Merge branch 'feature/remove-deprecated-code' into feature/remove-dep…

…recated-code-types

.github/workflows/double-precision.yml

@@ -1,5 +1,5 @@
 #
-name: double precision build and test with GCC+TPLs (no GPUs)
+name: Build and Test - Ubuntu/gcc double precision (TPLs, no GPUs)
 
 on:
   push:

.github/workflows/extended-precision.yml

@@ -1,5 +1,5 @@
 #
-name: extended precision build and test with GCC+TPLs (no GPUs)
+name: Build and Test - Ubuntu/gcc extended precision (TPLs, no GPUs)
 
 on:
   pull_request:

.github/workflows/macos-latest.yml

@@ -1,4 +1,4 @@
-name: MacOS short test
+name: Build and Test - MacOS (short)
 
 on:
   pull_request:
@@ -14,7 +14,7 @@ env:
   BUILD_TYPE: Release
 
 jobs:
-  build:
+  build_and_test:
     # The CMake configure and build commands are platform agnostic and should work equally
     # well on Windows or Mac.  You can convert this to a matrix build if you need
     # cross-platform coverage.

.github/workflows/single-precision.yml

@@ -1,5 +1,5 @@
 #
-name: single precision build and test with GCC+TPLs (no GPUs)
+name: Build and Test - Ubuntu/gcc single precision (TPLs, no GPUs)
 
 on:
   pull_request:

.github/workflows/spack-develop.yml

@@ -1,5 +1,5 @@
 #
-name: spack@develop build and test with GCC+TPLs (no GPUs)
+name: Build and Test - Ubuntu/gcc spack@develop (TPLs, no GPUs)
 
 on:
   pull_request:

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

@@ -1,4 +1,4 @@
-name: Ubuntu (clang) short test
+name: Build - Ubuntu/Clang (no TPLs)
 
 on:
   pull_request:
@@ -14,9 +14,15 @@ env:
   BUILD_TYPE: Release
 
 jobs:
-  build:
+  build_cycle_log_levels:
     runs-on: ubuntu-latest
 
+    strategy:
+      fail-fast: false
+      matrix:
+        # 2 is what all other builds use (its the default), so skip it here
+        logging_level: [0, 1, 3, 4, 5] 
+
     steps:
     - name: Install LLVM and Clang
       uses: KyleMayes/install-llvm-action@v1
@@ -28,14 +34,32 @@ jobs:
     - 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++)
+      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}}
 
     - name: Build
       # Build your program with the given configuration
       run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
 
-    - name: Test
-      working-directory: ${{github.workspace}}/build
-      # Execute tests defined by the CMake configuration.
-      # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
-      run: ctest -C ${{env.BUILD_TYPE}}
+  build_cycle_profiling:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        profiling: ['OFF', 'ON']
+
+    steps:
+    - name: Install LLVM and Clang
+      uses: KyleMayes/install-llvm-action@v1
+      with:
+        version: "14.0"
+
+    - 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}}
+
+    - name: Build
+      # Build your program with the given configuration
+      run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}

.github/workflows/windows-latest-mingw.yml

@@ -1,4 +1,4 @@
-name: Windows (mingw) short test
+name: Build and Test - Windows/mingw (short)
 
 on:
   pull_request:
@@ -14,7 +14,7 @@ env:
   BUILD_TYPE: Release
 
 jobs:
-  build:
+  buil_and_test:
     runs-on: windows-latest
 
     steps:

.github/workflows/windows-latest.yml

@@ -1,4 +1,4 @@
-name: Windows short test
+name: Build and Test - Windows/MSVC (short)
 
 on:
   pull_request:
@@ -14,7 +14,7 @@ env:
   BUILD_TYPE: Release
 
 jobs:
-  build:
+  build_and_test:
     runs-on: windows-latest
 
     steps:

CHANGELOG.md

@@ -9,6 +9,21 @@ can be used by including the header file `sundials_types_old.h`.
 
 ## Changes to SUNDIALS in release X.X.X
 
+Added the `SUNAdaptController` base class, ported ARKODE's internal
+implementations of time step controllers into implementations of this class,
+and updated ARKODE to use these objects instead of its own implementations.
+Added `ARKStepSetAdaptController` and `ERKStepSetAdaptController` routines
+so that users can modify controller parameters, or even provide custom
+implementations.
+
+Added the routines `ARKStepSetAdaptivityAdjustment` and
+`ERKStepSetAdaptivityAdjustment`, that allow users to adjust the
+value for the method order supplied to the temporal adaptivity controllers.
+The ARKODE default for this adjustment has been -1 since its initial
+release, but for some applications a value of 0 is more appropriate.
+Users who notice that their simulations encounter a large number of
+temporal error test failures may want to experiment with adjusting this value.
+
 Fixed a regression introduced by the stop time bug fix in v6.6.1 where ARKODE,
 CVODE, CVODES, IDA, and IDAS would return at the stop time rather than the
 requested output time if the stop time was reached in the same step in which the
@@ -47,6 +62,9 @@ method `ARKODE_VERNER_16_8_9`.
 Changed the `SUNProfiler` so that it does not rely on `MPI_WTime` in any case.
 This fixes https://github.com/LLNL/sundials/issues/312. 
 
+**Breaking change**
+Functions, types and header files that were previously deprecated have been
+removed. 
 
 ## Changes to SUNDIALS in release 6.6.1
 
@@ -61,6 +79,20 @@ the stop time. Additionally, with ARKODE, CVODE, and CVODES this fix removes an
 unnecessary interpolation of the solution at the stop time that could occur in
 this case.
 
+Fixed a bug in ERKStep where methods with `c[s-1] = 1` but `a[s-1,j] != b[j]`
+were incorrectly treated as having the first same as last (FSAL) property.
+
+Fixed a bug in `MRIStepCoupling_Write` where explicit coupling tables were not
+written to the output file pointer.
+
+ARKStep, ERKStep, MRIStep, and SPRKStep were updated to remove a potentially
+unnecessary right-hand side evaluation at the end of an integration. ARKStep was
+additionally updated to remove extra right-hand side evaluations when using an
+explicit method or an implicit method with an explicit first stage.
+
+The `MRIStepInnerStepper` class in MRIStep was updated to make supplying an
+`MRIStepInnerFullRhsFn` optional.
+
 ## Changes to SUNDIALS in release 6.6.0
 
 A new time-stepping module, `SPRKStep`, was added to ARKODE. This time-stepper

cmake/SundialsBuildOptionsPre.cmake

@@ -76,12 +76,12 @@ sundials_option(SUNDIALS_BUILD_WITH_PROFILING BOOL "${DOCSTR}" OFF)
 # ---------------------------------------------------------------
 
 set(DOCSTR "Build with logging capabilities enabled (0 = no logging, 1 = errors, 2 = +warnings, 3 = +info, 4 = +debug, 5 = +extras")
-sundials_option(SUNDIALS_LOGGING_LEVEL STRING "${DOCSTR}" 3
+sundials_option(SUNDIALS_LOGGING_LEVEL STRING "${DOCSTR}" 2
                 OPTIONS "0;1;2;3;4;5")
 
-if(SUNDIALS_LOGGING_LEVEL GREATER_EQUAL 4)
+if(SUNDIALS_LOGGING_LEVEL GREATER_EQUAL 3)
   message(STATUS "SUNDIALS logging level set to ${SUNDIALS_LOGGING_LEVEL}")
-  message(WARNING "SUNDIALS built with debug logging turned on, performance may be affected.")
+  message(WARNING "SUNDIALS built with additional logging turned on, performance may be affected.")
 endif()
 
 set(DOCSTR "Build SUNDIALS logging with MPI support")

cmake/macros/SundialsAddLibrary.cmake

@@ -176,6 +176,15 @@ macro(sundials_add_library target)
       target_link_libraries(${obj_target} ${_all_libs})
     endif()
 
+    if(SUNDIALS_BUILD_WITH_PROFILING)
+      if(ENABLE_CALIPER)
+        target_link_libraries(${obj_target} PUBLIC caliper)
+      endif()
+      if(ENABLE_ADIAK)
+        target_link_libraries(${obj_target} PUBLIC adiak::adiak ${CMAKE_DL_LIBS})
+      endif()
+    endif()
+
     # add includes to object library
     target_include_directories(${obj_target}
       PUBLIC

doc/README.md

@@ -0,0 +1,10 @@
+# SUNDIALS Documentation
+
+The SUNDIALS documentation is written using reStructuredText and
+[Sphinx](https://www.sphinx-doc.org/).
+
+To build the documentation with Sphinx you will need Python 3.9+. Sphinx and the
+necessary extensions can be installed using the requirements file i.e.,
+`pip install -r requirements.txt`. Additionally, building the developer
+documentation requires [Graphviz](https://graphviz.org/) for generating
+flowcharts.

doc/arkode/guide/source/ARKodeButcherTable.rst

@@ -76,33 +76,35 @@ ARKodeButcherTable functions
 .. _ARKodeButcherTable.FunctionsTable:
 .. table:: ARKodeButcherTable functions
 
-   +----------------------------------------------+------------------------------------------------------------+
-   | **Function name**                            | **Description**                                            |
-   +----------------------------------------------+------------------------------------------------------------+
-   | :c:func:`ARKodeButcherTable_LoadERK()`       | Retrieve a given explicit Butcher table by its unique ID   |
-   +----------------------------------------------+------------------------------------------------------------+
-   | :c:func:`ARKodeButcherTable_LoadERKByName()` | Retrieve a given explicit Butcher table by its unique name |
-   +----------------------------------------------+------------------------------------------------------------+
-   | :c:func:`ARKodeButcherTable_LoadDIRK()`      | Retrieve a given implicit Butcher table by its unique ID   |
-   +----------------------------------------------+------------------------------------------------------------+
-   | :c:func:`ARKodeButcherTable_LoadDIRKByName()`| Retrieve a given implicit Butcher table by its unique name |
-   +----------------------------------------------+------------------------------------------------------------+
-   | :c:func:`ARKodeButcherTable_Alloc()`         | Allocate an empty Butcher table                            |
-   +----------------------------------------------+------------------------------------------------------------+
-   | :c:func:`ARKodeButcherTable_Create()`        | Create a new Butcher table                                 |
-   +----------------------------------------------+------------------------------------------------------------+
-   | :c:func:`ARKodeButcherTable_Copy()`          | Create a copy of a Butcher table                           |
-   +----------------------------------------------+------------------------------------------------------------+
-   | :c:func:`ARKodeButcherTable_Space()`         | Get the Butcher table real and integer workspace size      |
-   +----------------------------------------------+------------------------------------------------------------+
-   | :c:func:`ARKodeButcherTable_Free()`          | Deallocate a Butcher table                                 |
-   +----------------------------------------------+------------------------------------------------------------+
-   | :c:func:`ARKodeButcherTable_Write()`         | Write the Butcher table to an output file                  |
-   +----------------------------------------------+------------------------------------------------------------+
-   | :c:func:`ARKodeButcherTable_CheckOrder()`    | Check the order of a Butcher table                         |
-   +----------------------------------------------+------------------------------------------------------------+
-   | :c:func:`ARKodeButcherTable_CheckARKOrder()` | Check the order of an ARK pair of Butcher tables           |
-   +----------------------------------------------+------------------------------------------------------------+
+   +--------------------------------------------------+------------------------------------------------------------+
+   | **Function name**                                | **Description**                                            |
+   +--------------------------------------------------+------------------------------------------------------------+
+   | :c:func:`ARKodeButcherTable_LoadERK()`           | Retrieve a given explicit Butcher table by its unique ID   |
+   +--------------------------------------------------+------------------------------------------------------------+
+   | :c:func:`ARKodeButcherTable_LoadERKByName()`     | Retrieve a given explicit Butcher table by its unique name |
+   +--------------------------------------------------+------------------------------------------------------------+
+   | :c:func:`ARKodeButcherTable_LoadDIRK()`          | Retrieve a given implicit Butcher table by its unique ID   |
+   +--------------------------------------------------+------------------------------------------------------------+
+   | :c:func:`ARKodeButcherTable_LoadDIRKByName()`    | Retrieve a given implicit Butcher table by its unique name |
+   +--------------------------------------------------+------------------------------------------------------------+
+   | :c:func:`ARKodeButcherTable_Alloc()`             | Allocate an empty Butcher table                            |
+   +--------------------------------------------------+------------------------------------------------------------+
+   | :c:func:`ARKodeButcherTable_Create()`            | Create a new Butcher table                                 |
+   +--------------------------------------------------+------------------------------------------------------------+
+   | :c:func:`ARKodeButcherTable_Copy()`              | Create a copy of a Butcher table                           |
+   +--------------------------------------------------+------------------------------------------------------------+
+   | :c:func:`ARKodeButcherTable_Space()`             | Get the Butcher table real and integer workspace size      |
+   +--------------------------------------------------+------------------------------------------------------------+
+   | :c:func:`ARKodeButcherTable_Free()`              | Deallocate a Butcher table                                 |
+   +--------------------------------------------------+------------------------------------------------------------+
+   | :c:func:`ARKodeButcherTable_Write()`             | Write the Butcher table to an output file                  |
+   +--------------------------------------------------+------------------------------------------------------------+
+   | :c:func:`ARKodeButcherTable_IsStifflyAccurate()` | Determine if ``A[stages - 1][i] == b[i]``                  |
+   +--------------------------------------------------+------------------------------------------------------------+
+   | :c:func:`ARKodeButcherTable_CheckOrder()`        | Check the order of a Butcher table                         |
+   +--------------------------------------------------+------------------------------------------------------------+
+   | :c:func:`ARKodeButcherTable_CheckARKOrder()`     | Check the order of an ARK pair of Butcher tables           |
+   +--------------------------------------------------+------------------------------------------------------------+
 
 .. c:function:: ARKodeButcherTable ARKodeButcherTable_LoadERK(ARKODE_ERKTableID emethod)
 
@@ -252,6 +254,19 @@ ARKodeButcherTable functions
       The *outfile* argument can be ``stdout`` or ``stderr``, or it
       may point to a specific file created using ``fopen``.
 
+.. c:function:: void ARKodeButcherTable_IsStifflyAccurate(ARKodeButcherTable B)
+
+   Determine if the table satisfies ``A[stages - 1][i] == b[i]``
+
+   **Arguments:**
+      * *B* -- the Butcher table.
+
+   **Returns**
+      * ``SUNTRUE`` if the method is "stiffly accurate", otherwise returns
+        ``SUNFALSE``
+
+   .. versionadded:: vX.X.X
+
 .. c:function:: int ARKodeButcherTable_CheckOrder(ARKodeButcherTable B, int* q, int* p, FILE* outfile)
 
    Determine the analytic order of accuracy for the specified Butcher

doc/arkode/guide/source/Constants.rst

@@ -468,6 +468,8 @@ contains the ARKODE output constants.
    | :index:`ARK_RELAX_JAC_FAIL`         | -46  | The relaxation Jacobian function returned an unrecoverable |
    |                                     |      | error                                                      |
    +-------------------------------------+------+------------------------------------------------------------+
+   | :index:`ARK_CONTROLLER_ERR`         | -47  | An error with a SUNAdaptController object was encountered. |
+   +-------------------------------------+------+------------------------------------------------------------+
    | :index:`ARK_UNRECOGNIZED_ERROR`     | -99  | An unknown error was encountered.                          |
    +-------------------------------------+------+------------------------------------------------------------+
    |                                                                                                         |

doc/arkode/guide/source/Introduction.rst

@@ -133,6 +133,21 @@ Changes from previous versions
 Changes in vX.X.X
 -----------------
 
+Added the :c:type:`SUNAdaptController` base class, ported ARKODE's internal
+implementations of time step controllers into implementations of this class,
+and updated ARKODE to use these objects instead of its own implementations.  Added
+:c:func:`ARKStepSetAdaptController` and :c:func:`ERKStepSetAdaptController`
+routines so that users can modify controller parameters, or even provide custom
+implementations.
+
+Added the routines :c:func:`ARKStepSetAdaptivityAdjustment` and
+:c:func:`ERKStepSetAdaptivityAdjustment`, that allow users to adjust the
+value for the method order supplied to the temporal adaptivity controllers.
+The ARKODE default for this adjustment has been :math:`-1` since its initial
+release, but for some applications a value of :math:`0` is more appropriate.
+Users who notice that their simulations encounter a large number of
+temporal error test failures may want to experiment with adjusting this value.
+
 Fixed the build system support for MAGMA when using a NVIDIA HPC SDK installation of CUDA
 and fixed the targets used for rocBLAS and rocSPARSE.
 
@@ -167,6 +182,10 @@ This fixes `GitHub Issue #312 <https://github.com/LLNL/sundials/issues/312>`_.
 
 Added Fortran support for the LAPACK  dense ``SUNLinearSolver`` implementation.
 
+**Breaking change**
+Functions, types and header files that were previously deprecated have been
+removed. 
+
 
 Changes in v5.6.1
 -----------------
@@ -181,6 +200,21 @@ requested output time is the same as the stop time. Additionally, this fix
 removes an unnecessary interpolation of the solution at the stop time that could
 occur in this case.
 
+Fixed a bug in ERKStep where methods with :math:`c_s = 1` but
+:math:`a_{s,j} \neq b_j` were incorrectly treated as having the first same as
+last (FSAL) property.
+
+Fixed a bug in :c:func:`MRIStepCoupling_Write` where explicit coupling tables
+were not written to the output file pointer.
+
+ARKStep, ERKStep, MRIStep, and SPRKStep were updated to remove a potentially
+unnecessary right-hand side evaluation at the end of an integration. ARKStep was
+additionally updated to remove extra right-hand side evaluations when using an
+explicit method or an implicit method with an explicit first stage.
+
+The :c:type:`MRIStepInnerStepper` class in MRIStep was updated to make supplying
+an :c:func:`MRIStepInnerFullRhsFn` optional.
+
 Changes in v5.6.0
 -----------------