Merge branch 'develop' into docs/JOSS

.devcontainer/devcontainer.json

@@ -2,7 +2,7 @@
     "build": {
         "dockerfile": "Dockerfile",
         "args": {
-            "GEOS_TPL_TAG": "251-99"
+            "GEOS_TPL_TAG": "255-118"
         }
     },
     "runArgs": [

.github/workflows/build_and_test.yml

@@ -12,6 +12,10 @@ on:
       CMAKE_BUILD_TYPE:
         required: true
         type: string
+      CODE_COVERAGE:
+        required: false
+        type: boolean
+        default: false
       DOCKER_IMAGE_TAG:
         required: true
         type: string
@@ -127,6 +131,10 @@ jobs:
         script_args+=(--cmake-build-type ${{ inputs.CMAKE_BUILD_TYPE }})
         script_args+=(${{ inputs.BUILD_AND_TEST_CLI_ARGS }})
 
+        if ${{ inputs.CODE_COVERAGE }} == 'true'; then
+          script_args+=(--code-coverage)
+        fi
+
         # In case of integrated tests run, we still want to send the results to the cloud for inspection.
         # While for standard build (if even possible), pushing a failed build would be pointless.
         # GHA set `-e` to bash scripts by default to fail asap,
@@ -148,5 +156,13 @@ jobs:
             echo "Download the bundle at https://storage.googleapis.com/${{ inputs.GCP_BUCKET }}/${DATA_BASENAME}"
           fi
         fi
-        
         exit ${EXIT_STATUS}
+
+    - name: Upload coverage to Codecov
+      if: inputs.CODE_COVERAGE
+      uses: codecov/codecov-action@v3
+      with:
+        files: geos_coverage.info.cleaned
+        fail_ci_if_error: true
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/ci_tests.yml

@@ -1,5 +1,10 @@
 name: GEOS CI 
-on: pull_request
+
+on: 
+  push:
+    branches: 
+      - develop
+  pull_request:
 
 # Cancels in-progress workflows for a PR when updated
 concurrency:
@@ -12,12 +17,11 @@ jobs:
 
   # Jobs will be cancelled if PR is a draft.
   # PR status must be "Open" to run CI.
-  is_pull_request_a_draft:
+  is_not_draft_pull_request:
     # Everywhere in this workflow, we use the most recent ubuntu distribution available in Github Actions
     # to ensure maximum support of google cloud's sdk.
     runs-on: ubuntu-22.04
     outputs:
-      NUM_ASSIGNEES: ${{ steps.extract_pr_info.outputs.NUM_ASSIGNEES }}
       DOCKER_IMAGE_TAG: ${{ steps.extract_docker_image_tag.outputs.DOCKER_IMAGE_TAG }}
       LABELS: ${{ steps.extract_pr_info.outputs.LABELS }}
     steps:
@@ -34,7 +38,6 @@ jobs:
         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 "NUM_ASSIGNEES=$(echo ${pr_json} | jq '.assignees | length')" >> "$GITHUB_OUTPUT"
         echo "LABELS=$(echo ${pr_json} | jq -crM '[.labels[].name]')" >> "$GITHUB_OUTPUT"
     # The TPL tag is contained in the codespaces configuration to avoid duplications.
     - name: Checkout .devcontainer/devcontainer.json
@@ -53,19 +56,22 @@ jobs:
 
   # PR must be assigned to be merged.
   # This job will fail if this is not the case.
-  is_pull_request_assigned:
-    needs: [is_pull_request_a_draft]
+  if_not_unassigned_pull_request:
+    needs: [is_not_draft_pull_request]
     runs-on: ubuntu-22.04
     steps:
-    - name: Check that the PR is assigned
+    - name: If this is a PR, Check that it is assigned
       run: |
-        echo "There are ${{ needs.is_pull_request_a_draft.outputs.NUM_ASSIGNEES }} on this PR."
-        ${{ needs.is_pull_request_a_draft.outputs.NUM_ASSIGNEES > 0 }}
+        if [[ ${{github.event_name}} != 'pull_request' ]]; then exit 0 ; fi
+        pr_json=$(curl -H "Accept: application/vnd.github+json" https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.number }})
+        NUM_ASSIGNEES=$(echo ${pr_json} | jq '.assignees | length')
+        echo "There are ${NUM_ASSIGNEES} assignees on this PR."
+        if [[ $NUM_ASSIGNEES == 0 ]]; then exit 1 ; fi
 
   # Validates that the PR is still pointing to the HEAD of the main branch of the submodules repositories.
   # (There are exceptions, read the script about those).
   are_submodules_in_sync:
-    needs: [is_pull_request_a_draft]
+    needs: [is_not_draft_pull_request]
     runs-on: ubuntu-22.04
     steps:
     # The integrated test submodule repository contains large data (using git lfs).
@@ -82,7 +88,7 @@ jobs:
 
   check_code_style_and_documentation:
     name: ${{ matrix.name }}
-    needs: [is_pull_request_a_draft]
+    needs: [is_not_draft_pull_request]
     strategy:
       fail-fast : false
       matrix:
@@ -97,7 +103,7 @@ jobs:
     with:
       BUILD_AND_TEST_CLI_ARGS: ${{ matrix.BUILD_AND_TEST_ARGS }}
       CMAKE_BUILD_TYPE: Release
-      DOCKER_IMAGE_TAG: ${{ needs.is_pull_request_a_draft.outputs.DOCKER_IMAGE_TAG }}
+      DOCKER_IMAGE_TAG: ${{ needs.is_not_draft_pull_request.outputs.DOCKER_IMAGE_TAG }}
       DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc9
       RUNS_ON: ubuntu-22.04
       USE_SCCACHE: false
@@ -106,7 +112,7 @@ jobs:
   # Those are quite fast and can efficiently benefit from the `sccache' tool to make them even faster.
   cpu_builds:
     name: ${{ matrix.name }}
-    needs: [is_pull_request_a_draft]
+    needs: [is_not_draft_pull_request]
     strategy:
       # In-progress jobs will not be cancelled if there is a failure
       fail-fast : false
@@ -161,7 +167,7 @@ jobs:
     uses: ./.github/workflows/build_and_test.yml
     with:
       CMAKE_BUILD_TYPE: ${{ matrix.CMAKE_BUILD_TYPE }}
-      DOCKER_IMAGE_TAG: ${{ needs.is_pull_request_a_draft.outputs.DOCKER_IMAGE_TAG }}
+      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: ${{ matrix.ENABLE_TRILINOS }}
@@ -174,29 +180,45 @@ jobs:
   # Note: The integrated tests are optional and are (for the moment) run for convenience only.
   run_integrated_tests:
     needs:
-      - is_pull_request_a_draft
+      - is_not_draft_pull_request
       - cpu_builds
-    if: "${{ contains( fromJSON( needs.is_pull_request_a_draft.outputs.LABELS ), 'ci: run integrated tests') }}"
+    if: "${{ contains( fromJSON( needs.is_not_draft_pull_request.outputs.LABELS ), 'ci: run integrated tests') }}"
     uses: ./.github/workflows/build_and_test.yml
     secrets: inherit
     with:
       BUILD_AND_TEST_CLI_ARGS: --build-exe-only
       BUILD_TYPE: integrated_tests
       CMAKE_BUILD_TYPE: Release
-      DOCKER_IMAGE_TAG: ${{ needs.is_pull_request_a_draft.outputs.DOCKER_IMAGE_TAG }}
+      DOCKER_IMAGE_TAG: ${{ needs.is_not_draft_pull_request.outputs.DOCKER_IMAGE_TAG }}
       DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc11
       ENABLE_HYPRE: ON
       ENABLE_TRILINOS: OFF
       GCP_BUCKET: geosx/integratedTests
       RUNS_ON: ubuntu-22.04
-
+
+  code_coverage:
+    needs:
+      - is_not_draft_pull_request
+    uses: ./.github/workflows/build_and_test.yml
+    secrets: inherit
+    with:
+      BUILD_AND_TEST_CLI_ARGS: "--no-run-unit-tests"
+      CMAKE_BUILD_TYPE: Debug
+      CODE_COVERAGE: true
+      DOCKER_IMAGE_TAG: ${{ needs.is_not_draft_pull_request.outputs.DOCKER_IMAGE_TAG }}
+      DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc11
+      ENABLE_HYPRE: ON
+      ENABLE_TRILINOS: OFF
+      GCP_BUCKET: geosx/ubuntu22.04-gcc11
+      RUNS_ON: ubuntu-22.04
+
   # If the 'ci: ready to be merged' PR label is found, the cuda jobs run immediately along side linux jobs.
   # Note: CUDA jobs should only be run if PR is ready to merge.
   cuda_builds:
     name: ${{ matrix.name }}
     needs:
-      - is_pull_request_a_draft
-    if: "${{ contains( fromJSON( needs.is_pull_request_a_draft.outputs.LABELS ), 'ci: ready to be merged') }}"
+      - 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
@@ -237,7 +259,7 @@ jobs:
     with:
       BUILD_AND_TEST_CLI_ARGS: ${{ matrix.BUILD_AND_TEST_CLI_ARGS }}
       CMAKE_BUILD_TYPE: ${{ matrix.CMAKE_BUILD_TYPE }}
-      DOCKER_IMAGE_TAG: ${{ needs.is_pull_request_a_draft.outputs.DOCKER_IMAGE_TAG }}
+      DOCKER_IMAGE_TAG: ${{ needs.is_not_draft_pull_request.outputs.DOCKER_IMAGE_TAG }}
       DOCKER_REPOSITORY: ${{ matrix.DOCKER_REPOSITORY }}
       ENABLE_HYPRE_DEVICE: ${{ matrix.ENABLE_HYPRE_DEVICE }}
       ENABLE_HYPRE: ${{ matrix.ENABLE_HYPRE }}
@@ -250,7 +272,7 @@ jobs:
   check_that_all_jobs_succeeded:
     runs-on: ubuntu-22.04
     needs:
-    - is_pull_request_assigned
+    - if_not_unassigned_pull_request
     - are_submodules_in_sync
     - check_code_style_and_documentation
     - cpu_builds
@@ -259,7 +281,7 @@ jobs:
     steps:
     - run: |
         ${{
-          needs.is_pull_request_assigned.result == 'success' &&
+          needs.if_not_unassigned_pull_request.result == 'success' &&
           needs.are_submodules_in_sync.result == 'success' &&
           needs.check_code_style_and_documentation.result == 'success' &&
           needs.cpu_builds.result == 'success' &&

.gitlab-ci.yml

@@ -21,6 +21,10 @@ stages:
     - git submodule set-url integratedTests [email protected]:GEOS-DEV/integratedTests.git
     - git submodule set-url src/coreComponents/fileIO/coupling/hdf5_interface https://github.com/GEOS-DEV/hdf5_interface.git
 
+    # Clean up directory and submodules when pre-initialized from previous CI run
+    - git clean -x -f -d
+    - git submodule foreach --recursive git clean -x -f -d
+
     # Update submodules
     - git submodule update --init --recursive src/cmake/blt
     - git submodule update --init --recursive src/coreComponents/LvArray

README.md

@@ -1,4 +1,7 @@
 [![DOI](https://zenodo.org/badge/131810578.svg)](https://zenodo.org/badge/latestdoi/131810578)
+[![codecov](https://codecov.io/github/GEOS-DEV/GEOS/graph/badge.svg?token=0VTEHPQG58)](https://codecov.io/github/GEOS-DEV/GEOS)
+![CI](https://github.com/GEOS-DEV/GEOS/actions/workflows/ci_tests.yml/badge.svg)
+[![docs](https://readthedocs.com/projects/geosx-geosx/badge/?version=latest)](https://geosx-geosx.readthedocs-hosted.com/en/latest/)
 
 Welcome to the GEOS project!
 -----------------------------

host-configs/LBL/cori-gcc@8.1.0.cmake

@@ -24,7 +24,6 @@ set(MPI_Fortran_COMPILER ${MPI_HOME}/bin/mpifort CACHE PATH "")
 set(MPIEXEC              /usr/bin/srun CACHE PATH "")
 set(MPIEXEC_NUMPROC_FLAG "-n" CACHE STRING "")
 
-set(GEOSX_ENABLE_FPE OFF CACHE BOOL "" FORCE)
 set(GEOSX_TPL_DIR "/global/project/projectdirs/m1411/GEOSX/tpls/install-cori-gcc\@8.1.0-release-24-07-20" CACHE PATH "" )
 
 

host-configs/LBL/cori-intel.cmake

@@ -24,7 +24,6 @@ set(MPI_Fortran_COMPILER "ftn" CACHE PATH "" FORCE)
 set(MPIEXEC              "/usr/bin/srun" CACHE PATH "")
 set(MPIEXEC_NUMPROC_FLAG "-n" CACHE STRING "")
 
-set(GEOSX_ENABLE_FPE OFF CACHE BOOL "" FORCE)
 set(GEOSX_TPL_DIR "/global/project/projectdirs/m1411/GEOSX/tpls/install-cori-intel-release-22-07-20" CACHE PATH "" )
 
 set(GEOSX_LINK_PREPEND_FLAG  "-Wl,--whole-archive"    CACHE STRING "" FORCE)

host-configs/TOTAL/pangea3-gcc8.4.1-openmpi-4.1.2.cmake

@@ -1,7 +1,5 @@
 # hostconfig for pangea3
 #
-# export MODULEPATH=/workrd/SCR/NUM/geosx_num/module_files:$MODULEPATH
-# module load cmake/3.21.4 gcc/8.4.1 cuda/11.0.3 ompi/4.1.2 openblas/0.3.18 python4geosx/p3/gcc8.4.1-ompi4.1.2
 #
 set(CONFIG_NAME "pangea3-gcc8.4.1-ompi-4.1.2" CACHE PATH "")
 
@@ -56,15 +54,15 @@ if (DEFINED ENV{CUDA_ROOT})
   set(CMAKE_CUDA_COMPILER ${CUDA_TOOLKIT_ROOT_DIR}/bin/nvcc CACHE STRING "")
   set(CUDA_ARCH sm_70 CACHE STRING "")
   set(CMAKE_CUDA_ARCHITECTURES 70 CACHE STRING "")
-  set(CMAKE_CUDA_FLAGS "-restrict -arch ${CUDA_ARCH} --expt-extended-lambda -Werror cross-execution-space-call,reorder,deprecated-declarations" CACHE STRING "")
+  set(CMAKE_CUDA_FLAGS "-restrict -arch ${CUDA_ARCH} --expt-relaxed-constexpr --expt-extended-lambda -Werror cross-execution-space-call,reorder,deprecated-declarations" CACHE STRING "")
   set(CMAKE_CUDA_FLAGS_RELEASE "-O3 -DNDEBUG -Xcompiler -DNDEBUG -Xcompiler -O3 -Xcompiler -mcpu=powerpc64le -Xcompiler -mtune=powerpc64le" CACHE STRING "")
   set(CMAKE_CUDA_FLAGS_RELWITHDEBINFO "-g -lineinfo ${CMAKE_CUDA_FLAGS_RELEASE}" CACHE STRING "")
   set(CMAKE_CUDA_FLAGS_DEBUG "-g -G -O0 -Xcompiler -O0" CACHE STRING "")
 
   # Uncomment this line to make nvcc output register usage for each kernel.
   # set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} --resource-usage" CACHE STRING "" FORCE)
 else()
-  message(FATAL_ERROR "You must have CUDA_ROOT environment variable set, we advise loading module cuda/11.0.3")
+  message(FATAL_ERROR "You must have CUDA_ROOT environment variable set, we advise loading module cuda/11.5.0")
 endif()
 
 # GTEST options
@@ -108,7 +106,7 @@ set(ENABLE_PETSC OFF CACHE BOOL "")
 set(ENABLE_HYPRE ON CACHE BOOL "")
 set(ENABLE_HYPRE_DEVICE "CUDA" CACHE BOOL "")
 
-# activate workaround for fmt formatter
-set(ENABLE_FMT_CONST_FORMATTER_WORKAROUND ON CACHE BOOL "")
+# disable benchmarks, they are incompatible with P3's nvcc version (cuda 11.5.0)
+set(ENABLE_BENCHMARKS OFF CACHE BOOL "")
 
 include( ${CMAKE_CURRENT_LIST_DIR}/../tpls.cmake )

inputFiles/compositionalMultiphaseFlow/4comp_2ph_1d.xml

@@ -7,6 +7,8 @@
       logLevel="1"
       discretization="fluidTPFA"
       targetRegions="{ Region1 }"
+      initialDt="1e5"
+      targetFlowCFL="2"
       temperature="297.15">
       <NonlinearSolverParameters
         newtonTol="1.0e-6"
@@ -45,26 +47,12 @@
     maxTime="2e7">
     <PeriodicEvent
       name="outputs"
-      timeFrequency="1e6"
-      target="/Outputs/siloOutput"/>
+      timeFrequency="5e6"
+      target="/Outputs/vtkOutput"/>
 
     <PeriodicEvent
       name="solverApplications1"
-      forceDt="1e3"
-      endTime="1e4"
-      target="/Solvers/compflow"/>
-
-    <PeriodicEvent
-      name="solverApplications2"
-      forceDt="1e4"
-      beginTime="1e4"
-      endTime="1e5"
-      target="/Solvers/compflow"/>
-
-    <PeriodicEvent
-      name="solverApplications3"
-      forceDt="1e5"
-      beginTime="1e5"
+      endTime="2e7"
       target="/Solvers/compflow"/>
 
     <PeriodicEvent
@@ -262,8 +250,8 @@
   </FieldSpecifications>
 
   <Outputs>
-    <Silo
-      name="siloOutput"/>
+    <VTK
+      name="vtkOutput"/>
 
     <Restart
       name="restartOutput"/>

inputFiles/compositionalMultiphaseFlow/co2_flux_3d.xml

@@ -119,6 +119,7 @@
   <Constitutive>
     <CO2BrinePhillipsFluid
       name="fluid"
+      logLevel="1"
       phaseNames="{ gas, water }"
       componentNames="{ co2, water }"
       componentMolarWeight="{ 44e-3, 18e-3 }"

inputFiles/compositionalMultiphaseFlow/deadoil_3ph_corey_1d_fractured.xml

@@ -10,7 +10,8 @@
       useMass="0"
       targetRegions="{ Domain, Fracture }">
       <NonlinearSolverParameters
-        newtonTol="1.0e-10"
+        lineSearchAction="None"
+        newtonTol="1.0e-8"
         newtonMaxIter="15"
         maxTimeStepCuts="2"
         lineSearchMaxCuts="2"/>
@@ -23,7 +24,7 @@
     <EmbeddedSurfaceGenerator
       name="SurfaceGenerator"
       logLevel="1"
-      discretization="fluidTPFA"
+      discretization="FE1"
       targetRegions="{ Domain, Fracture }"
       targetObjects="{ FracturePlane }"
       fractureRegion="Fracture"/>
@@ -99,6 +100,11 @@
       <TwoPointFluxApproximation
         name="fluidTPFA"/>
     </FiniteVolume>
+    <FiniteElements>
+    <FiniteElementSpace
+        name="FE1"
+        order="1"/>
+    </FiniteElements>
   </NumericalMethods>
 
   <ElementRegions>