Merge remote-tracking branch 'origin/develop' into feature/frankfei/p…

…ressurePerm

.github/workflows/build_and_test.yml

@@ -9,13 +9,20 @@ on:
         required: false
         type: string
         default: build
+      DOCKER_CERTS_UPDATE_COMMAND:
+        required: false
+        type: string
       CMAKE_BUILD_TYPE:
         required: true
         type: string
       CODE_COVERAGE:
         required: false
         type: boolean
         default: false
+      DOCKER_CERTS_DIR:
+        required: false
+        type: string
+        default: ''
       DOCKER_IMAGE_TAG:
         required: true
         type: string
@@ -40,20 +47,41 @@ on:
       HOST_CONFIG:
         required: false
         type: string
+      NPROC:
+        required: false
+        type: string
+        default: ''
       RUNS_ON:
         required: true
         type: string
+      UPLOAD_BASELINES:
+        required: false
+        type: string
       USE_SCCACHE:
         required: false
         type: boolean
         default: true
+      REQUIRED_LABEL:
+        required: false
+        type: string
     secrets:
       GOOGLE_CLOUD_GCP:
         required: false
 jobs:
   build_test_deploy:
     runs-on: ${{ inputs.RUNS_ON }}
     steps:
+    - name: does_pr_have_necessary_labels
+      if: ${{inputs.REQUIRED_LABEL && github.event_name == 'pull_request'}}
+      run: | 
+        pr_json=$(curl -H "Accept: application/vnd.github+json" https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.number }})
+        LABELS=$(echo ${pr_json} | jq -crM '[.labels[].name]')
+        echo " the labels are ${LABELS}"
+        echo " the required label is ${{inputs.REQUIRED_LABEL}}"
+        if [[ "${LABELS}" != *"${{inputs.REQUIRED_LABEL}}"* ]]; then
+          exit 1
+        fi
+      
     - name: 'Cleanup build folder'
       run: |
         pwd
@@ -64,15 +92,15 @@ jobs:
         ls -la ./
 
     - name: Checkout Repository
-      uses: actions/[email protected].1
+      uses: actions/[email protected].4
       with:
         submodules: true
         lfs: ${{ inputs.BUILD_TYPE == 'integrated_tests' }}
         fetch-depth: 1
 
     - id: 'auth'
       if: ${{ inputs.GCP_BUCKET || inputs.USE_SCCACHE }}
-      uses: 'google-github-actions/[email protected].0'
+      uses: 'google-github-actions/[email protected].2'
       with:
         credentials_json: '${{ secrets.GOOGLE_CLOUD_GCP }}'
         create_credentials_file: true
@@ -93,7 +121,20 @@ jobs:
         docker_args=()
         script_args=()
 
+        if [[ -n "${{ inputs.DOCKER_CERTS_DIR }}" ]]; then
+          DOCKER_CERTS_DIR=${{ inputs.DOCKER_CERTS_DIR }}
+          docker_args+=(-e DOCKER_CERTS_DIR=${DOCKER_CERTS_DIR})
+        fi
+
+        if [[ -n "${{ inputs.DOCKER_CERTS_UPDATE_COMMAND }}" ]]; then
+          DOCKER_CERTS_UPDATE_COMMAND=${{ inputs.DOCKER_CERTS_UPDATE_COMMAND }}
+          docker_args+=(-e DOCKER_CERTS_UPDATE_COMMAND=${DOCKER_CERTS_UPDATE_COMMAND})
+        fi
 
+        if [[ -n "${{ inputs.NPROC }}" ]]; then
+          NPROC=${{ inputs.NPROC }}
+          script_args+=(--nproc ${NPROC})
+        fi
 
         docker_args+=(${{ inputs.DOCKER_RUN_ARGS }})
 
@@ -128,11 +169,6 @@ jobs:
           script_args+=(--sccache-credentials $(basename ${GOOGLE_GHA_CREDS_PATH}))
         fi
 
-        if [ ${{ inputs.RUNS_ON }} == 'streak' ] || [ ${{ inputs.RUNS_ON }} == 'streak2' ]; then
-          RUNNER_CERTIFICATES_DIR=/etc/pki/ca-trust/source/anchors/
-          mkdir -p ${GITHUB_WORKSPACE}/certificates
-          cp ${RUNNER_CERTIFICATES_DIR}/*.crt* ${GITHUB_WORKSPACE}/certificates
-        fi
         # We need to know where the code folder is mounted inside the container so we can run the script at the proper location!
         # Since this information is repeated twice, we use a variable.
         GITHUB_WORKSPACE_MOUNT_POINT=/tmp/geos
@@ -154,7 +190,8 @@ jobs:
         script_args+=(--cmake-build-type ${{ inputs.CMAKE_BUILD_TYPE }})
         script_args+=(${{ inputs.BUILD_AND_TEST_CLI_ARGS }})
 
-        
+
+        DOCKER_REPOSITORY=${{ inputs.DOCKER_REPOSITORY }}
         SPLIT_DOCKER_REPOSITORY=(${DOCKER_REPOSITORY//// })
         CONTAINER_NAME=geosx_build_${SPLIT_DOCKER_REPOSITORY[1]}_${GITHUB_SHA:0:7}
         echo "CONTAINER_NAME: ${CONTAINER_NAME}"
@@ -168,6 +205,14 @@ jobs:
           script_args+=(--code-coverage)
         fi
 
+
+        echo running "docker run \
+          ${docker_args[@]} \
+          -h=`hostname` \
+          ${{ inputs.DOCKER_REPOSITORY }}:${{ inputs.DOCKER_IMAGE_TAG }} \
+          ${GITHUB_WORKSPACE_MOUNT_POINT}/scripts/ci_build_and_test_in_container.sh \
+          ${script_args[@]}"
+
         # In case of integrated tests run, we still want to send the results to the cloud for inspection.
         # While for standard build (if even possible), pushing a failed build would be pointless.
         # GHA set `-e` to bash scripts by default to fail asap,
@@ -186,8 +231,25 @@ jobs:
         # Send to the bucket and print the download link when it makes sense.
         if [[ ! -z "${{ inputs.GCP_BUCKET }}" ]]; then
           if [[ "${{ inputs.BUILD_TYPE }}" = "integrated_tests" || ${EXIT_STATUS} -eq 0 ]]; then
-            CLOUDSDK_PYTHON=python3 gsutil cp -a public-read ${DATA_EXCHANGE_DIR}/${DATA_BASENAME} gs://${{ inputs.GCP_BUCKET }}/
-            echo "Download the bundle at https://storage.googleapis.com/${{ inputs.GCP_BUCKET }}/${DATA_BASENAME}"
+            if [ -f ${DATA_EXCHANGE_DIR}/${DATA_BASENAME} ]; then
+              CLOUDSDK_PYTHON=python3 gsutil cp -a public-read ${DATA_EXCHANGE_DIR}/${DATA_BASENAME} gs://${{ inputs.GCP_BUCKET }}/
+              echo "Download the bundle at https://storage.googleapis.com/${{ inputs.GCP_BUCKET }}/${DATA_BASENAME}"
+            fi
+
+            if [ -f ${DATA_EXCHANGE_DIR}/test_logs_${DATA_BASENAME} ]; then
+              CLOUDSDK_PYTHON=python3 gsutil cp -a public-read ${DATA_EXCHANGE_DIR}/test_logs_${DATA_BASENAME} gs://${{ inputs.GCP_BUCKET }}/
+              echo "Download integrated test logs here: https://storage.googleapis.com/${{ inputs.GCP_BUCKET }}/test_logs_${DATA_BASENAME}"
+            fi
+
+            # if $UPLOAD_BASELINES; then
+              if [ -f ${DATA_EXCHANGE_DIR}/baseline_${DATA_BASENAME} ];then
+                CLOUDSDK_PYTHON=python3 gsutil cp -a public-read ${DATA_EXCHANGE_DIR}/baseline_${DATA_BASENAME} gs://${{ inputs.GCP_BUCKET }}/
+                echo "Download test baselines here: https://storage.googleapis.com/${{ inputs.GCP_BUCKET }}/baseline_${DATA_BASENAME}"
+                echo "New baseline ID: baseline_${DATA_BASENAME::-7}"
+              else
+                echo "Baselines ${DATA_EXCHANGE_DIR}/baseline_${DATA_BASENAME} were not uploaded. Likeyly because no rebaseline was necessary."
+              fi
+            # fi
           fi
         fi
         
@@ -200,7 +262,7 @@ jobs:
 
     - name: Upload coverage to Codecov
       if: inputs.CODE_COVERAGE
-      uses: codecov/codecov-action@v4.0.1
+      uses: codecov/codecov-action@v4.3.1
       with:
         files: geos_coverage.info.cleaned
         fail_ci_if_error: true

.github/workflows/ci_tests.yml

@@ -23,7 +23,6 @@ jobs:
     runs-on: ubuntu-22.04
     outputs:
       DOCKER_IMAGE_TAG: ${{ steps.extract_docker_image_tag.outputs.DOCKER_IMAGE_TAG }}
-      LABELS: ${{ steps.extract_pr_info.outputs.LABELS }}
     steps:
     - name: Check that the PR is not a draft (cancel rest of jobs otherwise)
       id: extract_pr_info
@@ -37,17 +36,12 @@ jobs:
           draft_status=$(echo ${pr_json} | jq '.draft')
           echo "Draft status of PR is ${draft_status}."
           if [[ $draft_status == true ]]; then exit 1 ; fi
-          
-          # If the workflow is meant to continue, we extract additional information for the json of the pr.
-          echo "LABELS=$(echo ${pr_json} | jq -crM '[.labels[].name]')" >> "$GITHUB_OUTPUT"
-        else
-          echo "LABELS=['ci: ready to be merged']" >> "$GITHUB_OUTPUT"
         fi
 
         
     # The TPL tag is contained in the codespaces configuration to avoid duplications.
     - name: Checkout .devcontainer/devcontainer.json
-      uses: actions/[email protected].1
+      uses: actions/[email protected].4
       with:
         sparse-checkout: |
           .devcontainer/devcontainer.json
@@ -83,7 +77,7 @@ jobs:
     # The integrated test submodule repository contains large data (using git lfs).
     # To save time (and money) we do not let Github Actions automatically clone all our (lfs) subrepositories and do it by hand.
     - name: Checkout Repository
-      uses: actions/[email protected].1
+      uses: actions/[email protected].4
       with:
         # Let script update submodules; Github Actions submodule history causes error
         submodules: false
@@ -194,7 +188,6 @@ jobs:
     needs:
       - is_not_draft_pull_request
       - cpu_builds
-    if: "${{ contains( fromJSON( needs.is_not_draft_pull_request.outputs.LABELS ), 'ci: run integrated tests') || github.event_name != 'pull_request' }}"
     uses: ./.github/workflows/build_and_test.yml
     secrets: inherit
     with:
@@ -207,7 +200,27 @@ jobs:
       ENABLE_TRILINOS: OFF
       GCP_BUCKET: geosx/integratedTests
       RUNS_ON: streak2
-      DOCKER_RUN_ARGS: "--cpus=32 --memory=384g"
+      NPROC: 32
+      DOCKER_RUN_ARGS: "--cpus=32 --memory=384g -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"
+      REQUIRED_LABEL: "ci: run integrated tests"
+      UPLOAD_BASELINES: "ci: upload test baselines"
+
+  baseline_log:
+    needs: [is_not_draft_pull_request]
+    runs-on: ubuntu-22.04
+    steps:
+    - name: Checkout Repository
+      uses: actions/[email protected]
+      with:
+        submodules: false
+        lfs: false
+        fetch-depth: 0
+        sparse-checkout: |
+          scripts
+    - name: Check that the baseline logs are modified if rebaselines are detected
+      run: "scripts/check_baseline_log.sh"
 
   code_coverage:
     needs:
@@ -231,7 +244,6 @@ jobs:
     name: ${{ matrix.name }}
     needs:
       - is_not_draft_pull_request
-    if: "${{ contains( fromJSON( needs.is_not_draft_pull_request.outputs.LABELS ), 'ci: ready to be merged') }}"
     strategy:
       # In-progress jobs will not be cancelled if there is a failure
       fail-fast : false
@@ -244,8 +256,12 @@ jobs:
             ENABLE_HYPRE_DEVICE: CUDA
             ENABLE_HYPRE: ON
             ENABLE_TRILINOS: OFF
-            RUNS_ON: Runner_8core_32GB
-
+            RUNS_ON: streak2
+            NPROC: 16
+            DOCKER_RUN_ARGS: "--cpus=16 --memory=256g --runtime=nvidia -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: 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
@@ -254,13 +270,20 @@ jobs:
             ENABLE_HYPRE: ON
             ENABLE_TRILINOS: OFF
             RUNS_ON: streak
-            DOCKER_RUN_ARGS: "--cpus=8 --memory=256g --runtime=nvidia --gpus all"
+            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-certificates"
 
           - name: Centos (7.7, gcc 8.3.1, open-mpi 1.10.7, cuda 11.8.89)
             BUILD_AND_TEST_CLI_ARGS: "--no-run-unit-tests --no-install-schema"
             CMAKE_BUILD_TYPE: Release
             DOCKER_REPOSITORY: geosx/centos7.7-gcc8.3.1-cuda11.8.89
-            RUNS_ON: Runner_4core_16GB
+            RUNS_ON: streak2
+            NPROC: 16
+            DOCKER_RUN_ARGS: "--cpus=16 --memory=256g --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.
           - name: Pecan GPU (centos 7.7, gcc 8.2.0, open-mpi 4.0.1, mkl 2019.5, cuda 11.5.119)
@@ -285,6 +308,8 @@ jobs:
     with:
       BUILD_AND_TEST_CLI_ARGS: ${{ matrix.BUILD_AND_TEST_CLI_ARGS }}
       CMAKE_BUILD_TYPE: ${{ matrix.CMAKE_BUILD_TYPE }}
+      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 }}
       DOCKER_REPOSITORY: ${{ matrix.DOCKER_REPOSITORY }}
       DOCKER_RUN_ARGS: ${{ matrix.DOCKER_RUN_ARGS }}
@@ -293,7 +318,9 @@ jobs:
       ENABLE_TRILINOS: ${{ matrix.ENABLE_TRILINOS }}
       GCP_BUCKET: ${{ matrix.GCP_BUCKET }}
       HOST_CONFIG: ${{ matrix.HOST_CONFIG }}
+      NPROC: ${{ matrix.NPROC }}
       RUNS_ON: ${{ matrix.RUNS_ON }}
+      REQUIRED_LABEL: "ci: ready to be merged"
     secrets: inherit
 
   # Convenience job - passes when all other jobs have passed (must pass the CUDA jobs).

.gitmodules

@@ -7,9 +7,6 @@
 [submodule "src/coreComponents/constitutive/PVTPackage"]
 	path = src/coreComponents/constitutive/PVTPackage
 	url = ../../GEOS-DEV/PVTPackage.git
-[submodule "integratedTests"]
-	path = integratedTests
-	url = ../../GEOS-DEV/integratedTests.git
 [submodule "src/coreComponents/fileIO/coupling/hdf5_interface"]
 	path = src/coreComponents/fileIO/coupling/hdf5_interface
 	url = ../../GEOS-DEV/hdf5_interface.git

.integrated_tests.yaml

@@ -0,0 +1,8 @@
+---
+baselines:
+  bucket: geosx
+  baseline: integratedTests/baseline_integratedTests-pr3105-4885-a1a85c1
+
+allow_fail:
+  all: ''
+  streak: pennyShapedToughnessDominated_smoke_01,pennyShapedViscosityDominated_smoke_01,pknViscosityDominated_smoke_01

.readthedocs.yml

@@ -33,5 +33,4 @@ formats: all
 submodules:
   include: 
   - src/coreComponents/constitutive/PVTPackage
-  - integratedTests
   recursive: true

BASELINE_NOTES.md

@@ -0,0 +1,26 @@
+
+Notes
+==========
+
+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 #3105 (2024-05-08)
+======================
+
+Added missing derivative for temperature, hence small numerical diffs in thermal tests results and numeracal behavior
+
+
+PR #2917 (2024-05-07)
+======================
+
+New fields for wellsControls: wellControls1_ConstantMassRate_table, targetMassRate, massDensity, ...
+
+
+PR #3044 (2024-05-02)
+======================
+
+Removed old integratedTests submodule
+Implemented new baseline storage
+Implemented new CI integrated tests

host-configs/LLNL/quartz-base.cmake

@@ -58,9 +58,9 @@ set(MKL_LIBRARIES ${MKL_ROOT}/lib/intel64/libmkl_intel_lp64.so
 
 # ATS
 set(ATS_ARGUMENTS "--machine slurm36"  CACHE STRING "")
-# set(USER $ENV{USER} CACHE STRING "")
-# set(ATS_WORKING_DIR "/p/lustre2/${USER}/integratedTests/${CONFIG_NAME}"  CACHE PATH "")
-# set(ATS_BASELINE_DIR "/p/lustre2/${USER}/integratedTests/baselines"  CACHE PATH "")
+set(USER $ENV{USER} CACHE STRING "")
+set(ATS_WORKING_DIR "/p/lustre2/${USER}/integratedTestsGEOS/${CONFIG_NAME}"  CACHE PATH "")
+set(ATS_BASELINE_DIR "/p/lustre2/${USER}/integratedTestsGEOS/baselines"  CACHE PATH "")
 
 # Temporary argument for python module change testing
 # set(GEOS_PYTHON_PACKAGES_BRANCH "feature/sherman/outOfPlaceATS" CACHE STRING "" FORCE)