Feature/remove deprecated code

.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

@@ -56,6 +56,10 @@ 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
 
 Updated the Tpetra NVector interface to support Trilinos 14.

benchmarks/advection_reaction_3D/kokkos/arkode_driver.cpp

@@ -38,7 +38,7 @@ typedef struct
 #define LOCAL_NLS(NLS)       ( GET_NLS_CONTENT(NLS)->local_nls )
 
 /* SUNNonlinearSolver constructor */
-SUNNonlinearSolver TaskLocalNewton(SUNContext ctx, N_Vector y, FILE* DFID);
+SUNNonlinearSolver TaskLocalNewton(SUNContext ctx, N_Vector y);
 
 
 /* --------------------------------------------------------------
@@ -59,7 +59,6 @@ int EvolveProblemDIRK(N_Vector y, UserData* udata, UserOptions* uopt)
   long int nfe, nfi;          /* RHS stats                    */
   long int nni, ncnf;         /* nonlinear solver stats       */
   long int nli, npsol;        /* linear solver stats          */
-  FILE*    DFID = NULL;       /* diagnostics output file      */
   char     fname[MXSTR];
 
   /* Additively split methods should not add the advection and reaction terms */
@@ -85,16 +84,6 @@ int EvolveProblemDIRK(N_Vector y, UserData* udata, UserOptions* uopt)
   retval = ARKStepSetMaxNumSteps(arkode_mem, 100000);
   if (check_retval(&retval, "ARKStepSetMaxNumSteps", 1, udata->myid)) return 1;
 
-  /* Open output file for integrator diagnostics */
-  if (uopt->save)
-  {
-    sprintf(fname, "%s/diagnostics.%06d.txt", uopt->outputdir, udata->myid);
-    DFID = fopen(fname, "w");
-
-    retval = ARKStepSetDiagnostics(arkode_mem, DFID);
-    if (check_retval(&retval, "ARKStepSetDiagnostics", 1, udata->myid)) return 1;
-  }
-
   /* Create the (non)linear solver */
   if (uopt->nls == "newton")
   {
@@ -107,7 +96,7 @@ int EvolveProblemDIRK(N_Vector y, UserData* udata, UserOptions* uopt)
     if (check_retval(&retval, "ARKStepSetNonlinearSolver", 1, udata->myid)) return 1;
 
     /* Create linear solver */
-    LS = uopt->precond ? SUNLinSol_SPGMR(y, PREC_LEFT, 0, udata->ctx) : SUNLinSol_SPGMR(y, PREC_NONE, 0, udata->ctx);
+    LS = uopt->precond ? SUNLinSol_SPGMR(y, SUN_PREC_LEFT, 0, udata->ctx) : SUNLinSol_SPGMR(y, SUN_PREC_NONE, 0, udata->ctx);
     if (check_retval((void *)LS, "SUNLinSol_SPGMR", 0, udata->myid)) return 1;
 
     /* Attach linear solver */
@@ -169,9 +158,6 @@ int EvolveProblemDIRK(N_Vector y, UserData* udata, UserOptions* uopt)
     iout++;
   } while (iout < uopt->nout);
 
-  /* close output stream */
-  if (uopt->save) fclose(DFID);
-
   /* Get final statistics */
   retval = ARKStepGetNumSteps(arkode_mem, &nst);
   check_retval(&retval, "ARKStepGetNumSteps", 1, udata->myid);
@@ -234,7 +220,6 @@ int EvolveProblemIMEX(N_Vector y, UserData* udata, UserOptions* uopt)
   long int nfe, nfi;          /* RHS stats                    */
   long int nni, ncnf;         /* nonlinear solver stats       */
   long int nli, npsol;        /* linear solver stats          */
-  FILE*    DFID = NULL;       /* diagnostics output file      */
   char     fname[MXSTR];
 
   /* Additively split methods should not add the advection and reaction terms */
@@ -260,16 +245,6 @@ int EvolveProblemIMEX(N_Vector y, UserData* udata, UserOptions* uopt)
   retval = ARKStepSetMaxNumSteps(arkode_mem, 100000);
   if (check_retval(&retval, "ARKStepSetMaxNumSteps", 1, udata->myid)) return 1;
 
-  /* Open output file for integrator diagnostics */
-  if (uopt->save)
-  {
-    sprintf(fname, "%s/diagnostics.%06d.txt", uopt->outputdir, udata->myid);
-    DFID = fopen(fname, "w");
-
-    retval = ARKStepSetDiagnostics(arkode_mem, DFID);
-    if (check_retval(&retval, "ARKStepSetDiagnostics", 1, udata->myid)) return 1;
-  }
-
   /* Create the (non)linear solver */
   if (uopt->nls == "newton")
   {
@@ -282,7 +257,7 @@ int EvolveProblemIMEX(N_Vector y, UserData* udata, UserOptions* uopt)
     if (check_retval(&retval, "ARKStepSetNonlinearSolver", 1, udata->myid)) return 1;
 
     /* Create linear solver */
-    LS = SUNLinSol_SPGMR(y, PREC_LEFT, 0, udata->ctx);
+    LS = SUNLinSol_SPGMR(y, SUN_PREC_LEFT, 0, udata->ctx);
     if (check_retval((void *)LS, "SUNLinSol_SPGMR", 0, udata->myid)) return 1;
 
     /* Attach linear solver */
@@ -297,7 +272,7 @@ int EvolveProblemIMEX(N_Vector y, UserData* udata, UserOptions* uopt)
   {
     /* The custom task-local nonlinear solver handles the linear solve
        as well, so we do not need a SUNLinearSolver. */
-    NLS = TaskLocalNewton(udata->ctx, y, DFID);
+    NLS = TaskLocalNewton(udata->ctx, y);
     if (check_retval((void *)NLS, "TaskLocalNewton", 0, udata->myid)) return 1;
 
     /* Attach nonlinear solver */
@@ -355,9 +330,6 @@ int EvolveProblemIMEX(N_Vector y, UserData* udata, UserOptions* uopt)
     iout++;
   } while (iout < uopt->nout);
 
-  /* close output stream */
-  if (uopt->save) fclose(DFID);
-
   /* Get final statistics */
   retval = ARKStepGetNumSteps(arkode_mem, &nst);
   check_retval(&retval, "ARKStepGetNumSteps", 1, udata->myid);
@@ -415,7 +387,6 @@ int EvolveProblemExplicit(N_Vector y, UserData* udata, UserOptions* uopt)
   int      iout;              /* output counter                */
   long int nst, nst_a, netf;  /* step stats                    */
   long int nfe;               /* RHS stats                     */
-  FILE*    DFID;              /* diagnostics output file       */
   char     fname[MXSTR];
 
   /* Additively split methods should not add the advection and reaction terms */
@@ -445,16 +416,6 @@ int EvolveProblemExplicit(N_Vector y, UserData* udata, UserOptions* uopt)
   retval = ERKStepSetFixedStep(arkode_mem, 1e-5);
   if (check_retval(&retval, "ERKStepSetFixedStep", 1, udata->myid)) return 1;
 
-  /* Open output file for integrator diagnostics */
-  if (uopt->save)
-  {
-    sprintf(fname, "%s/diagnostics.%06d.txt", uopt->outputdir, udata->myid);
-    DFID = fopen(fname, "w");
-
-    retval = ERKStepSetDiagnostics(arkode_mem, DFID);
-    if (check_retval(&retval, "ERKStepSetDiagnostics", 1, udata->myid)) return 1;
-  }
-
   /* Output initial condition */
   if (uopt->nout > 0)
   {
@@ -490,9 +451,6 @@ int EvolveProblemExplicit(N_Vector y, UserData* udata, UserOptions* uopt)
     iout++;
   } while (iout < uopt->nout);
 
-  /* close output stream */
-  if (uopt->save) fclose(DFID);
-
   /* Get final statistics */
   retval = ERKStepGetNumSteps(arkode_mem, &nst);
   check_retval(&retval, "ERKStepGetNumSteps", 1, udata->myid);
@@ -718,7 +676,7 @@ int TaskLocalNewton_GetNumConvFails(SUNNonlinearSolver NLS,
 }
 
 
-SUNNonlinearSolver TaskLocalNewton(SUNContext ctx, N_Vector y, FILE* DFID)
+SUNNonlinearSolver TaskLocalNewton(SUNContext ctx, N_Vector y)
 {
   SUNNonlinearSolver NLS;
   TaskLocalNewton_Content content;
@@ -771,12 +729,5 @@ SUNNonlinearSolver TaskLocalNewton(SUNContext ctx, N_Vector y, FILE* DFID)
 
   content->ncnf = 0;
 
-  /* Setup the local nonlinear solver monitoring */
-  if (DFID != NULL)
-  {
-    SUNNonlinSolSetInfoFile_Newton(LOCAL_NLS(NLS), DFID);
-    SUNNonlinSolSetPrintLevel_Newton(LOCAL_NLS(NLS), 1);
-  }
-
   return NLS;
 }

benchmarks/advection_reaction_3D/kokkos/cvode_driver.cpp

@@ -70,7 +70,7 @@ int EvolveProblemBDF(N_Vector y, UserData* udata, UserOptions* uopt)
     if (check_retval(&retval, "CVodeSetNonlinearSolver", 1, udata->myid)) return 1;
 
     /* Create linear solver */
-    LS = uopt->precond ? SUNLinSol_SPGMR(y, PREC_LEFT, 0, udata->ctx) : SUNLinSol_SPGMR(y, PREC_NONE, 0, udata->ctx);
+    LS = uopt->precond ? SUNLinSol_SPGMR(y, SUN_PREC_LEFT, 0, udata->ctx) : SUNLinSol_SPGMR(y, SUN_PREC_NONE, 0, udata->ctx);
     if (check_retval((void *)LS, "SUNLinSol_SPGMR", 0, udata->myid)) return 1;
 
     /* Attach linear solver */

benchmarks/advection_reaction_3D/kokkos/ida_driver.cpp

@@ -92,7 +92,7 @@ int EvolveDAEProblem(N_Vector y, UserData* udata, UserOptions* uopt)
     if (check_retval(&retval, "IDASetNonlinearSolver", 1, udata->myid)) return 1;
 
     /* Create linear solver */
-    LS = uopt->precond ? SUNLinSol_SPGMR(y, PREC_LEFT, 0, udata->ctx) : SUNLinSol_SPGMR(y, PREC_NONE, 0, udata->ctx);
+    LS = uopt->precond ? SUNLinSol_SPGMR(y, SUN_PREC_LEFT, 0, udata->ctx) : SUNLinSol_SPGMR(y, SUN_PREC_NONE, 0, udata->ctx);
     if (check_retval((void *)LS, "SUNLinSol_SPGMR", 0, udata->myid)) return 1;
 
     /* Attach linear solver */