Merge branch 'develop' into feature/udpating-answers-instructions

.github/workflows/double-precision.yml

@@ -25,10 +25,18 @@ jobs:
         with:
           indexsize: ${{ matrix.indexsize }}
           precision: ${{ matrix.precision }}
-      - name: Archive files from failed build
+      - name: Archive build files from failed build
         uses: actions/[email protected]
         if: failure()
         with:
           name: build_files
           path: |
             ${{ github.workspace }}/test/build_*
+            !${{ github.workspace }}/test/build_*/Testing/output
+      - name: Archive output files from failed build
+        uses: actions/[email protected]
+        if: failure()
+        with:
+          name: output_files
+          path: |
+            ${{ github.workspace }}/test/build_*/Testing/output

.github/workflows/extended-precision.yml

@@ -24,10 +24,18 @@ jobs:
         with:
           indexsize: ${{ matrix.indexsize }}
           precision: ${{ matrix.precision }}
-      - name: Archive files from failed build
+      - name: Archive build files from failed build
         uses: actions/[email protected]
         if: failure()
         with:
           name: build_files
           path: |
             ${{ github.workspace }}/test/build_*
+            !${{ github.workspace }}/test/build_*/Testing/output
+      - name: Archive output files from failed build
+        uses: actions/[email protected]
+        if: failure()
+        with:
+          name: output_files
+          path: |
+            ${{ github.workspace }}/test/build_*/Testing/output

.github/workflows/single-precision.yml

@@ -24,10 +24,18 @@ jobs:
         with:
           indexsize: ${{ matrix.indexsize }}
           precision: ${{ matrix.precision }}
-      - name: Archive files from failed build
+      - name: Archive build files from failed build
         uses: actions/[email protected]
         if: failure()
         with:
           name: build_files
           path: |
             ${{ github.workspace }}/test/build_*
+            !${{ github.workspace }}/test/build_*/Testing/output
+      - name: Archive output files from failed build
+        uses: actions/[email protected]
+        if: failure()
+        with:
+          name: output_files
+          path: |
+            ${{ github.workspace }}/test/build_*/Testing/output

.github/workflows/spack-develop.yml

@@ -27,10 +27,18 @@ jobs:
         with:
           indexsize: ${{ matrix.indexsize }}
           precision: ${{ matrix.precision }}
-      - name: Archive files from failed build
+      - name: Archive build files from failed build
         uses: actions/[email protected]
         if: failure()
         with:
           name: build_files
           path: |
             ${{ github.workspace }}/test/build_*
+            !${{ github.workspace }}/test/build_*/Testing/output
+      - name: Archive output files from failed build
+        uses: actions/[email protected]
+        if: failure()
+        with:
+          name: output_files
+          path: |
+            ${{ github.workspace }}/test/build_*/Testing/output

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

@@ -21,7 +21,7 @@ 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 -G "MinGW Makefiles" -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}
+      run: cmake -G "MinGW Makefiles" -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DSUNDIALS_BUILD_WITH_PROFILING=ON -DSUNDIALS_LOGGING_LEVEL=2 -DSUNDIALS_TEST_UNITTESTS=OFF -DEXAMPLES_ENABLE_CXX=ON
 
     - name: Build
       # Build your program with the given configuration

.github/workflows/windows-latest.yml

@@ -17,7 +17,7 @@ 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}} -DBUILD_STATIC_LIBS=OFF
+      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DBUILD_STATIC_LIBS=OFF -DSUNDIALS_BUILD_WITH_PROFILING=ON -DSUNDIALS_LOGGING_LEVEL=2 -DSUNDIALS_TEST_UNITTESTS=ON -DEXAMPLES_ENABLE_CXX=ON
 
     - name: Build
       # Build your program with the given configuration

CHANGELOG.md

@@ -27,7 +27,7 @@ Fixed scaling bug in `SUNMatScaleAddI_Sparse` for non-square matrices.
 Fixed missing soversions in some `SUNLinearSolver` and `SUNNonlinearSolver`
 CMake targets.
 
-Added Fortran support for the LAPACK dense `SUNLinearSolver` implementations.
+Added Fortran support for the LAPACK dense `SUNLinearSolver` implementation.
 
 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.
@@ -38,6 +38,8 @@ ERK method `ARKODE_SOFRONIOU_SPALETTA_5_3_4`, the sixth order ERK method
 the eighth order ERK method `ARKODE_VERNER_13_7_8`, and the ninth order ERK
 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. 
 
 ## Changes to SUNDIALS in release 6.6.1
 

cmake/SundialsSetupCompilers.cmake

@@ -223,13 +223,6 @@ if(SUNDIALS_POSIX_TIMERS AND POSIX_TIMERS_NEED_POSIX_C_SOURCE)
   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D_POSIX_C_SOURCE=${SUNDIALS_POSIX_C_SOURCE}")
 endif()
 
-# Check if profiling is being built with no timers.
-if(SUNDIALS_BUILD_WITH_PROFILING AND
-   (NOT ENABLE_CALIPER) AND
-   (NOT ENABLE_MPI) AND
-   (NOT SUNDIALS_POSIX_TIMERS))
-  message(SEND_ERROR "The SUNDIALS native profiler requires POSIX timers or MPI_Wtime, but neither were found.")
-endif()
 
 # ---------------------------------------------------------------
 # Check for deprecated attribute with message

cmake/macros/SundialsAddLibrary.cmake

@@ -152,6 +152,8 @@ macro(sundials_add_library target)
     # create the target for the object library
     add_library(${obj_target} OBJECT ${sources})
 
+    set_target_properties(${obj_target} PROPERTIES FOLDER "obj")
+
     # add all object libraries to object library
     if(sundials_add_library_OBJECT_LIBRARIES)
       target_link_libraries(${obj_target}
@@ -229,6 +231,8 @@ macro(sundials_add_library target)
 
       add_library(${_actual_target_name} ${_libtype} $<TARGET_OBJECTS:${obj_target}>)
 
+      set_target_properties(${_actual_target_name} PROPERTIES FOLDER "src")
+
       # add any object library dependencies
       if(sundials_add_library_OBJECT_LIBRARIES)
         if(${_libtype} MATCHES "STATIC")

doc/arkode/guide/source/Introduction.rst

@@ -162,6 +162,9 @@ ERK method ``ARKODE_SOFRONIOU_SPALETTA_5_3_4``, the sixth order ERK method
 the eighth order ERK method ``ARKODE_VERNER_13_7_8``, and the ninth order ERK
 method ``ARKODE_VERNER_16_8_9``.
 
+Changed the ``SUNProfiler`` so that it does not rely on ``MPI_WTime`` in any case.
+This fixes `GitHub Issue #312 <https://github.com/LLNL/sundials/issues/312>`_. 
+
 Added Fortran support for the LAPACK  dense ``SUNLinearSolver`` implementation.
 
 Changes in v5.6.1
@@ -993,7 +996,6 @@ utilize a zero initial guess.
 A bug was fixed in the ARKODE stepper modules where the stop time may be passed
 after resetting the integrator.
 
-
 Changes in v4.7.0
 -----------------
 

doc/arkode/guide/source/Usage/ARKStep_c_interface/User_callable.rst

@@ -726,11 +726,8 @@ the user has set a stop time (with a call to the optional input function
         in :numref:`ARKODE.Mathematics.Interpolation`).
 
         The *ARK_ONE_STEP* option tells the solver to only take a
-        single internal step :math:`y_{n-1} \to y_{n}` and then return
-        control back to the calling program.  If this step will
-        overtake *tout* then the solver will again return an
-        interpolated result; otherwise it will return a copy of the
-        internal solution :math:`y_{n}` in the vector *yout*.
+        single internal step, :math:`y_{n-1} \to y_{n}`, and return the solution
+        at that point, :math:`y_{n}`, in the vector *yout*.
 
    **Return value:**
       * *ARK_SUCCESS* if successful.
@@ -795,8 +792,8 @@ the user has set a stop time (with a call to the optional input function
       only to get the direction and a rough scale of the independent
       variable.
 
-      All failure return values are negative and so testing the return argument for
-      negative values will trap all :c:func:`ARKStepEvolve()` failures.
+      All failure return values are negative and so testing the return argument
+      for negative values will trap all :c:func:`ARKStepEvolve()` failures.
 
       Since interpolation may reduce the accuracy in the reported
       solution, if full method accuracy is desired the user should issue

doc/arkode/guide/source/Usage/ERKStep_c_interface/User_callable.rst

@@ -352,11 +352,8 @@ has requested rootfinding.
         :numref:`ARKODE.Mathematics.Interpolation`).
 
         The *ARK_ONE_STEP* option tells the solver to only take a
-        single internal step :math:`y_{n-1} \to y_{n}` and then return
-        control back to the calling program.  If this step will
-        overtake *tout* then the solver will again return an
-        interpolated result; otherwise it will return a copy of the
-        internal solution :math:`y_{n}` in the vector *yout*.
+        single internal step, :math:`y_{n-1} \to y_{n}`, and return the solution
+        at that point, :math:`y_{n}`, in the vector *yout*.
 
    **Return value:**
       * *ARK_SUCCESS* if successful.
@@ -399,7 +396,9 @@ has requested rootfinding.
 
       In *ARK_ONE_STEP* mode, *tout* is used only on the first call, and
       only to get the direction and a rough scale of the independent
-      variable. All failure return values are negative and so testing the
+      variable.
+
+      All failure return values are negative and so testing the
       return argument for negative values will trap all
       :c:func:`ERKStepEvolve()` failures.
 

doc/arkode/guide/source/Usage/MRIStep_c_interface/User_callable.rst

@@ -545,11 +545,8 @@ the user has set a stop time (with a call to the optional input function
         in :numref:`ARKODE.Mathematics.Interpolation`).
 
         The *ARK_ONE_STEP* option tells the solver to only take a
-        single internal step :math:`y_{n-1} \to y_{n}` and then return
-        control back to the calling program.  If this step will
-        overtake *tout* then the solver will again return an
-        interpolated result; otherwise it will return a copy of the
-        internal solution :math:`y_{n}` in the vector *yout*.
+        single internal step, :math:`y_{n-1} \to y_{n}`, and return the solution
+        at that point, :math:`y_{n}`, in the vector *yout*.
 
    **Return value:**
       * *ARK_SUCCESS* if successful.
@@ -604,8 +601,8 @@ the user has set a stop time (with a call to the optional input function
       only to get the direction and a rough scale of the independent
       variable.
 
-      All failure return values are negative and so testing the return argument for
-      negative values will trap all :c:func:`MRIStepEvolve()` failures.
+      All failure return values are negative and so testing the return argument
+      for negative values will trap all :c:func:`MRIStepEvolve()` failures.
 
       Since interpolation may reduce the accuracy in the reported
       solution, if full method accuracy is desired the user should issue

doc/arkode/guide/source/Usage/SPRKStep_c_interface/User_callable.rst

@@ -152,11 +152,8 @@ has requested rootfinding.
                  :numref:`ARKODE.Mathematics.Interpolation`).
 
                  The *ARK_ONE_STEP* option tells the solver to only take a
-                 single internal step :math:`y_{n-1} \to y_{n}` and then return
-                 control back to the calling program.  If this step will
-                 overtake *tout* then the solver will again return an
-                 interpolated result; otherwise it will return a copy of the
-                 internal solution :math:`y_{n}` in the vector *yout*.
+                 single internal step, :math:`y_{n-1} \to y_{n}`, and return the
+                 solution at that point, :math:`y_{n}`, in the vector *yout*.
 
    :retval ARK_SUCCESS: if successful.
    :retval ARK_ROOT_RETURN: if :c:func:`SPRKStepEvolve()` succeeded, and
@@ -191,7 +188,9 @@ has requested rootfinding.
 
       In *ARK_ONE_STEP* mode, *tout* is used only on the first call, and
       only to get the direction and a rough scale of the independent
-      variable. All failure return values are negative and so testing the
+      variable.
+
+      All failure return values are negative and so testing the
       return argument for negative values will trap all
       :c:func:`SPRKStepEvolve()` failures.
 

doc/cvode/guide/source/Introduction.rst

@@ -129,6 +129,9 @@ Fixed scaling bug in ``SUNMatScaleAddI_Sparse`` for non-square matrices.
 Fixed missing soversions in some ``SUNLinearSolver`` and ``SUNNonlinearSolver``
 CMake targets.
 
+Changed the ``SUNProfiler`` so that it does not rely on ``MPI_WTime`` in any case.
+This fixes `GitHub Issue #312 <https://github.com/LLNL/sundials/issues/312>`_. 
+
 Added Fortran support for the LAPACK  dense ``SUNLinearSolver`` implementation.
 
 Changes in v6.6.1

doc/cvodes/guide/source/Introduction.rst

@@ -132,6 +132,9 @@ Fixed scaling bug in ``SUNMatScaleAddI_Sparse`` for non-square matrices.
 Fixed missing soversions in some ``SUNLinearSolver`` and ``SUNNonlinearSolver``
 CMake targets.
 
+Changed the ``SUNProfiler`` so that it does not rely on ``MPI_WTime`` in any case.
+This fixes `GitHub Issue #312 <https://github.com/LLNL/sundials/issues/312>`_. 
+
 Added Fortran support for the LAPACK  dense ``SUNLinearSolver`` implementation.
 
 Changes in v6.6.1

doc/ida/guide/source/Introduction.rst

@@ -90,6 +90,9 @@ Fixed scaling bug in ``SUNMatScaleAddI_Sparse`` for non-square matrices.
 Fixed missing soversions in some ``SUNLinearSolver`` and ``SUNNonlinearSolver``
 CMake targets.
 
+Changed the ``SUNProfiler`` so that it does not rely on ``MPI_WTime`` in any case.
+This fixes `GitHub Issue #312 <https://github.com/LLNL/sundials/issues/312>`_. 
+
 Added Fortran support for the LAPACK  dense ``SUNLinearSolver`` implementation.
 
 Changes in v6.6.1

doc/idas/guide/source/Introduction.rst

@@ -107,6 +107,9 @@ Fixed scaling bug in ``SUNMatScaleAddI_Sparse`` for non-square matrices.
 Fixed missing soversions in some ``SUNLinearSolver`` and ``SUNNonlinearSolver``
 CMake targets.
 
+Changed the ``SUNProfiler`` so that it does not rely on ``MPI_WTime`` in any case.
+This fixes `GitHub Issue #312 <https://github.com/LLNL/sundials/issues/312>`_. 
+
 Added Fortran support for the LAPACK  dense ``SUNLinearSolver`` implementation.
 
 Changes in v5.6.1

doc/kinsol/guide/source/Introduction.rst

@@ -112,6 +112,9 @@ Updated the Tpetra NVector interface to support Trilinos 14.
 Fixed a memory leak when destroying a CUDA, HIP, SYCL, or system SUNMemoryHelper
 object.
 
+Changed the ``SUNProfiler`` so that it does not rely on ``MPI_WTime`` in any case.
+This fixes `GitHub Issue #312 <https://github.com/LLNL/sundials/issues/312>`_. 
+
 Changes in v6.6.0
 -----------------
 

doc/shared/Install.rst

@@ -1022,6 +1022,7 @@ illustration only.
 .. cmakeoption:: SUNDIALS_BUILD_WITH_PROFILING
 
    Build SUNDIALS with capabilties for fine-grained profiling.
+   This requires POSIX timers or the Windows ``profileapi.h`` timers.
 
    Default: OFF
 

doc/shared/sundials/Profiling.rst

@@ -48,6 +48,11 @@ If Caliper is enabled, then users should refer to the `Caliper documentation <ht
 for information on getting profiler output. In most cases, this involves
 setting the ``CALI_CONFIG`` environment variable.
 
+
+.. note:: 
+
+   The SUNDIALS profiler requires POSIX timers or the Windows ``profileapi.h`` timers.
+
 .. warning::
 
    While the SUNDIALS profiling scheme is relatively lightweight, enabling
@@ -149,6 +154,31 @@ are available.
       * Returns zero if successful, or non-zero if an error occurred
 
 
+.. c:function:: int SUNProfiler_GetElapsedTime(SUNProfiler p, const char* name, double* time)
+
+   Get the elapsed time for the timer "name" in seconds.
+
+   **Arguments:**
+      * ``p`` -- a ``SUNProfiler`` object
+      * ``name`` -- the name for the profiling region of interest
+      * ``time`` -- upon return, the elapsed time for the timer
+
+   **Returns:**
+      * Returns zero if successful, or non-zero if an error occurred
+
+
+.. c:function:: int SUNProfiler_GetTimerResolution(SUNProfiler p, double* resolution)
+
+   Get the timer resolution in seconds.
+
+   **Arguments:**
+      * ``p`` -- a ``SUNProfiler`` object
+      * ``resolution`` -- upon return, the resolution for the timer
+
+   **Returns:**
+      * Returns zero if successful, or non-zero if an error occurred
+
+
 .. c:function:: int SUNProfiler_Print(SUNProfiler p, FILE* fp)
 
    Prints out a profiling summary. When constructed with an MPI comm the summary