Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20241122_175815 branch to master

.github/workflows/AT2.yml

@@ -92,7 +92,7 @@ jobs:
 
           printf "\n\n\n"
 
-          echo "image: ${AT2_IMAGE:-unknown}"
+          echo "image: ${AT2_IMAGE_FULLPATH:-${AT2_IMAGE:-unknown}}"
 
           python3 ${GITHUB_WORKSPACE}/packages/framework/pr_tools/PullRequestLinuxDriverTest.py \
             --target-branch-name ${{ github.event.pull_request.base.ref }} \
@@ -107,14 +107,16 @@ jobs:
             --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
+            --filename-packageenables ./packageEnables.cmake \
+            --max-cores-allowed=29 \
+            --num-concurrent-tests=16
       - 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 "image: ${AT2_IMAGE_FULLPATH:-${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)
@@ -183,7 +185,7 @@ jobs:
 
           printf "\n\n\n"
 
-          echo "image: ${AT2_IMAGE:-unknown}"
+          echo "image: ${AT2_IMAGE_FULLPATH:-${AT2_IMAGE:-unknown}}"
 
           python3 ${GITHUB_WORKSPACE}/packages/framework/pr_tools/PullRequestLinuxDriverTest.py \
             --target-branch-name ${{ github.event.pull_request.base.ref }} \
@@ -198,14 +200,16 @@ jobs:
             --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
+            --filename-packageenables ./packageEnables.cmake \
+            --max-cores-allowed=29 \
+            --num-concurrent-tests=16
       - 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 "image: ${AT2_IMAGE_FULLPATH:-${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)
@@ -273,7 +277,7 @@ jobs:
 
           printf "\n\n\n"
 
-          echo "image: ${AT2_IMAGE:-unknown}"
+          echo "image: ${AT2_IMAGE_FULLPATH:-${AT2_IMAGE:-unknown}}"
           type python
           python3 ${GITHUB_WORKSPACE}/packages/framework/pr_tools/PullRequestLinuxDriverTest.py \
             --target-branch-name ${{ github.event.pull_request.base.ref }} \
@@ -297,7 +301,7 @@ jobs:
         working-directory: /home/Trilinos/build
         run: |
           echo "## Image" >> $GITHUB_STEP_SUMMARY
-          echo "image: ${AT2_IMAGE:-unknown}" >> $GITHUB_STEP_SUMMARY
+          echo "image: ${AT2_IMAGE_FULLPATH:-${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)
@@ -365,7 +369,7 @@ jobs:
 
           printf "\n\n\n"
 
-          echo "image: ${AT2_IMAGE:-unknown}"
+          echo "image: ${AT2_IMAGE_FULLPATH:-${AT2_IMAGE:-unknown}}"
           type python
           python3 ${GITHUB_WORKSPACE}/packages/framework/pr_tools/PullRequestLinuxDriverTest.py \
             --target-branch-name ${{ github.event.pull_request.base.ref }} \
@@ -387,7 +391,7 @@ jobs:
         working-directory: /home/Trilinos/build
         run: |
           echo "## Image" >> $GITHUB_STEP_SUMMARY
-          echo "image: ${AT2_IMAGE:-unknown}" >> $GITHUB_STEP_SUMMARY
+          echo "image: ${AT2_IMAGE_FULLPATH:-${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)

.github/workflows/codeql.yml

@@ -45,7 +45,7 @@ jobs:
       uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@662472033e021d55d94146f66f6058822b0b39fd # v3.27.0
+      uses: github/codeql-action/init@ea9e4e37992a54ee68a9622e985e60c8e8f12d9f # v3.27.4
       with:
         languages: ${{ matrix.language }}
         build-mode: ${{ matrix.build-mode }}
@@ -108,6 +108,6 @@ jobs:
           ninja -j 16
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@662472033e021d55d94146f66f6058822b0b39fd # v3.27.0
+      uses: github/codeql-action/analyze@ea9e4e37992a54ee68a9622e985e60c8e8f12d9f # v3.27.4
       with:
         category: "/language:${{matrix.language}}"

.github/workflows/dependency-review.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
+        uses: step-security/harden-runner@0080882f6c36860b6ba35c610c98ce87d4e2f26f # v2.10.2
         with:
           egress-policy: audit
 

.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@662472033e021d55d94146f66f6058822b0b39fd # v3.27.0
+        uses: github/codeql-action/upload-sarif@ea9e4e37992a54ee68a9622e985e60c8e8f12d9f # v3.27.4
         with:
           sarif_file: results.sarif

.gitignore

@@ -163,3 +163,7 @@ rsync.*
 
 # pycharm ide
 .idea
+
+# clangd server stuff
+.cache/
+compile_commands.json

packages/amesos2/src/Amesos2_EpetraCrsMatrix_MatrixAdapter_def.hpp

@@ -36,7 +36,8 @@ namespace Amesos2 {
       o_map = rcpFromRef(this->mat_->RowMap());
       t_map = Util::tpetra_map_to_epetra_map<local_ordinal_t,global_ordinal_t,global_size_t,node_t>(*map);
 
-      RCP<Epetra_CrsMatrix> t_mat = rcp(new Epetra_CrsMatrix(Copy, *t_map, this->getMaxRowNNZ()));
+      int maxRowNNZ = 0; // this->getMaxRowNNZ();
+      RCP<Epetra_CrsMatrix> t_mat = rcp(new Epetra_CrsMatrix(Copy, *t_map, maxRowNNZ));
 
       Epetra_Import importer(*t_map, *o_map);
       t_mat->Import(*(this->mat_), importer, Insert);

packages/amesos2/src/Amesos2_ShyLUBasker_def.hpp

@@ -557,7 +557,7 @@ bool
 ShyLUBasker<Matrix,Vector>::loadA_impl(EPhase current_phase)
 {
   using Teuchos::as;
-  if(current_phase == SOLVE) return (false);
+  if(current_phase == SOLVE || current_phase == PREORDERING ) return( false );
 
   #ifdef HAVE_AMESOS2_TIMERS
   Teuchos::TimeMonitor convTimer(this->timers_.mtxConvTime_);
@@ -573,7 +573,8 @@ ShyLUBasker<Matrix,Vector>::loadA_impl(EPhase current_phase)
   {
 
     // Only the root image needs storage allocated
-    if( this->root_ ){
+    if( this->root_ && current_phase == SYMBFACT )
+    {
       Kokkos::resize(nzvals_view_, this->globalNumNonZeros_);
       Kokkos::resize(rowind_view_, this->globalNumNonZeros_);
       Kokkos::resize(colptr_view_, this->globalNumCols_ + 1); //this will be wrong for case of gapped col ids, e.g. 0,2,4,9; num_cols = 10 ([0,10)) but num GIDs = 4...

packages/framework/pr_tools/PullRequestLinuxDriver.sh

@@ -52,6 +52,8 @@ function bootstrap_modules() {
         module unload sems-python
         module load sems-git/2.37.0
         module load sems-python/3.9.0
+        execute_command_checked "module load sems-ccache"
+        configure_ccache
 
         module list
     else

packages/intrepid2/src/Cell/Intrepid2_CellData.cpp

@@ -21,6 +21,9 @@ const CellTopologyData*
 Intrepid2::getCellTopologyData(const unsigned& cellTopologyKey){
     const CellTopologyData* cellTopologyData;
     switch (cellTopologyKey) {
+      case shards::Node::key:
+      cellTopologyData = shards::getCellTopologyData<shards::Node>();
+      break;
       case shards::Line<2>::key:
       cellTopologyData = shards::getCellTopologyData<shards::Line<2>>();
       break;

packages/muelu/doc/UsersGuide/masterList.xml

@@ -876,6 +876,14 @@
       <comment-ML>parameter not existing in ML</comment-ML>
     </parameter>
 
+    <parameter>
+      <name>aggregation: output file: aggregate qualities</name>
+      <type>bool</type>
+      <default>false</default>
+      <description>Whether to plot the aggregate quality.</description>
+      <comment-ML>parameter not existing in ML</comment-ML>
+    </parameter>
+
     <parameter>
       <name>aggregation: params</name>
       <type>\parameterlist</type>

packages/muelu/doc/UsersGuide/options_aggregation.tex

@@ -62,6 +62,8 @@
 
 \cbb{aggregation: output file: build colormap}{bool}{false}{Whether to output a random colormap in a separate XML file.}
 
+\cbb{aggregation: output file: aggregate qualities}{bool}{false}{Whether to plot the aggregate quality.}
+
 \cbb{aggregation: mesh layout}{string}{Global Lexicographic}{Type of ordering for structured mesh aggregation. Possible values: "Global Lexicographic" and "Local Lexicographic".}
 
 \cbb{aggregation: output type}{string}{Aggregates}{Type of object holding the aggregation data. Possible values: "Aggregates" or "CrsGraph".}

packages/muelu/doc/UsersGuide/paramlist.tex

@@ -115,6 +115,8 @@
 
 \cbb{aggregation: output file: build colormap}{bool}{false}{Whether to output a random colormap in a separate XML file.}
 
+\cbb{aggregation: output file: aggregate qualities}{bool}{false}{Whether to plot the aggregate quality.}
+
 \cbb{aggregation: mesh layout}{string}{Global Lexicographic}{Type of ordering for structured mesh aggregation. Possible values: "Global Lexicographic" and "Local Lexicographic".}
 
 \cbb{aggregation: output type}{string}{Aggregates}{Type of object holding the aggregation data. Possible values: "Aggregates" or "CrsGraph".}

packages/muelu/doc/UsersGuide/paramlist_hidden.tex

@@ -183,6 +183,8 @@
 
 \cbb{aggregation: output file: build colormap}{bool}{false}{Whether to output a random colormap in a separate XML file.}
 
+\cbb{aggregation: output file: aggregate qualities}{bool}{false}{Whether to plot the aggregate quality.}
+
 \cba{aggregation: params}{\parameterlist}{Sublist of options for use by aggregation.}
 
 \cba{strength-of-connection: params}{\parameterlist}{Sublist of options for use by coalesce/drop.}

packages/muelu/src/Graph/MatrixTransformation/MueLu_CoalesceDropFactory_def.hpp

@@ -1251,6 +1251,7 @@ void CoalesceDropFactory<Scalar, LocalOrdinal, GlobalOrdinal, Node>::Build(Level
               isBoundary = pointBoundaryNodes[row];
             } else {
               // The amalgamated row is marked as Dirichlet iff all point rows are Dirichlet
+              isBoundary = true;
               for (LO j = 0; j < blkSize; j++) {
                 if (!pointBoundaryNodes[row * blkSize + j]) {
                   isBoundary = false;
@@ -1514,7 +1515,7 @@ void CoalesceDropFactory<Scalar, LocalOrdinal, GlobalOrdinal, Node>::Build(Level
       }
     }
 
-    if ((GetVerbLevel() & Statistics1) && !(A->GetFixedBlockSize() > 1 && threshold != STS::zero())) {
+    if (GetVerbLevel() & Statistics1) {
       RCP<const Teuchos::Comm<int>> comm = A->getRowMap()->getComm();
       GO numGlobalTotal, numGlobalDropped;
       MueLu_sumAll(comm, numTotal, numGlobalTotal);

packages/muelu/src/Graph/UncoupledAggregation/MueLu_AggregationPhase2bAlgorithm_decl.hpp

@@ -73,17 +73,13 @@ class AggregationPhase2bAlgorithm : public MueLu::AggregationAlgorithmBase<Local
                        typename AggregationAlgorithmBase<LocalOrdinal, GlobalOrdinal, Node>::AggStatType& aggStat,
                        LO& numNonAggregatedNodes) const;
 
-  void BuildAggregatesRandom(const ParameterList& params,
-                             const LWGraph_kokkos& graph,
-                             Aggregates& aggregates,
-                             typename AggregationAlgorithmBase<LocalOrdinal, GlobalOrdinal, Node>::AggStatType& aggStat,
-                             LO& numNonAggregatedNodes) const;
-
-  void BuildAggregatesDeterministic(const ParameterList& params,
-                                    const LWGraph_kokkos& graph,
-                                    Aggregates& aggregates,
-                                    typename AggregationAlgorithmBase<LocalOrdinal, GlobalOrdinal, Node>::AggStatType& aggStat,
-                                    LO& numNonAggregatedNodes) const;
+  template <bool deterministic>
+  void BuildAggregates(const ParameterList& params,
+                       const LWGraph_kokkos graph,
+                       Aggregates& aggregates,
+                       typename AggregationAlgorithmBase<LocalOrdinal, GlobalOrdinal, Node>::AggStatType aggStat,
+                       LO& numNonAggregatedNodes) const;
+
   //@}
 
   std::string description() const { return "Phase 2b (expansion)"; }