Add pygeosx unit tests to CI; fix gcc version pragma in LvArray

.devcontainer/devcontainer.json

@@ -2,7 +2,7 @@
     "build": {
         "dockerfile": "Dockerfile",
         "args": {
-            "GEOS_TPL_TAG": "260-235"
+            "GEOS_TPL_TAG": "259-158"
         }
     },
     "runArgs": [

.github/workflows/build_and_test.yml

@@ -31,6 +31,9 @@ on:
       ENABLE_HYPRE_DEVICE:
         required: false
         type: string
+      ENABLE_PYGEOSX:
+        required: false
+        type: string
       ENABLE_TRILINOS:
         required: false
         type: string
@@ -149,6 +152,12 @@ jobs:
         docker_args+=(-e ENABLE_HYPRE_DEVICE=${ENABLE_HYPRE_DEVICE:-CPU})
         docker_args+=(-e ENABLE_TRILINOS=${ENABLE_TRILINOS:-ON})
 
+
+        # pygeosx testing
+        if [ "${{ inputs.ENABLE_PYGEOSX }}" == 'ON' ]; then
+          script_args+=(--run-pygeosx-tests)
+        fi
+
         docker_args+=(--cap-add=SYS_PTRACE --rm)
 
         script_args+=(--cmake-build-type ${{ inputs.CMAKE_BUILD_TYPE }})

.github/workflows/ci_tests.yml

@@ -127,27 +127,32 @@ jobs:
           - name: Ubuntu (20.04, gcc 9.4.0, open-mpi 4.0.3)
             CMAKE_BUILD_TYPE: Release
             DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc9
+            ENABLE_PYGEOSX: 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
+            ENABLE_PYGEOSX: 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
+            ENABLE_PYGEOSX: 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
+            ENABLE_PYGEOSX: 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
+            ENABLE_PYGEOSX: ON
 
           - name: Ubuntu (22.04, clang 15.0.7, open-mpi 4.1.2)
             CMAKE_BUILD_TYPE: Release
@@ -182,6 +187,7 @@ jobs:
       DOCKER_IMAGE_TAG: ${{ needs.is_not_draft_pull_request.outputs.DOCKER_IMAGE_TAG }}
       DOCKER_REPOSITORY: ${{ matrix.DOCKER_REPOSITORY }}
       ENABLE_HYPRE: ${{ matrix.ENABLE_HYPRE }}
+      ENABLE_PYGEOSX: ${{ matrix.ENABLE_PYGEOSX }}
       ENABLE_TRILINOS: ${{ matrix.ENABLE_TRILINOS }}
       GCP_BUCKET: ${{ matrix.GCP_BUCKET }}
       HOST_CONFIG: ${{ matrix.HOST_CONFIG }}

host-configs/environment.cmake

@@ -24,6 +24,17 @@ else()
   set(ENABLE_HYPRE OFF CACHE BOOL "" FORCE)
 endif()
 
+# pygeosx
+if(NOT DEFINED ENABLE_PYGEOSX)
+  set(ENABLE_PYGEOSX "$ENV{ENABLE_PYGEOSX}" CACHE BOOL "" FORCE)
+endif()
+if(ENABLE_PYGEOSX)
+  set(Python3_EXECUTABLE /usr/bin/python3 CACHE PATH "")
+  set(ENABLE_PYLVARRAY ON CACHE BOOL "")
+else()
+  set(ENABLE_PYGEOSX OFF CACHE BOOL "" FORCE)
+endif()
+
 # Same pattern
 if(NOT DEFINED ENABLE_TRILINOS)
   set(ENABLE_TRILINOS "$ENV{ENABLE_TRILINOS}" CACHE BOOL "" FORCE)

scripts/ci_build_and_test_in_container.sh

@@ -51,7 +51,9 @@ Usage: $0
   --no-run-unit-tests
       Do not run the unit tests (but they will be built).
   --repository /path/to/repository
-      Internal mountpoint where the geos repository will be available. 
+      Internal mountpoint where the geos repository will be available.
+  --run-pygeosx-tests
+      Runs the pygeosx tests.
   --run-integrated-tests
       Run the integrated tests. Then bundle and send the results to the cloud.
   --sccache-credentials credentials.json
@@ -68,13 +70,14 @@ exit 1
 or_die cd $(dirname $0)/..
 
 # Parsing using getopt
-args=$(or_die getopt -a -o h --long build-exe-only,cmake-build-type:,code-coverage,data-basename:,exchange-dir:,host-config:,install-dir-basename:,no-install-schema,no-run-unit-tests,repository:,run-integrated-tests,sccache-credentials:,test-code-style,test-documentation,help -- "$@")
+args=$(or_die getopt -a -o h --long build-exe-only,cmake-build-type:,code-coverage,data-basename:,exchange-dir:,host-config:,install-dir-basename:,no-install-schema,no-run-unit-tests,repository:,run-pygeosx-tests,run-integrated-tests,sccache-credentials:,test-code-style,test-documentation,help -- "$@")
 
 # Variables with default values
 BUILD_EXE_ONLY=false
 GEOSX_INSTALL_SCHEMA=true
 HOST_CONFIG="host-configs/environment.cmake"
 RUN_UNIT_TESTS=true
+RUN_PYGEOSX_TESTS=false
 RUN_INTEGRATED_TESTS=false
 TEST_CODE_STYLE=false
 TEST_DOCUMENTATION=false
@@ -105,6 +108,7 @@ do
     --no-install-schema)     GEOSX_INSTALL_SCHEMA=false; shift;;
     --no-run-unit-tests)     RUN_UNIT_TESTS=false;       shift;;
     --repository)            GEOS_SRC_DIR=$2;            shift 2;;
+    --run-pygeosx-tests)     RUN_PYGEOSX_TESTS=true;     shift;;
     --run-integrated-tests)  RUN_INTEGRATED_TESTS=true;  shift;;
     --code-coverage)         CODE_COVERAGE=true;         shift;;
     --sccache-credentials)   SCCACHE_CREDS=$2;           shift 2;;
@@ -180,6 +184,10 @@ if [[ "${RUN_INTEGRATED_TESTS}" = true ]]; then
   ATS_CMAKE_ARGS="-DATS_ARGUMENTS=\"--machine openmpi --ats openmpi_mpirun=/usr/bin/mpirun --ats openmpi_args=--allow-run-as-root --ats openmpi_procspernode=4 --ats openmpi_maxprocs=4\" -DPython3_ROOT_DIR=${ATS_PYTHON_HOME}"
 fi
 
+# Set CMake option for pygeosx
+if [[ "${RUN_PYGEOSX_TESTS}" = true ]]; then
+  PYGEOSX_CMAKE_ARG="-DENABLE_PYGEOSX=ON"
+fi
 
 if [[ "${CODE_COVERAGE}" = true ]]; then
   or_die apt-get update
@@ -212,7 +220,8 @@ or_die python3 scripts/config-build.py \
                -DGEOSX_INSTALL_SCHEMA=${GEOSX_INSTALL_SCHEMA} \
                -DENABLE_COVERAGE=$([[ "${CODE_COVERAGE}" = true ]] && echo 1 || echo 0) \
                ${SCCACHE_CMAKE_ARGS} \
-               ${ATS_CMAKE_ARGS}
+               ${ATS_CMAKE_ARGS} \
+               ${PYGEOSX_CMAKE_ARG}
 
 # The configuration step is now over, we can now move to the build directory for the build!
 or_die cd ${GEOSX_BUILD_DIR}
@@ -236,6 +245,12 @@ else
   or_die ninja -j $NPROC
   or_die ninja install
 
+  if [[ "${RUN_PYGEOSX_TESTS}" = true ]]; then
+    or_die ninja pygeosx
+    or_die ninja geosx_python_tools
+    or_die ninja pygeosx_unit_tests
+  fi
+
   if [[ ! -z "${DATA_BASENAME_WE}" ]]; then
     # Here we pack the installation.
     # The `--transform` parameter provides consistency between the tarball name and the unpacked folder.

scripts/spack_packages/packages/geosx/package.py

@@ -473,6 +473,7 @@ def geos_hostconfig(self, spec, prefix, py_site_pkgs_dir=None):
 
             if '+pygeosx' in spec:
                 cfg.write(cmake_cache_option('ENABLE_PYGEOSX', True))
+                cfg.write(cmake_cache_option('ENABLE_PYLVARRAY', True))
             else:
                 cfg.write(cmake_cache_option('ENABLE_PYGEOSX', False))