Merge Pull Request #13794 from trilinos/Trilinos/master_merge_2025020…

…7_175815 Automatically Merged using Trilinos Master Merge AutoTester PR Title: b'Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20250207_175815 branch to master' PR Author: trilinos-autotester
trilinos · Feb 8, 2025 · 62ff542 · 62ff542
2 parents bd59c87 + 95b49d7
commit 62ff542
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diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -45,7 +45,7 @@ jobs:
       uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@17a820bf2e43b47be2c72b39cc905417bc1ab6d0 # v3.28.6
+      uses: github/codeql-action/init@dd746615b3b9d728a6a37ca2045b68ca76d4841a # v3.28.8
       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@17a820bf2e43b47be2c72b39cc905417bc1ab6d0 # v3.28.6
+      uses: github/codeql-action/analyze@dd746615b3b9d728a6a37ca2045b68ca76d4841a # v3.28.8
       with:
         category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/scorecards.yml b/.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@17a820bf2e43b47be2c72b39cc905417bc1ab6d0 # v3.28.6
+        uses: github/codeql-action/upload-sarif@dd746615b3b9d728a6a37ca2045b68ca76d4841a # v3.28.8
         with:
           sarif_file: results.sarif
diff --git a/cmake/ProjectCompilerPostConfig.cmake b/cmake/ProjectCompilerPostConfig.cmake
@@ -76,6 +76,7 @@ set(promoted_warnings
     sequence-point
     sign-compare
     strict-aliasing
+    switch
     type-limits
     uninitialized
     unused-function
@@ -95,4 +96,6 @@ elseif("${Trilinos_WARNINGS_MODE}" STREQUAL "ERROR")
     disable_warnings_for_deprecated_packages()
 endif()
 
-disable_warnings("${explicitly_disabled_warnings}")
+if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+    disable_warnings("${explicitly_disabled_warnings}")
+endif()
diff --git a/packages/amesos2/example/SimpleSolve_File.cpp b/packages/amesos2/example/SimpleSolve_File.cpp
@@ -64,6 +64,7 @@ int main(int argc, char *argv[]) {
 
   Teuchos::oblackholestream blackhole;
 
+  bool multi_solve     = false;
   bool printMatrix     = false;
   bool printSolution   = false;
   bool checkSolution   = false;
@@ -83,6 +84,7 @@ int main(int argc, char *argv[]) {
   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("multi-solve","no-multi-solve",&multi_solve,"Test multiple numFacto & solve per symbolic.");
   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.");
@@ -104,7 +106,7 @@ int main(int argc, char *argv[]) {
   const size_t numVectors = 1;
 
   // Read matrix
-  RCP<const MAT> A = Tpetra::MatrixMarket::Reader<MAT>::readSparseFile(mat_filename, comm);
+  RCP<MAT> A = Tpetra::MatrixMarket::Reader<MAT>::readSparseFile(mat_filename, comm);
 
   // get the map (Range Map used for both X & B)
   RCP<const Map<LO,GO> > rngmap = A->getRangeMap();
@@ -217,11 +219,34 @@ int main(int argc, char *argv[]) {
     stackedTimer = rcp(new Teuchos::StackedTimer("Amesos2 SimpleSolve-File"));
     Teuchos::TimeMonitor::setStackedTimer(stackedTimer);
   }
-  solver->symbolicFactorization().numericFactorization().solve();
+  solver->symbolicFactorization(); comm->barrier();
+  solver->numericFactorization();  comm->barrier();
+  solver->solve(); comm->barrier();
+  if (multi_solve) {
+    {
+      // change (1,1) diagonal entry value
+      Teuchos::Array<GO> gblColIndsBuf (1);
+      Teuchos::Array<Scalar> valsBuf (1);
+      valsBuf[0] = 7.0;
+      gblColIndsBuf[0] = 0;
+
+      Teuchos::ArrayView<GO> gblColInds = gblColIndsBuf.view (0, 1);
+      Teuchos::ArrayView<Scalar> vals = valsBuf.view (0, 1);
+
+      A->resumeFill();
+      A->replaceGlobalValues (0, gblColInds, vals);
+      A->fillComplete();
+    }
+    // perform numeric for the second time
+    solver->numericFactorization();
+
+    // chage RHS, and re-do solve
+    B->putScalar(10);
+    solver->solve();
+  }
   if(useStackedTimer) {
     stackedTimer->stopBaseTimer();
   }
-
   if( printSolution ){
     // Print the solution
     RCP<Map<LO,GO> > root_map

diff --git a/packages/amesos2/src/Amesos2_KLU2_def.hpp b/packages/amesos2/src/Amesos2_KLU2_def.hpp
@@ -453,7 +453,7 @@ KLU2<Matrix,Vector>::loadA_impl(EPhase current_phase)
         Kokkos::resize(host_col_ptr_view_, this->globalNumRows_ + 1);
     }
 
-    local_ordinal_type nnz_ret = 0;
+    local_ordinal_type nnz_ret = -1;
     bool gather_supported = (this->matrixA_->getComm()->getSize() > 1 && (std::is_same<scalar_type, float>::value || std::is_same<scalar_type, double>::value));
     {
 #ifdef HAVE_AMESOS2_TIMERS

diff --git a/packages/amesos2/src/Amesos2_ShyLUBasker_def.hpp b/packages/amesos2/src/Amesos2_ShyLUBasker_def.hpp
@@ -587,7 +587,7 @@ ShyLUBasker<Matrix,Vector>::loadA_impl(EPhase current_phase)
       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...
     }
 
-    local_ordinal_type nnz_ret = 0;
+    local_ordinal_type nnz_ret = -1;
     bool gather_supported = (this->matrixA_->getComm()->getSize() > 1 && (std::is_same<scalar_type, float>::value || std::is_same<scalar_type, double>::value));
     {
     #ifdef HAVE_AMESOS2_TIMERS

diff --git a/packages/amesos2/src/Amesos2_TpetraCrsMatrix_MatrixAdapter_def.hpp b/packages/amesos2/src/Amesos2_TpetraCrsMatrix_MatrixAdapter_def.hpp
@@ -98,16 +98,18 @@ namespace Amesos2 {
                     const EPhase current_phase) const
     {
       typedef Tpetra::Map< local_ordinal_t, global_ordinal_t, node_t> contiguous_map_type;
-      auto rowMap = this->mat_->getRowMap();
-      auto colMap = this->mat_->getColMap();
-      auto rowComm = rowMap->getComm();
-      auto colComm = colMap->getComm();
-
+      using Teuchos::RCP;
+      using Teuchos::rcp;
 #ifdef HAVE_AMESOS2_TIMERS
       auto reindexTimer = Teuchos::TimeMonitor::getNewTimer("Time to re-index matrix gids");
       Teuchos::TimeMonitor ReindexTimer(*reindexTimer);
 #endif
 
+      auto rowMap = this->mat_->getRowMap();
+      auto colMap = this->mat_->getColMap();
+      auto rowComm = rowMap->getComm();
+      auto colComm = colMap->getComm();
+
       GlobalOrdinal indexBase = rowMap->getIndexBase();
       GlobalOrdinal numDoFs = this->mat_->getGlobalNumRows();
       LocalOrdinal nRows = this->mat_->getLocalNumRows();
@@ -120,12 +122,17 @@ namespace Amesos2 {
         global_ordinal_t frow = tmpMap->getMinGlobalIndex();
 
         // Create new GID list for RowMap
-        Kokkos::View<global_ordinal_t*, HostExecSpaceType> rowIndexList ("indexList", nRows);
+        Kokkos::View<global_ordinal_t*, HostExecSpaceType> rowIndexList ("rowIndexList", nRows);
         for (local_ordinal_t k = 0; k < nRows; k++) {
           rowIndexList(k) = frow+k; // based on index-base of rowMap
         }
         // Create new GID list for ColMap
-        Kokkos::View<global_ordinal_t*, HostExecSpaceType> colIndexList ("indexList", nCols);
+        Kokkos::View<global_ordinal_t*, HostExecSpaceType> colIndexList ("colIndexList", nCols);
+        // initialize to catch col GIDs that are not in row GIDs
+        // they will be all assigned to (n+1)th columns
+        for (local_ordinal_t k = 0; k < nCols; k++) {
+          colIndexList(k) = numDoFs+indexBase;
+        }
         typedef Tpetra::MultiVector<global_ordinal_t,
                                     local_ordinal_t,
                                     global_ordinal_t,
@@ -307,9 +314,11 @@ namespace Amesos2 {
                 recvDispls(p+1) = recvDispls(p) + recvCounts(p);
               }
             }
-            // -- convert to global colids & convert to 0-base
+            // -- convert to global colids & ** convert to base-zero **
             KV_GO lclColind_ ("localColind_", lclColind.extent(0));
-            for (int i = 0; i < int(lclColind.extent(0)); i++) lclColind_(i) = (colMap->getGlobalElement((lclColind(i))) - colIndexBase);
+            for (int i = 0; i < int(lclColind.extent(0)); i++) {
+              lclColind_(i) = (colMap->getGlobalElement((lclColind(i))) - colIndexBase);
+            }
             if (column_major || need_to_perm) {
               Kokkos::resize(indices_t, indices.extent(0));
               Teuchos::gatherv<int, LocalOrdinal> (lclColind_.data(), lclColind_.extent(0), indices_t.data(),
@@ -326,6 +335,7 @@ namespace Amesos2 {
             Teuchos::RCP< Teuchos::Time > gatherTime = Teuchos::TimeMonitor::getNewCounter ("Amesos2::gather(transpose index)");
             Teuchos::TimeMonitor GatherTimer(*gatherTime);
 #endif
+            // (note: column idexes are now in base-0)
             if (column_major) {
               // Map to transpose
               Kokkos::resize(transpose_map, ret);
@@ -347,9 +357,14 @@ namespace Amesos2 {
                 int i = perm_l2g(row);
                 for (int k=pointers_t(i); k<pointers_t(i+1); k++) {
                   int col = indices_t(k);
-                  transpose_map(k) = pointers(1+col);
-                  indices(pointers(1+col)) = row;
-                  pointers(1+col) ++;
+                  if (col < nRows) {
+                    transpose_map(k) = pointers(1+col);
+                    indices(pointers(1+col)) = row;
+                    pointers(1+col) ++;
+                  } else {
+                    // extra columns
+                    transpose_map(k) = -1;
+                  }
                 }
               }
             } else if (need_to_perm) {
@@ -366,9 +381,13 @@ namespace Amesos2 {
                 int row = perm_g2l(i);
                 for (int k=pointers_t(i); k<pointers_t(i+1); k++) {
                   int col = indices_t(k);
-                  transpose_map(k) = pointers(1+row);
-                  indices(pointers(1+row)) = col;
-                  pointers(1+row) ++;
+                  if (col < nRows) {
+                    transpose_map(k) = pointers(1+row);
+                    indices(pointers(1+row)) = col;
+                    pointers(1+row) ++;
+                  } else {
+                    transpose_map(k) = -1;
+                  }
                 }
               }
             } else {
@@ -409,7 +428,9 @@ namespace Amesos2 {
 #endif
             if (transpose_map.extent(0) > 0) {
               for (int k=0; k<ret; k++) {
-                nzvals(transpose_map(k)) = nzvals_t(k);
+                if (transpose_map(k) >= 0) {
+                  nzvals(transpose_map(k)) = nzvals_t(k);
+                }
               }
             }
           }

diff --git a/packages/amesos2/test/solvers/CMakeLists.txt b/packages/amesos2/test/solvers/CMakeLists.txt
@@ -390,14 +390,22 @@ IF (${PACKAGE_NAME}_ENABLE_ShyLU_NodeBasker)
     STANDARD_PASS_OUTPUT
     )
 
-    ##Copy shylubasker_test.xml, but do not test
-    ##depends on not included matrices
+    ##Copy shylubasker_test.xml
     TRIBITS_COPY_FILES_TO_BINARY_DIR(SolverTestCopyShyLUBaskerFiles
     SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}
     SOURCE_FILES shylubasker_test.xml
     EXEDEPS Solver_Test
     )
 
+    ##Test only if ShyLU-Basker is enabled
+    TRIBITS_ADD_TEST(
+    Solver_Test
+    NAME ShyLUBasker_Solver_Test
+    ARGS "--xml-params=shylubasker_test.xml --filedir=${CMAKE_CURRENT_BINARY_DIR}/../matrices/ --multiple-solves --refactor"
+    STANDARD_PASS_OUTPUT
+    NUM_MPI_PROCS 2
+    COMM serial mpi
+    )
 ENDIF()
 
 ##### MUMPS Tests ####

diff --git a/packages/amesos2/test/solvers/shylubasker_test.xml b/packages/amesos2/test/solvers/shylubasker_test.xml
@@ -6,7 +6,7 @@
 
   <!-- Wathen120 is a bad performance matrix that is symm with nice supernodes -->
   <ParameterList name="wathen120.mtx">
-    <ParameterList name="Basker">
+    <ParameterList name="ShyLUBasker">
 
       <!-- Test Epetra objects first -->
       <ParameterList name="epetra">
@@ -221,13 +221,13 @@
 	   </ParameterList> <!-- end solver_run_params -->
 	</ParameterList> <!-- end run-int-long-p#-default -->
       </ParameterList> <!-- end tpetra -->
-    </ParameterList> <!-- end Basker -->
+    </ParameterList> <!-- end ShyLUBasker -->
   </ParameterList> <!-- end wathen120 -->
 
 
   <!-- Asic_680ks is a key matrix with medium performance first btf blk small -->
   <ParameterList name="asic_680ks.mtx">
-    <ParameterList name="Basker">
+    <ParameterList name="ShyLUBasker">
 
       <!-- Test Epetra objects first -->
       <ParameterList name="epetra">
@@ -442,12 +442,12 @@
 	   </ParameterList> <!-- end solver_run_params -->
 	</ParameterList> <!-- end run-int-long-p#-default -->
       </ParameterList> <!-- end tpetra -->
-    </ParameterList> <!-- end Basker -->
+    </ParameterList> <!-- end ShyLUBasker -->
   </ParameterList> <!-- end asic680ks -->
 
   <!-- G2 Very bad matrix sym large supernodes -->
   <ParameterList name="G2_circuit.mtx">
-    <ParameterList name="Basker">
+    <ParameterList name="ShyLUBasker">
 
       <!-- Test Epetra objects first -->
       <ParameterList name="epetra">
@@ -662,12 +662,12 @@
 	   </ParameterList> <!-- end solver_run_params -->
 	</ParameterList> <!-- end run-int-long-p#-default -->
       </ParameterList> <!-- end tpetra -->
-    </ParameterList> <!-- end Basker -->
+    </ParameterList> <!-- end ShyLUBasker -->
   </ParameterList> <!-- end G2_circuit -->
 
   <!-- Private Large Power Simulation Matrix, good very btf matrix -->
   <ParameterList name="power0.mtx">
-    <ParameterList name="Basker">
+    <ParameterList name="ShyLUBasker">
 
       <!-- Test Epetra objects first -->
       <ParameterList name="epetra">
@@ -882,12 +882,12 @@
 	   </ParameterList> <!-- end solver_run_params -->
 	</ParameterList> <!-- end run-int-long-p#-default -->
       </ParameterList> <!-- end tpetra -->
-    </ParameterList> <!-- end Basker -->
+    </ParameterList> <!-- end ShyLUBasker -->
   </ParameterList> <!-- end power0 -->
 
   <!-- hvdc2, interesting matrix with need for pivoting -->
   <ParameterList name="hvdc2.mtx">
-    <ParameterList name="Basker">
+    <ParameterList name="ShyLUBasker">
 
       <!-- Test Epetra objects first -->
       <ParameterList name="epetra">
@@ -1102,12 +1102,12 @@
 	   </ParameterList> <!-- end solver_run_params -->
 	</ParameterList> <!-- end run-int-long-p#-default -->
       </ParameterList> <!-- end tpetra -->
-    </ParameterList> <!-- end Basker -->
+    </ParameterList> <!-- end ShyLUBasker -->
   </ParameterList> <!-- end hvdc2 -->
 
   <!-- amesos_test_mat1 has good tests (limit to 4 threads) -->
   <ParameterList name="amesos2_test_mat1.mtx">
-    <ParameterList name="Basker">
+    <ParameterList name="ShyLUBasker">
 
       <!-- Test Epetra objects first -->
       <ParameterList name="epetra">
@@ -1272,12 +1272,12 @@
 	   </ParameterList> <!-- end solver_run_params -->
 	</ParameterList> <!-- end run-int-long-p#-default -->
       </ParameterList> <!-- end tpetra -->
-    </ParameterList> <!-- end Basker -->
+    </ParameterList> <!-- end ShyLUBasker -->
   </ParameterList> <!-- end amesos2_test_mat1 -->
 
   <!-- amesos2_test_mat4 has good tests (limit to 4 threads) -->
   <ParameterList name="amesos2_test_mat4.mtx">
-    <ParameterList name="Basker">
+    <ParameterList name="ShyLUBasker">
 
       <!-- Test Epetra objects first -->
       <ParameterList name="epetra">
@@ -1442,7 +1442,7 @@
 	   </ParameterList> <!-- end solver_run_params -->
 	</ParameterList> <!-- end run-int-long-p#-default -->
       </ParameterList> <!-- end tpetra -->
-    </ParameterList> <!-- end Basker -->
+    </ParameterList> <!-- end ShyLUBasker -->
   </ParameterList> <!-- end amesos2_test_mat4 -->
  <!-- TO BE CONT... -->
 </ParameterList> <!-- end test_parms -->