Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20250131_175819 branch to master

.github/workflows/AT2.yml

@@ -35,7 +35,7 @@ jobs:
           with:
             skip_after_successful_duplicate: 'true'
 
-  gcc10-openmpi416-EXPERIMENTAL:
+  gcc10-openmpi4:
     needs: pre-checks
     runs-on: [self-hosted, gcc-10.3.0_openmpi-4.1.6]
     if: ${{ needs.pre-checks.outputs.should_skip != 'true' && (github.event.action == 'synchronize' || github.event.action == 'opened' || github.event.review.state == 'APPROVED') }}
@@ -221,7 +221,7 @@ jobs:
           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
 
-  cuda11-EXPERIMENTAL:
+  cuda11:
     needs: pre-checks
     runs-on: [self-hosted, cuda-11.4.2_gcc-10.3.0_openmpi-4.1.6]
     if: ${{ needs.pre-checks.outputs.should_skip != 'true' && (github.event.action == 'synchronize' || github.event.action == 'opened' || github.event.review.state == 'APPROVED') }}

.github/workflows/codeql.yml

@@ -45,7 +45,7 @@ jobs:
       uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@b6a472f63d85b9c78a3ac5e89422239fc15e9b3c # v3.28.1
+      uses: github/codeql-action/init@17a820bf2e43b47be2c72b39cc905417bc1ab6d0 # v3.28.6
       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@b6a472f63d85b9c78a3ac5e89422239fc15e9b3c # v3.28.1
+      uses: github/codeql-action/analyze@17a820bf2e43b47be2c72b39cc905417bc1ab6d0 # v3.28.6
       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@b6a472f63d85b9c78a3ac5e89422239fc15e9b3c # v3.28.1
+        uses: github/codeql-action/upload-sarif@17a820bf2e43b47be2c72b39cc905417bc1ab6d0 # v3.28.6
         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@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9.0.0
+    - uses: actions/stale@5bef64f19d7facfb25b37b414482c7164d639639 # v9.1.0
       with:
         debug-only: false
         ascending: true

commonTools/framework/github_issue_creator/create_trilinos_github_test_failure_issue_unit_tests.py

@@ -7,7 +7,6 @@
 
 
 import sys
-import imp
 import shutil
 import unittest
 

packages/amesos2/src/Amesos2_EpetraCrsMatrix_MatrixAdapter_decl.hpp

@@ -113,13 +113,20 @@ namespace Amesos2 {
         int myNRows = this->mat_->NumMyRows();
         int myNnz = this->mat_->NumMyNonzeros();
         if(current_phase == PREORDERING || current_phase == SYMBFACT) {
-          // workspace for column major
-          KV_GS pointers_t;
-          KV_GO indices_t;
-
           // gether rowptr
           Kokkos::resize(recvCounts, nRanks);
           Kokkos::resize(recvDispls, nRanks+1);
+
+          // index-bases
+          global_ordinal_t rowIndexBase = rowMap->getIndexBase();
+          global_ordinal_t colIndexBase = colMap->getIndexBase();
+          // map from global to local
+          host_ordinal_type_array  perm_g2l;
+          host_ordinal_type_array  perm_l2g;
+          // workspace for column major
+          KV_GS pointers_t;
+          KV_GO indices_t;
+          bool need_to_perm = false;
           {
 #ifdef HAVE_AMESOS2_TIMERS
             Teuchos::RCP< Teuchos::Time > gatherTime = Teuchos::TimeMonitor::getNewCounter ("Amesos2::gather(rowptr)");
@@ -142,13 +149,38 @@ namespace Amesos2 {
               }
               recvDispls(nRanks) = 0;
             }
-            if (myRank == 0 && column_major) {
+            // gether g2l perm (convert to 0-base)
+            {
+              host_ordinal_type_array lclMap;
+              Kokkos::resize(lclMap, myNRows);
+              if (myRank == 0) {
+                Kokkos::resize(perm_g2l, nRows);
+                Kokkos::resize(perm_l2g, nRows);
+              } else {
+                Kokkos::resize(perm_g2l, 1);
+              }
+              for (int i=0; i < myNRows; i++) {
+                lclMap(i) = rowMap->getGlobalElement(i);
+              }
+              Teuchos::gatherv<int, local_ordinal_t> (lclMap.data(), myNRows, perm_g2l.data(),
+                                                      recvCounts.data(), recvDispls.data(),
+                                                      0, *comm);
+              if (myRank == 0) {
+                for (int i=0; i < nRows; i++) {
+                  perm_g2l(i) -= rowIndexBase;
+                  perm_l2g(perm_g2l(i)) = i;
+                  if (i != perm_g2l(i)) need_to_perm = true;
+                }
+              }
+            }
+            if (myRank == 0 && (column_major || need_to_perm)) {
               Kokkos::resize(pointers_t, nRows+1);
             } else if (myRank != 0) {
               Kokkos::resize(pointers_t, 2);
             }
-            int *pointers_ = (myRank != 0 || column_major ? pointers_t.data() : pointers.data());
-            Teuchos::gatherv<int, local_ordinal_t> (&lclRowptr[1], myNRows, &pointers_[1], 
+            local_ordinal_t sendIdx = (myNRows > 0 ? 1 : 0); // To skip sending the first rowptr entry (note: 0, if local matrix is empty)
+            local_ordinal_t *pointers_ = ((myRank != 0 || (column_major || need_to_perm)) ? pointers_t.data() : pointers.data());
+            Teuchos::gatherv<int, local_ordinal_t> (&lclRowptr[sendIdx], myNRows, &pointers_[1],
                                                     recvCounts.data(), recvDispls.data(),
                                                     0, *comm);
             if (myRank == 0) {
@@ -157,13 +189,17 @@ namespace Amesos2 {
               recvCounts(0) = pointers_[recvDispls(1)];
               local_ordinal_t displs = recvCounts(0);
               for (int p = 1; p < nRanks; p++) {
-                // save recvCounts from pth MPI
-                recvCounts(p) = pointers_[recvDispls(p+1)];
-                // shift pointers for pth MPI to global
-                for (int i = 1+recvDispls(p); i <= recvDispls(p+1); i++) {
-                  pointers_[i] += displs;
+                // skip "Empty" submatrix (no rows)
+                //  recvCounts(p) is zero, while pointers_[recvDispls(p+1)] now contains nnz from p-1
+                if (recvDispls(p+1) > recvDispls(p)) {
+                  // save recvCounts from pth MPI
+                  recvCounts(p) = pointers_[recvDispls(p+1)];
+                  // shift pointers for pth MPI to global
+                  for (int i = 1+recvDispls(p); i <= recvDispls(p+1); i++) {
+                    pointers_[i] += displs;
+                  }
+                  displs += recvCounts(p);
                 }
-                displs += recvCounts(p);
               }
               ret = pointers_[nRows];
             }
@@ -182,43 +218,70 @@ namespace Amesos2 {
             }
             // -- convert to global colids
             KV_GO lclColind_ ("localColind_", myNnz);
-            for (int i = 0; i < int(myNnz); i++) lclColind_(i) = colMap->getGlobalElement((lclColind[i]));
-            if (column_major) {
+            for (int i = 0; i < int(myNnz); i++) lclColind_(i) = (colMap->getGlobalElement((lclColind[i])) - colIndexBase);
+            if (column_major || need_to_perm) {
               Kokkos::resize(indices_t, indices.extent(0));
-              Teuchos::gatherv<int, local_ordinal_t> (lclColind_.data(), myNnz, indices_t.data(), 
+              Teuchos::gatherv<int, local_ordinal_t> (lclColind_.data(), myNnz, indices_t.data(),
                                                       recvCounts.data(), recvDispls.data(),
                                                       0, *comm);
             } else {
-              Teuchos::gatherv<int, local_ordinal_t> (lclColind_.data(), myNnz, indices.data(), 
+              Teuchos::gatherv<int, local_ordinal_t> (lclColind_.data(), myNnz, indices.data(),
                                                       recvCounts.data(), recvDispls.data(),
                                                       0, *comm);
             }
           }
-          if (myRank == 0 && column_major) {
+          if (myRank == 0) {
 #ifdef HAVE_AMESOS2_TIMERS
             Teuchos::RCP< Teuchos::Time > gatherTime = Teuchos::TimeMonitor::getNewCounter ("Amesos2::gather(transpose index)");
             Teuchos::TimeMonitor GatherTimer(*gatherTime);
 #endif
-            // Map to transpose
-            Kokkos::resize(transpose_map, ret);
-            // Transopose to convert to CSC
-            for (int i=0; i<=nRows; i++) {
-              pointers(i) = 0;
-            }
-            for (int k=0; k<ret; k++) {
-              if (indices_t(k) < nRows-1) {
-                pointers(indices_t(k)+2) ++;
+            if (column_major) {
+              // Map to transpose
+              Kokkos::resize(transpose_map, ret);
+              // Transopose to convert to CSC
+              for (int i=0; i<=nRows; i++) {
+                pointers(i) = 0;
               }
-            }
-            for (int i=1; i < nRows; i++) {
-              pointers(i+1) += pointers(i);
-            }
-            for (int i=0; i<nRows; i++) {
-              for (int k=pointers_t(i); k<pointers_t(i+1); k++) {
-                transpose_map(k) = pointers(1+indices_t(k));
-                indices(pointers(1+indices_t(k))) = i;
-                pointers(1+indices_t(k)) ++;
+              for (int k=0; k<ret; k++) {
+                int col = indices_t(k);
+                if (col < nRows-1) {
+                  pointers(col+2) ++;
+                }
+              }
+              for (int i=1; i < nRows; i++) {
+                pointers(i+1) += pointers(i);
+              }
+              // nonzeroes in each column are sorted in ascending row
+              for (int row=0; row<nRows; row++) {
+                int i = perm_g2l(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) ++;
+                }
               }
+            } else if (need_to_perm) {
+              // Map to permute
+              Kokkos::resize(transpose_map, ret);
+              for (int i=0; i<nRows; i++) {
+                int row = perm_g2l(i);
+                pointers(row+2) = pointers_t(i+1)-pointers_t(i);
+              }
+              for (int i=1; i < nRows; i++) {
+                pointers(i+1) += pointers(i);
+              }
+              for (int i=0; i<nRows; i++) {
+                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) ++;
+                }
+              }
+            } else {
+              Kokkos::resize(transpose_map, 0);
             }
           }
         }
@@ -229,22 +292,25 @@ namespace Amesos2 {
             Teuchos::RCP< Teuchos::Time > gatherTime = Teuchos::TimeMonitor::getNewCounter ("Amesos2::gather(nzvals)");
             Teuchos::TimeMonitor GatherTimer(*gatherTime);
 #endif
-            if (column_major) {
+            // gather nzvals
+            if (transpose_map.extent(0) > 0) {
               Kokkos::resize(nzvals_t, nzvals.extent(0));
-              Teuchos::gatherv<int, scalar_t> (lclNzvals, myNnz, nzvals_t.data(), 
+              Teuchos::gatherv<int, scalar_t> (lclNzvals, myNnz, nzvals_t.data(),
                                                recvCounts.data(), recvDispls.data(),
                                                0, *comm);
             } else {
-              Teuchos::gatherv<int, scalar_t> (lclNzvals, myNnz, nzvals.data(), 
+              Teuchos::gatherv<int, scalar_t> (lclNzvals, myNnz, nzvals.data(),
                                                recvCounts.data(), recvDispls.data(),
                                                0, *comm);
             }
           }
-          if (myRank == 0 && column_major) {
+          if (myRank == 0) {
             // Insert Numerical values to transopose matrix
             ret = pointers(nRows);
-            for (int k=0; k<ret; k++) {
-              nzvals(transpose_map(k)) = nzvals_t(k);
+            if (transpose_map.extent(0) > 0) {
+              for (int k=0; k<ret; k++) {
+                nzvals(transpose_map(k)) = nzvals_t(k);
+              }
             }
           }
         }

packages/amesos2/src/Amesos2_Superlu_FunctionMap.hpp

@@ -45,6 +45,8 @@ namespace SLU {
 #include "slu_util.h"
 #include "superlu_enum_consts.h"
 
+#undef EMPTY
+
 void
 at_plus_a(
           const int n,      /* number of columns in matrix A. */

packages/amesos2/src/Amesos2_Superludist_TypeMap.hpp

@@ -77,6 +77,8 @@ namespace SLUD {
   }
 #endif  // HAVE_TEUCHOS_COMPLEX
 
+#undef EMPTY
+
 // multiplication of SLUD types
 template <typename slu_scalar_t, typename slu_mag_t>
 struct slu_dist_mult {};