Merge branch 'develop' into docs/JOSS

.github/workflows/ci_tests.yml

@@ -5,6 +5,7 @@ on:
     branches: 
       - develop
   pull_request:
+  workflow_dispatch:
 
 # Cancels in-progress workflows for a PR when updated
 concurrency:
@@ -14,7 +15,6 @@ concurrency:
 # Please define `build.args.GEOS_TPL_TAG` in `.devcontainer/devcontainer.json`
 
 jobs:
-
   # Jobs will be cancelled if PR is a draft.
   # PR status must be "Open" to run CI.
   is_not_draft_pull_request:
@@ -28,17 +28,23 @@ jobs:
     - name: Check that the PR is not a draft (cancel rest of jobs otherwise)
       id: extract_pr_info
       run: |
-        # We do not rely on the `github.event.pull_request.labels` information since it's cached at the job.
-        # Changing labels or assignee in the PR would not allow to simply re-run the job with a different outcome.
-        pr_json=$(curl -H "Accept: application/vnd.github+json" https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.number }})
-        
-        # We stop the workflow if the pr is draft
-        draft_status=$(echo ${pr_json} | jq '.draft')
-        echo "Draft status of PR is ${draft_status}."
-        if [[ $draft_status == true ]]; then exit 1 ; fi
+        if [[ ${{github.event_name}} == 'pull_request' ]]; then 
+          # We do not rely on the `github.event.pull_request.labels` information since it's cached at the job.
+          # Changing labels or assignee in the PR would not allow to simply re-run the job with a different outcome.
+          pr_json=$(curl -H "Accept: application/vnd.github+json" https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.number }})
+          
+          # We stop the workflow if the pr is draft
+          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
+
         
-        # 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"
     # The TPL tag is contained in the codespaces configuration to avoid duplications.
     - name: Checkout .devcontainer/devcontainer.json
       uses: actions/checkout@v3
@@ -280,6 +286,11 @@ jobs:
     if: ${{ always() }}
     steps:
     - run: |
+        echo "if_not_unassigned_pull_request: ${{needs.if_not_unassigned_pull_request.result}}"
+        echo "are_submodules_in_sync: ${{needs.are_submodules_in_sync.result}}"
+        echo "check_code_style_and_documentation: ${{needs.check_code_style_and_documentation.result}}"
+        echo "cpu_builds: ${{needs.cpu_builds.result}}"
+        echo "cuda_builds: ${{needs.cuda_builds.result}}"
         ${{
           needs.if_not_unassigned_pull_request.result == 'success' &&
           needs.are_submodules_in_sync.result == 'success' &&

.gitmodules

@@ -13,3 +13,6 @@
 [submodule "src/coreComponents/fileIO/coupling/hdf5_interface"]
 	path = src/coreComponents/fileIO/coupling/hdf5_interface
 	url = ../../GEOS-DEV/hdf5_interface.git
+[submodule "scripts/uberenv"]
+	path = scripts/uberenv
+	url = ../../LLNL/uberenv.git

.uberenv_config.json

@@ -0,0 +1,11 @@
+{
+"package_name": "geosx",
+"package_version": "develop",
+"package_final_phase": "lvarray_hostconfig",
+"package_source_dir": "../..",
+"spack_url": "https://github.com/spack/spack",
+"spack_commit": "e8658d6493887ef702dd38f0e9ee5870a1651c1e",
+"spack_configs_path": "scripts/spack_configs",
+"spack_packages_path": "scripts/spack_packages/packages",
+"spack_concretizer": "clingo"
+}

scripts/pygeosx_configs/blueos_3_ppc64le_ib_p9/spack.yaml

@@ -0,0 +1,137 @@
+#------------------------------------------------------------------------------------------------------------
+# SPDX-License-Identifier: LGPL-2.1-only
+#
+# Copyright (c) 2018-2020 Lawrence Livermore National Security LLC
+# Copyright (c) 2018-2020 The Board of Trustees of the Leland Stanford Junior University
+# Copyright (c) 2018-2020 TotalEnergies
+# Copyright (c) 2019-     GEOSX Contributors
+# All rights reserved
+#
+# See top level LICENSE, COPYRIGHT, CONTRIBUTORS, NOTICE, and ACKNOWLEDGEMENTS files for details.
+#------------------------------------------------------------------------------------------------------------
+
+# %[email protected]
+#
+# Uberenv command to build pygeosx dependencies:
+# python3 ./scripts/uberenv/uberenv.py --spec="%[email protected]" --project-json="scripts/pygeosx_configs/pygeosx.json"
+
+spack:
+  config:
+    install_tree:
+      root: $spack/..
+      projections:
+        all: '{compiler.name}-{compiler.version}/{name}-{version}-{hash}'
+    misc_cache: $spack/../misc_cache
+    test_stage: $spack/../test_stage
+    build_stage::
+    - $spack/../build_stage
+
+  view:
+    default:
+      root: ../view
+      projections: 
+        all: '{name}-{version}'
+
+  compilers::
+  - compiler:
+      spec: [email protected]
+      paths:
+        cc: /usr/tce/packages/gcc/gcc-8.3.1/bin/gcc
+        cxx: /usr/tce/packages/gcc/gcc-8.3.1/bin/g++
+        f77: /usr/tce/packages/gcc/gcc-8.3.1/bin/gfortran
+        fc: /usr/tce/packages/gcc/gcc-8.3.1/bin/gfortran
+      flags:
+        # Fix for "undefined reference to `_gfortran_transfer_integer_write'"
+        ldlibs: -lgfortran
+      operating_system: rhel7
+      target: ppc64le
+      modules: []
+      environment: {}
+      extra_rpaths: []
+
+  packages:
+    all:
+      compiler: [gcc]
+      providers:
+        mpi: [spectrum-mpi]
+        blas: [openblas]
+        lapack: [openblas]
+
+    spectrum-mpi:
+      buildable: False
+      externals:
+        - spec: spectrum-mpi@release%[email protected]
+          prefix: /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-8.3.1
+
+    cuda:
+      buildable: False
+      externals:
+      - spec: [email protected] +allow-unsupported-compilers
+        prefix: /usr/tce/packages/cuda/cuda-11.2.0
+
+  # System level packages to not build
+    cmake:
+      buildable: False
+      externals:
+      - spec: [email protected]
+        prefix: /usr/tce/packages/cmake/cmake-3.21.1
+    readline:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /collab/usr/gapps/python/build/spack-coralea.3/opt/spack/linux-rhel7-ppc64le/gcc-4.9.3/readline-7.0-owal6z2zh5zotgvdmwow6sgdn6cqfn43/
+    m4:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    perl:
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+    pkg-config:
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+    diffutils:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr/bin/
+    autoconf:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    automake:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    libtool:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    bison:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    flex:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    tk:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    tcl:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr

scripts/pygeosx_configs/pygeosx.json

@@ -0,0 +1,11 @@
+{
+"package_name": "pygeosx",
+"package_version": "fakeversion",
+"package_final_phase": "",
+"package_source_dir": "../..",
+"spack_url": "https://github.com/spack/spack",
+"spack_commit": "e8658d6493887ef702dd38f0e9ee5870a1651c1e",
+"spack_configs_path": "scripts/pygeosx_configs",
+"spack_packages_path": "scripts/spack_packages/packages",
+"spack_concretizer": "clingo"
+}

scripts/pygeosx_configs/toss_4_x86_64_ib/spack.yaml

@@ -0,0 +1,142 @@
+#------------------------------------------------------------------------------------------------------------
+# SPDX-License-Identifier: LGPL-2.1-only
+#
+# Copyright (c) 2018-2020 Lawrence Livermore National Security LLC
+# Copyright (c) 2018-2020 The Board of Trustees of the Leland Stanford Junior University
+# Copyright (c) 2018-2020 TotalEnergies
+# Copyright (c) 2019-     GEOSX Contributors
+# All rights reserved
+#
+# See top level LICENSE, COPYRIGHT, CONTRIBUTORS, NOTICE, and ACKNOWLEDGEMENTS files for details.
+#------------------------------------------------------------------------------------------------------------
+
+#  %[email protected]
+#
+# Uberenv command to build pygeosx dependencies:
+# python3 ./scripts/uberenv/uberenv.py --spec="%[email protected]" --project-json="scripts/pygeosx_configs/pygeosx.json"
+
+spack:
+  config:
+    install_tree:
+      root: $spack/..
+      projections:
+        all: '{compiler.name}-{compiler.version}/{name}-{version}-{hash}'
+    misc_cache: $spack/../misc_cache
+    test_stage: $spack/../test_stage
+    build_stage::
+    - $spack/../build_stage
+
+  view:
+    default:
+      root: ../view
+      projections: 
+        all: '{name}-{version}'
+
+  compilers::
+  - compiler:
+      spec: [email protected]
+      paths:
+        cc: /usr/tce/packages/gcc/gcc-10.3.1-magic/bin/gcc
+        cxx: /usr/tce/packages/gcc/gcc-10.3.1-magic/bin/g++
+        f77: /usr/tce/packages/gcc/gcc-10.3.1-magic/bin/gfortran
+        fc: /usr/tce/packages/gcc/gcc-10.3.1-magic/bin/gfortran
+      operating_system: rhel8
+      target: x86_64
+      modules: []
+      environment: {}
+      extra_rpaths: []
+
+  packages:
+    all:
+      target: [ivybridge]
+      compiler: [clang]
+      providers:
+        mpi: [mvapich2]
+        blas: [intel-oneapi-mkl]
+        lapack: [intel-oneapi-mkl]
+
+   # Lock down which MPI we are using
+    mvapich2:
+      buildable: False
+      externals:
+        - spec: [email protected]%[email protected]
+          prefix:  /usr/tce/packages/mvapich2/mvapich2-2.3.6-gcc-10.3.1-magic
+
+    intel-oneapi-mkl:
+      externals:
+        - spec: "[email protected]"
+          prefix: /opt/intel/oneapi
+      buildable: False
+
+    # System level packages to not build
+    papi:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr/tce/packages/papi/papi-6.0.0.1/
+    cmake:
+      version: [3.26.3]
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr/tce/packages/cmake/cmake-3.26.3
+    readline:
+      externals:
+      - spec: [email protected]
+        prefix: /collab/usr/gapps/python/build/spack-toss3.3/opt/spack/linux-rhel7-x86_64/gcc-4.9.3/readline-7.0-e5jqqjmcjknidgwvi353pd6umpixzxr2
+      buildable: false
+    m4:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    perl:
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+    pkg-config:
+      buildable: false
+      externals:
+      - spec: [email protected]
+        prefix: /usr
+    diffutils:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr/bin
+    autoconf:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    automake:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    libtool:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    bison:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    flex:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    tk:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr
+    tcl:
+      buildable: False
+      externals:
+        - spec: [email protected]
+          prefix: /usr