dev merge

.devcontainer/devcontainer.json

@@ -2,7 +2,7 @@
     "build": {
         "dockerfile": "Dockerfile",
         "args": {
-            "GEOS_TPL_TAG": "278-500"
+            "GEOS_TPL_TAG": "284-535"
         }
     },
     "runArgs": [

.github/CODEOWNERS

@@ -10,6 +10,7 @@
 /.github/ @rrsettgast
 
 /BASELINE_NOTES.md
+/.integrated_tests.yaml                               @CusiniM @cssherman @rrsettgast @wrtobin @castelletto1 @jhuang2601 @paveltomin
 /inputFiles/                                          @CusiniM @cssherman @jhuang2601 @rrsettgast
 /src/coreComponents/LvArray                           @rrsettgast @wrtobin @corbett5 @CusiniM 
 /src/coreComponents/codingUtilities                   @rrsettgast @untereiner @corbett5 @wrtobin

.github/ISSUE_TEMPLATE/bug-report.md

@@ -27,7 +27,7 @@ If applicable, add screenshots to help explain your problem.
 **Platform (please complete the following information):**
 - Machine [e.g. LLNL/Quartz] 
 - Compiler: [e.g. gcc 8.1.0]
-- GEOSX Version [e.g. 0.2]
+- GEOS Version [e.g. 0.2]
 
 **Additional context**
 Add any other context about the problem here.

.github/workflows/build_and_test.yml

@@ -5,6 +5,10 @@ on:
       BUILD_AND_TEST_CLI_ARGS:
         required: false
         type: string
+      BUILD_SHARED_LIBS:
+        required: false
+        type: string
+        default: 'ON'
       BUILD_TYPE:
         required: false
         type: string
@@ -51,6 +55,9 @@ on:
         required: false
         type: string
         default: ''
+      HOST_ARCH:
+        required: false
+        type: string
       RUNS_ON:
         required: true
         type: string
@@ -63,7 +70,11 @@ on:
         type: string
       LOCAL_BASELINE_DIR:
         required: false
-        type: string  
+        type: string
+      BUILD_GENERATOR:
+        required: false
+        type: string
+        default: '--ninja'
     secrets:
       GOOGLE_CLOUD_GCP:
         required: false
@@ -100,20 +111,26 @@ jobs:
 
     - id: 'auth'
       if: ${{ inputs.GCP_BUCKET || inputs.USE_SCCACHE }}
-      uses: 'google-github-actions/[email protected].3'
+      uses: 'google-github-actions/[email protected].5'
       with:
         credentials_json: '${{ secrets.GOOGLE_CLOUD_GCP }}'
         create_credentials_file: true
 
     - name: 'Set up Cloud SDK'
       if: inputs.GCP_BUCKET
-      uses: 'google-github-actions/[email protected].0'
+      uses: 'google-github-actions/[email protected].1'
       with:
         version: '>= 363.0.0'
 
     - name: Print environment
       run: printenv
 
+    - name: Setup QEMU for ${{ inputs.HOST_ARCH }} emulation
+      if: ${{ inputs.HOST_ARCH }}
+      uses: docker/setup-qemu-action@v3
+      with:
+        platforms: ${{ inputs.HOST_ARCH }}
+
     - name: Build, test, deploy.
       run: |
         # Those two bash arrays will be populated depending on the required options,
@@ -136,6 +153,10 @@ jobs:
           script_args+=(--nproc ${NPROC})
         fi
 
+        if [[ -n "${{ inputs.BUILD_GENERATOR }}" ]]; then
+          script_args+=(${{ inputs.BUILD_GENERATOR }})
+        fi
+
         docker_args+=(${{ inputs.DOCKER_RUN_ARGS }})
 
         COMMIT=${{ github.event.pull_request.head.sha }}
@@ -184,6 +205,7 @@ jobs:
         docker_args+=(-e ENABLE_HYPRE=${ENABLE_HYPRE:-OFF})
         docker_args+=(-e ENABLE_HYPRE_DEVICE=${ENABLE_HYPRE_DEVICE:-CPU})
         docker_args+=(-e ENABLE_TRILINOS=${ENABLE_TRILINOS:-ON})
+        docker_args+=(-e GEOS_BUILD_SHARED_LIBS=${{ inputs.BUILD_SHARED_LIBS }})
 
         docker_args+=(--cap-add=SYS_PTRACE --rm)
 

.github/workflows/ci_tests.yml

@@ -5,7 +5,7 @@ on:
     branches: 
       - develop
   pull_request:
-      types: [opened, synchronize, reopened, edited]
+      types: [opened, synchronize, reopened]
   workflow_dispatch:
 
 # Cancels in-progress workflows for a PR when updated
@@ -149,43 +149,49 @@ jobs:
           - name: Ubuntu (20.04, gcc 9.4.0, open-mpi 4.0.3)
             CMAKE_BUILD_TYPE: Release
             DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc9
+            BUILD_SHARED_LIBS: ON
 
           - name: Ubuntu debug (20.04, gcc 10.5.0, open-mpi 4.0.3) - github codespaces
             CMAKE_BUILD_TYPE: Debug
             DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc10
+            BUILD_SHARED_LIBS: ON
 
           - name: Ubuntu (20.04, gcc 10.5.0, open-mpi 4.0.3) - github codespaces
             CMAKE_BUILD_TYPE: Release
             DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc10
+            BUILD_SHARED_LIBS: ON
 
           - name: Ubuntu (22.04, gcc 11.4.0, open-mpi 4.1.2)
             CMAKE_BUILD_TYPE: Release
             DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc11
             ENABLE_HYPRE: ON
             ENABLE_TRILINOS: OFF
             GCP_BUCKET: geosx/ubuntu22.04-gcc11
+            BUILD_SHARED_LIBS: ON
 
           - name: Ubuntu (22.04, gcc 12.3.0, open-mpi 4.1.2)
             CMAKE_BUILD_TYPE: Release
             DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc12
             ENABLE_HYPRE: ON
             ENABLE_TRILINOS: OFF
+            BUILD_SHARED_LIBS: ON
 
           - name: Ubuntu (22.04, clang 15.0.7, open-mpi 4.1.2)
             CMAKE_BUILD_TYPE: Release
             DOCKER_REPOSITORY: geosx/ubuntu22.04-clang15
             ENABLE_HYPRE: ON
             ENABLE_TRILINOS: OFF
+            BUILD_SHARED_LIBS: ON
 
     uses: ./.github/workflows/build_and_test.yml
     with:
+      BUILD_SHARED_LIBS: ${{ matrix.BUILD_SHARED_LIBS }}
       CMAKE_BUILD_TYPE: ${{ matrix.CMAKE_BUILD_TYPE }}
       DOCKER_IMAGE_TAG: ${{ needs.is_not_draft_pull_request.outputs.DOCKER_IMAGE_TAG }}
       DOCKER_REPOSITORY: ${{ matrix.DOCKER_REPOSITORY }}
       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
 
@@ -244,6 +250,8 @@ jobs:
       ENABLE_TRILINOS: OFF
       GCP_BUCKET: geosx/ubuntu22.04-gcc11
       RUNS_ON: Runner_4core_16GB
+      REQUIRED_LABEL: "ci: run code coverage"
+
 
   # mac_builds:
   #   needs:
@@ -269,6 +277,7 @@ jobs:
           - name: Ubuntu CUDA debug (20.04, clang 10.0.0 + gcc 9.4.0, open-mpi 4.0.3, cuda-11.8.89)
             BUILD_AND_TEST_CLI_ARGS: "--build-exe-only --no-install-schema"
             CMAKE_BUILD_TYPE: Debug
+            BUILD_GENERATOR: "--ninja"
             DOCKER_REPOSITORY: geosx/ubuntu20.04-clang10.0.0-cuda11.8.89
             ENABLE_HYPRE_DEVICE: CUDA
             ENABLE_HYPRE: ON
@@ -282,6 +291,7 @@ jobs:
           - name: Ubuntu CUDA (20.04, clang 10.0.0 + gcc 9.4.0, open-mpi 4.0.3, cuda-11.8.89)
             BUILD_AND_TEST_CLI_ARGS: "--no-install-schema"
             CMAKE_BUILD_TYPE: Release
+            BUILD_GENERATOR: "--ninja"
             DOCKER_REPOSITORY: geosx/ubuntu20.04-clang10.0.0-cuda11.8.89
             ENABLE_HYPRE_DEVICE: CUDA
             ENABLE_HYPRE: ON
@@ -291,35 +301,59 @@ jobs:
             DOCKER_RUN_ARGS: "--cpus=8 --memory=256g --runtime=nvidia --gpus all -v /etc/pki/ca-trust/source/anchors/:/usr/local/share/ca-certificates/llnl:ro"
             DOCKER_CERTS_DIR: "/usr/local/share/ca-certificates"
             DOCKER_CERTS_UPDATE_COMMAND: "update-ca-certificates"
+
+          - name: Rockylinux CUDA (8, clang 17.0.6, cuda 12.5.1)
+            BUILD_AND_TEST_CLI_ARGS: "--no-install-schema"
+            CMAKE_BUILD_TYPE: Release
+            BUILD_GENERATOR: "--ninja"
+            ENABLE_HYPRE_DEVICE: CUDA
+            ENABLE_HYPRE: ON
+            ENABLE_TRILINOS: OFF
+            DOCKER_REPOSITORY: geosx/rockylinux8-clang17-cuda12.5
+            RUNS_ON: streak
+            NPROC: 8
+            DOCKER_RUN_ARGS: "--cpus=8 --memory=256g --runtime=nvidia --gpus all -v /etc/pki/ca-trust/source/anchors/:/usr/local/share/ca-certificates/llnl:ro"
+            DOCKER_CERTS_DIR: "/usr/local/share/ca-certificates"
+            DOCKER_CERTS_UPDATE_COMMAND: "update-ca-trust"
 
-          # compiler error in ElasticFirstOrderWaveEquationSEMKernel::StressComputation::launch in call to FE_TYPE::computeFirstOrderStiffnessTermX
-          # - name: Rockylinux (8, clang 17.0.6, cuda 12.5)
-          #   BUILD_AND_TEST_CLI_ARGS: "--no-run-unit-tests --no-install-schema"
-          #   CMAKE_BUILD_TYPE: Release
-          #   DOCKER_REPOSITORY: geosx/rockylinux8-clang17-cuda12.5
-          #   RUNS_ON: streak2
-          #   NPROC: 2
-          #   DOCKER_RUN_ARGS: "--cpus=1 --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"
-
-          # compiler error in ElasticFirstOrderWaveEquationSEMKernel::StressComputation::launch in call to FE_TYPE::computeFirstOrderStiffnessTermX
-          # - name: Rockylinux (8, gcc 8.5, cuda 12.5)
-          #   BUILD_AND_TEST_CLI_ARGS: "--no-run-unit-tests --no-install-schema"
-          #   CMAKE_BUILD_TYPE: Release
-          #   DOCKER_REPOSITORY: geosx/rockylinux8-gcc8-cuda12.5
-          #   RUNS_ON: streak2
-          #   NPROC: 2
-          #   DOCKER_RUN_ARGS: "--cpus=1 --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"  
+          - name: Rockylinux CUDA (8, gcc 8.5, cuda 12.5.1)
+            BUILD_AND_TEST_CLI_ARGS: "--no-run-unit-tests --no-install-schema"
+            CMAKE_BUILD_TYPE: Release
+            BUILD_GENERATOR: "--ninja"
+            ENABLE_HYPRE_DEVICE: CUDA
+            ENABLE_HYPRE: ON
+            ENABLE_TRILINOS: OFF
+            DOCKER_REPOSITORY: geosx/rockylinux8-gcc8-cuda12.5
+            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"
+
+          - name: Pangea 3 (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"
+            DOCKER_REPOSITORY: geosx/pangea3-almalinux8-gcc9.4-openmpi4.1.2-cuda11.5.0-openblas0.3.18
+            HOST_CONFIG: host-configs/TOTAL/pangea3-gcc8.4.1-openmpi-4.1.2-wave-solver.cmake
+            ENABLE_HYPRE_DEVICE: CUDA
+            ENABLE_HYPRE: ON
+            ENABLE_TRILINOS: OFF
+            HOST_ARCH: ppc64le
+            RUNS_ON: streak2
+            NPROC: 8
+            DOCKER_RUN_ARGS: "--cpus=8 --memory=128g -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.
 
     uses: ./.github/workflows/build_and_test.yml
     with:
       BUILD_AND_TEST_CLI_ARGS: ${{ matrix.BUILD_AND_TEST_CLI_ARGS }}
       CMAKE_BUILD_TYPE: ${{ matrix.CMAKE_BUILD_TYPE }}
+      BUILD_GENERATOR: ${{ matrix.BUILD_GENERATOR }}
       DOCKER_CERTS_DIR: ${{ matrix.DOCKER_CERTS_DIR }}
       DOCKER_CERTS_UPDATE_COMMAND: ${{ matrix.DOCKER_CERTS_UPDATE_COMMAND }}
       DOCKER_IMAGE_TAG: ${{ needs.is_not_draft_pull_request.outputs.DOCKER_IMAGE_TAG }}
@@ -329,6 +363,7 @@ jobs:
       ENABLE_HYPRE: ${{ matrix.ENABLE_HYPRE }}
       ENABLE_TRILINOS: ${{ matrix.ENABLE_TRILINOS }}
       GCP_BUCKET: ${{ matrix.GCP_BUCKET }}
+      HOST_ARCH: ${{ matrix.HOST_ARCH }}
       HOST_CONFIG: ${{ matrix.HOST_CONFIG }}
       NPROC: ${{ matrix.NPROC }}
       RUNS_ON: ${{ matrix.RUNS_ON }}

.gitignore

@@ -19,6 +19,7 @@
 /Debug/
 uberenv_libs
 spack-*.txt
+/src/docs/sphinx/datastructure
 *~
 __pycache__
 

.integrated_tests.yaml

@@ -1,7 +1,7 @@
 baselines:
   bucket: geosx
-  baseline: integratedTests/baseline_integratedTests-pr3197-6679-a003f43
+  baseline: integratedTests/baseline_integratedTests-pr2878-8188-ed2ded2
 
 allow_fail:
   all: ''
-  streak: pennyShapedToughnessDominated_smoke_01,pennyShapedViscosityDominated_smoke_01,pknViscosityDominated_smoke_01
+  streak: ''

.readthedocs.yml

@@ -15,6 +15,8 @@ build:
     nodejs: "16"
     python: "3.10"
   jobs:
+    pre_build:
+    - python3 scripts/SchemaToRSTDocumentation.py -s src/coreComponents/schema/schema.xsd -o src/docs/sphinx
     post_install:
     - npm install -g [email protected]
     - npm install -g @mermaid-js/[email protected]
@@ -30,9 +32,12 @@ python:
 sphinx:
   configuration: src/conf.py
   builder: html
+  fail_on_warning: true
+
 
 # Optionally build your docs in additional formats such as PDF and ePub
-formats: all
+formats:
+  - pdf
 
 submodules:
   include: