merge develop

.devcontainer/devcontainer.json

@@ -2,7 +2,7 @@
     "build": {
         "dockerfile": "Dockerfile",
         "args": {
-            "GEOS_TPL_TAG": "286-547"
+            "GEOS_TPL_TAG": "290-594"
         }
     },
     "runArgs": [

.github/workflows/ci_tests.yml

@@ -183,6 +183,15 @@ jobs:
             ENABLE_TRILINOS: OFF
             BUILD_SHARED_LIBS: ON
 
+          - name: Sherlock CPU (centos 7.9.2009, gcc 10.1.0, open-mpi 4.1.2, openblas 0.3.10)
+            CMAKE_BUILD_TYPE: Release
+            DOCKER_REPOSITORY: geosx/sherlock-gcc10.1.0-openmpi4.1.2-openblas0.3.10-zlib1.2.11
+            ENABLE_HYPRE: ON
+            ENABLE_TRILINOS: OFF
+            GCP_BUCKET: geosx/Sherlock-CPU
+            HOST_CONFIG: host-configs/Stanford/sherlock-gcc10.cmake
+            BUILD_SHARED_LIBS: ON
+
     uses: ./.github/workflows/build_and_test.yml
     with:
       BUILD_SHARED_LIBS: ${{ matrix.BUILD_SHARED_LIBS }}
@@ -192,6 +201,7 @@ jobs:
       ENABLE_HYPRE: ${{ matrix.ENABLE_HYPRE }}
       ENABLE_TRILINOS: ${{ matrix.ENABLE_TRILINOS }}
       GCP_BUCKET: ${{ matrix.GCP_BUCKET }}
+      HOST_CONFIG: ${{ matrix.HOST_CONFIG }}
       RUNS_ON: ubuntu-22.04
     secrets: inherit
 
@@ -330,7 +340,7 @@ jobs:
             DOCKER_CERTS_DIR: "/etc/pki/ca-trust/source/anchors"
             DOCKER_CERTS_UPDATE_COMMAND: "update-ca-trust"
 
-          - name: Pangea 3 (AlmaLinux 8.8, gcc 9.4.0, open-mpi 4.1.2, cuda 11.5.0, openblas 0.3.10)
+          - name: Pangea 3 CUDA (AlmaLinux 8.8, gcc 9.4.0, open-mpi 4.1.2, cuda 11.5.0, openblas 0.3.10)
             BUILD_AND_TEST_CLI_ARGS: "--build-exe-only --no-install-schema"
             CMAKE_BUILD_TYPE: Release
             BUILD_GENERATOR: "--makefile"
@@ -346,6 +356,21 @@ jobs:
             DOCKER_CERTS_DIR: "/etc/pki/ca-trust/source/anchors"
             DOCKER_CERTS_UPDATE_COMMAND: "update-ca-trust"
 
+          - name: Sherlock GPU (centos 7.9.2009, gcc 10.1.0, open-mpi 4.1.2, openblas 0.3.10, cuda 12.4.0,)
+            BUILD_AND_TEST_CLI_ARGS: "--no-run-unit-tests --no-install-schema"
+            BUILD_GENERATOR: "--ninja"
+            CMAKE_BUILD_TYPE: Release
+            DOCKER_REPOSITORY: geosx/sherlock-gcc10.1.0-openmpi4.1.2-cuda12.4.0-openblas0.3.10-zlib1.2.11
+            ENABLE_HYPRE_DEVICE: CUDA
+            ENABLE_HYPRE: ON
+            ENABLE_TRILINOS: OFF
+            GCP_BUCKET: geosx/Sherlock-GPU
+            HOST_CONFIG: host-configs/Stanford/sherlock-gcc10-cuda12-sm70.cmake
+            RUNS_ON: streak2
+            NPROC: 8
+            DOCKER_RUN_ARGS: "--cpus=8 --memory=128g --runtime=nvidia -v /etc/pki/ca-trust/source/anchors/:/etc/pki/ca-trust/source/anchors/llnl:ro"
+            DOCKER_CERTS_DIR: "/etc/pki/ca-trust/source/anchors"
+            DOCKER_CERTS_UPDATE_COMMAND: "update-ca-trust"
 
           # Below this line, jobs that deploy to Google Cloud.
 

.integrated_tests.yaml

@@ -1,6 +1,7 @@
 baselines:
   bucket: geosx
-  baseline: integratedTests/baseline_integratedTests-pr3339-8707-7c55c70
+  baseline: integratedTests/baseline_integratedTests-pr3395-9832-31f145e
+
 allow_fail:
   all: ''
   streak: ''

BASELINE_NOTES.md

@@ -6,6 +6,85 @@ This file is designed to track changes to the integrated test baselines.
 Any developer who updates the baseline ID in the .integrated_tests.yaml file is expected to create an entry in this file with the pull request number, date, and their justification for rebaselining.
 These notes should be in reverse-chronological order, and use the following time format: (YYYY-MM-DD).
 
+PR  #3395 (2024-01-22)
+=====================
+Add new fields and change the default input for some tests.
+
+PR #3416 (2024-01-21)
+=====================
+Refactoring of induced seismicity EQ solvers to add coupling.
+
+PR #3310 (2024-01-21)
+======================
+Scalable rock toughness required new field.
+
+PR #3228 (2024-01-15)
+=====================
+deltaVolume added in multiphase.
+
+PR #3495 (2024-01-08)
+=====================
+Add missing logic to support switching from fixed mass rate injection rate constraint to max injection pressure.
+
+PR #3384 (2024-01-07)
+=====================
+Added plastic strain output.
+
+PR #3486 (2025-01-06)
+=====================
+useNewGravity became gravityDensityScheme.
+
+PR #3479 (2024-12-15)
+=====================
+Refine inputFiles/compositionalMultiphaseFlow: shift reference pressures to initial pressures, make nonlinear tuning more reasonable, minimize output.
+
+PR #3450 (2024-12-14)
+=====================
+Fix timestep selector flaw in SolidMechanicsLagrangeContact.
+
+PR #3450 (2024-12-08)
+=====================
+Added test for explicit runge kutta sprinslider.
+
+PR #3480 (2024-12-06)
+=====================
+Add "logLevel" parameter under /Problem/Outputs in baseline files
+
+PR #3361 (2024-12-03)
+=====================
+Revert default gravity treatment to old version. Make the way introduced in #3337 optional.
+
+PR #3361 (2024-12-03)
+=====================
+Baseline diffs after reimplementation of wave equation acoustic gradient for velocity and density parameters: new field "partialGradient2" and "pressureForward" field replacing "pressureDoubleDerivative".
+
+PR #3393 (2024-12-02)
+=====================
+Fix netToGross bug.
+
+PR #3381 (2024-12-01)
+=====================
+A few baseline diffs for order FaceElementSubRegion::m_toFacesRelation map. Not sure why this was changed by this PR, but the previous order seems incorrect for a couple of cases.
+
+PR #2957 (2024-11-27)
+=====================
+Added ExternalDataRepository.
+
+PR #3448 (2024-11-21)
+=====================
+Switched the FaceElementSubRegion::m_toFacesRelation and FaceElementSubRegion::m_2dElemToElems back to array2d instead of ArrayOfArray. This results in a reordering m_toFacesRelation back to the "correct" assumed order of "original face first". This fixes a bug that failed to remove the CellStencil entry when a FaceElement splits two cells.
+
+PR #2637 (2024-11-21)
+=====================
+Added numberOfTargetProcesses.
+
+PR #3439 (2024-11-20)
+=====================
+EDFM bugfixes: derivatives sign, frac/cell element volume, fix apertures inconsistency in test cases.
+
+PR ##3440 (2024-11-18)
+=====================
+Added Lagrange multiplier with bubble functions stabilization (sli only) and possibility to specify a slip.
 
 PR #3339 (2024-11-14)
 =====================

COPYRIGHT

@@ -8,7 +8,7 @@ contributors. The following copyright applies to each file in the GEOS
 distribution, unless otherwise stated in the file:
 
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2024 Total, S.A
+ * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
  * Copyright (c) 2023-2024 Chevron 
  * Copyright (c) 2019-     GEOS/GEOSX Contributors

examples/ObjectCatalog/Base.hpp

@@ -3,9 +3,9 @@
  * SPDX-License-Identifier: LGPL-2.1-only
  *
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2024 Total, S.A
+ * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
- * Copyright (c) 2023-2024 Chevron 
+ * Copyright (c) 2023-2024 Chevron
  * Copyright (c) 2019-     GEOS/GEOSX Contributors
  * All rights reserved
  *
@@ -46,7 +46,7 @@ class Parameter
 class Base
 {
 public:
-  Base( int junk, double const & junk2, Parameter& pbv )
+  Base( int junk, double const & junk2, Parameter & pbv )
   {
     GEOS_LOG( "calling Base constructor with arguments (" << junk << " " << junk2 << ")" );
   }
@@ -56,14 +56,20 @@ class Base
     GEOS_LOG( "calling Base destructor" );
   }
 
-  using CatalogInterface = dataRepository::CatalogInterface< Base, int, double const &, Parameter& >;
-  static CatalogInterface::CatalogType& getCatalog()
+  using CatalogInterface = dataRepository::CatalogInterface< Base, int, double const &, Parameter & >;
+  static CatalogInterface::CatalogType & getCatalog()
   {
     static CatalogInterface::CatalogType catalog;
     return catalog;
   }
 
   virtual std::string const getName() const = 0;
+
+  static DataContext const & getDataContext()
+  {
+    static DataFileContext const context = DataFileContext( "Base Test Class", __FILE__, __LINE__ );
+    return context;
+  }
 };
 
 #endif

examples/ObjectCatalog/Derived1.cpp

@@ -3,7 +3,7 @@
  * SPDX-License-Identifier: LGPL-2.1-only
  *
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2024 Total, S.A
+ * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
  * Copyright (c) 2023-2024 Chevron 
  * Copyright (c) 2019-     GEOS/GEOSX Contributors

examples/ObjectCatalog/Derived1.hpp

@@ -3,7 +3,7 @@
  * SPDX-License-Identifier: LGPL-2.1-only
  *
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2024 Total, S.A
+ * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
  * Copyright (c) 2023-2024 Chevron 
  * Copyright (c) 2019-     GEOS/GEOSX Contributors

examples/ObjectCatalog/Derived2.cpp

@@ -2,10 +2,11 @@
  * ------------------------------------------------------------------------------------------------------------
  * SPDX-License-Identifier: LGPL-2.1-only
  *
- * Copyright (c) 2018-2020 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2020 The Board of Trustees of the Leland Stanford Junior University
- * Copyright (c) 2018-2020 Total, S.A
- * Copyright (c) 2019-     GEOSX Contributors
+ * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
+ * Copyright (c) 2018-2024 TotalEnergies
+ * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
+ * Copyright (c) 2023-2024 Chevron
+ * Copyright (c) 2019-     GEOS/GEOSX Contributors
  * All rights reserved
  *
  * See top level LICENSE, COPYRIGHT, CONTRIBUTORS, NOTICE, and ACKNOWLEDGEMENTS files for details.

examples/ObjectCatalog/Derived2.hpp

@@ -3,7 +3,7 @@
  * SPDX-License-Identifier: LGPL-2.1-only
  *
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2024 Total, S.A
+ * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
  * Copyright (c) 2023-2024 Chevron 
  * Copyright (c) 2019-     GEOS/GEOSX Contributors

examples/ObjectCatalog/main.cpp

@@ -3,9 +3,9 @@
  * SPDX-License-Identifier: LGPL-2.1-only
  *
  * Copyright (c) 2016-2024 Lawrence Livermore National Security LLC
- * Copyright (c) 2018-2024 Total, S.A
+ * Copyright (c) 2018-2024 TotalEnergies
  * Copyright (c) 2018-2024 The Board of Trustees of the Leland Stanford Junior University
- * Copyright (c) 2023-2024 Chevron 
+ * Copyright (c) 2023-2024 Chevron
  * Copyright (c) 2019-     GEOS/GEOSX Contributors
  * All rights reserved
  *
@@ -31,10 +31,14 @@ int main( int argc, char *argv[] )
 
 
   GEOS_LOG( "Attempting to create a Derived1 object" );
-  std::unique_ptr<Base> derived1 = Base::CatalogInterface::Factory( "derived1", junk, junk2, param );
+  std::unique_ptr< Base > derived1 = Base::CatalogInterface::factory( "derived1",
+                                                                      Base::getDataContext(),
+                                                                      junk, junk2, param );
   GEOS_LOG( "Attempting to create a Derived2 object" );
-  std::unique_ptr<Base> derived2 = Base::CatalogInterface::Factory( "derived2", junk, junk3, param );
+  std::unique_ptr< Base > derived2 = Base::CatalogInterface::factory( "derived2",
+                                                                      Base::getDataContext(),
+                                                                      junk, junk3, param );
 
-  Base::CatalogInterface::catalog_cast<Derived1>( *(derived2.get()));
+  Base::CatalogInterface::catalog_cast< Derived1 >( *(derived2.get()));
   GEOS_LOG( "EXITING MAIN" );
 }

examples/pygeosxExamples/modifyBoundaryCondition/pkn_example.xml

@@ -62,7 +62,7 @@
     <SurfaceGenerator
       name="SurfaceGen"
       targetRegions="{ Domain }"
-      rockToughness="1e6"
+      initialRockToughness="1e6"
       nodeBasedSIF="1"
       mpiCommOrder="1"/>
   </Solvers>