Merge Pull Request trilinos#13056 from trilinos/Trilinos/master_merge…

…_20240531_175842 Automatically Merged using Trilinos Master Merge AutoTester PR Title: b'Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20240531_175842 branch to master' PR Author: trilinos-autotester
jennloe · Jun 1, 2024 · ee6599d · ee6599d
2 parents aeccfde + 056b8ee
commit ee6599d
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diff --git a/.github/workflows/clang_format.yml b/.github/workflows/clang_format.yml
@@ -2,8 +2,10 @@ name: Check packages with clang-format
 
 on: [pull_request]
 
-permissions: read-all
-
+permissions:
+  contents: read
+  issues: write
+
 jobs:
   build:
     runs-on: ubuntu-latest

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -62,7 +62,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@b7cec7526559c32f1616476ff32d17ba4c59b2d6 # v3.25.5
+      uses: github/codeql-action/init@9fdb3e49720b44c48891d036bb502feb25684276 # v3.25.6
       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@b7cec7526559c32f1616476ff32d17ba4c59b2d6 # v3.25.5
+      uses: github/codeql-action/analyze@9fdb3e49720b44c48891d036bb502feb25684276 # v3.25.6
       with:
         category: "/language:${{matrix.language}}"
diff --git a/.github/workflows/dependency-review.yml b/.github/workflows/dependency-review.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Harden Runner
-        uses: step-security/harden-runner@a4aa98b93cab29d9b1101a6143fb8bce00e2eac4 # v2.7.1
+        uses: step-security/harden-runner@f086349bfa2bd1361f7909c78558e816508cdc10 # v2.8.0
         with:
           egress-policy: audit
 

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@b7cec7526559c32f1616476ff32d17ba4c59b2d6 # v3.25.5
+        uses: github/codeql-action/upload-sarif@9fdb3e49720b44c48891d036bb502feb25684276 # v3.25.6
         with:
           sarif_file: results.sarif
diff --git a/packages/amesos2/src/Amesos2_Tacho_decl.hpp b/packages/amesos2/src/Amesos2_Tacho_decl.hpp
@@ -227,6 +227,7 @@ class TachoSolver : public SolverCore<Amesos2::TachoSolver, Matrix, Vector>
     // TODO: Implement the paramter options - confirm which we want and which have been implemented
     int method;
     int variant;
+    int small_problem_threshold_size;
     // int num_kokkos_threads;
     // int max_num_superblocks;
   } data_;

diff --git a/packages/amesos2/src/Amesos2_Tacho_def.hpp b/packages/amesos2/src/Amesos2_Tacho_def.hpp
@@ -107,6 +107,7 @@ TachoSolver<Matrix,Vector>::symbolicFactorization_impl()
 
     data_.solver.setSolutionMethod(data_.method);
     data_.solver.setLevelSetOptionAlgorithmVariant(data_.variant);
+    data_.solver.setSmallProblemThresholdsize(data_.small_problem_threshold_size);
 
     // TODO: Confirm param options
     // data_.solver.setMaxNumberOfSuperblocks(data_.max_num_superblocks);
@@ -247,6 +248,8 @@ TachoSolver<Matrix,Vector>::setParameters_impl(const Teuchos::RCP<Teuchos::Param
   }
   // solver type
   data_.variant = parameterList->get<int> ("variant", 2);
+  // small problem threshold
+  data_.small_problem_threshold_size = parameterList->get<int> ("small problem threshold size", 1024);
   // TODO: Confirm param options
   // data_.num_kokkos_threads = parameterList->get<int>("kokkos-threads", 1);
   // data_.max_num_superblocks = parameterList->get<int>("max-num-superblocks", 4);
@@ -264,6 +267,7 @@ TachoSolver<Matrix,Vector>::getValidParameters_impl() const
 
     pl->set("method", "chol", "Type of factorization, chol, ldl, or lu");
     pl->set("variant", 2, "Type of solver variant, 0, 1, or 2");
+    pl->set("small problem threshold size", 1024, "Problem size threshold below with Tacho uses LAPACK.");
 
     // TODO: Confirm param options
     // pl->set("kokkos-threads", 1, "Number of threads");

diff --git a/packages/framework/ini-files/config-specs.ini b/packages/framework/ini-files/config-specs.ini
@@ -2046,7 +2046,7 @@ use PACKAGE-ENABLES|ALL
 use rhel7_sems-clang-11.0.1-openmpi-1.10.1-serial_release-debug_shared_no-kokkos-arch_no-asan_no-complex_no-fpic_mpi_no-pt_no-rdc_no-uvm_deprecated-on_no-package-enables
 use PACKAGE-ENABLES|ALL
 
-[rhel7_sems-clang-11.0.1-openmpi-1.10.7-serial_release-debug_shared_no-kokkos-arch_no-asan_no-complex_no-fpic_mpi_no-pt_no-rdc_no-uvm_deprecated-on_no-package-enables]
+[rhel8_sems-clang-11.0.1-openmpi-4.0.5-serial_release-debug_shared_no-kokkos-arch_no-asan_no-complex_no-fpic_mpi_no-pt_no-rdc_no-uvm_deprecated-on_no-package-enables]
 # uses sems-v2 modules
 use RHEL7_SEMS_COMPILER|CLANG
 use NODE-TYPE|SERIAL
@@ -2067,11 +2067,17 @@ opt-set-cmake-var Teko_DISABLE_LSCSTABALIZED_TPETRA_ALPAH_INV_D BOOL       : ON
 
 use RHEL7_TEST_DISABLES|CLANG
 
+opt-set-cmake-var SuperLU_LIBRARY_NAMES STRING : superlu;m
+opt-set-cmake-var ML_ENABLE_SuperLU BOOL FORCE : OFF
+
+opt-set-cmake-var Pliris_vector_random_MPI_3_DISABLE BOOL : ON
+opt-set-cmake-var Pliris_vector_random_MPI_4_DISABLE BOOL : ON
+
 use RHEL7_POST
 
-[rhel7_sems-clang-11.0.1-openmpi-1.10.7-serial_release-debug_shared_no-kokkos-arch_no-asan_no-complex_no-fpic_mpi_no-pt_no-rdc_no-uvm_deprecated-on_all]
+[rhel8_sems-clang-11.0.1-openmpi-4.0.5-serial_release-debug_shared_no-kokkos-arch_no-asan_no-complex_no-fpic_mpi_no-pt_no-rdc_no-uvm_deprecated-on_all]
 # uses sems-v2 modules
-use rhel7_sems-clang-11.0.1-openmpi-1.10.7-serial_release-debug_shared_no-kokkos-arch_no-asan_no-complex_no-fpic_mpi_no-pt_no-rdc_no-uvm_deprecated-on_no-package-enables
+use rhel8_sems-clang-11.0.1-openmpi-4.0.5-serial_release-debug_shared_no-kokkos-arch_no-asan_no-complex_no-fpic_mpi_no-pt_no-rdc_no-uvm_deprecated-on_no-package-enables
 use PACKAGE-ENABLES|ALL
 
 [rhel7_sems-intel-19.0.5-mpich-3.2-serial_release-debug_static_no-kokkos-arch_no-asan_no-complex_fpic_mpi_no-pt_no-rdc_no-uvm_deprecated-on_no-package-enables]

diff --git a/packages/framework/ini-files/supported-envs.ini b/packages/framework/ini-files/supported-envs.ini
@@ -178,6 +178,7 @@ gcc-openmpi
 gcc-serial
 aue-gcc-openmpi
 sems-cuda-11.4.2-sems-gnu-10.1.0-sems-openmpi-4.1.4
+sems-clang-11.0.1-openmpi-4.0.5-serial
 
 [ats2]
 cuda-11.2.152-gnu-8.3.1-spmpi-rolling
diff --git a/packages/framework/pr_tools/trilinosprhelpers/TrilinosPRConfigurationBase.py b/packages/framework/pr_tools/trilinosprhelpers/TrilinosPRConfigurationBase.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 This file contains the base class for the Pull Request test driver.

diff --git a/packages/framework/pr_tools/trilinosprhelpers/TrilinosPRConfigurationInstallation.py b/packages/framework/pr_tools/trilinosprhelpers/TrilinosPRConfigurationInstallation.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 Custom PR Executor for Installation testing

diff --git a/packages/framework/pr_tools/trilinosprhelpers/TrilinosPRConfigurationStandard.py b/packages/framework/pr_tools/trilinosprhelpers/TrilinosPRConfigurationStandard.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 Custom PR Executor for Standard testing

diff --git a/packages/framework/pr_tools/trilinosprhelpers/__init__.py b/packages/framework/pr_tools/trilinosprhelpers/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 
 from .sysinfo import *

diff --git a/packages/framework/pr_tools/trilinosprhelpers/gitutility/GitUtility.py b/packages/framework/pr_tools/trilinosprhelpers/gitutility/GitUtility.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 This class contains a set of utilities for using and querying

diff --git a/packages/framework/pr_tools/trilinosprhelpers/gitutility/unittests/__init__.py b/packages/framework/pr_tools/trilinosprhelpers/gitutility/unittests/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 This file is required to enable Python to locate the package files in the parent

diff --git a/packages/framework/pr_tools/trilinosprhelpers/gitutility/unittests/test_GitUtility.py b/packages/framework/pr_tools/trilinosprhelpers/gitutility/unittests/test_GitUtility.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8; mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 """

diff --git a/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/EnvvarHelper.py b/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/EnvvarHelper.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 """

diff --git a/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/JenkinsEnv.py b/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/JenkinsEnv.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 from .EnvvarHelper import EnvvarHelper
 

diff --git a/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/TrilinosJenkinsEnv.py b/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/TrilinosJenkinsEnv.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 from .JenkinsEnv import JenkinsEnv
 

diff --git a/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/__init__.py b/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 
 from .EnvvarHelper import EnvvarHelper

diff --git a/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/unittests/__init__.py b/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/unittests/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 This file is required to enable Python to locate the package files in the parent

diff --git a/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/unittests/test_EnvvarHelper.py b/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/unittests/test_EnvvarHelper.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8; mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 """

diff --git a/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/unittests/test_JenkinsEnv.py b/packages/framework/pr_tools/trilinosprhelpers/jenkinsenv/unittests/test_JenkinsEnv.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8; mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 """

diff --git a/...ages/framework/pr_tools/trilinosprhelpers/jenkinsenv/unittests/test_TrilinosJenkinsEnv.py b/...ages/framework/pr_tools/trilinosprhelpers/jenkinsenv/unittests/test_TrilinosJenkinsEnv.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8; mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 """

diff --git a/packages/framework/pr_tools/trilinosprhelpers/sysinfo/SysInfo.py b/packages/framework/pr_tools/trilinosprhelpers/sysinfo/SysInfo.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 System information helpers are contained in this file.

diff --git a/packages/framework/pr_tools/trilinosprhelpers/sysinfo/unittests/__init__.py b/packages/framework/pr_tools/trilinosprhelpers/sysinfo/unittests/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 This file is required to enable Python to locate the package files in the parent

diff --git a/packages/framework/pr_tools/trilinosprhelpers/sysinfo/unittests/test_SysInfo.py b/packages/framework/pr_tools/trilinosprhelpers/sysinfo/unittests/test_SysInfo.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8; mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 """

diff --git a/packages/framework/pr_tools/trilinosprhelpers/sysinfo/unittests/test_gpu_utils.py b/packages/framework/pr_tools/trilinosprhelpers/sysinfo/unittests/test_gpu_utils.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8; mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 """

diff --git a/packages/framework/pr_tools/trilinosprhelpers/unittests/__init__.py b/packages/framework/pr_tools/trilinosprhelpers/unittests/__init__.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
 This file is required to enable Python to locate the package files in the parent

diff --git a/packages/framework/pr_tools/trilinosprhelpers/unittests/test_TrilinosPRConfigurationBase.py b/packages/framework/pr_tools/trilinosprhelpers/unittests/test_TrilinosPRConfigurationBase.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8; mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 """

diff --git a/...ramework/pr_tools/trilinosprhelpers/unittests/test_TrilinosPRConfigurationInstallation.py b/...ramework/pr_tools/trilinosprhelpers/unittests/test_TrilinosPRConfigurationInstallation.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- coding: utf-8; mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-
 """
 """

diff --git a/packages/framework/pr_tools/unittests/__init__.py b/packages/framework/pr_tools/unittests/__init__.py
@@ -1,3 +1,3 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 # -*- mode: python; py-indent-offset: 4; py-continuation-offset: 4 -*-