Merge Pull Request #12805 from trilinos/Trilinos/master_merge_2024030…

…8_175834

Automatically Merged using Trilinos Master Merge AutoTester
PR Title: b'Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20240308_175834 branch to master'
PR Author: trilinos-autotester

.github/dependabot.yml

@@ -0,0 +1,16 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: daily
+
+  - package-ecosystem: pip
+    directory: /cmake/tribits/doc/sphinx
+    schedule:
+      interval: daily
+
+  - package-ecosystem: pip
+    directory: /packages/kokkos-kernels/docs
+    schedule:
+      interval: daily

.github/workflows/PR-gcc-openmpi.yml

@@ -11,8 +11,14 @@ on:
     - develop
   workflow_dispatch:
 
+permissions:
+  contents: read
+
 jobs:
   trilogpu02-gcc:
+    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, trilogpu02]
     container:
       image: registry-ex.sandia.gov/trilinos-project/trilinos-containers/rhel8/trilinos-pr-env:gcc-8.5.0
@@ -29,7 +35,7 @@ jobs:
           bash -l -c "module list"
           printenv PATH
       - name: Cancel Previous Runs
-        uses: styfle/[email protected]
+        uses: styfle/cancel-workflow-action@b173b6ec0100793626c2d9e6b90435061f4fc3e5 # 0.11.0
         with:
           access_token: ${{ github.token }}
       - name: make dirs
@@ -38,7 +44,7 @@ jobs:
           mkdir -p /home/Trilinos/src/Trilinos
           mkdir -p /home/Trilinos/build
       - name: Clone trilinos
-        uses: actions/checkout@v4
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
         with:
           fetch-depth: 0
       - name: Repo status

.github/workflows/clang_format.yml

@@ -7,8 +7,8 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - uses: DoozyX/[email protected]
+    - uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
+    - uses: DoozyX/clang-format-lint-action@1566bcec081dcb246ab02e7c5f9786c0b629dd4d # v0.16.2
       with:
         source: './packages/muelu ./packages/tempus ./packages/teko ./packages/xpetra'
         exclude: './packages/tempus/examples'
@@ -18,7 +18,7 @@ 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@v4
+    - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4.3.1
       id: upload-artf
       if: ${{ hashFiles('format_patch.txt') != '' }}
       with:
@@ -32,13 +32,13 @@ jobs:
 
     # This does not work for PRs from forks.
     - name: Post artifact in issue comment
-      uses: mshick/[email protected]
+      uses: mshick/add-pr-comment@7c0890544fb33b0bdd2e59467fbacb62e028a096 # v2.8.1
       if: ${{ (hashFiles('format_patch.txt') != '') && (github.event.pull_request.head.repo.full_name == github.repository) }}
       with:
         message: |
           Your PR updated files that did not respect package clang formatting settings.  Please apply the patch found [here](${{ steps.upload-artf.outputs.artifact-url }})
 
-    - uses: actions/github-script@v3
+    - uses: actions/github-script@ffc2c79a5b2490bd33e0a41c1de74b877714d736 # v3.2.0
       if: ${{ hashFiles('format_patch.txt') != '' }}
       with:
         script: |

.github/workflows/dependency-review.yml

@@ -0,0 +1,27 @@
+# Dependency Review Action
+#
+# This Action will scan dependency manifest files that change as part of a Pull Request,
+# surfacing known-vulnerable versions of the packages declared or updated in the PR.
+# Once installed, if the workflow run is marked as required,
+# PRs introducing known-vulnerable packages will be blocked from merging.
+#
+# Source repository: https://github.com/actions/dependency-review-action
+name: 'Dependency Review'
+on: [pull_request]
+
+permissions:
+  contents: read
+
+jobs:
+  dependency-review:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Harden Runner
+        uses: step-security/harden-runner@63c24ba6bd7ba022e95695ff85de572c04a18142 # v2.7.0
+        with:
+          egress-policy: audit
+
+      - name: 'Checkout Repository'
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
+      - name: 'Dependency Review'
+        uses: actions/dependency-review-action@0efb1d1d84fc9633afcdaad14c485cbbc90ef46c # v2.5.1

.github/workflows/detect-git-lfs.yml

@@ -3,13 +3,16 @@ name: Check for git LFS pointers
 on:
   pull_request:
 
+permissions:
+  contents: read
+
 jobs:
   build:
     runs-on: ubuntu-latest
 
     steps:
     - name: Check out code
-      uses: actions/checkout@v3
+      uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
       with:
         fetch-depth: 0
 

.github/workflows/detect-mpi-comm-world.yml

@@ -3,13 +3,16 @@ name: Check MPI_COMM_WORLD
 on:
   pull_request:
 
+permissions:
+  contents: read
+
 jobs:
   build:
     runs-on: ubuntu-latest
 
     steps:
     - name: Check out code
-      uses: actions/checkout@v3
+      uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
       with:
         fetch-depth: 0
 

.github/workflows/flag_prs_to_master.yml

@@ -19,12 +19,12 @@ jobs:
 
     steps:
     - name: Add label
-      uses: actions-ecosystem/action-add-labels@v1     
+      uses: actions-ecosystem/action-add-labels@18f1af5e3544586314bbe15c0273249c770b2daf # v1.1.3     
       if: "!contains(github.event.sender.login,'trilinos-autotester')"
       with:
         labels: "AT: WIP"     
     - name: Add comment
-      uses: mshick/add-pr-comment@v2
+      uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2.8.2
       if: "!contains(github.event.sender.login,'trilinos-autotester')"
       with:
          message: |

.github/workflows/scorecards.yml

@@ -0,0 +1,71 @@
+# This workflow uses actions that are not certified by GitHub. They are provided
+# by a third-party and are governed by separate terms of service, privacy
+# policy, and support documentation.
+
+name: Scorecard supply-chain security
+on:
+  # For Branch-Protection check. Only the default branch is supported. See
+  # https://github.com/ossf/scorecard/blob/main/docs/checks.md#branch-protection
+  branch_protection_rule:
+  # To guarantee Maintained check is occasionally updated. See
+  # https://github.com/ossf/scorecard/blob/main/docs/checks.md#maintained
+  schedule:
+    - cron: '20 7 * * 2'
+  push:
+    branches: ["master"]
+
+# Declare default permissions as read only.
+permissions: read-all
+
+jobs:
+  analysis:
+    name: Scorecard analysis
+    runs-on: ubuntu-latest
+    permissions:
+      # Needed to upload the results to code-scanning dashboard.
+      security-events: write
+      # Needed to publish results and get a badge (see publish_results below).
+      id-token: write
+      contents: read
+      actions: read
+
+    steps:
+      - name: "Checkout code"
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
+        with:
+          persist-credentials: false
+
+      - name: "Run analysis"
+        uses: ossf/scorecard-action@99c53751e09b9529366343771cc321ec74e9bd3d # v2.0.6
+        with:
+          results_file: results.sarif
+          results_format: sarif
+          # (Optional) "write" PAT token. Uncomment the `repo_token` line below if:
+          # - you want to enable the Branch-Protection check on a *public* repository, or
+          # - you are installing Scorecards on a *private* repository
+          # To create the PAT, follow the steps in https://github.com/ossf/scorecard-action#authentication-with-pat.
+          # repo_token: ${{ secrets.SCORECARD_TOKEN }}
+
+          # Public repositories:
+          #   - Publish results to OpenSSF REST API for easy access by consumers
+          #   - Allows the repository to include the Scorecard badge.
+          #   - See https://github.com/ossf/scorecard-action#publishing-results.
+          # For private repositories:
+          #   - `publish_results` will always be set to `false`, regardless
+          #     of the value entered here.
+          publish_results: true
+
+      # 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@a8a3f3ad30e3422c9c7b888a15615d19a852ae32 # v3.1.3
+        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@a56a03b370b87b26fde6d680755f818cfda0372b # v2.24.5
+        with:
+          sarif_file: results.sarif

.github/workflows/stale.yml

@@ -26,7 +26,7 @@ jobs:
       pull-requests: write  # for actions/stale to close stale PRs
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/stale@v4
+    - uses: actions/stale@a20b814fb01b71def3bd6f56e7494d667ddf28da # v4.1.1
       with:
         debug-only: false
         ascending: true

.github/workflows/title_to_mention.yml

@@ -18,14 +18,14 @@ jobs:
 
     steps:
     - name: Mention MueLu
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@67dcc547d311b736a8e6c5c236542148a47adc3d # v2.1.1
       if: (contains(github.event.action, 'labeled') && contains(github.event.label.name, 'MueLu')) || (contains(github.event.action, 'opened') && contains(github.event.issue.title, 'MueLu'))  
       with:
         issue-number: ${{ github.event.issue.number }}  
         body: |
           Automatic mention of the @trilinos/muelu team
     - name: Mention Ifpack2
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@67dcc547d311b736a8e6c5c236542148a47adc3d # v2.1.1
       if: (contains(github.event.action, 'labeled') && contains(github.event.label.name, 'Ifpack2')) || (contains(github.event.action, 'opened') && contains(github.event.issue.title, 'Ifpack2'))
       with:
         issue-number: ${{ github.event.issue.number }}  

.github/workflows/tpetra_muelu_label_to_project.yml

@@ -13,13 +13,13 @@ permissions:
 jobs:
   assign_one_project:
     permissions:
-      issues: write  # for actions/github-script@v6
+      issues: write  # for actions/github-script@d7906e4ad0b1822421a7e6a35d5ca353c962f410 # v6.4.1
       repository-projects: write  # for srggrs/assign-one-project-github-action to assign issues and PRs to repo project
     name: Assign to MueLu or Tpetra Project
     runs-on: ubuntu-latest
     steps:
     - name: Add MueLu Label
-      uses: actions/github-script@v6
+      uses: actions/github-script@d7906e4ad0b1822421a7e6a35d5ca353c962f410 # v6.4.1
       if: contains(github.event.issue.title, 'MueLu')
       with:
         script: |
@@ -30,7 +30,7 @@ jobs:
             labels: ["pkg: MueLu"]
           })
     - name: Add Tpetra Label
-      uses: actions/github-script@v6
+      uses: actions/github-script@d7906e4ad0b1822421a7e6a35d5ca353c962f410 # v6.4.1
       if: contains(github.event.issue.title, 'Tpetra')
       with:
         script: |
@@ -41,13 +41,13 @@ jobs:
             labels: ["pkg: Tpetra"]
           })          
     - name: Add to MueLu Project
-      uses: srggrs/[email protected]
+      uses: srggrs/assign-one-project-github-action@37de3321023f8c12ea85372d748ab2017b995bfd # 1.3.0
       if: contains(github.event.label.name, 'MueLu') || contains(github.event.issue.title, 'MueLu')
       with:
         project: 'https://github.com/trilinos/Trilinos/projects/5'
         column_name: 'Backlog'
     - name: Add to Tpetra Project
-      uses: srggrs/[email protected]    
+      uses: srggrs/assign-one-project-github-action@37de3321023f8c12ea85372d748ab2017b995bfd # 1.3.0    
       if: contains(github.event.label.name, 'Tpetra') || contains(github.event.issue.title, 'Tpetra')
       with:
         project: 'https://github.com/trilinos/Trilinos/projects/2'

packages/belos/src/BelosBiCGStabSolMgr.hpp

@@ -782,6 +782,15 @@ ReturnType BiCGStabSolMgr<ScalarType,MV,OP>::solve ()
                                "Belos::BiCGStabSolMgr::solve(): Invalid return from BiCGStabIter::iterate().");
           }
         }
+        catch (const StatusTestNaNError& e) {
+          // A NaN was detected in the solver.  Set the solution to zero and return unconverged.
+          achievedTol_ = MT::one();
+          Teuchos::RCP<MV> X = problem_->getLHS();
+          MVT::MvInit( *X, SCT::zero() );
+          printer_->stream(Warnings) << "Belos::BiCGStabSolMgr::solve(): Warning! NaN has been detected!" 
+                                     << std::endl;
+          return Unconverged; 
+        }
         catch (const std::exception &e) {
           printer_->stream(Errors) << "Error! Caught std::exception in BiCGStabIter::iterate() at iteration "
                                    << bicgstab_iter->getNumIters() << std::endl

packages/belos/src/BelosBlockCGSolMgr.hpp

@@ -1015,6 +1015,15 @@ ReturnType BlockCGSolMgr<ScalarType,MV,OP,true>::solve() {
               "to the Belos developers.");
           }
         }
+        catch (const StatusTestNaNError& e) {
+          // A NaN was detected in the solver.  Set the solution to zero and return unconverged.
+          achievedTol_ = MT::one();
+          Teuchos::RCP<MV> X = problem_->getLHS();
+          MVT::MvInit( *X, SCT::zero() );
+          printer_->stream(Warnings) << "Belos::BlockCGSolMgr::solve(): Warning! NaN has been detected!" 
+                                     << std::endl;
+          return Unconverged;
+        }
         catch (const std::exception &e) {
           std::ostream& err = printer_->stream (Errors);
           err << "Error! Caught std::exception in CGIteration::iterate() at "

packages/belos/src/BelosBlockGCRODRSolMgr.hpp

@@ -1964,7 +1964,7 @@ ReturnType BlockGCRODRSolMgr<ScalarType,MV,OP>::solve() {
           tmpNumBlocks = dim / blockSize_;  // Allow for a good breakdown.
         else{
           tmpNumBlocks = ( dim - blockSize_) / blockSize_;  // Allow for restarting.
-          printer_->stream(Warnings) << "Belos::BlockGmresSolMgr::solve():  Warning! Requested Krylov subspace dimension is larger than operator dimension!"
+          printer_->stream(Warnings) << "Belos::BlockGCRODRSolMgr::solve():  Warning! Requested Krylov subspace dimension is larger than operator dimension!"
                                      << std::endl << "The maximum number of blocks allowed for the Krylov subspace will be adjusted to " << tmpNumBlocks << std::endl;
           primeList.set("Num Blocks",Teuchos::as<int>(tmpNumBlocks));
         }
@@ -2019,7 +2019,7 @@ ReturnType BlockGCRODRSolMgr<ScalarType,MV,OP>::solve() {
           if ( expConvTest_->getLOADetected() ) {
             // we don't have convergence
             loaDetected_ = true;
-            printer_->stream(Warnings) << "Belos::BlockGmresSolMgr::solve(): Warning! Solver has experienced a loss of accuracy!" << std::endl;
+            printer_->stream(Warnings) << "Belos::BlockGCRODRSolMgr::solve(): Warning! Solver has experienced a loss of accuracy!" << std::endl;
           }
         }
         // *******************************************
@@ -2054,6 +2054,15 @@ ReturnType BlockGCRODRSolMgr<ScalarType,MV,OP>::solve() {
             isConverged = false;
         }
       } // end catch (const GmresIterationOrthoFailure &e)
+      catch (const StatusTestNaNError& e) {
+        // A NaN was detected in the solver.  Set the solution to zero and return unconverged.
+        achievedTol_ = MT::one();
+        Teuchos::RCP<MV> X = problem_->getLHS();
+        MVT::MvInit( *X, SCT::zero() );
+        printer_->stream(Warnings) << "Belos::BlockGCRODRSolMgr::solve(): Warning! NaN has been detected!" 
+                                     << std::endl;
+        return Unconverged;
+      }
       catch (const std::exception &e) {
         printer_->stream(Errors) << "Error! Caught std::exception in BlockGmresIter::iterate() at iteration "
                                  << block_gmres_iter->getNumIters() << std::endl

packages/belos/src/BelosBlockGmresSolMgr.hpp

@@ -1142,6 +1142,15 @@ ReturnType BlockGmresSolMgr<ScalarType,MV,OP>::solve() {
             break;
           }
         }
+        catch (const StatusTestNaNError& e) {
+          // A NaN was detected in the solver.  Set the solution to zero and return unconverged.
+          achievedTol_ = MT::one();
+          Teuchos::RCP<MV> X = problem_->getLHS();
+          MVT::MvInit( *X, SCT::zero() );
+          printer_->stream(Warnings) << "Belos::BlockGmresSolMgr::solve(): Warning! NaN has been detected!" 
+                                     << std::endl;
+          return Unconverged;
+        }
         catch (const std::exception &e) {
           printer_->stream(Errors) << "Error! Caught std::exception in BlockGmresIter::iterate() at iteration "
                                    << block_gmres_iter->getNumIters() << std::endl