Merge branch 'develop' into feature/tbeltzun/level-names-vtk

GEOS-DEV · Nov 15, 2023 · 1ac8cb3 · 1ac8cb3
2 parents 4971115 + c60be25
commit 1ac8cb3
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Showing 408 changed files with 29,387 additions and 2,732 deletions.
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -2,7 +2,7 @@
     "build": {
         "dockerfile": "Dockerfile",
         "args": {
-            "GEOS_TPL_TAG": "238-63"
+            "GEOS_TPL_TAG": "245-86"
         }
     },
     "runArgs": [

diff --git a/.github/workflows/build_and_test.yml b/.github/workflows/build_and_test.yml
@@ -35,6 +35,10 @@ on:
       OS:
         required: true
         type: string
+      USE_SCCACHE:
+        required: false
+        type: boolean
+        default: true
     secrets:
       GOOGLE_CLOUD_GCP:
         required: false
@@ -52,6 +56,7 @@ jobs:
       HOST_CONFIG: ${{ inputs.HOST_CONFIG }}
       COMMIT: ${{ inputs.COMMIT }}
       GEOSX_TPL_TAG: ${{ inputs.GEOSX_TPL_TAG }}
+      USE_SCCACHE: ${{ inputs.USE_SCCACHE }}
     steps:
     - name: Checkout Repository
       uses: actions/checkout@v3
@@ -60,10 +65,11 @@ jobs:
         lfs: false
 
     - id: 'auth'
-      if: env.GCP_BUCKET
+      if: ${{ env.GCP_BUCKET || env.USE_SCCACHE }}
       uses: 'google-github-actions/auth@v1'
       with:
         credentials_json: '${{ secrets.GOOGLE_CLOUD_GCP }}'
+        create_credentials_file: true
     - name: 'Set up Cloud SDK'
       if: env.GCP_BUCKET
       uses: 'google-github-actions/setup-gcloud@v1'

diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -7,7 +7,7 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  GEOSX_TPL_TAG: 228-73
+  GEOSX_TPL_TAG: 245-86
 
 jobs:
 
@@ -204,7 +204,7 @@ jobs:
 
           - name: Ubuntu CUDA (20.04, clang 10.0.0 + gcc 9.4.0, open-mpi 4.0.3, cuda-11.8.89)
             DOCKER_REPOSITORY: geosx/ubuntu20.04-clang10.0.0-cuda11.8.89
-            OS: ubuntu-22.04
+            OS: Runner_4core_16GB
             CMAKE_BUILD_TYPE: Release
             BUILD_AND_TEST_ARGS: "--disable-unit-tests --disable-schema-deployment"
             ENABLE_HYPRE: ON
@@ -213,14 +213,14 @@ jobs:
 
           - name: Centos (7.7, gcc 8.3.1, open-mpi 1.10.7, cuda 11.8.89)
             DOCKER_REPOSITORY: geosx/centos7.7-gcc8.3.1-cuda11.8.89
-            OS: ubuntu-22.04
+            OS: Runner_4core_16GB
             CMAKE_BUILD_TYPE: Release
             BUILD_AND_TEST_ARGS: "--disable-unit-tests --disable-schema-deployment"
 
           # Matrix job that deploys to Google Cloud
           - name: Pecan GPU (centos 7.7, gcc 8.2.0, open-mpi 4.0.1, mkl 2019.5, cuda 11.5.119)
             DOCKER_REPOSITORY: geosx/pecan-gpu-gcc8.2.0-openmpi4.0.1-mkl2019.5-cuda11.5.119
-            OS: ubuntu-22.04
+            OS: Runner_4core_16GB
             CMAKE_BUILD_TYPE: Release
             BUILD_AND_TEST_ARGS: "--build-exe-only --disable-unit-tests --disable-schema-deployment"
             HOST_CONFIG: host-configs/TOTAL/pecan-GPU.cmake

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -28,7 +28,7 @@ stages:
     - git submodule update --init --recursive integratedTests
     - git submodule update --init --recursive src/coreComponents/fileIO/coupling/hdf5_interface
 
-    - mkdir ${SYSTEM}
+    - mkdir ${SYSTEM_COMPILER}
 
     # newer geosxats needs python3 to run
     - module load python/3
@@ -39,24 +39,24 @@ stages:
     # CONFIGURE
     - echo "~~~~~~~~~~ START - configure ~~~~~~~~~~~"
     - config_code=0
-    - python scripts/config-build.py -hc host-configs/LLNL/${HOST_CONFIG} -bt Release -bp build -DENABLE_DOXYGEN=OFF 2>&1 | tee ${SYSTEM}/${SYSTEM}_configure.log || config_code=$?
-    - mv ${SYSTEM}/${SYSTEM}_configure.log ${SYSTEM}/${SYSTEM}_configure_$([ $config_code == 0 ] && echo "SUCCESS" || echo "FAILURE").log
+    - python scripts/config-build.py -hc host-configs/LLNL/${HOST_CONFIG} -bt Release -bp build -DENABLE_DOXYGEN=OFF 2>&1 | tee ${SYSTEM_COMPILER}/${SYSTEM_COMPILER}_configure.log || config_code=$?
+    - mv ${SYSTEM_COMPILER}/${SYSTEM_COMPILER}_configure.log ${SYSTEM_COMPILER}/${SYSTEM_COMPILER}_configure_$([ $config_code == 0 ] && echo "SUCCESS" || echo "FAILURE").log
     - echo "~~~~~~~~~~ END - configure ~~~~~~~~~~~~~"
 
     # BUILD
     - echo "~~~~~~~~~~ START - build ~~~~~~~~~~~"
     - build_code=0
-    - ${ALLOC_COMMAND} make VERBOSE=1 -C build -j ${NPROC:-16} 2>&1 | tee ${SYSTEM}/${SYSTEM}_build.log || build_code=$?
-    - mv ${SYSTEM}/${SYSTEM}_build.log ${SYSTEM}/${SYSTEM}_build_$([ $build_code == 0 ] && echo "SUCCESS" || echo "FAILURE").log
+    - ${ALLOC_COMMAND} make VERBOSE=1 -C build -j ${NPROC:-16} 2>&1 | tee ${SYSTEM_COMPILER}/${SYSTEM_COMPILER}_build.log || build_code=$?
+    - mv ${SYSTEM_COMPILER}/${SYSTEM_COMPILER}_build.log ${SYSTEM_COMPILER}/${SYSTEM_COMPILER}_build_$([ $build_code == 0 ] && echo "SUCCESS" || echo "FAILURE").log
     - echo "~~~~~~~~~~ END - build ~~~~~~~~~~~~~"
 
     # UNIT TEST
     - echo "~~~~~~~~~~ START - unit tests ~~~~~~~~~~~"
     - unit_code=0
     - cd build
-    - ${ALLOC_COMMAND} ctest --output-on-failure  2>&1 | tee ../${SYSTEM}/${SYSTEM}_unit_test.log || unit_code=$?
+    - ${ALLOC_COMMAND} ctest --output-on-failure  2>&1 | tee ../${SYSTEM_COMPILER}/${SYSTEM_COMPILER}_unit_test.log || unit_code=$?
     - cd ..
-    - mv ${SYSTEM}/${SYSTEM}_unit_test.log ${SYSTEM}/${SYSTEM}_unit_test_$([ $unit_code == 0 ] && echo "SUCCESS" || echo "FAILURE").log
+    - mv ${SYSTEM_COMPILER}/${SYSTEM_COMPILER}_unit_test.log ${SYSTEM_COMPILER}/${SYSTEM_COMPILER}_unit_test_$([ $unit_code == 0 ] && echo "SUCCESS" || echo "FAILURE").log
     - echo "~~~~~~~~~~ END - unit tests ~~~~~~~~~~~~~"
 
     # INTEGRATED TEST
@@ -66,11 +66,11 @@ stages:
     - make ats_environment
     # Hard code integrated test failure status until optional fail flag fixed
     - integrated_code=1
-    - ${INTEGRATED_ALLOC_COMMAND} ./integratedTests/geos_ats.sh --failIfTestsFail 2>&1 | tee ../${SYSTEM}/${SYSTEM}_integrated_test.log || integrated_code=1
-    #- ${INTEGRATED_ALLOC_COMMAND} ./integratedTests/geos_ats.sh --failIfTestsFail 2>&1 | tee ../${SYSTEM}/${SYSTEM}_integrated_test.log || integrated_code=$?
+    - ${INTEGRATED_ALLOC_COMMAND} ./integratedTests/geos_ats.sh --failIfTestsFail 2>&1 | tee ../${SYSTEM_COMPILER}/${SYSTEM_COMPILER}_integrated_test.log || integrated_code=1
+    #- ${INTEGRATED_ALLOC_COMMAND} ./integratedTests/geos_ats.sh --failIfTestsFail 2>&1 | tee ../${SYSTEM_COMPILER}/${SYSTEM_COMPILER}_integrated_test.log || integrated_code=$?
     - cd ..
-    - mv ${SYSTEM}/${SYSTEM}_integrated_test.log ${SYSTEM}/${SYSTEM}_integrated_test_$([ $integrated_code == 0 ] && echo "SUCCESS" || echo "FAILURE").log
-    - cp -rL build/integratedTests/TestResults ${SYSTEM}/
+    - mv ${SYSTEM_COMPILER}/${SYSTEM_COMPILER}_integrated_test.log ${SYSTEM_COMPILER}/${SYSTEM_COMPILER}_integrated_test_$([ $integrated_code == 0 ] && echo "SUCCESS" || echo "FAILURE").log
+    - cp -rL build/integratedTests/TestResults ${SYSTEM_COMPILER}/
     - echo "~~~~~~~~~~ END - integrated tests ~~~~~~~~~~~~~"
 
     # CLEANUP + PRINT SUCCESS/FAILURES
@@ -95,9 +95,9 @@ stages:
   artifacts:
     when: always
     paths:
-      - quartz/
-      - lassen/
-      - tioga/
+      - quartz*/
+      - lassen*/
+      - tioga*/
   # Allow job to always fail, so nightly-job in next stage will run
   allow_failure: true
 
@@ -108,7 +108,6 @@ stages:
   variables:
     ALLOC_COMMAND: "salloc -N1 -ppdebug"
     INTEGRATED_ALLOC_COMMAND: "salloc -N1 -n 36 -ppdebug"
-    SYSTEM: "quartz"
   tags:
     - shell
     - quartz
@@ -121,7 +120,6 @@ stages:
   variables:
     ALLOC_COMMAND: "salloc -N1 -ppdebug"
     INTEGRATED_ALLOC_COMMAND: "salloc -N 10 -p pbatch"
-    SYSTEM: "tioga"
   before_script:
     - module load rocm/5.4.3
     - module load cce/15.0.0
@@ -138,43 +136,64 @@ stages:
   variables:
     ALLOC_COMMAND: "lalloc 1"
     INTEGRATED_ALLOC_COMMAND: "lalloc 10"
-    SYSTEM: "lassen"
   tags:
     - shell
     - lassen
   extends: [.build_script]
 
 ####
-# quartz job
+# quartz jobs
 quartz_clang_14_build:
   variables:
     HOST_CONFIG: "quartz-clang-14.cmake"
+    SYSTEM_COMPILER: "quartz-clang-14"
+  extends: [.build_on_quartz]
+
+quartz_gcc_12_build:
+  variables:
+    HOST_CONFIG: "quartz-gcc-12.cmake"
+    SYSTEM_COMPILER: "quartz-gcc-12"
   extends: [.build_on_quartz]
 
 ####
 # tioga job
 tioga_cce_15_build:
   variables:
     HOST_CONFIG: "tioga-cce-15.cmake"
+    SYSTEM_COMPILER: "tioga-cce-15"
   extends: [.build_on_tioga]
 
 ####
-# lassen job
+# lassen jobs
 lassen_clang_10_cuda_11_build:
   variables:
     HOST_CONFIG: "lassen-clang-10-cuda-11.cmake"
+    SYSTEM_COMPILER: "lassen-clang-10-cuda-11"
+  extends: [.build_on_lassen]
+
+lassen_gcc_8_cuda_11_build:
+  variables:
+    HOST_CONFIG: "lassen-gcc-8-cuda-11.cmake"
+    SYSTEM_COMPILER: "lassen-gcc-8-cuda-11"
   extends: [.build_on_lassen]
 
 ####
 # Pull nightlyTests repo and update files
+# Note: Arguments to update.sh need to be kept updated with build jobs
 nightly-job:
   stage: nightly
   script:
-    - echo "~~~~~~~~~~ START - write to nightlyTests Repo ~~~~~~~~~~~~~"
-    - git clone [email protected]:GEOS-DEV/nightlyTests.git
-    - cd nightlyTests
-    - ./update.sh
-    - echo "~~~~~~~~~~ END - write to nightlyTests Repo ~~~~~~~~~~~~~"
+    - |
+      echo "~~~~~~~~~~ START - write to nightlyTests Repo ~~~~~~~~~~~~~"
+      git clone [email protected]:GEOS-DEV/nightlyTests.git
+      cd nightlyTests
+      ./update.sh \
+          quartz-clang-14 \
+          quartz-gcc-12 \
+          lassen-clang-10-cuda-11 \
+          lassen-gcc-8-cuda-11 \
+          tioga-cce-15
+      echo "~~~~~~~~~~ END - write to nightlyTests Repo ~~~~~~~~~~~~~"
   only:
     refs:
       - schedules

diff --git a/inputFiles/compositionalMultiphaseFlow/co2_flux_3d.xml b/inputFiles/compositionalMultiphaseFlow/co2_flux_3d.xml
@@ -8,6 +8,8 @@
       discretization="fluidTPFA"
       temperature="368.15"
       useMass="1"
+      useTotalMassEquation="0"
+      useSimpleAccumulation="1"
       targetRegions="{ region }">
       <NonlinearSolverParameters
         newtonTol="1.0e-5"

diff --git a/inputFiles/compositionalMultiphaseWell/staircase_co2_wells_3d.xml b/inputFiles/compositionalMultiphaseWell/staircase_co2_wells_3d.xml
@@ -121,7 +121,7 @@
     <CellElementRegion
       name="Channel"
       cellBlocks="{ b08, b00, b01, b05, b06, b14, b15, b11 }"
-      materialList="{ fluid1, rock, relperm, cappres }"/>
+      materialList="{ fluid1, rock, relperm, cappres, diffusion }"/>
 
     <CellElementRegion
       name="Barrier"
@@ -182,6 +182,13 @@
     <ConstantPermeability
       name="rockPerm"
       permeabilityComponents="{ 2.0e-16, 2.0e-16, 2.0e-16 }"/>
+
+    <ConstantDiffusion
+      name="diffusion"
+      phaseNames="{ gas, water }"
+      defaultPhaseDiffusivityMultipliers="{ 20, 1 }"
+      diffusivityComponents="{ 1e-9, 1e-9, 1e-9 }"/>
+
   </Constitutive>
 
   <FieldSpecifications>

diff --git a/inputFiles/hydraulicFracturing/heterogeneousInSitu_base.xml b/inputFiles/hydraulicFracturing/heterogeneousInSitu_base.xml
@@ -14,16 +14,18 @@
       contactRelationName="fractureContact"
       maxNumResolves="2">
       <NonlinearSolverParameters
-        newtonTol="1.0e-6"
+        newtonTol="1.0e-5"
         newtonMaxIter="40"
         lineSearchMaxCuts="3"/>
       <LinearSolverParameters
+        logLevel="1"
         solverType="gmres"
-        preconditionerType="amg"/>
+        preconditionerType="mgr"/>
     </Hydrofracture>
 
     <SolidMechanicsLagrangianSSLE
       name="lagsolve"
+      logLevel="1"
       timeIntegrationOption="QuasiStatic"
       discretization="FE1"
       targetRegions="{ Domain, Fracture }"
@@ -37,6 +39,7 @@
 
     <SinglePhaseFVM
       name="SinglePhaseFlow"
+      logLevel="1"
       discretization="singlePhaseTPFA"
       targetRegions="{ Fracture }">
       <NonlinearSolverParameters
@@ -155,7 +158,7 @@
 
     <FrictionlessContact
       name="fractureContact"
-      penaltyStiffness="0.0e8"
+      penaltyStiffness="1e12"
       apertureTableName="apertureTable"/>
 
     <ParallelPlatesPermeability

diff --git a/inputFiles/materialPointMethod/dfgMovingGrid/FTable.dat b/inputFiles/materialPointMethod/dfgMovingGrid/FTable.dat
@@ -0,0 +1,2 @@
+0	1	1	1
+0.1	1	0.95	1
diff --git a/inputFiles/materialPointMethod/dfgMovingGrid/mpmHeaderFile_dfgMovingGrid b/inputFiles/materialPointMethod/dfgMovingGrid/mpmHeaderFile_dfgMovingGrid
@@ -0,0 +1,4 @@
+2	1
+stiff	0
+compliant	1
+CPDI	8
diff --git a/inputFiles/materialPointMethod/dfgMovingGrid/mpmParticleFile_dfgMovingGrid b/inputFiles/materialPointMethod/dfgMovingGrid/mpmParticleFile_dfgMovingGrid
@@ -0,0 +1,8 @@
+1 0.125	0.125	0.0	0	0	0	1.0	0.0	0.0	0	0	0	0	1.0	0.125	0	0	0	0.125	0	0	0	0.5	
+2 0.125	0.375	0.0	0	0	0	1.0	0.0	0.0	0	0	1	0	1.0	0.125	0	0	0	0.125	0	0	0	0.5	
+3 0.125	0.625	0.0	0	0	0	1.0	0.0	0.0	1	0	1	0	1.0	0.125	0	0	0	0.125	0	0	0	0.5	
+4 0.125	0.875	0.0	0	0	0	1.0	0.0	0.0	1	0	0	0	1.0	0.125	0	0	0	0.125	0	0	0	0.5	
+5 0.375	0.125	0.0	0	0	0	1.0	0.0	0.0	0	0	1	0	1.0	0.125	0	0	0	0.125	0	0	0	0.5	
+6 0.375	0.375	0.0	0	0	0	1.0	0.0	0.0	0	0	1	0	1.0	0.125	0	0	0	0.125	0	0	0	0.5	
+7 0.375	0.625	0.0	0	0	0	1.0	0.0	0.0	1	0	1	0	1.0	0.125	0	0	0	0.125	0	0	0	0.5	
+8 0.375	0.875	0.0	0	0	0	1.0	0.0	0.0	1	0	1	0	1.0	0.125	0	0	0	0.125	0	0	0	0.5