Merge Pull Request trilinos#12917 from trilinos/Trilinos/master_merge…

…_20240412_175845

Automatically Merged using Trilinos Master Merge AutoTester
PR Title: b'Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20240412_175845 branch to master'
PR Author: trilinos-autotester

.github/workflows/codeql.yml

@@ -0,0 +1,87 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL: Linear Solvers"
+
+on:
+  #push:
+  #  branches: [ "muelu-sync-workflow" ]
+  pull_request:
+    branches: [ "develop" ]
+  schedule:
+    - cron: '41 23 * * 2'
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - language: c-cpp
+          build-mode: manual
+        #- language: python
+        #  build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
+        config: |
+          query-filters:
+          - exclude:
+             tags: cpp/integer-multiplication-cast-to-long
+           
+    - if: matrix.build-mode == 'manual'
+      name: Configure Trilinos            
+      run: |
+          mkdir -p trilinos_build
+          cd trilinos_build 
+          cmake -G 'Unix Makefiles' -DTrilinos_ENABLE_TESTS=OFF -DTrilinos_ENABLE_Epetra=OFF -DTrilinos_ENABLE_AztecOO=OFF -DTrilinos_ENABLE_Ifpack=OFF -DTrilinos_ENABLE_ML=OFF -D Trilinos_ENABLE_Triutils=OFF -DTrilinos_ENABLE_Tpetra=ON -DTrilinos_ENABLE_MueLu=ON -DTrilinos_ENABLE_Krino=OFF ..
+      
+    - if: matrix.build-mode == 'manual'
+      name: Build Trilinos
+      run: |
+          cd trilinos_build 
+          make -j 2
+      
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/scorecards.yml

@@ -66,6 +66,6 @@ jobs:
 
       # Upload the results to GitHub's code scanning dashboard.
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@1b1aada464948af03b950897e5eb522f92603cc2 # v3.24.9
+        uses: github/codeql-action/upload-sarif@4355270be187e1b672a7a1c7c7bae5afdc1ab94a # v3.24.10
         with:
           sarif_file: results.sarif

.github/workflows/spack.yml

@@ -9,8 +9,14 @@ on:
       - submitted
   workflow_dispatch:
 
+permissions:
+  contents: read
+
 jobs:
   gcc10-openmpi416:
+    permissions:
+      actions: write  # for styfle/cancel-workflow-action to cancel/stop running workflows
+      contents: read  # for actions/checkout to fetch code
     runs-on: [self-hosted, gcc-10.3.0_openmpi-4.1.6]
     steps:
       - name: Cancel Previous Runs

cmake/tribits/doc/sphinx/requirements.txt

@@ -1,2 +1,2 @@
-Sphinx==4.0.2
+Sphinx==7.2.6
 sphinx-rtd-theme==0.5.2

packages/framework/ini-files/config-specs.ini

@@ -1722,6 +1722,7 @@ opt-set-cmake-var Tpetra_INST_SERIAL BOOL FORCE : ON
 opt-set-cmake-var Zoltan_ENABLE_Scotch BOOL FORCE : OFF
 
 [CUDA11-RUN-SERIAL-TESTS]
+opt-set-cmake-var KokkosKernels_sparse_cuda_MPI_1_SET_RUN_SERIAL BOOL FORCE : ON
 opt-set-cmake-var KokkosKernels_batched_dla_cuda_MPI_1_SET_RUN_SERIAL BOOL FORCE : ON
 opt-set-cmake-var Intrepid2_unit-test_MonolithicExecutable_Intrepid2_Tests_MPI_1_SET_RUN_SERIAL BOOL FORCE : ON
 
@@ -2838,6 +2839,48 @@ opt-set-cmake-var Stratimikos_Galeri_xpetra_complex_double_Jacobi_MPI_4_DISABLE
 use GCC_PACKAGE_SPECIFIC_WARNING_FLAGS
 use RHEL8_POST
 
+[rhel8_gcc-serial_release-debug_shared_no-kokkos-arch_no-asan_no-complex_no-fpic_no-mpi_no-pt_no-rdc_no-uvm_deprecated-on_no-package-enables]
+# gcc-serial containerized environment
+use COMPILER|GNU
+use NODE-TYPE|SERIAL
+use BUILD-TYPE|RELEASE-DEBUG
+
+use RHEL8_LIB-TYPE|SHARED
+use KOKKOS-ARCH|NO-KOKKOS-ARCH
+
+use USE-ASAN|NO
+use USE-COMPLEX|NO
+use USE-FPIC|NO
+use USE-MPI|NO
+use USE-PT|NO
+use USE-RDC|NO
+use USE-UVM|NO
+use USE-DEPRECATED|YES
+use PACKAGE-ENABLES|NO-PACKAGE-ENABLES
+
+use COMMON_SPACK_TPLS
+
+opt-set-cmake-var CMAKE_CXX_FLAGS                STRING       : -Wall -Wno-clobbered -Wno-vla -Wno-pragmas -Wno-unknown-pragmas -Wno-parentheses -Wno-unused-local-typedefs -Wno-literal-suffix -Wno-deprecated-declarations -Wno-misleading-indentation -Wno-int-in-bool-context -Wno-maybe-uninitialized -Wno-class-memaccess -Wno-nonnull-compare -Wno-address -Wno-inline -Wno-unused-but-set-variable -Wno-unused-variable -Wno-unused-label -Werror -DTRILINOS_HIDE_DEPRECATED_HEADER_WARNINGS
+
+opt-set-cmake-var TPL_BLAS_LIBRARY_DIRS     STRING FORCE : ${OPENBLAS_ROOT|ENV}/lib
+opt-set-cmake-var TPL_BLAS_LIBRARIES        STRING FORCE : ${OPENBLAS_ROOT|ENV}/lib/libopenblas.a;-L${OPENBLAS_ROOT|ENV}/lib;-lgfortran;-lgomp;-lm
+opt-set-cmake-var TPL_LAPACK_LIBRARY_DIRS   STRING FORCE : ${OPENBLAS_ROOT|ENV}/lib
+opt-set-cmake-var TPL_LAPACK_LIBRARIES      STRING FORCE : ${OPENBLAS_ROOT|ENV}/lib/libopenblas.a;-L${OPENBLAS_ROOT|ENV}/lib;-lgfortran;-lgomp;-lm
+
+opt-set-cmake-var TPL_Netcdf_LIBRARIES      STRING FORCE : ""
+
+opt-set-cmake-var TPL_ENABLE_ParMETIS       BOOL FORCE   : OFF
+opt-set-cmake-var TPL_ENABLE_Pnetcdf        BOOL FORCE   : OFF
+
+opt-set-cmake-var Trilinos_ENABLE_TrilinosFrameworkTests BOOL FORCE : OFF
+opt-set-cmake-var Trilinos_ENABLE_TrilinosBuildStats     BOOL FORCE : OFF
+
+# Turned off to bypass: ML CONFIGURATION ERROR:  SuperLU_5.0 detected - only SuperLU version < 5.0 currently supported for this package.
+opt-set-cmake-var ML_ENABLE_SuperLU BOOL FORCE : OFF
+
+use GCC_PACKAGE_SPECIFIC_WARNING_FLAGS
+use RHEL8_POST
+
 [rhel8_aue-gcc-openmpi_debug_shared_no-kokkos-arch_no-asan_complex_no-fpic_mpi_no-pt_no-rdc_no-uvm_deprecated-on_no-package-enables]
 use COMPILER|GNU
 use NODE-TYPE|SERIAL
@@ -2886,6 +2929,10 @@ use PACKAGE-ENABLES|ALL
 opt-set-cmake-var Trilinos_ENABLE_TrilinosFrameworkTests BOOL FORCE : OFF
 opt-set-cmake-var Trilinos_ENABLE_TrilinosBuildStats BOOL FORCE : OFF
 
+[rhel8_gcc-serial_release-debug_shared_no-kokkos-arch_no-asan_no-complex_no-fpic_no-mpi_no-pt_no-rdc_no-uvm_deprecated-on_all]
+use rhel8_gcc-serial_release-debug_shared_no-kokkos-arch_no-asan_no-complex_no-fpic_no-mpi_no-pt_no-rdc_no-uvm_deprecated-on_no-package-enables
+use PACKAGE-ENABLES|ALL
+
 [rhel8_aue-gcc-openmpi_debug_shared_no-kokkos-arch_no-asan_complex_no-fpic_mpi_no-pt_no-rdc_no-uvm_deprecated-on_all]
 use rhel8_aue-gcc-openmpi_debug_shared_no-kokkos-arch_no-asan_complex_no-fpic_mpi_no-pt_no-rdc_no-uvm_deprecated-on_no-package-enables
 use PACKAGE-ENABLES|ALL

packages/framework/ini-files/environment-specs.ini

@@ -158,6 +158,8 @@ envvar-find-in-path MPIF90 : mpif90
 
 [rhel8_gcc-openmpi]
 
+[rhel8_gcc-serial]
+
 [rhel8_aue-gcc-openmpi]
 
 [rhel8_oneapi-intelmpi]

packages/framework/ini-files/supported-envs.ini

@@ -174,6 +174,7 @@ gnu
 [rhel8]
 oneapi-intelmpi
 gcc-openmpi
+gcc-serial
 aue-gcc-openmpi
 sems-cuda-11.4.2-sems-gnu-10.1.0-sems-openmpi-4.1.4
 

packages/kokkos-kernels/batched/dense/impl/KokkosBatched_Trsm_Team_Impl.hpp

@@ -99,6 +99,48 @@ struct TeamTrsm<MemberType, Side::Right, Uplo::Upper, Trans::NoTranspose,
   }
 };
 
+///
+/// R/L/NT
+///
+/// B := (alpha*B) inv(tril(A))
+/// A(n x n), B(m x n)
+
+template <typename MemberType, typename ArgDiag>
+struct TeamTrsm<MemberType, Side::Right, Uplo::Lower, Trans::NoTranspose,
+                ArgDiag, Algo::Trsm::Unblocked> {
+  template <typename ScalarType, typename AViewType, typename BViewType>
+  KOKKOS_INLINE_FUNCTION static int invoke(const MemberType &member,
+                                           const ScalarType alpha,
+                                           const AViewType &A,
+                                           const BViewType &B) {
+    return TeamTrsmInternalLeftUpper<Algo::Trsm::Unblocked>::invoke(
+        member, ArgDiag::use_unit_diag, B.extent(1), B.extent(0), alpha,
+        A.data(), A.stride_1(), A.stride_0(), B.data(), B.stride_1(),
+        B.stride_0());
+  }
+};
+
+template <typename MemberType, typename ArgDiag>
+struct TeamTrsm<MemberType, Side::Right, Uplo::Lower, Trans::NoTranspose,
+                ArgDiag, Algo::Trsm::Blocked> {
+  template <typename ScalarType, typename AViewType, typename BViewType>
+  KOKKOS_INLINE_FUNCTION static int invoke(const MemberType &member,
+                                           const ScalarType alpha,
+                                           const AViewType &A,
+                                           const BViewType &B) {
+    return TeamTrsmInternalLeftUpper<Algo::Trsm::Blocked>::invoke(
+        member, ArgDiag::use_unit_diag, B.extent(1), B.extent(0), alpha,
+        A.data(), A.stride_1(), A.stride_0(), B.data(), B.stride_1(),
+        B.stride_0());
+  }
+};
+
+///
+/// R/U/T
+///
+/// B := (alpha*B) inv(triu(A))
+/// A(n x n), B(m x n)
+
 template <typename MemberType, typename ArgDiag>
 struct TeamTrsm<MemberType, Side::Right, Uplo::Upper, Trans::Transpose, ArgDiag,
                 Algo::Trsm::Unblocked> {
@@ -107,7 +149,7 @@ struct TeamTrsm<MemberType, Side::Right, Uplo::Upper, Trans::Transpose, ArgDiag,
                                            const ScalarType alpha,
                                            const AViewType &A,
                                            const BViewType &B) {
-    return TeamTrsmInternalLeftLower<Algo::Trsm::Unblocked>::invoke(
+    return TeamTrsmInternalLeftUpper<Algo::Trsm::Unblocked>::invoke(
         member, ArgDiag::use_unit_diag, B.extent(1), B.extent(0), alpha,
         A.data(), A.stride_0(), A.stride_1(), B.data(), B.stride_1(),
         B.stride_0());
@@ -122,7 +164,7 @@ struct TeamTrsm<MemberType, Side::Right, Uplo::Upper, Trans::Transpose, ArgDiag,
                                            const ScalarType alpha,
                                            const AViewType &A,
                                            const BViewType &B) {
-    return TeamTrsmInternalLeftLower<Algo::Trsm::Blocked>::invoke(
+    return TeamTrsmInternalLeftUpper<Algo::Trsm::Blocked>::invoke(
         member, ArgDiag::use_unit_diag, B.extent(1), B.extent(0), alpha,
         A.data(), A.stride_0(), A.stride_1(), B.data(), B.stride_1(),
         B.stride_0());