -79,7 +79,7 @@ EmptyLineAfterAccessModifier                  : Never
 EmptyLineBeforeAccessModifier                 : Always
 ExperimentalAutoDetectBinPacking              : false
 FixNamespaceComments                          : true
-IncludeBlocks                   : Regroup
+IncludeBlocks                   : Preserve
 IncludeCategories               :
 - Regex                           : '^(<|"(gtest|gmock|isl|json)/)'
   Priority                        : 1

.github/workflows/macos-latest.yml

@@ -25,9 +25,13 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Configure CMake
-      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
-      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
-      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
+      # Configure CMake in a 'build' subdirectory.
+      run: |
+        cmake \
+        -B ${{github.workspace}}/build \
+        -D CMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} \
+        -D ENABLE_ALL_WARNINGS=ON \
+        -D ENABLE_WARNINGS_AS_ERRORS=ON
 
     - name: Build
       # Build your program with the given configuration

.github/workflows/ubuntu-clang-latest.yml

@@ -21,8 +21,9 @@ jobs:
       fail-fast: false
       max-parallel: 2
       matrix:
-        # 2 is what all other builds use (its the default), so skip it here
-        logging_level: [0, 1, 3, 4, 5] 
+        # Level 2 is also used in other builds (it's the default) but include it
+        # here to ensure it's tested with all warning flags
+        logging_level: [0, 1, 2, 3, 4, 5]
 
     steps:
     - name: Install LLVM and Clang
@@ -33,9 +34,16 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Configure CMake
-      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
-      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
-      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DCMAKE_C_COMPILER=$(which clang) -DCMAKE_CXX_COMPILER=$(which clang++) -DSUNDIALS_LOGGING_LEVEL=${{matrix.logging_level}}
+      # Configure CMake in a 'build' subdirectory.
+      run: |
+        cmake \
+        -B ${{github.workspace}}/build \
+        -D CMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} \
+        -D CMAKE_C_COMPILER=$(which clang) \
+        -D CMAKE_CXX_COMPILER=$(which clang++) \
+        -D SUNDIALS_LOGGING_LEVEL=${{matrix.logging_level}} \
+        -D ENABLE_ALL_WARNINGS=ON \
+        -D ENABLE_WARNINGS_AS_ERRORS=ON
 
     - name: Build
       # Build your program with the given configuration
@@ -57,9 +65,16 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Configure CMake
-      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
-      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
-      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DCMAKE_C_COMPILER=$(which clang) -DCMAKE_CXX_COMPILER=$(which clang++) -DSUNDIALS_BUILD_WITH_PROFILING=${{matrix.profiling}}
+      # Configure CMake in a 'build' subdirectory.
+      run: |
+        cmake \
+        -B ${{github.workspace}}/build \
+        -D CMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} \
+        -D CMAKE_C_COMPILER=$(which clang) \
+        -D CMAKE_CXX_COMPILER=$(which clang++) \
+        -D SUNDIALS_BUILD_WITH_PROFILING=${{matrix.profiling}} \
+        -D ENABLE_ALL_WARNINGS=ON \
+        -D ENABLE_WARNINGS_AS_ERRORS=ON
 
     - name: Build
       # Build your program with the given configuration

.readthedocs.yaml

@@ -14,6 +14,7 @@ build:
     - graphviz
 
 # Build documentation in the doc/ directory with Sphinx
+# TODO(DJG): Once multiple references are fixed, add fail_on_warning: true
 sphinx:
    configuration: doc/superbuild/source/conf.py
 

CHANGELOG.md

@@ -38,6 +38,12 @@ Added the following MRI coupling tables
 Added `ARKodeButcherTable_ERKIDToName` and `ARKodeButcherTable_DIRKIDToName` to
 convert a Butcher table ID to a string representation.
 
+Added the function ``ARKodeSetAutonomous`` in ARKODE to indicate that the
+implicit right-hand side function does not explicitly depend on time. When using
+the trivial predictor, an autonomous problem may reuse implicit function
+evaluations across stage solves to reduce the total number of function
+evaluations.
+
 Users may now disable interpolated output in ARKODE by passing `ARK_INTERP_NONE`
 to `ARKodeSetInterpolantType`. When interpolation is disabled, rootfinding is
 not supported, implicit methods must use the trivial predictor (the default
@@ -120,6 +126,11 @@ Deprecated the `ARKStepSetOptimalParams` function. Since this function does not
 ARKODE-wide equivalent, instructions have been added to the user guide for how
 to retain the current functionality using other user-callable functions.
 
+The unsupported implementations of `N_VGetArrayPointer` and `N_VSetArrayPointer`
+for the *hypre* and PETSc vectors are now deprecated.  Users should access the
+underlying wrapped external library vector objects instead with
+`N_VGetVector_ParHyp` and `N_VGetVector_Petsc`, respectively.
+
 ## Changes to SUNDIALS in release v7.0.0
 
 ### Major Feature

benchmarks/CMakeLists.txt

@@ -22,6 +22,12 @@ endif()
 
 sundials_option(BENCHMARK_NVECTOR BOOL "NVector benchmarks are on" ON)
 
+# Disable some warnings for benchmarks
+if(ENABLE_ALL_WARNINGS)
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-unused-parameter")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-parameter")
+endif()
+
 #----------------------------------------
 # Add specific benchmarks
 #----------------------------------------

cmake/SundialsSetupCompilers.cmake

@@ -93,8 +93,21 @@ if(ENABLE_ALL_WARNINGS)
     set(CMAKE_CXX_FLAGS "-Wmissing-declarations -Wcast-qual ${CMAKE_CXX_FLAGS}")
   endif()
 
-  set(CMAKE_C_FLAGS "-Wall -Wpedantic -Wextra -Wshadow -Wno-unused-parameter -Wno-unused-function ${CMAKE_C_FLAGS}")
-  set(CMAKE_CXX_FLAGS "-Wall -Wpedantic -Wextra -Wshadow -Wno-unused-parameter -Wno-unused-function ${CMAKE_CXX_FLAGS}")
+  set(CMAKE_C_FLAGS "-Wall -Wpedantic -Wextra -Wshadow ${CMAKE_C_FLAGS}")
+  set(CMAKE_CXX_FLAGS "-Wall -Wpedantic -Wextra -Wshadow ${CMAKE_CXX_FLAGS}")
+
+  # TODO(DJG): Add -fcheck=all,no-pointer,no-recursion once Jenkins is updated
+  # to use gfortran > 5.5 which segfaults with -fcheck=array-temps,bounds,do,mem
+  # no- options were added in gfortran 6
+  #
+  # Exclude run-time pointer checks (no-pointer) because passing null objects
+  # to SUNDIALS functions (e.g., sunmat => null() to SetLinearSolver) causes a
+  # run-time error with this check
+  #
+  # Exclude checks for subroutines and functions not marked as recursive
+  # (no-recursion) e.g., ark_brusselator1D_task_local_nls_f2003 calls
+  # SUNNonlinsolFree from within a custom nonlinear solver implementation of
+  # SUNNonlinsolFree which causes a run-time error with this check
   set(CMAKE_Fortran_FLAGS "-Wall -Wpedantic -Wno-unused-dummy-argument -Wno-c-binding-type -ffpe-summary=none ${CMAKE_Fortran_FLAGS}")
 endif()
 
@@ -205,6 +218,17 @@ if(NOT (SUNDIALS_C_COMPILER_HAS_ATTRIBUTE_ASSUME OR SUNDIALS_C_COMPILER_HAS_BUIL
   " SUNDIALS_C_COMPILER_HAS_ASSUME)
 endif()
 
+# ---------------------------------------------------------------
+# Check for unused extension
+# ---------------------------------------------------------------
+
+check_c_source_compiles("
+  int main(void) {
+    __attribute__((unused)) double a = 0.0;
+    return 0;
+  }
+" SUNDIALS_C_COMPILER_HAS_ATTRIBUTE_UNUSED)
+
 # ---------------------------------------------------------------
 # Check for POSIX timers
 # ---------------------------------------------------------------

doc/arkode/examples/source/conf.py

@@ -11,8 +11,8 @@
 # -----------------------------------------------------------------------------
 
 import sys, os
-sys.path.append(os.path.dirname(os.path.abspath('../../../shared/versions.py')))
-from versions import *
+sys.path.append(os.path.dirname(os.path.abspath('../../../shared/sundials_vars.py')))
+from sundials_vars import *
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the

doc/arkode/guide/source/ARKodeButcherTable.rst

@@ -18,55 +18,66 @@
 Butcher Table Data Structure
 ==============================
 
-To store the Butcher table defining a Runge--Kutta method ARKODE provides the
-:c:type:`ARKodeButcherTable` type and several related utility routines. We use
-the following Butcher table notation (shown for a 3-stage method):
+To store a Butcher table, :math:`B`, defining a Runge--Kutta method ARKODE
+provides the :c:type:`ARKodeButcherTable` type and several related utility
+routines. We use the following notation
 
 .. math::
 
+   B \; \equiv \;
    \begin{array}{r|c}
      c & A \\
      \hline
      q & b \\
      p & \tilde{b}
    \end{array}
-   \quad = \quad
-   \begin{array}{r|ccc}
-     c_1 & a_{1,1} & a_{1,2} & a_{1,3} \\
-     c_2 & a_{2,1} & a_{2,2} & a_{2,3} \\
-     c_3 & a_{3,1} & a_{3,2} & a_{3,3} \\
-     \hline
-     q & b_1 & b_2 & b_3 \\
-     p & \tilde{b}_1 & \tilde{b}_2 & \tilde{b}_3
-   \end{array}
-
-where the method and embedding share stage :math:`A` and abscissa :math:`c`
-values, but use their stages :math:`z_i` differently through the coefficients
-:math:`b` and :math:`\tilde{b}` to generate methods of orders :math:`q` (the
-main method) and :math:`p` (the embedding, typically :math:`q = p+1`, though
-sometimes this is reversed). :c:type:`ARKodeButcherTable` is defined as
+   \; = \;
+   \begin{array}{c|cccc}
+   c_1    & a_{1,1} & \cdots & a_{1,s-1} & a_{1,s} \\
+   c_2    & a_{2,1} & \cdots & a_{2,s-1} & a_{2,s} \\
+   \vdots & \vdots  & \vdots & \vdots    & \vdots  \\
+   c_s    & a_{s,1} & \cdots & a_{s,s-1} & a_{s,s} \\
+   \hline
+   q      & b_1         & \cdots & b_{s-1}         & b_s \\
+   p      & \tilde{b}_1 & \cdots & \tilde{b}_{s-1} & \tilde{b}_s
+   \end{array}.
+
+An :c:type:`ARKodeButcherTable` is a pointer to the
+:c:struct:`ARKodeButcherTableMem` structure:
 
 .. c:type:: ARKodeButcherTableMem* ARKodeButcherTable
 
-where ``ARKodeButcherTableMem`` is the structure
+.. c:struct:: ARKodeButcherTableMem
+
+   Structure for storing a Butcher table
+
+   .. c:member:: int q
+
+      The method order of accuracy
+
+   .. c:member:: int p
+
+      The embedding order of accuracy, typically :math:`q = p + 1`
+
+   .. c:member:: int stages
+
+      The number of stages in the method, :math:`s`
+
+   .. c:member:: sunrealtype **A
+
+      The method coefficients :math:`A \in \mathbb{R}^s`
+
+   .. c:member:: sunrealtype *c
 
-.. code-block:: c
+      The method abscissa :math:`c \in \mathbb{R}^s`
 
-   typedef struct ARKodeButcherTableMem {
+   .. c:member:: sunrealtype *b
 
-     int q;
-     int p;
-     int stages;
-     sunrealtype **A;
-     sunrealtype *c;
-     sunrealtype *b;
-     sunrealtype *d;
+      The method coefficients :math:`b \in \mathbb{R}^s`
 
-   };
+   .. c:member:: sunrealtype *d
 
-where ``stages`` is the number of stages in the RK method, the variables ``q``,
-``p``, ``A``, ``c``, and ``b`` have the same meaning as in the Butcher table
-above, and ``d`` is used to store :math:`\tilde{b}`.
+      The method embedding coefficients :math:`\tilde{b} \in \mathbb{R}^s`
 
 .. _ARKodeButcherTable.Functions:
 

doc/arkode/guide/source/Butcher.rst

@@ -438,10 +438,10 @@ Knoth-Wolke-3-3
 .. index:: Knoth-Wolke-3-3 ERK method
 
 Accessible via the constant ``ARKODE_KNOTH_WOLKE_3_3`` to
-:c:func:`ARKStepSetTableNum`, :c:func:`ERKStepSetTableNum` or
+:c:func:`ARKStepSetTableNum`, :c:func:`ERKStepSetTableNum`, or
 :c:func:`ARKodeButcherTable_LoadERK`.
 Accessible via the string ``"ARKODE_KNOTH_WOLKE_3_3"`` to
-:c:func:`ARKStepSetTableName`, :c:func:`ERKStepSetTableName` or
+:c:func:`ARKStepSetTableName`, :c:func:`ERKStepSetTableName`, or
 :c:func:`ARKodeButcherTable_LoadERKByName`.
 This is the default 3th order slow and fast MRIStep method (from
 :cite:p:`KnWo:98`).
@@ -511,10 +511,10 @@ Zonneveld-5-3-4
 .. index:: Zonneveld-5-3-4 ERK method
 
 Accessible via the constant ``ARKODE_ZONNEVELD_5_3_4`` to
-:c:func:`ARKStepSetTableNum`, :c:func:`ERKStepSetTableNum`
-or :c:func:`ARKodeButcherTable_LoadERK`.
+:c:func:`ARKStepSetTableNum`, :c:func:`ERKStepSetTableNum`, or
+:c:func:`ARKodeButcherTable_LoadERK`.
 Accessible via the string ``"ARKODE_ZONNEVELD_5_3_4"`` to
-:c:func:`ARKStepSetTableName`, :c:func:`ERKStepSetTableName` or
+:c:func:`ARKStepSetTableName`, :c:func:`ERKStepSetTableName`, or
 :c:func:`ARKodeButcherTable_LoadERKByName`.
 This is the default 4th order explicit method
 (from :cite:p:`Zon:63`).
@@ -2227,9 +2227,11 @@ Symplectic Partitioned Butcher tables
 -------------------------------------
 
 In the category of symplectic partitioned Runge-Kutta (SPRK) methods, ARKODE
-includes methods that have orders :math:`q = \{1,2,3,4,5,6,8,10\}`. Each of
-the ARKODE SPRK tables are specified via a unique ID and name.
+includes methods that have orders :math:`q = \{1,2,3,4,5,6,8,10\}`.
+
+.. c:enum:: ARKODE_SPRKMethodID
 
+   Each of the ARKODE SPRK tables are specified via a unique ID and name.
 
 ARKODE_SPRK_EULER_1_1
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/arkode/guide/source/Constants.rst

@@ -578,8 +578,18 @@ contains the ARKODE output constants.
    |                                     |      | :c:type:`SUNLinearSolver` module.                          |
    +-------------------------------------+------+------------------------------------------------------------+
 
+.. c:enum:: ARKRelaxSolver
 
+   Nonlinear solver identifiers used to specify the method for solving
+   :eq:`ARKODE_RELAX_NLS` when relaxation is enabled.
 
+   .. c:enumerator:: ARK_RELAX_NEWTON
+
+      Newton's method
+
+   .. c:enumerator:: ARK_RELAX_BRENT
+
+      Brent's method
 ..
    Commented-out table rows:
 

doc/arkode/guide/source/Usage/ARKStep/Relaxation.rst

@@ -211,12 +211,10 @@ relaxation.
 
    Sets the nonlinear solver method used to compute the relaxation parameter.
 
-   The default value is ``ARK_RELAX_NEWTON``.
+   The default value is :c:enumerator:`ARK_RELAX_NEWTON`
 
    :param arkode_mem: the ARKStep memory structure
-   :param solver: the nonlinear solver to use: ``ARK_RELAX_BRENT`` or
-                  ``ARK_RELAX_NEWTON``
-
+   :param solver: the nonlinear solver to use
    :retval ARK_SUCCESS: the value was successfully set
    :retval ARK_MEM_NULL: ``arkode_mem`` was ``NULL``
    :retval ARK_RELAX_MEM_NULL: the internal relaxation memory structure was

doc/arkode/guide/source/Usage/ARKStep/XBraid.rst

@@ -234,15 +234,15 @@ to store a snapshot of solution data at a single point in time and this
 structure simply contains an N_Vector. Specifically, the structure is defined
 as follows:
 
-.. code-block:: C
+.. c:type:: struct _braid_Vector_struct *SUNBraidVector;
 
-   struct _braid_Vector_struct
-   {
-     N_Vector y;
-   };
+   Pointer to vector wrapper (same as braid_Vector)
+
+.. c:struct:: _braid_Vector_struct
+
+   .. c:member:: N_Vector y
 
-   /* Poiner to vector wrapper (same as braid_Vector) */
-   typedef struct _braid_Vector_struct *SUNBraidVector;
+      SUNDIALS N_Vector wrapped by the ``braid_Vector``
 
 To assist in creating creating and destroying this structure the following
 utility functions are provided.

doc/arkode/guide/source/Usage/ERKStep/Relaxation.rst

@@ -205,12 +205,10 @@ relaxation.
 
    Sets the nonlinear solver method used to compute the relaxation parameter.
 
-   The default value is ``ARK_RELAX_NEWTON``.
+   The default value is :c:enumerator:`ARK_RELAX_NEWTON`
 
    :param arkode_mem: the ERKStep memory structure
-   :param solver: the nonlinear solver to use: ``ARK_RELAX_BRENT`` or
-                  ``ARK_RELAX_NEWTON``
-
+   :param solver: the nonlinear solver to use
    :retval ARK_SUCCESS: the value was successfully set
    :retval ARK_MEM_NULL: ``arkode_mem`` was ``NULL``
    :retval ARK_RELAX_MEM_NULL: the internal relaxation memory structure was