Merge branch 'feature/aronson/strainOutput' of https://github.com/GEO…

…S-DEV/GEOS into feature/aronson/strainOutput
GEOS-DEV · Jun 20, 2024 · 0956ef2 · 0956ef2
2 parents b33ab2d + 0255567
commit 0956ef2
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -2,7 +2,7 @@
     "build": {
         "dockerfile": "Dockerfile",
         "args": {
-            "GEOS_TPL_TAG": "263-252"
+            "GEOS_TPL_TAG": "262-349"
         }
     },
     "runArgs": [

diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh
@@ -2,7 +2,6 @@
 /usr/bin/ln -s /workspaces/GEOS/.vscode-codespaces /workspaces/GEOS/.vscode
 # Activate the appropriate submodules
 git submodule init
-git submodule deinit integratedTests
 git submodule update
 # Load the pretty printer for LvArray
 echo "source /workspaces/GEOS/src/coreComponents/LvArray/scripts/gdb-printers-shallow.py" > ~/.gdbinit
diff --git a/.github/workflows/build_and_test.yml b/.github/workflows/build_and_test.yml
@@ -54,16 +54,16 @@ on:
       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
+      LOCAL_BASELINE_DIR:
+        required: false
+        type: string  
     secrets:
       GOOGLE_CLOUD_GCP:
         required: false
@@ -142,7 +142,7 @@ jobs:
         SHORT_COMMIT=${COMMIT:0:7}
         script_args+=(--install-dir-basename GEOSX-${SHORT_COMMIT})
 
-        # All the data exchanged with the docker container is eventually meant to be send to the cloud. 
+        # All the data exchanged with the docker container is eventually meant to be sent to the cloud. 
         if [[ ! -z "${{ inputs.GCP_BUCKET }}" ]]; then
           if [ "${{ inputs.BUILD_TYPE }}" = "build" ]; then
             DATA_BASENAME=GEOSX-and-TPL-${SHORT_COMMIT}.tar.gz
@@ -205,6 +205,45 @@ jobs:
           script_args+=(--code-coverage)
         fi
 
+        if [[ -n "${{ inputs.LOCAL_BASELINE_DIR }}" ]]; then
+          # Extract the 'baseline' value 
+           
+          # Define the path to the YAML file
+          YAML_FILE_PATH="${GITHUB_WORKSPACE}/.integrated_tests.yaml"
+          
+          # Verify the YAML file path
+          if [[ ! -f "${YAML_FILE_PATH}" ]]; then
+            echo "Error: File $YAML_FILE_PATH does not exist."
+          else
+            echo "Found integratedTests file: $YAML_FILE_PATH."
+          fi
+
+          # Extract the baseline field 
+          BASELINE_FULL_PATH=$(grep -A 2 'baselines:' "${YAML_FILE_PATH}" | grep 'baseline:' | awk '{print $2}')
+
+          # Remove the 'integratedTests/' prefix
+          BASELINE_TAG=${BASELINE_FULL_PATH#integratedTests/}
+          echo "Baseline: ${BASELINE_TAG}"
+
+          # Extract the folder name
+          PR_NUMBER=$(echo "$BASELINE_TAG" | grep -o 'pr[0-9]*')
+          PR_BASELINE_FOLDER_NAME=baselines_${PR_NUMBER}
+          echo "Baseline folder name: ${PR_BASELINE_FOLDER_NAME}"
+
+          CURRENT_BASELINE_DIR=${{ inputs.LOCAL_BASELINE_DIR }}/${PR_BASELINE_FOLDER_NAME}
+          echo "Current baseline dir: ${CURRENT_BASELINE_DIR}"
+
+          if [ -d ${CURRENT_BASELINE_DIR} ];then
+            echo "Current baseline dir found."
+            ls -l ${CURRENT_BASELINE_DIR}
+                    
+            # We defined a mount point and mount it read-only inside the container.
+            CURRENT_BASELINE_DIR_MOUNT=/tmp/geos/baselines
+            docker_args+=(--volume=${CURRENT_BASELINE_DIR}:${CURRENT_BASELINE_DIR_MOUNT}:ro)
+          else
+            echo "Current baselines directory (${CURRENT_BASELINE_DIR}) not found"
+          fi
+        fi
 
         echo running "docker run \
           ${docker_args[@]} \
@@ -241,22 +280,33 @@ jobs:
               echo "Download integrated test logs here: https://storage.googleapis.com/${{ 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."
+            if [ -f ${DATA_EXCHANGE_DIR}/baseline_${DATA_BASENAME} ];then
+
+              if [[ -n "${{ inputs.LOCAL_BASELINE_DIR }}" ]]; then
+                # 1. We copy the baselines to a local directory to store them 
+                
+                # 1.a Create the new target directory to store the new baselines
+                THIS_PR_NUMBER=pr${{ github.event.number }}
+                NEW_PR_BASELINE_FOLDER_NAME=baselines_${THIS_PR_NUMBER}
+                TARGET_DIR="${{ inputs.LOCAL_BASELINE_DIR }}/${NEW_PR_BASELINE_FOLDER_NAME}"
+                echo "Create folder ${TARGET_DIR}"
+                mkdir -p "${TARGET_DIR}"
+          
+                # 1.b We copy the new baselines to the new target directory
+                SOURCE_FILE="${DATA_EXCHANGE_DIR}/baseline_${DATA_BASENAME}"
+                echo "Copy ${SOURCE_FILE} to ${TARGET_DIR}"
+                cp "${SOURCE_FILE}" "${TARGET_DIR}"
               fi
-            # fi
+                
+              # 2. We push the baselines to the cloud
+              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
-        
-        # manually remove the workspace to avoid issues with the next job when using self-hosted runners
-        if [ -d "${GITHUB_WORKSPACE}/integratedTests" ]; then
-          rm -rf ${GITHUB_WORKSPACE}/integratedTests
-        fi
 
         exit ${EXIT_STATUS}
 

diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml
@@ -199,13 +199,13 @@ jobs:
       ENABLE_HYPRE: ON
       ENABLE_TRILINOS: OFF
       GCP_BUCKET: geosx/integratedTests
-      RUNS_ON: streak2
+      RUNS_ON: streak2-32core
       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"
+      LOCAL_BASELINE_DIR: /data/GEOS/baselines
 
   baseline_log:
     needs: [is_not_draft_pull_request]

diff --git a/.integrated_tests.yaml b/.integrated_tests.yaml
@@ -1,7 +1,6 @@
----
 baselines:
   bucket: geosx
-  baseline: integratedTests/baseline_integratedTests-pr3125-5101-7764ffb
+  baseline: integratedTests/baseline_integratedTests-pr3170-5687-d6e16c7
 
 allow_fail:
   all: ''

diff --git a/BASELINE_NOTES.md b/BASELINE_NOTES.md
@@ -6,44 +6,128 @@ 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 #3170 (2024-06-19)
+======================
+Fix tutorial example for thermal debonding wellbore problem. Test case modified.
+
+
+PR #3130 (2024-06-19)
+======================
+New solver for contact mechanics based on the Augmented Lagrangian Method (ALM). New test case added.
+
+
+PR #3160 (2024-06-18)
+======================
+Two experimental options for compositional flow solver. Rebaseline because of the new input flags.
+
+
+PR #3165 (2024-06-18)
+======================
+Small bug fix. Rebaseline required due to appearance of useTotalMassEquation in well solver params. No real results change.
+
+
+PR #3088 (2024-06-17)
+======================
+Adding temperature-dependent Solid Volumetric Heat Capacity. Rebaseline because of the parameter change in SolidInternalEnergy.
+
+
+PR #3100 (2024-06-14)
+======================
+Adding pressure stabilization for single phase poromechanics.
+
+
+PR #3133 (2024-06-14)
+======================
+Fix node ordering for faceElements.
+
+
+PR #3021 (2024-06-13)
+======================
+Preparatory work for fractures + wells. New test case added.
+
+
+PR #3152 (2024-06-13)
+======================
+Some random things. Baseline update because of the new parameter (minScalingFactor).
+
+
+PR #3138 (2024-06-11)
+======================
+Properly sync nonlinear solver params for coupled solver. Baseline update mostly due to number of iterations change in baseline files.
+
+
+PR #3140 (2024-06-11)
+======================
+Fixed derivative in EzrokhiBrineDensity
+
+
+PR #3080 (2024-06-07)
+=====================
+Rebaseline after adding viscoelastic wave propagator.
+
+
+PR #3075 (2024-06-05)
+=====================
+Introduce configuration tolerance. Rebaseline because of the new parameter in NonlinearSolverParameters.
+
+
+PR #3120 (2024-06-05)
+=====================
+Add missing compositionalMultiphaseFlow tests into ATS and adjust output naming. Rebaseline accordingly.
+
+
+PR #3113 (2024-06-05)
+=====================
+Add general version updateConfiguration. Rebaseline of some edfm cases is needed.
+
+
+PR #3050 (2024-05-20)
+=====================
+Spatially varying grain bulk modulus. Rebaseline of all poromechanics cases needed.
+
+
+PR #3141 (2024-05-28)
+=====================
+Test cashing baselines locally.
+
+
 PR #3125 (2024-05-16)
 =====================
 Remove field to store pressure gradient cell-wise for solvers that don't need it.
 
+
 PR #2110 (2024-05-13)
 =====================
 new field to store pressure gradient cell-wise.
 
+
 PR #3060 (2024-05-13)
 ======================
-
 Rebaselined after addition of elastic VTI wave propagator. 
 
+
 PR #4950 (2024-05-10)
 ======================
-
 Added smoke tests for SeismicityRate solver in inducedSeismicity.
 
+
 PR #3086 (2024-05-09)
 ======================
-
 Added a presure-dependent permeability model and the transmissibility calculation in the CellElementStencil
 
+
 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
diff --git a/host-configs/LLNL/lassen-base.cmake b/host-configs/LLNL/lassen-base.cmake
@@ -43,7 +43,6 @@ set(ESSL_LIBRARIES /usr/tcetmp/packages/essl/essl-6.3.0.2/lib64/libesslsmpcuda.s
 # TPL
 set(ENABLE_PAPI OFF CACHE BOOL "")
 set(SILO_BUILD_TYPE powerpc64-unknown-linux-gnu CACHE STRING "")
-set(ENABLE_FESAPI OFF CACHE BOOL "" FORCE)
 
 # GEOSX specific options
 set(ENABLE_PVTPackage ON CACHE BOOL "")

diff --git a/host-configs/LLNL/quartz-base.cmake b/host-configs/LLNL/quartz-base.cmake
@@ -41,8 +41,6 @@ set(YAPF_EXECUTABLE /usr/gapps/GEOSX/thirdPartyLibs/python/quartz-gcc-python/pyt
 set(SPHINX_EXECUTABLE /usr/gapps/GEOSX/thirdPartyLibs/python/quartz-gcc-python/python/bin/sphinx-build CACHE PATH "" FORCE)
 
 
-set(ENABLE_FESAPI OFF CACHE BOOL "" FORCE)
-
 # caliper 
 set(ENABLE_CALIPER ON CACHE BOOL "" FORCE)
 set(ENABLE_CALIPER_HYPRE ON CACHE BOOL "" FORCE)

diff --git a/host-configs/TOTAL/pangea4-base.cmake b/host-configs/TOTAL/pangea4-base.cmake
@@ -0,0 +1,65 @@
+#######################################
+#
+# Pangea4 - base config for CPU cluster
+#
+#   - RAJA   CPU
+#   - CHAI   CPU
+#   - CUDA   OFF
+#   - OPENMP OFF
+#   - HYPRE ON
+#
+#######################################
+
+#######################################
+# SCIENTIFIC LIBRARIES
+#######################################
+
+set( ENABLE_HYPRE       ON  CACHE BOOL "" FORCE )
+set( ENABLE_MATHPRESSO  ON  CACHE BOOL "" FORCE )
+set( ENABLE_PAMELA      ON  CACHE BOOL "" FORCE )
+set( ENABLE_PETSC       OFF CACHE BOOL "" FORCE )
+set( ENABLE_PVTPackage  ON  CACHE BOOL "" FORCE )
+set( ENABLE_SCOTCH      ON  CACHE BOOL "" FORCE )
+set( ENABLE_SUITESPARSE ON  CACHE BOOL "" FORCE )
+set( ENABLE_TRILINOS    OFF CACHE BOOL "" FORCE )
+set( ENABLE_VTK         ON  CACHE BOOL "" FORCE )
+
+#######################################
+# DEVELOPMENT TOOLS
+#######################################
+
+set( ENABLE_DOXYGEN           ON CACHE BOOL "" FORCE )
+set( ENABLE_GTEST_DEATH_TESTS ON CACHE BOOL "" FORCE )
+set( ENABLE_SPHINX            ON CACHE BOOL "" FORCE )
+set( ENABLE_UNCRUSTIFY        ON CACHE BOOL "" FORCE )
+set( ENABLE_XML_UPDATES       ON CACHE BOOL "" FORCE )
+
+#######################################
+# PERFORMANCE TOOLS
+#######################################
+
+set( ENABLE_BENCHMARKS ON CACHE BOOL "" FORCE )
+set( ENABLE_CALIPER    ON CACHE BOOL "" FORCE )
+
+#######################################
+# RAJA/CHAI SETUP
+#######################################
+
+set( ENABLE_OPENMP      OFF         CACHE BOOL "" FORCE )
+set( ENABLE_CUDA        OFF         CACHE BOOL "" FORCE )
+
+set( ENABLE_CHAI        ON          CACHE BOOL   "" FORCE )
+set( CHAI_BUILD_TYPE    "cpu-no-rm" CACHE STRING "" FORCE )
+set( CHAI_ARGS          ""          CACHE STRING "" FORCE )
+
+set( ENABLE_RAJA        ON          CACHE BOOL "" FORCE )
+set( RAJA_ENABLE_HIP    OFF         CACHE BOOL "" FORCE )
+set( RAJA_ENABLE_OPENMP OFF         CACHE BOOL "" FORCE )
+set( RAJA_ENABLE_TBB    OFF         CACHE BOOL "" FORCE )
+
+#######################################
+# PYTHON SETUP
+#######################################
+
+set( ENABLE_PYGEOSX         ON CACHE BOOL "" )
+set( ENABLE_VTK_WRAP_PYTHON ON CACHE BOOL "" )