Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20241213_175815 branch to master

.github/workflows/AT2.yml

@@ -288,7 +288,7 @@ jobs:
             --workspace-dir /home/runner/_work/Trilinos \
             --source-dir ${GITHUB_WORKSPACE} \
             --build-dir /home/Trilinos/build \
-            --dashboard-build-name=PR-${{ github.event.pull_request.number }}_${AT2_IMAGE}_release_static_uvm \
+            --dashboard-build-name=PR-${{ github.event.pull_request.number }}_${AT2_IMAGE}_release_static \
             --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 \
@@ -385,7 +385,7 @@ 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 \
+            --skip-create-packageenables \
       - name: Summary
         if: ${{ !cancelled() }}
         shell: bash -l {0}

.github/workflows/codeql.yml

@@ -45,7 +45,7 @@ jobs:
       uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@f09c1c0a94de965c15400f5634aa42fac8fb8f88 # v3.27.5
+      uses: github/codeql-action/init@aa578102511db1f4524ed59b8cc2bae4f6e88195 # v3.27.6
       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@f09c1c0a94de965c15400f5634aa42fac8fb8f88 # v3.27.5
+      uses: github/codeql-action/analyze@aa578102511db1f4524ed59b8cc2bae4f6e88195 # v3.27.6
       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@f09c1c0a94de965c15400f5634aa42fac8fb8f88 # v3.27.5
+        uses: github/codeql-action/upload-sarif@aa578102511db1f4524ed59b8cc2bae4f6e88195 # v3.27.6
         with:
           sarif_file: results.sarif

packages/amesos2/cmake/Amesos2_config.h.in

@@ -110,3 +110,9 @@
 
 /* Define to 1 if SuperLU's *gssvx and *gsisx routines need a GlobalLU_t argument. */
 #cmakedefine HAVE_AMESOS2_SUPERLU5_API
+
+#cmakedefine HAVE_AMESOS2_XPETRA
+#cmakedefine HAVE_AMESOS2_ZOLTAN2CORE
+#ifdef HAVE_AMESOS2_ZOLTAN2CORE
+#  define HAVE_AMESOS2_ZOLTAN2
+#endif

packages/amesos2/cmake/Dependencies.cmake

@@ -5,7 +5,7 @@
 SET(LIB_REQUIRED_DEP_PACKAGES Teuchos Tpetra TrilinosSS Kokkos)
 SET(LIB_OPTIONAL_DEP_PACKAGES Epetra EpetraExt ShyLU_NodeBasker ShyLU_NodeTacho)
 SET(TEST_REQUIRED_DEP_PACKAGES)
-SET(TEST_OPTIONAL_DEP_PACKAGES ShyLU_NodeBasker ShyLU_NodeTacho Kokkos TrilinosSS)
+SET(TEST_OPTIONAL_DEP_PACKAGES ShyLU_NodeBasker ShyLU_NodeTacho Kokkos TrilinosSS Xpetra Zoltan2Core)
 # SET(LIB_REQUIRED_DEP_TPLS SuperLU)
 SET(LIB_REQUIRED_DEP_TPLS )
 SET(LIB_OPTIONAL_DEP_TPLS MPI SuperLU SuperLUMT SuperLUDist LAPACK UMFPACK PARDISO_MKL CSS_MKL ParMETIS METIS Cholmod MUMPS STRUMPACK CUSPARSE CUSOLVER)

packages/amesos2/example/GappedMtxGIDs-1proc.cpp

@@ -160,8 +160,10 @@ int main(int argc, char *argv[]) {
          "does not result in the same Map.");
     }
 
-    if ( myRank == 0 && verbose ) {
-      *fos << "\nrowMap->describe output:" << endl;
+    if ( verbose ) {
+      if ( myRank == 0 ) {
+        *fos << "\nrowMap->describe output:" << endl;
+      }
       rowMap->describe(*fos, Teuchos::VERB_EXTREME);
     }
 
@@ -186,16 +188,20 @@ int main(int argc, char *argv[]) {
       A = readCrsMatrixFromFile (mtx_name, fos, rowMap, domainMap, rangeMap, convert_mtx_to_zero_base, num_header_lines);
     }
 
-    if ( myRank == 0 && verbose ) {
-      *fos << "A->describe" << endl;
+    if ( verbose ) {
+      if ( myRank == 0 ) {
+        *fos << "A->describe" << endl;
+      }
       A->describe(*fos, Teuchos::VERB_EXTREME);
     }
 
 
     RCP<MV> RHS;
     RHS = Tpetra::MatrixMarket::Reader<MAT>::readDenseFile (rhs_name, comm, rangeMap);
-    if ( myRank == 0 && verbose ) {
-      *fos << "RHS->describe" << endl;
+    if ( verbose ) {
+      if ( myRank == 0 ) {
+        *fos << "RHS->describe" << endl;
+      }
       RHS->describe(*fos, Teuchos::VERB_EXTREME);
     }
 
@@ -410,6 +416,8 @@ readCrsMatrixFromFile (const std::string& matrixFilename,
     for (typename Teuchos::Array<GO>::size_type i=0; i<gblRowInds.size(); i++) {
       A->insertGlobalValues (gblRowInds[i], gblColInds(i,1), vals(i,1));
     }
+  } else {
+    A = Teuchos::rcp(new MAT(rowMap, 0));
   }
 
   A->fillComplete (domainMap, rangeMap);

packages/amesos2/example/SimpleSolve_File.cpp

@@ -12,6 +12,9 @@
 #include <Teuchos_oblackholestream.hpp>
 #include <Teuchos_VerboseObject.hpp>
 #include <Teuchos_CommandLineProcessor.hpp>
+#include <Teuchos_StackedTimer.hpp>
+#include <Teuchos_ParameterList.hpp>
+#include <Teuchos_ParameterXMLFileReader.hpp>
 
 #include <Tpetra_Core.hpp>
 #include <Tpetra_Map.hpp>
@@ -22,8 +25,16 @@
 #include <MatrixMarket_Tpetra.hpp>
 #include <Tpetra_Import.hpp>
 
-#include "Amesos2.hpp"
-#include "Amesos2_Version.hpp"
+#include <Amesos2.hpp>
+#include <Amesos2_Version.hpp>
+
+#if defined(HAVE_AMESOS2_XPETRA) && defined(HAVE_AMESOS2_ZOLTAN2)
+# include <Zoltan2_OrderingProblem.hpp>
+# include <Zoltan2_PartitioningProblem.hpp>
+# include <Zoltan2_TpetraRowGraphAdapter.hpp>
+# include <Zoltan2_TpetraCrsMatrixAdapter.hpp>
+# include <Zoltan2_XpetraMultiVectorAdapter.hpp>
+#endif
 
 
 int main(int argc, char *argv[]) {
@@ -32,7 +43,9 @@ int main(int argc, char *argv[]) {
   typedef Tpetra::CrsMatrix<>::scalar_type Scalar;
   typedef Tpetra::Map<>::local_ordinal_type LO;
   typedef Tpetra::Map<>::global_ordinal_type GO;
+  typedef Tpetra::Map<>::node_type NO;
 
+  typedef Tpetra::RowGraph<LO, GO, NO> Graph;
   typedef Tpetra::CrsMatrix<Scalar,LO,GO> MAT;
   typedef Tpetra::MultiVector<Scalar,LO,GO> MV;
 
@@ -51,24 +64,32 @@ int main(int argc, char *argv[]) {
 
   Teuchos::oblackholestream blackhole;
 
-  bool printMatrix   = false;
-  bool printSolution = false;
-  bool checkSolution = false;
-  bool printTiming   = false;
-  bool allprint      = false;
+  bool printMatrix     = false;
+  bool printSolution   = false;
+  bool checkSolution   = false;
+  bool printTiming     = false;
+  bool useStackedTimer = false;
+  bool allprint        = false;
   bool verbose = (myRank==0);
+  bool useZoltan2 = false;
+  bool useParMETIS = false;
   std::string mat_filename("arc130.mtx");
   std::string rhs_filename("");
   std::string solvername("Superlu");
+  std::string xml_filename("");
   Teuchos::CommandLineProcessor cmdp(false,true);
   cmdp.setOption("verbose","quiet",&verbose,"Print messages and results.");
   cmdp.setOption("filename",&mat_filename,"Filename for Matrix-Market test matrix.");
   cmdp.setOption("rhs_filename",&rhs_filename,"Filename for Matrix-Market right-hand-side.");
   cmdp.setOption("solvername",&solvername,"Name of solver.");
+  cmdp.setOption("xml_filename",&xml_filename,"XML Filename for Solver parameters.");
   cmdp.setOption("print-matrix","no-print-matrix",&printMatrix,"Print the full matrix after reading it.");
   cmdp.setOption("print-solution","no-print-solution",&printSolution,"Print solution vector after solve.");
   cmdp.setOption("check-solution","no-check-solution",&checkSolution,"Check solution vector after solve.");
+  cmdp.setOption("use-zoltan2","no-zoltan2",&useZoltan2,"Use Zoltan2 (Hypergraph) for repartitioning");
+  cmdp.setOption("use-parmetis","no-parmetis",&useParMETIS,"Use ParMETIS for repartitioning");
   cmdp.setOption("print-timing","no-print-timing",&printTiming,"Print solver timing statistics");
+  cmdp.setOption("use-stacked-timer","no-stacked-timer",&useStackedTimer,"Use StackedTimer to print solver timing statistics");
   cmdp.setOption("all-print","root-print",&allprint,"All processors print to out");
   if (cmdp.parse(argc,argv) != Teuchos::CommandLineProcessor::PARSE_SUCCESSFUL) {
     return -1;
@@ -78,27 +99,17 @@ int main(int argc, char *argv[]) {
   RCP<Teuchos::FancyOStream> fos = Teuchos::fancyOStream(Teuchos::rcpFromRef(out));
 
   // Say hello
-  out << myRank << " : " << Amesos2::version() << std::endl << std::endl;
+  out << myRank << " : " << Amesos2::version() << " on " << comm->getSize() << " MPIs" << std::endl << std::endl;
 
   const size_t numVectors = 1;
 
-  RCP<MAT> A = Tpetra::MatrixMarket::Reader<MAT>::readSparseFile(mat_filename, comm);
-  if( printMatrix ){
-    A->describe(*fos, Teuchos::VERB_EXTREME);
-  }
-  else if( verbose ){
-    std::cout << std::endl << A->description() << std::endl << std::endl;
-  }
+  // Read matrix
+  RCP<const MAT> A = Tpetra::MatrixMarket::Reader<MAT>::readSparseFile(mat_filename, comm);
 
-  // get the maps
-  RCP<const Map<LO,GO> > dmnmap = A->getDomainMap();
+  // get the map (Range Map used for both X & B)
   RCP<const Map<LO,GO> > rngmap = A->getRangeMap();
-
-  GO nrows = dmnmap->getGlobalNumElements();
-  RCP<Map<LO,GO> > root_map
-    = rcp( new Map<LO,GO>(nrows,myRank == 0 ? nrows : 0,0,comm) );
-  RCP<MV> Xhat = rcp( new MV(root_map,numVectors) );
-  RCP<Import<LO,GO> > importer = rcp( new Import<LO,GO>(dmnmap,root_map) );
+  RCP<const Map<LO,GO> > dmnmap = A->getDomainMap();
+  GO nrows = A->getGlobalNumRows();
 
   // Create random X
   RCP<MV> X = rcp(new MV(dmnmap,numVectors));
@@ -122,6 +133,69 @@ int main(int argc, char *argv[]) {
     B = Tpetra::MatrixMarket::Reader<MAT>::readDenseFile (rhs_filename, comm, rngmap);
   }
 
+  if (useZoltan2 || useParMETIS) {
+#if defined(HAVE_AMESOS2_XPETRA) && defined(HAVE_AMESOS2_ZOLTAN2)
+    // Specify partitioning parameters
+    Teuchos::ParameterList zoltan_params;
+    zoltan_params.set("partitioning_approach", "partition");
+    //
+    if (useParMETIS) {
+      if (comm->getRank() == 0) {
+        std::cout << "Using Zoltan2(ParMETIS)" << std::endl;
+      }
+      zoltan_params.set("algorithm", "parmetis");
+      zoltan_params.set("symmetrize_input", "transpose");
+      zoltan_params.set("partitioning_objective", "minimize_cut_edge_weight");
+    } else {
+      if (comm->getRank() == 0) {
+        std::cout << "Using Zoltan2(HyperGraph)" << std::endl;
+      }
+      zoltan_params.set("algorithm", "phg");
+    }
+
+    // Create an input adapter for the Tpetra matrix.
+    Zoltan2::TpetraRowGraphAdapter<Graph>
+      zoltan_graph(A->getGraph());
+
+    // Create and solve partitioning problem
+    Zoltan2::PartitioningProblem<Zoltan2::TpetraRowGraphAdapter<Graph>>
+      problem(&zoltan_graph, &zoltan_params);
+    problem.solve();
+
+    // Redistribute matrix
+    RCP<MAT> zoltan_A;
+    Zoltan2::TpetraCrsMatrixAdapter<MAT> zoltan_matrix(A);
+    zoltan_matrix.applyPartitioningSolution (*A, zoltan_A, problem.getSolution());
+    // Set it as coefficient matrix, and update range map
+    A = zoltan_A;
+    rngmap = A->getRangeMap();
+
+    // Redistribute RHS
+    RCP<MV> zoltan_b;
+    Zoltan2::XpetraMultiVectorAdapter<MV> adapterRHS(rcpFromRef (*B));
+    adapterRHS.applyPartitioningSolution (*B, zoltan_b, problem.getSolution());
+    // Set it as RHS
+    B = zoltan_b;
+
+    // Redistribute Sol
+    RCP<MV> zoltan_x;
+    Zoltan2::XpetraMultiVectorAdapter<MV> adapterSol(rcpFromRef (*X));
+    adapterSol.applyPartitioningSolution (*X, zoltan_x, problem.getSolution());
+    // Set it as Sol
+    X = zoltan_x;
+#else
+    TEUCHOS_TEST_FOR_EXCEPTION(
+      useZoltan2, std::invalid_argument,
+      "Both Xpetra and Zoltan2 are needed to use Zoltan2.");
+#endif
+  }
+  if( printMatrix ){
+    A->describe(*fos, Teuchos::VERB_EXTREME);
+  }
+  else if( verbose ){
+    std::cout << std::endl << A->description() << std::endl << std::endl;
+  }
+
   // Constructor from Factory
   RCP<Amesos2::Solver<MAT,MV> > solver;
   if( !Amesos2::query(solvername) ){
@@ -130,11 +204,30 @@ int main(int argc, char *argv[]) {
   }
 
   solver = Amesos2::create<MAT,MV>(solvername, A, X, B);
+  if (xml_filename != "") {
+    Teuchos::ParameterList test_params =
+      Teuchos::ParameterXMLFileReader(xml_filename).getParameters();
+    Teuchos::ParameterList& amesos2_params = test_params.sublist("Amesos2");
+    *fos << amesos2_params.currentParametersString() << std::endl;
+    solver->setParameters( Teuchos::rcpFromRef(amesos2_params) );
+  }
 
+  RCP<Teuchos::StackedTimer> stackedTimer;
+  if(useStackedTimer) {
+    stackedTimer = rcp(new Teuchos::StackedTimer("Amesos2 SimpleSolve-File"));
+    Teuchos::TimeMonitor::setStackedTimer(stackedTimer);
+  }
   solver->symbolicFactorization().numericFactorization().solve();
+  if(useStackedTimer) {
+    stackedTimer->stopBaseTimer();
+  }
 
   if( printSolution ){
     // Print the solution
+    RCP<Map<LO,GO> > root_map
+      = rcp( new Map<LO,GO>(nrows,myRank == 0 ? nrows : 0,0,comm) );
+    RCP<MV> Xhat = rcp( new MV(root_map,numVectors) );
+    RCP<Import<LO,GO> > importer = rcp( new Import<LO,GO>(rngmap,root_map) );
     if( allprint ){
       if( myRank == 0 ) *fos << "Solution :" << std::endl;
       Xhat->describe(*fos,Teuchos::VERB_EXTREME);
@@ -167,11 +260,20 @@ int main(int argc, char *argv[]) {
     if (myRank == 0) *fos << std::endl;
   }
 
-  if( printTiming ){
+  if(useStackedTimer) {
+    Teuchos::StackedTimer::OutputOptions options;
+    options.num_histogram=3;
+    options.print_warnings = false;
+    options.output_histogram = true;
+    options.output_fraction=true;
+    options.output_minmax = true;
+    stackedTimer->report(std::cout, comm, options);
+  } else if( printTiming ){
     // Print some timing statistics
     solver->printTiming(*fos);
+  } else {
+    Teuchos::TimeMonitor::summarize();
   }
-  Teuchos::TimeMonitor::summarize();
 
   // We are done.
   return 0;