Merge Pull Request #12966 from trilinos/Trilinos/master_merge_2024042…

…6_175835 Automatically Merged using Trilinos Master Merge AutoTester PR Title: b'Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20240426_175835 branch to master' PR Author: trilinos-autotester
trilinos · Apr 27, 2024 · 8205a1b · 8205a1b
2 parents c1660db + ccc05fe
commit 8205a1b
Show file tree

Hide file tree

Showing 38 changed files with 1,358 additions and 76 deletions.
diff --git a/.github/workflows/AT2.yml b/.github/workflows/AT2.yml
@@ -32,7 +32,7 @@ jobs:
           bash -l -c "module list"
           printenv PATH
       - name: Cancel Previous Runs
-        uses: styfle/[email protected]
+        uses: styfle/cancel-workflow-action@85880fa0301c86cca9da44039ee3bb12d3bedbfa # 0.12.1
         with:
           access_token: ${{ github.token }}
       - name: make dirs
@@ -41,7 +41,7 @@ jobs:
           mkdir -p /home/Trilinos/src/Trilinos
           mkdir -p /home/Trilinos/build
       - name: Clone trilinos
-        uses: actions/[email protected].2
+        uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4.1.3
         with:
           fetch-depth: 0
       - name: Repo status
@@ -90,7 +90,7 @@ jobs:
           bash -l -c "module list"
           printenv PATH
       - name: Cancel Previous Runs
-        uses: styfle/[email protected]
+        uses: styfle/cancel-workflow-action@85880fa0301c86cca9da44039ee3bb12d3bedbfa # 0.12.1
         with:
           access_token: ${{ github.token }}
       - name: make dirs
@@ -99,7 +99,7 @@ jobs:
           mkdir -p /home/Trilinos/src/Trilinos
           mkdir -p /home/Trilinos/build
       - name: Clone trilinos
-        uses: actions/[email protected].2
+        uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4.1.3
         with:
           fetch-depth: 0
       - name: Repo status

diff --git a/.github/workflows/clang_format.yml b/.github/workflows/clang_format.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
+    - uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4.1.3
     - uses: DoozyX/clang-format-lint-action@11b773b1598aa4ae3b32f023701bca5201c3817d # v0.17
       with:
         source: './packages/muelu ./packages/tempus ./packages/teko ./packages/xpetra'
@@ -20,7 +20,7 @@ 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@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4.3.1
+    - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
       id: upload-artf
       if: ${{ hashFiles('format_patch.txt') != '' }}
       with:

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -58,11 +58,11 @@ jobs:
         # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
     steps:
     - name: Checkout repository
-      uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+      uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4.1.3
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@df5a14dc28094dc936e103b37d749c6628682b60 # v3.25.0
+      uses: github/codeql-action/init@8f596b4ae3cb3c588a5c46780b86dd53fef16c52 # v3.25.2
       with:
         languages: ${{ matrix.language }}
         build-mode: ${{ matrix.build-mode }}
@@ -85,6 +85,6 @@ jobs:
           make -j 2
       
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@df5a14dc28094dc936e103b37d749c6628682b60 # v3.25.0
+      uses: github/codeql-action/analyze@8f596b4ae3cb3c588a5c46780b86dd53fef16c52 # v3.25.2
       with:
         category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/dependency-review.yml b/.github/workflows/dependency-review.yml
@@ -22,6 +22,6 @@ jobs:
           egress-policy: audit
 
       - name: 'Checkout Repository'
-        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
+        uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4.1.3
       - name: 'Dependency Review'
         uses: actions/dependency-review-action@5bbc3ba658137598168acb2ab73b21c432dd411b # v4.2.5
diff --git a/.github/workflows/detect-git-lfs.yml b/.github/workflows/detect-git-lfs.yml
@@ -12,7 +12,7 @@ jobs:
 
     steps:
     - name: Check out code
-      uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
+      uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4.1.3
       with:
         fetch-depth: 0
 

diff --git a/.github/workflows/detect-mpi-comm-world.yml b/.github/workflows/detect-mpi-comm-world.yml
@@ -12,7 +12,7 @@ jobs:
 
     steps:
     - name: Check out code
-      uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
+      uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4.1.3
       with:
         fetch-depth: 0
 

diff --git a/.github/workflows/scorecards.yml b/.github/workflows/scorecards.yml
@@ -31,7 +31,7 @@ jobs:
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
+        uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4.1.3
         with:
           persist-credentials: false
 
@@ -58,14 +58,14 @@ jobs:
       # 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@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4.3.1
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
         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@4355270be187e1b672a7a1c7c7bae5afdc1ab94a # v3.24.10
+        uses: github/codeql-action/upload-sarif@8f596b4ae3cb3c588a5c46780b86dd53fef16c52 # v3.25.2
         with:
           sarif_file: results.sarif
diff --git a/.github/workflows/spack.yml b/.github/workflows/spack.yml
@@ -24,7 +24,7 @@ jobs:
         with:
           access_token: ${{ github.token }}
       - name: Clone Trilinos
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@1d96c772d19495a3b5c517cd2bc0cb401ea0529f # v4.1.3
         with:
           fetch-depth: 1
       - name: Spack build

diff --git a/SECURITY.md b/SECURITY.md
@@ -0,0 +1,9 @@
+# Security Policy
+
+## Supported Versions
+
+The latest released version of Trilinos is the only version supported with security updates.  You can find that at: https://github.com/trilinos/Trilinos/releases.
+
+## Reporting a Vulnerability
+
+For run-of-the mill memory errors, etc., please file a Github issue.  For specific, sensitive security issues, please click on "Report a vulnerability" at https://github.com/trilinos/Trilinos/security.
diff --git a/packages/amesos2/src/Amesos2_PardisoMKL_def.hpp b/packages/amesos2/src/Amesos2_PardisoMKL_def.hpp
@@ -291,27 +291,31 @@ namespace Amesos2 {
 
     RCP<const Teuchos::ParameterList> valid_params = getValidParameters_impl();
 
+    // Fill-in reordering: 0 = minimum degree, 2 = METIS 4.0.1 (default), 3 = METIS 5.1, 4 = AMD,
     if( parameterList->isParameter("IPARM(2)") )
     {
       RCP<const ParameterEntryValidator> fillin_validator = valid_params->getEntry("IPARM(2)").validator();
       parameterList->getEntry("IPARM(2)").setValidator(fillin_validator);
       iparm_[1] = getIntegralValue<int>(*parameterList, "IPARM(2)");
     }
 
+    // Iterative-direct algorithm
     if( parameterList->isParameter("IPARM(4)") )
     {
       RCP<const ParameterEntryValidator> prec_validator = valid_params->getEntry("IPARM(4)").validator();
       parameterList->getEntry("IPARM(4)").setValidator(prec_validator);
       iparm_[3] = getIntegralValue<int>(*parameterList, "IPARM(4)");
     }
 
+    // Max numbers of iterative refinement steps
     if( parameterList->isParameter("IPARM(8)") )
     {
       RCP<const ParameterEntryValidator> refine_validator = valid_params->getEntry("IPARM(8)").validator();
       parameterList->getEntry("IPARM(8)").setValidator(refine_validator);
       iparm_[7] = getIntegralValue<int>(*parameterList, "IPARM(8)");
     }
-
+
+    // Perturb the pivot elements
     if( parameterList->isParameter("IPARM(10)") )
     {
       RCP<const ParameterEntryValidator> pivot_perturb_validator = valid_params->getEntry("IPARM(10)").validator();
@@ -323,34 +327,47 @@ namespace Amesos2 {
     // Then solver specific options can override this.
     iparm_[11] = this->control_.useTranspose_ ? 2 : 0;
 
+    // Normal solve (0), or a transpose solve (1)
     if( parameterList->isParameter("IPARM(12)") )
     {
       RCP<const ParameterEntryValidator> trans_validator = valid_params->getEntry("IPARM(12)").validator();
       parameterList->getEntry("IPARM(12)").setValidator(trans_validator);
       iparm_[11] = getIntegralValue<int>(*parameterList, "IPARM(12)");
     }
 
+    // (Non-)symmetric matchings : detault 1 for nonsymmetric and 0 for symmetric matrix (default is nonsymmetric)
+    if( parameterList->isParameter("IPARM(13)") )
+    {
+      RCP<const ParameterEntryValidator> trans_validator = valid_params->getEntry("IPARM(13)").validator();
+      parameterList->getEntry("IPARM(13)").setValidator(trans_validator);
+      iparm_[12] = getIntegralValue<int>(*parameterList, "IPARM(13)");
+    }
+
+    // Output: Number of nonzeros in the factor LU
     if( parameterList->isParameter("IPARM(18)") )
     {
       RCP<const ParameterEntryValidator> report_validator = valid_params->getEntry("IPARM(18)").validator();
       parameterList->getEntry("IPARM(18)").setValidator(report_validator);
       iparm_[17] = getIntegralValue<int>(*parameterList, "IPARM(18)");
     }
 
+    // Scheduling method for the parallel numerical factorization
     if( parameterList->isParameter("IPARM(24)") )
     {
       RCP<const ParameterEntryValidator> par_fact_validator = valid_params->getEntry("IPARM(24)").validator();
       parameterList->getEntry("IPARM(24)").setValidator(par_fact_validator);
       iparm_[23] = getIntegralValue<int>(*parameterList, "IPARM(24)");
     }
 
+    // Parallelization scheme for the forward and backward solv
     if( parameterList->isParameter("IPARM(25)") )
     {
       RCP<const ParameterEntryValidator> par_fbsolve_validator = valid_params->getEntry("IPARM(25)").validator();
       parameterList->getEntry("IPARM(25)").setValidator(par_fbsolve_validator);
       iparm_[24] = getIntegralValue<int>(*parameterList, "IPARM(25)");
     } 
 
+    // Graph compression scheme for METIS.
     if( parameterList->isParameter("IPARM(60)") )
     {
       RCP<const ParameterEntryValidator> ooc_validator = valid_params->getEntry("IPARM(60)").validator();
@@ -433,7 +450,14 @@ PardisoMKL<Matrix,Vector>::getValidParameters_impl() const
                                       "Transposed"),
                                       tuple<int>(0, 1, 2),
                                       pl.getRawPtr());
-
+
+    setStringToIntegralParameter<int>("IPARM(13)", toString(iparm_temp[12]),
+                                      "Use weighted matching",
+                                      tuple<string>("0", "1"),
+                                      tuple<string>("No matching", "Use matching"),
+                                      tuple<int>(0, 1),
+                                      pl.getRawPtr());
+
     setStringToIntegralParameter<int>("IPARM(24)", toString(iparm_temp[23]),
                                       "Parallel factorization control",
                                       tuple<string>("0", "1"),

diff --git a/packages/intrepid2/perf-test/CMakeLists.txt b/packages/intrepid2/perf-test/CMakeLists.txt
@@ -2,6 +2,6 @@ TRIBITS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
 
 ADD_SUBDIRECTORY(ComputeBasis)
 ADD_SUBDIRECTORY(DynRankView)
-
+ADD_SUBDIRECTORY(Sierra)
 
 
diff --git a/packages/intrepid2/perf-test/ComputeBasis/test_hgrad.hpp b/packages/intrepid2/perf-test/ComputeBasis/test_hgrad.hpp
@@ -157,8 +157,10 @@ namespace Intrepid2 {
           refBasisValues("refBasisValues", numDofs, numPoints),
           refBasisGrads ("refBasisGrads",  numDofs, numPoints, spaceDim);
 
-        ImplBasisType::getValues<DeviceSpaceType>(refBasisValues, refPoints, OPERATOR_VALUE);
-        ImplBasisType::getValues<DeviceSpaceType>(refBasisGrads,  refPoints, OPERATOR_GRAD);
+        auto space = typename DeviceSpaceType::execution_space();
+
+        ImplBasisType::getValues<DeviceSpaceType>(space, refBasisValues, refPoints, OPERATOR_VALUE);
+        ImplBasisType::getValues<DeviceSpaceType>(space, refBasisGrads,  refPoints, OPERATOR_GRAD);
 
 	std::cout << " Ref completed\n";
 

diff --git a/packages/intrepid2/perf-test/Sierra/CMakeLists.txt b/packages/intrepid2/perf-test/Sierra/CMakeLists.txt
@@ -0,0 +1,23 @@
+TRIBITS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
+
+SET(SIERRA_GRAD_PROJECTION_SOURCES
+  SierraGradProjection.cpp
+  )
+
+TRIBITS_ADD_EXECUTABLE(
+  SierraGradProjection
+  SOURCES ${SIERRA_GRAD_PROJECTION_SOURCES}
+  CATEGORIES BASIC PERFORMANCE
+  )
+
+# Performance test representing gradient projection as used in Sierra 
+TRIBITS_ADD_TEST(
+   SierraGradProjection
+   NAME "SierraGradProjection"
+   ARGS ""
+   COMM mpi
+   NUM_MPI_PROCS 1
+   CATEGORIES PERFORMANCE
+   RUN_SERIAL
+   )
+
Original file line number	Diff line number	Diff line change
Expand Up		@@ -2,6 +2,6 @@ TRIBITS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})

		ADD_SUBDIRECTORY(ComputeBasis)
		ADD_SUBDIRECTORY(DynRankView)

		ADD_SUBDIRECTORY(Sierra)