Merge Pull Request #13525 from trilinos/Trilinos/master_merge_2024101…

…1_175835 Automatically Merged using Trilinos Master Merge AutoTester PR Title: b'Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20241011_175835 branch to master' PR Author: trilinos-autotester
trilinos · Oct 12, 2024 · 5665193 · 5665193
2 parents a90610d + f0d5905
commit 5665193
Show file tree

Hide file tree

Showing 114 changed files with 2,656 additions and 1,085 deletions.
diff --git a/.github/workflows/AT2.yml b/.github/workflows/AT2.yml
@@ -13,15 +13,17 @@ on:
     - develop
   workflow_dispatch:
 
-# actions: write needed by skip-duplicate-actions
-permissions:
-  actions: write
+# actions: write needed by skip-duplicate-actions (handled below as per OpenSSF scorecard)
+permissions: 
   contents: read
 
 jobs:
   # Jobs depend on the output of pre-checks to run
   pre-checks:
         runs-on: ubuntu-latest
+        # actions: write needed by skip-duplicate-actions
+        permissions:
+          actions: write
         outputs:
             should_skip: ${{ steps.skip_check.outputs.should_skip }}
         steps:
@@ -55,7 +57,7 @@ jobs:
           mkdir -p /home/Trilinos/src/Trilinos
           mkdir -p /home/Trilinos/build
       - name: Clone trilinos
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
         with:
           fetch-depth: 0
       - name: Repo status
@@ -82,8 +84,8 @@ jobs:
           popd
 
           export TRILINOS_DIR=${GITHUB_WORKSPACE:?}
-          export PYTHONPATH=${PYTHONPATH}:${GITHUB_WORKSPACE}/packages/framework/GenConfig
-          export PYTHONPATH=${PYTHONPATH}:${GITHUB_WORKSPACE}/packages/framework/pr_tools
+          export PYTHONPATH=${PYTHONPATH}:${TRILINOS_DIR}/packages/framework/GenConfig
+          export PYTHONPATH=${PYTHONPATH}:${TRILINOS_DIR}/packages/framework/pr_tools
 
           printf "\n\n\n"
 
@@ -146,7 +148,7 @@ jobs:
           mkdir -p /home/Trilinos/src/Trilinos
           mkdir -p /home/Trilinos/build
       - name: Clone trilinos
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
         with:
           fetch-depth: 0
       - name: Repo status
@@ -173,8 +175,8 @@ jobs:
           popd
 
           export TRILINOS_DIR=${GITHUB_WORKSPACE:?}
-          export PYTHONPATH=${PYTHONPATH}:${GITHUB_WORKSPACE}/packages/framework/GenConfig
-          export PYTHONPATH=${PYTHONPATH}:${GITHUB_WORKSPACE}/packages/framework/pr_tools
+          export PYTHONPATH=${PYTHONPATH}:${TRILINOS_DIR}/packages/framework/GenConfig
+          export PYTHONPATH=${PYTHONPATH}:${TRILINOS_DIR}/packages/framework/pr_tools
 
           printf "\n\n\n"
 
@@ -237,7 +239,7 @@ jobs:
           mkdir -p /home/Trilinos/src/Trilinos
           mkdir -p /home/Trilinos/build
       - name: Clone trilinos
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
         with:
           fetch-depth: 0
       - name: Repo status
@@ -263,8 +265,8 @@ jobs:
           popd
 
           export TRILINOS_DIR=${GITHUB_WORKSPACE:?}
-          export PYTHONPATH=${PYTHONPATH}:${GITHUB_WORKSPACE}/packages/framework/GenConfig
-          export PYTHONPATH=${PYTHONPATH}:${GITHUB_WORKSPACE}/packages/framework/pr_tools
+          export PYTHONPATH=${PYTHONPATH}:${TRILINOS_DIR}/packages/framework/GenConfig
+          export PYTHONPATH=${PYTHONPATH}:${TRILINOS_DIR}/packages/framework/pr_tools
 
           printf "\n\n\n"
 
@@ -303,3 +305,94 @@ jobs:
           echo "## Helpful Links" >> $GITHUB_STEP_SUMMARY
           echo "https://github.com/trilinos/Trilinos/wiki/Containers" >> $GITHUB_STEP_SUMMARY
           echo "https://gitlab-ex.sandia.gov/trilinos-project/trilinos-containers/-/wikis/Containers-at-Sandia" >> $GITHUB_STEP_SUMMARY
+
+  framework-tests-EXPERIMENTAL:
+    needs: pre-checks
+    runs-on: [self-hosted, python-3.9]
+    if: ${{ needs.pre-checks.outputs.should_skip != 'true' && (github.event.action == 'synchronize' || github.event.action == 'opened' || github.event.review.state == 'APPROVED') }}
+    steps:
+      - name: env
+        env:
+          GITHUB_CONTEXT: ${{ toJson(github) }}
+        run: |
+          env
+      - name: module list
+        shell: bash
+        run: |
+          bash -l -c "module list"
+          printenv PATH
+      - name: Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@85880fa0301c86cca9da44039ee3bb12d3bedbfa # 0.12.1
+        with:
+          access_token: ${{ github.token }}
+      - name: make dirs
+        working-directory: /
+        run: |
+          mkdir -p /home/Trilinos/src/Trilinos
+          mkdir -p /home/Trilinos/build
+      - name: Clone trilinos
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+        with:
+          fetch-depth: 0
+      - name: Repo status
+        run: |
+          git fetch --all
+          pwd
+          ls -lhat
+          git status
+          git branch -vv
+          git branch -a
+      - name: get dependencies
+        working-directory: ./packages/framework
+        run: |
+          bash -l -c "./get_dependencies.sh --container"
+      - name: PullRequestLinuxDriverTest.py
+        shell: bash -l {0}
+        working-directory: /home/Trilinos/build
+        run: |
+          mkdir bin
+          pushd bin
+          ln -s $(type -p python3) python
+          export PATH=$(pwd):${PATH}
+          popd
+
+          export TRILINOS_DIR=${GITHUB_WORKSPACE:?}
+          export PYTHONPATH=${PYTHONPATH}:${TRILINOS_DIR}/packages/framework/GenConfig
+          export PYTHONPATH=${PYTHONPATH}:${TRILINOS_DIR}/packages/framework/pr_tools
+
+          printf "\n\n\n"
+
+          echo "image: ${AT2_IMAGE:-unknown}"
+          type python
+          python3 ${GITHUB_WORKSPACE}/packages/framework/pr_tools/PullRequestLinuxDriverTest.py \
+            --target-branch-name ${{ github.event.pull_request.base.ref }} \
+            --genconfig-build-name rhel8_python_debug_shared_no-kokkos-arch_no-asan_no-complex_no-fpic_no-mpi_no-pt_no-rdc_no-uvm_deprecated-on_pr-framework \
+            --pullrequest-number ${{ github.event.pull_request.number }} \
+            --pullrequest-env-config-file ${GITHUB_WORKSPACE}/packages/framework/pr_tools/trilinos_pr.ini \
+            --pullrequest-gen-config-file ${GITHUB_WORKSPACE}/packages/framework/GenConfig/src/gen-config.ini \
+            --workspace-dir /home/runner/_work/Trilinos \
+            --source-dir ${GITHUB_WORKSPACE} \
+            --build-dir /home/Trilinos/build \
+            --dashboard-build-name `cat /etc/hostname` \
+            --ctest-driver /home/runner/_work/Trilinos/Trilinos/cmake/SimpleTesting/cmake/ctest-driver.cmake \
+            --ctest-drop-site sems-cdash-son.sandia.gov/cdash \
+            --filename-subprojects ./package_subproject_list.cmake \
+            --filename-packageenables ./packageEnables.cmake \
+      - name: Summary
+        if: ${{ !cancelled() }}
+        shell: bash -l {0}
+        working-directory: /home/Trilinos/build
+        run: |
+          echo "## Image" >> $GITHUB_STEP_SUMMARY
+          echo "image: ${AT2_IMAGE:-unknown}" >> $GITHUB_STEP_SUMMARY
+          echo "## CDash Links" >> $GITHUB_STEP_SUMMARY
+          echo "### Current Build" >> $GITHUB_STEP_SUMMARY
+          AT2_URL=$(</home/runner/AT2_URL.txt)
+          echo $AT2_URL >> $GITHUB_STEP_SUMMARY
+          echo "### All Builds" >> $GITHUB_STEP_SUMMARY
+          AT2_ALL_BUILDS=$(</home/runner/AT2_ALL_BUILDS.txt)
+          echo $AT2_ALL_BUILDS >> $GITHUB_STEP_SUMMARY
+          echo "## Helpful Links" >> $GITHUB_STEP_SUMMARY
+          echo "https://github.com/trilinos/Trilinos/wiki/Containers" >> $GITHUB_STEP_SUMMARY
+          echo "https://gitlab-ex.sandia.gov/trilinos-project/trilinos-containers/-/wikis/Containers-at-Sandia" >> $GITHUB_STEP_SUMMARY
+
diff --git a/.github/workflows/clang_format.yml b/.github/workflows/clang_format.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+    - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
     - uses: DoozyX/clang-format-lint-action@c71d0bf4e21876ebec3e5647491186f8797fde31 # v0.18.2
       with:
         source: './packages/muelu ./packages/tempus ./packages/teko ./packages/xpetra'
@@ -22,7 +22,7 @@ jobs:
     - run: git diff HEAD > format_patch.txt
     - run: if [ "$(cat format_patch.txt)" == "" ] ; then rm format_patch.txt ; else cat format_patch.txt; fi
 
-    - uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
+    - uses: actions/upload-artifact@604373da6381bf24206979c74d06a550515601b9 # v4.4.1
       id: upload-artf
       if: ${{ hashFiles('format_patch.txt') != '' }}
       with:

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -58,11 +58,11 @@ jobs:
         # 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@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+      uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@294a9d92911152fe08befb9ec03e240add280cb3 # v3.26.8
+      uses: github/codeql-action/init@c36620d31ac7c881962c3d9dd939c40ec9434f2b # v3.26.12
       with:
         languages: ${{ matrix.language }}
         build-mode: ${{ matrix.build-mode }}
@@ -85,6 +85,6 @@ jobs:
           make -j 2
       
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@294a9d92911152fe08befb9ec03e240add280cb3 # v3.26.8
+      uses: github/codeql-action/analyze@c36620d31ac7c881962c3d9dd939c40ec9434f2b # v3.26.12
       with:
         category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/dependency-review.yml b/.github/workflows/dependency-review.yml
@@ -22,6 +22,6 @@ jobs:
           egress-policy: audit
 
       - name: 'Checkout Repository'
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
       - name: 'Dependency Review'
         uses: actions/dependency-review-action@5a2ce3f5b92ee19cbb1541a4984c76d921601d7c # v4.3.4
diff --git a/.github/workflows/detect-git-lfs.yml b/.github/workflows/detect-git-lfs.yml
@@ -12,7 +12,7 @@ jobs:
 
     steps:
     - name: Check out code
-      uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+      uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
       with:
         fetch-depth: 0
 

diff --git a/.github/workflows/detect-mpi-comm-world.yml b/.github/workflows/detect-mpi-comm-world.yml
@@ -12,7 +12,7 @@ jobs:
 
     steps:
     - name: Check out code
-      uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+      uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
       with:
         fetch-depth: 0
 

diff --git a/.github/workflows/per-commit.yml b/.github/workflows/per-commit.yml
@@ -0,0 +1,23 @@
+name: Per-Commit Checks
+
+on:
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  DCO-signoff:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Check out code
+      uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
+      with:
+        fetch-depth: 0
+
+    - name: Search for signoff statements in commit messages
+      run: |
+        $GITHUB_WORKSPACE/commonTools/test/utilities/check-commit-signoffs.sh \
+        origin/${{ github.event.pull_request.base.ref }} \
+        ${{ github.event.pull_request.head.sha }}
diff --git a/.github/workflows/scorecards.yml b/.github/workflows/scorecards.yml
@@ -31,7 +31,7 @@ jobs:
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
         with:
           persist-credentials: false
 
@@ -58,14 +58,14 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: "Upload artifact"
-        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
+        uses: actions/upload-artifact@604373da6381bf24206979c74d06a550515601b9 # v4.4.1
         with:
           name: SARIF file
           path: results.sarif
           retention-days: 5
 
       # Upload the results to GitHub's code scanning dashboard.
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@294a9d92911152fe08befb9ec03e240add280cb3 # v3.26.8
+        uses: github/codeql-action/upload-sarif@c36620d31ac7c881962c3d9dd939c40ec9434f2b # v3.26.12
         with:
           sarif_file: results.sarif
diff --git a/.github/workflows/spack.yml b/.github/workflows/spack.yml
@@ -24,7 +24,7 @@ jobs:
         with:
           access_token: ${{ github.token }}
       - name: Clone Trilinos
-        uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
         with:
           fetch-depth: 1
       - name: Spack build

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -78,3 +78,17 @@ When your changes are ready to be integrated into Trilinos' `develop` branch:
 ### Feedback
 
 At this point you'll enter into a stage where you and various Trilinos developers will iterate back and forth until your changes are in an acceptable state and can be merged in.  If you need to make changes to your pull request, make additional commits on your `<branchName>` branch and push them up to your fork.  Make sure you don't delete your remote feature branch or your fork of Trilinos before your pull request has been merged.
+
+
+## Sign-off Your Work
+
+The Developer Certificate of Origin ([DCO](https://developercertificate.org)) is a lightweight way for contributors to certify that they wrote or otherwise have the right to submit the code they are contributing to the project. Contributors must sign-off that they adhere to these requirements by adding a Signed-off-by line to commit messages.
+
+Example:
+```
+This is a commit message
+
+Signed-off-by: John A. Doe <[email protected]>
+```
+
+See [`git commit --signoff`](https://git-scm.com/docs/git-commit#Documentation/git-commit.txt---signoff)
diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 
 
 [![OpenSSF Scorecard](https://api.securityscorecards.dev/projects/github.com/trilinos/Trilinos/badge)](https://securityscorecards.dev/viewer/?uri=github.com/trilinos/Trilinos)
-
+[![OpenSSF Best Practices](https://www.bestpractices.dev/projects/9452/badge)](https://www.bestpractices.dev/projects/9452)
 
 
 The Trilinos Project is an effort to develop algorithms and enabling

diff --git a/SECURITY.md b/SECURITY.md
@@ -6,4 +6,20 @@ The latest released version of Trilinos is the only version supported with secur
 
 ## Reporting a Vulnerability
 
-For run-of-the mill memory errors, etc., please file a Github issue.  For specific, sensitive security issues, please click on "Report a vulnerability" at https://github.com/trilinos/Trilinos/security.
+For run-of-the mill memory errors, etc., please file a Github issue.  
+
+If you discover a security vulnerability within Trilinos, please follow these steps to report it:
+
+1. **Do Not Create a Public Issue**: Please do not disclose the vulnerability publicly until it has been addressed.
+2. **Contact Us**: Please click on "Report a vulnerability" at https://github.com/trilinos/Trilinos/security.
+3. **Provide Details**: Include as much information as possible about the vulnerability, including:
+   - A description of the vulnerability
+   - Steps to reproduce the issue
+   - Any relevant logs or screenshots
+   - Your contact information (optional, but helpful for follow-up)
+
+## Response Process
+
+We will acknowledge your report within 5 days and aim to provide a resolution or further information within 30 days. 
+
+We appreciate your help in keeping our project secure!
diff --git a/cmake/TPLs/FindTPLMKL.cmake b/cmake/TPLs/FindTPLMKL.cmake
@@ -15,10 +15,32 @@
 # pseudorandom number generators.  That's why we require a header
 # file, to access the function declarations.
 
-TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( MKL
-  REQUIRED_HEADERS mkl.h
-  REQUIRED_LIBS_NAMES mkl_rt
-  )
+IF(Kokkos_ENABLE_SYCL)
+  # For OneAPI MKL on GPU, use the CMake target
+  # Temporarily change CMAKE_CXX_COMPILER to icpx to convince MKL to add the DPCPP target
+  # If it sees that CMAKE_CXX_COMPILER is just ".../mpicxx", it won't do this.
+  set(CMAKE_CXX_COMPILER_PREVIOUS "${CMAKE_CXX_COMPILER}")
+  set(CMAKE_CXX_COMPILER "icpx")
+  # Use the BLAS95 and LAPACK95 interfaces (int32_t for dimensions and indices)
+  set(MKL_INTERFACE lp64)
+  find_package(MKL REQUIRED COMPONENTS MKL::MKL MKL::MKL_SYCL)
+  IF (NOT MKL_FOUND)
+    MESSAGE(FATAL_ERROR "MKL (as CMake package) was not found! This is required for SYCL+MKL")
+  ENDIF()
+  set(CMAKE_CXX_COMPILER "${CMAKE_CXX_COMPILER_PREVIOUS}")
+
+  tribits_extpkg_create_imported_all_libs_target_and_config_file( MKL
+    INNER_FIND_PACKAGE_NAME MKL
+    IMPORTED_TARGETS_FOR_ALL_LIBS MKL::MKL MKL::MKL_SYCL
+    )
+ELSE ()
+  # For host MKL, the single library libmkl_rt is sufficient.
+  # This works for older versions of MKL that don't provide MKLConfig.cmake.
+  TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( MKL
+    REQUIRED_HEADERS mkl.h
+    REQUIRED_LIBS_NAMES mkl_rt
+    )
+ENDIF()
 
 # In the past, MKL users had to link with a long list of libraries.
 # The choice of libraries enables specific functionality.  Intel
@@ -69,7 +91,3 @@ TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( MKL
 # where the MKLROOT environment variable points to my MKL install
 # directory.
 
-
-
-
-