Merge branch 'develop' into cmake/lapack-target

LLNL · Jul 17, 2024 · 074e7d6 · 074e7d6
2 parents b7e2a2f + e9a6d86
commit 074e7d6
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diff --git a/.github/workflows/check-spelling.yml b/.github/workflows/check-spelling.yml
@@ -0,0 +1,44 @@
+name: Checks - spelling
+
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  spelling_check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Install python3-pip
+        run: |
+          sudo apt update
+          sudo apt install -y --no-install-recommends python3-pip
+
+      - name: Install codespell
+        run: pip install codespell
+
+      - name: Print codespell version
+        run: codespell --version
+
+      - name: Check out repository code
+        uses: actions/checkout@v4
+        with:
+          submodules: true
+
+      - name: Run codespell
+        run: |
+          ./scripts/spelling.sh
+
+      - name: Run git diff to see if anything changed
+        run: /usr/bin/git diff --name-only --exit-code
+
+      - name: Run git diff if we failed
+        if: failure()
+        run: /usr/bin/git diff > spelling.patch
+
+      - name: Archive diff as a patch if we failed
+        uses: actions/upload-artifact@v3
+        if: failure()
+        with:
+          name: spelling.patch
+          path: |
+            ${{ github.workspace }}/spelling.patch
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1789,7 +1789,7 @@ update their code to set the corresponding `ops` structure member,
 `matvecsetup`, to `NULL`.
 
 The generic SUNMatrix API now defines error codes to be returned by SUNMatrix
-operations. Operations which return an integer flag indiciating success/failure
+operations. Operations which return an integer flag indicating success/failure
 may return different values than previously.
 
 A new SUNMatrix (and SUNLinearSolver) implementation was added to facilitate
@@ -1901,7 +1901,7 @@ function signatures have been changed including MRIStepCreate which now
 takes an ARKStep memory structure for the fast integration as an input.
 
 The reinitialization functions `ERKStepReInit`, `ARKStepReInit`, and
-`MRIStepReInit` have been updated to retain the minimum and maxiumum step
+`MRIStepReInit` have been updated to retain the minimum and maximum step
 size values from before reinitialization rather than resetting them to the
 default values.
 
@@ -1926,7 +1926,7 @@ being built.
 
 Fixed a memory leak in the PETSc `N_Vector` clone function.
 
-Fixed a memeory leak in the ARKODE, CVODE, and IDA F77 interfaces when not using
+Fixed a memory leak in the ARKODE, CVODE, and IDA F77 interfaces when not using
 the default nonlinear solver.
 
 Fixed a bug in the ARKStep time-stepping module in ARKODE that would result in
@@ -2638,7 +2638,7 @@ with sparse direct solvers.
 
 #### KINSOL
 
-The Picard iteration return was chanegd to always return the newest iterate upon
+The Picard iteration return was changed to always return the newest iterate upon
 success.
 
 A minor bug in the line search was fixed to prevent an infinite loop when the

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -187,7 +187,7 @@ include(SundialsSetupCompilers)
 include(SundialsSetupTPLs)
 
 # ===============================================================
-# Build options to be proccessed last
+# Build options to be processed last
 # ===============================================================
 
 include(SundialsBuildOptionsPost)

diff --git a/CODEOWNERS b/CODEOWNERS
@@ -3,6 +3,6 @@
 
 # These owners will be the default owners for everything in
 # the repo. Unless a later match takes precedence,
-# globabl owners will be requested for review when someone
+# global owners will be requested for review when someone
 # opens a pull request.
 * @balos1 @gardner48 @cswoodward @drreynolds
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,6 +1,6 @@
 # Contributing to SUNDIALS
 
-There are two primary ways of contributing to SUNDIALS. The first way is by particpating
+There are two primary ways of contributing to SUNDIALS. The first way is by participating
 in the development of SUNDIALS directly through contributions of code to the primary
 [SUNDIALS repository](https://github.com/LLNL/sundials). This is the best way to contribute
 bug fixes and minor improvements. At this time, the SUNDIALS team does not have the resources

diff --git a/benchmarks/advection_reaction_3D/kokkos/ParallelGrid.hpp b/benchmarks/advection_reaction_3D/kokkos/ParallelGrid.hpp
@@ -72,7 +72,7 @@ class ParallelGrid
 public:
   // Constructor that creates a new ParallelGrid object.
   // [in] - the memory helper to use for allocating the MPI buffers
-  // [in,out] comm - on input, the overal MPI communicator, on output, the cartesian communicator
+  // [in,out] comm - on input, the overall MPI communicator, on output, the cartesian communicator
   // [in] a[] - an array of length 3 which defines the domain [a,b]
   // [in] b[] - an array of length 3 which defines the domain [a,b]
   // [in] npts[] - an array of length 3 which defines the number of mesh points in each dimension
@@ -563,7 +563,7 @@ class ParallelGrid
 
   GLOBALINT nx, ny, nz;   /* number of intervals globally       */
   int nxl, nyl, nzl;      /* number of intervals locally        */
-  int npx, npy, npz;      /* numner of processes                */
+  int npx, npy, npz;      /* number of processes                */
   sunrealtype dx, dy, dz; /* mesh spacing                       */
   sunrealtype ax, ay, az; /* domain in [a, b]                   */
   sunrealtype bx, by, bz;

diff --git a/benchmarks/advection_reaction_3D/kokkos/arkode_driver.cpp b/benchmarks/advection_reaction_3D/kokkos/arkode_driver.cpp
@@ -33,7 +33,7 @@ typedef struct
   SUNNonlinearSolver local_nls;
 }* TaskLocalNewton_Content;
 
-/* Content accessor macors */
+/* Content accessor macros */
 #define GET_NLS_CONTENT(NLS) ((TaskLocalNewton_Content)(NLS->content))
 #define LOCAL_NLS(NLS)       (GET_NLS_CONTENT(NLS)->local_nls)
 

diff --git a/benchmarks/advection_reaction_3D/kokkos/check_retval.h b/benchmarks/advection_reaction_3D/kokkos/check_retval.h
@@ -23,7 +23,7 @@
  * opt == 0  means the function allocates memory and returns a
  *           pointer so check if a NULL pointer was returned
  * opt == 1  means the function returns an integer where a
- *           value < 0 indicates an error occured
+ *           value < 0 indicates an error occurred
  * --------------------------------------------------------------*/
 static int check_retval(void* returnvalue, const char* funcname, int opt, int myid)
 {

diff --git a/benchmarks/advection_reaction_3D/kokkos/rhs3D.hpp b/benchmarks/advection_reaction_3D/kokkos/rhs3D.hpp
@@ -23,7 +23,7 @@
  * --------------------------------------------------------------*/
 
 /* Compute the advection term f(t,y) = -c (grad * y). This is done using
-   upwind 1st order finite differences.  At present, only periodic boudary
+   upwind 1st order finite differences.  At present, only periodic boundary
    conditions are supported, which are handled via MPI's Cartesian
    communicator (even for serial runs). */
 static int Advection(sunrealtype t, N_Vector y, N_Vector ydot, void* user_data)

diff --git a/benchmarks/advection_reaction_3D/raja/ParallelGrid.hpp b/benchmarks/advection_reaction_3D/raja/ParallelGrid.hpp
@@ -45,7 +45,7 @@ class ParallelGrid
 public:
   // Constructor that creates a new ParallelGrid object.
   // [in] - the memory helper to use for allocating the MPI buffers
-  // [in,out] comm - on input, the overal MPI communicator, on output, the cartesian communicator
+  // [in,out] comm - on input, the overall MPI communicator, on output, the cartesian communicator
   // [in] a[] - an array of length 3 which defines the domain [a,b]
   // [in] b[] - an array of length 3 which defines the domain [a,b]
   // [in] npts[] - an array of length 3 which defines the number of mesh points in each dimension
@@ -508,7 +508,7 @@ class ParallelGrid
 
   GLOBALINT nx, ny, nz; /* number of intervals globally       */
   int nxl, nyl, nzl;    /* number of intervals locally        */
-  int npx, npy, npz;    /* numner of processes                */
+  int npx, npy, npz;    /* number of processes                */
   REAL dx, dy, dz;      /* mesh spacing                       */
   REAL ax, ay, az;      /* domain in [a, b]                   */
   REAL bx, by, bz;

diff --git a/benchmarks/advection_reaction_3D/raja/advection_reaction_3D.hpp b/benchmarks/advection_reaction_3D/raja/advection_reaction_3D.hpp
@@ -89,7 +89,7 @@ struct UserData
   N_Vector vmask;
   N_Vector wmask;
 
-  /* problem paramaters */
+  /* problem parameters */
   sunrealtype xmax; /* maximum x value              */
   sunrealtype A;    /* concentration of species A   */
   sunrealtype B;    /* w source rate                */

diff --git a/benchmarks/advection_reaction_3D/raja/arkode_driver.cpp b/benchmarks/advection_reaction_3D/raja/arkode_driver.cpp
@@ -33,7 +33,7 @@ typedef struct
   SUNNonlinearSolver local_nls;
 }* TaskLocalNewton_Content;
 
-/* Content accessor macors */
+/* Content accessor macros */
 #define GET_NLS_CONTENT(NLS) ((TaskLocalNewton_Content)(NLS->content))
 #define LOCAL_NLS(NLS)       (GET_NLS_CONTENT(NLS)->local_nls)
 

diff --git a/benchmarks/advection_reaction_3D/raja/check_retval.h b/benchmarks/advection_reaction_3D/raja/check_retval.h
@@ -23,7 +23,7 @@
  * opt == 0  means the function allocates memory and returns a
  *           pointer so check if a NULL pointer was returned
  * opt == 1  means the function returns an integer where a
- *           value < 0 indicates an error occured
+ *           value < 0 indicates an error occurred
  * --------------------------------------------------------------*/
 static int check_retval(void* returnvalue, const char* funcname, int opt, int myid)
 {

diff --git a/benchmarks/diffusion_2D/diffusion_2D.cpp b/benchmarks/diffusion_2D/diffusion_2D.cpp
@@ -11,7 +11,7 @@
  * SPDX-License-Identifier: BSD-3-Clause
  * SUNDIALS Copyright End
  * -----------------------------------------------------------------------------
- * Shared implementaiton file for 2D diffusion benchmark problem
+ * Shared implementation file for 2D diffusion benchmark problem
  * ---------------------------------------------------------------------------*/
 
 #include "diffusion_2D.hpp"

diff --git a/benchmarks/diffusion_2D/diffusion_2D.hpp b/benchmarks/diffusion_2D/diffusion_2D.hpp
@@ -159,7 +159,7 @@ struct UserData
   sunrealtype* Ssend = NULL;
   sunrealtype* Nsend = NULL;
 
-  // Send requests for neighor exchange
+  // Send requests for neighbor exchange
   MPI_Request reqSW;
   MPI_Request reqSE;
   MPI_Request reqSS;
@@ -192,7 +192,7 @@ struct UserData
 
 struct UserOutput
 {
-  // Ouput variables
+  // Output variables
   int output     = 1;    // 0 = no output, 1 = stats output, 2 = output to disk
   int nout       = 20;   // number of output times
   N_Vector error = NULL; // error vector

diff --git a/benchmarks/diffusion_2D/main_arkode.cpp b/benchmarks/diffusion_2D/main_arkode.cpp
@@ -329,7 +329,7 @@ int main(int argc, char* argv[])
     sunrealtype dTout = udata.tf / uout.nout;
     sunrealtype tout  = dTout;
 
-    // Inital output
+    // Initial output
     flag = uout.open(&udata);
     if (check_flag(&flag, "UserOutput::open", 1)) { return 1; }
 
@@ -524,7 +524,7 @@ void UserOptions::help()
   cout << endl;
   cout << "Integrator command line options:" << endl;
   cout << "  --rtol <rtol>           : relative tolerance" << endl;
-  cout << "  --atol <atol>           : absoltue tolerance" << endl;
+  cout << "  --atol <atol>           : absolute tolerance" << endl;
   cout << "  --nonlinear             : disable linearly implicit flag" << endl;
   cout << "  --order <ord>           : method order" << endl;
   cout << "  --fixedstep <step>      : used fixed step size" << endl;

diff --git a/benchmarks/diffusion_2D/main_cvode.cpp b/benchmarks/diffusion_2D/main_cvode.cpp
@@ -310,7 +310,7 @@ int main(int argc, char* argv[])
     sunrealtype dTout = udata.tf / uout.nout;
     sunrealtype tout  = dTout;
 
-    // Inital output
+    // Initial output
     flag = uout.open(&udata);
     if (check_flag(&flag, "UserOutput::open", 1)) { return 1; }
 
@@ -479,7 +479,7 @@ void UserOptions::help()
   cout << endl;
   cout << "Integrator command line options:" << endl;
   cout << "  --rtol <rtol>           : relative tolerance" << endl;
-  cout << "  --atol <atol>           : absoltue tolerance" << endl;
+  cout << "  --atol <atol>           : absolute tolerance" << endl;
   cout << "  --ls <cg|gmres|sludist> : linear solver" << endl;
   cout << "  --lsinfo                : output residual history" << endl;
   cout << "  --liniters <iters>      : max number of iterations" << endl;

diff --git a/benchmarks/diffusion_2D/main_ida.cpp b/benchmarks/diffusion_2D/main_ida.cpp
@@ -305,7 +305,7 @@ int main(int argc, char* argv[])
     sunrealtype dTout = udata.tf / uout.nout;
     sunrealtype tout  = dTout;
 
-    // Inital output
+    // Initial output
     flag = uout.open(&udata);
     if (check_flag(&flag, "UserOutput::open", 1)) { return 1; }
 
@@ -460,7 +460,7 @@ void UserOptions::help()
   cout << endl;
   cout << "Integrator command line options:" << endl;
   cout << "  --rtol <rtol>           : relative tolerance" << endl;
-  cout << "  --atol <atol>           : absoltue tolerance" << endl;
+  cout << "  --atol <atol>           : absolute tolerance" << endl;
   cout << "  --ls <cg|gmres|sludist> : linear solver" << endl;
   cout << "  --liniters <iters>      : max number of iterations" << endl;
   cout << "  --epslin <factor>       : linear tolerance factor" << endl;

diff --git a/benchmarks/nvector/plot_nvector_performance_results.py b/benchmarks/nvector/plot_nvector_performance_results.py
@@ -15,7 +15,7 @@
 # This script plots the output from test_nector_performance_* and assumes:
 #   1. vector lengths are powers of two starting from 0, and
 #   2. output files are named: output_nelem_nvec_nsum_ntest_timing.txt
-# where nelem is the number of elements in the vector, nvec is the nuber of
+# where nelem is the number of elements in the vector, nvec is the number of
 # vectors, nsum is the number of sums, ntest is the number of tests, and timing
 # indicates if timing was enabled.
 # -----------------------------------------------------------------------------

diff --git a/benchmarks/nvector/plot_nvector_performance_speedup.py b/benchmarks/nvector/plot_nvector_performance_speedup.py
@@ -15,7 +15,7 @@
 # This script plots the output from test_nector_performance_* and assumes:
 #   1. vector lengths are powers of two starting from 0, and
 #   2. output files are named: output_nelem_nvec_nsum_ntest_timing.txt
-# where nelem is the number of elements in the vector, nvec is the nuber of
+# where nelem is the number of elements in the vector, nvec is the number of
 # vectors, nsum is the number of sums, ntest is the number of tests, and timing
 # indicates if timing was enabled.
 # -----------------------------------------------------------------------------

diff --git a/benchmarks/nvector/sycl/test_nvector_performance_sycl.cpp b/benchmarks/nvector/sycl/test_nvector_performance_sycl.cpp
@@ -118,7 +118,7 @@ int main(int argc, char* argv[])
                   ? "Yes"
                   : "No")
             << std::endl;
-  std::cout << " suports usm shared allocations? "
+  std::cout << " supports usm shared allocations? "
             << (dev.get_info<::sycl::info::device::usm_shared_allocations>()
                   ? "Yes"
                   : "No")

diff --git a/benchmarks/nvector/test_nvector_performance.h b/benchmarks/nvector/test_nvector_performance.h
@@ -17,7 +17,7 @@
 
 #include <math.h>
 
-/* define constatnts */
+/* define constants */
 #define NEG_ONE SUN_RCONST(-1.0)
 #define ZERO    SUN_RCONST(0.0)
 #define ONE     SUN_RCONST(1.0)

diff --git a/cmake/SundialsBuildOptionsPost.cmake b/cmake/SundialsBuildOptionsPost.cmake
@@ -11,7 +11,7 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # SUNDIALS Copyright End
 # ---------------------------------------------------------------
-# SUNDIALS build options that are interepreted after all other
+# SUNDIALS build options that are interpreted after all other
 # CMake configuration.
 # ---------------------------------------------------------------
 

diff --git a/cmake/SundialsBuildOptionsPre.cmake b/cmake/SundialsBuildOptionsPre.cmake
@@ -11,7 +11,7 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # SUNDIALS Copyright End
 # ---------------------------------------------------------------
-# SUNDIALS build options that are interepreted prior to any
+# SUNDIALS build options that are interpreted prior to any
 # other CMake configuration.
 # ---------------------------------------------------------------
 

diff --git a/cmake/SundialsSetupCXX.cmake b/cmake/SundialsSetupCXX.cmake
@@ -41,7 +41,7 @@ set(DOCSTR "Enable C++ compiler specific extensions")
 sundials_option(CMAKE_CXX_EXTENSIONS BOOL "${DOCSTR}" ON)
 message(STATUS "C++ extensions set to ${CMAKE_CXX_EXTENSIONS}")
 
-# SYCL requries C++17
+# SYCL requires C++17
 if(ENABLE_SYCL AND (CMAKE_CXX_STANDARD LESS "17"))
   message(SEND_ERROR "CMAKE_CXX_STANDARD must be >= 17 because ENABLE_SYCL=ON")
 endif()
diff --git a/cmake/SundialsSetupCompilers.cmake b/cmake/SundialsSetupCompilers.cmake
@@ -21,12 +21,12 @@
 include(SundialsIndexSize)
 
 # ===============================================================
-# Platform specifc settings
+# Platform specific settings
 # ===============================================================
 
 if(WIN32)
   # Under Windows, add compiler directive to inhibit warnings about use of
-  # unsecure functions.
+  # insecure functions.
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 
   # Under Windows, we need to have dll and exe files in the same directory to

diff --git a/cmake/SundialsSetupCuda.cmake b/cmake/SundialsSetupCuda.cmake
@@ -11,7 +11,7 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # SUNDIALS Copyright End
 # ---------------------------------------------------------------
-# Setup the CUDA languge and CUDA libraries.
+# Setup the CUDA language and CUDA libraries.
 # ---------------------------------------------------------------
 
 # ===============================================================

diff --git a/cmake/tpl/FindMAGMA.cmake b/cmake/tpl/FindMAGMA.cmake
@@ -97,7 +97,7 @@ if(MAGMA_LIBRARY AND MAGMA_INCLUDE_DIR)
         # Check if we need to find cusparse or cublas
         if(SUNDIALS_MAGMA_BACKENDS MATCHES "CUDA")
           # Replace cublas, cusparse with the CMake targets because the library
-          # path in the magma pkgconfig is not reliable. Sepcifically, the path
+          # path in the magma pkgconfig is not reliable. Specifically, the path
           # is wrong on systems like Perlmutter where the NVIDIA HPC SDK is
           # used.
           if(lib STREQUAL "-lcublas")

diff --git a/cmake/tpl/SundialsHypre.cmake b/cmake/tpl/SundialsHypre.cmake
@@ -37,12 +37,12 @@ endif()
 # -----------------------------------------------------------------------------
 
 if(ENABLE_HYPRE)
-  # Using hypre requres building with MPI enabled
+  # Using hypre requires building with MPI enabled
   if(NOT ENABLE_MPI)
     message(
       FATAL_ERROR "MPI is required for hypre support. Set ENABLE_MPI to ON.")
   endif()
-  # Using hypre requres C99 or newer
+  # Using hypre requires C99 or newer
   if(CMAKE_C_STANDARD STREQUAL "90")
     message(SEND_ERROR "CMAKE_C_STANDARD must be >= c99 with ENABLE_HYPRE=ON")
   endif()