Update to match GEOSgcm main as of 2024-Aug-20

.circleci/config.yml

@@ -1,85 +1,42 @@
 version: 2.1
 
-executors:
-  gfortran-large:
-    docker:
-      - image: gmao/ubuntu20-geos-env-mkl:v6.2.8-openmpi_4.0.6-gcc_11.2.0
-        auth:
-          username: $DOCKERHUB_USER
-          password: $DOCKERHUB_AUTH_TOKEN
-    environment:
-      OMPI_ALLOW_RUN_AS_ROOT: 1
-      OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
-      OMPI_MCA_btl_vader_single_copy_mechanism: none
-    resource_class: large
-    #MEDIUM# resource_class: medium
+parameters:
+  GHA_Actor:
+    type: string
+    default: ""
+  GHA_Action:
+    type: string
+    default: ""
+  GHA_Event:
+    type: string
+    default: ""
+  GHA_Meta:
+    type: string
+    default: ""
 
-  ifort-large:
-    docker:
-      - image: gmao/ubuntu20-geos-env:v6.2.8-intelmpi_2021.2.0-intel_2021.2.0
-        auth:
-          username: $DOCKERHUB_USER
-          password: $DOCKERHUB_AUTH_TOKEN
-    resource_class: large
-    #MEDIUM# resource_class: medium
+# Anchors to prevent forgetting to update a version
+os_version: &os_version ubuntu20
+baselibs_version: &baselibs_version v7.25.0
+bcs_version: &bcs_version v11.5.0
+tag_build_arg_name: &tag_build_arg_name fv3version
+
+orbs:
+  ci: geos-esm/circleci-tools@2
 
 workflows:
   build-test:
     jobs:
-      - build-GEOSctm:
-          name: build-GEOSctm-on-<< matrix.compiler >>
+
+      # Build GEOSfvdycore
+      - ci/build:
+          name: build-GEOSfvdycore-as-<< matrix.fv_precision >>-on-<< matrix.compiler >>
+          context:
+            - docker-hub-creds
           matrix:
             parameters:
-              compiler: [gfortran, ifort]
-          context: 
-            - docker-hub-creds
-
-jobs:
-  build-GEOSctm:
-    parameters:
-      compiler:
-        type: string
-    executor: << parameters.compiler >>-large
-    working_directory: /root/project
-    steps:
-      - checkout:
-          path: GEOSctm
-      - run:
-          name: "Versions etc"
-          command: mpirun --version && << parameters.compiler>> --version && echo $BASEDIR && pwd && ls
-      - run:
-          name: "Mepo clone external repos"
-          command: |
-            cd ${CIRCLE_WORKING_DIRECTORY}/GEOSctm
-            mepo clone
-            mepo status
-      - run:
-          name: "Mepo checkout-if-exists"
-          command: |
-            cd ${CIRCLE_WORKING_DIRECTORY}/GEOSctm
-            echo "${CIRCLE_BRANCH}"
-            if [ "${CIRCLE_BRANCH}" != "develop" ] && [ "${CIRCLE_BRANCH}" != "main" ]
-            then
-               mepo checkout-if-exists ${CIRCLE_BRANCH}
-            fi
-            mepo status
-      - run:
-          name: "CMake"
-          command: |
-            mkdir -p /logfiles
-            cd ${CIRCLE_WORKING_DIRECTORY}/GEOSctm
-            mkdir -p  ${CIRCLE_WORKING_DIRECTORY}/workspace/build-GEOSctm
-            cd ${CIRCLE_WORKING_DIRECTORY}/workspace/build-GEOSctm
-            cmake ${CIRCLE_WORKING_DIRECTORY}/GEOSctm -DBASEDIR=$BASEDIR/Linux -DCMAKE_Fortran_COMPILER=<< parameters.compiler >> -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX=${CIRCLE_WORKING_DIRECTORY}/workspace/install-GEOSctm -DUSE_F2PY=OFF |& tee /logfiles/cmake.log
-      - run:
-          name: "Build and install"
-          command: |
-            cd ${CIRCLE_WORKING_DIRECTORY}/workspace/build-GEOSctm
-            make -j"$(nproc)" install |& tee /logfiles/make.log
-            #MEDIUM# make -j4 install |& tee /logfiles/make.log
-      - run:
-          name: "Compress artifacts"
-          command: |
-            gzip -9 /logfiles/*
-      - store_artifacts:
-          path: /logfiles
+              compiler: [ifort, gfortran]
+              fv_precision: ["R8"]
+          baselibs_version: *baselibs_version
+          repo: GEOSctm
+          mepodevelop: false
+          persist_workspace: false # Needs to be true to run fv3/gcm experiment, costs extra

.editorconfig

@@ -0,0 +1,27 @@
+# Global Editor Config for MAPL
+#
+# This is an ini style configuration. See http://editorconfig.org/ for more information on this file.
+#
+# Top level editor config.
+root = true
+
+# Always use Unix style new lines with new line ending on every file and trim whitespace
+[*]
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+# Python: PEP8 defines 4 spaces for indentation
+[*.py]
+indent_style = space
+indent_size = 4
+
+# YAML format, 2 spaces
+[{*.yaml,*.yml}]
+indent_style = space
+indent_size = 2
+
+# CMake (from KitWare: https://github.com/Kitware/CMake/blob/master/.editorconfig)
+[{CMakeLists.txt,*.cmake,*.rst}]
+indent_style = space
+indent_size = 2

.github/CODEOWNERS

@@ -3,16 +3,16 @@
 # Order is important; the last matching pattern takes the most
 # precedence.
 
-# Everything in GEOSgcm should be owned by the GCM Gatekeepers
+# Everything in GEOSctm should be owned by the CTM Gatekeepers
 * @GEOS-ESM/ctm-gatekeepers
 
-# The GCM gatekeepers and CMake should know/approve these
+# The CTM gatekeepers and CMake should know/approve these
 /.github/    @GEOS-ESM/cmake-team @GEOS-ESM/ctm-gatekeepers
-/.circleci/    @GEOS-ESM/cmake-team @GEOS-ESM/ctm-gatekeepers
-/.codebuild/    @GEOS-ESM/cmake-team @GEOS-ESM/ctm-gatekeepers
+/.circleci/  @GEOS-ESM/cmake-team @GEOS-ESM/ctm-gatekeepers
+/.codebuild/ @GEOS-ESM/cmake-team @GEOS-ESM/ctm-gatekeepers
 
-# The GEOS CMake Team is the CODEOWNER for the CMakeLists.txt files in this repository
-CMakeLists.txt @GEOS-ESM/cmake-team
+# The GEOS CMake Team should be notified about changes to the CMakeLists.txt files in this repository
+CMakeLists.txt @GEOS-ESM/cmake-team @GEOS-ESM/ctm-gatekeepers
 
 # The GEOS CMake Team should be notified about and approve config changes
-/config/       @GEOS-ESM/cmake-team
+/config/ @GEOS-ESM/cmake-team @GEOS-ESM/ctm-gatekeepers

.github/workflows/enforce-labels.yml

@@ -8,22 +8,26 @@ jobs:
   require-label:
     runs-on: ubuntu-latest
     steps:
-      - uses: mheap/github-action-required-labels@v2
+      - uses: mheap/github-action-required-labels@v5
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           mode: minimum
           count: 1
-          labels: "0 diff,0 diff trivial,Non 0-diff,0 diff structural,0-diff trivial,Not 0-diff,0-diff,automatic,0-diff uncoupled"
+          labels: "0 diff,0 diff trivial,Non 0-diff,0 diff structural,0-diff trivial,Not 0-diff,0-diff,automatic,0-diff uncoupled,github_actions"
           add_comment: true
+          message: "This PR is being prevented from merging because you have not added one of our required labels: {{ provided }}. Please add one so that the PR can be merged."
+
   blocking-label:
     runs-on: ubuntu-latest
     steps:
-      - uses: mheap/github-action-required-labels@v2
+      - uses: mheap/github-action-required-labels@v5
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           mode: exactly
           count: 0
           labels: "Contingent - DNA,Needs Lead Approval,Contingent -- Do Not Approve"
           add_comment: true
+          message: "This PR is being prevented from merging because you have added one of our blocking labels: {{ provided }}. You'll need to remove it before this PR can be merged."
+

.github/workflows/workflow.yml

@@ -6,6 +6,8 @@ on:
     # Do not run if the only files changed cannot affect the build
     paths-ignore:
       - "**.md"
+      - "**.json"
+      - "ChangeLog-PreJason.txt"
       - "parallel_build.csh"
       - ".github/CODEOWNERS"
       - ".codebuild/**"
@@ -17,33 +19,41 @@ jobs:
     if: "!contains(github.event.pull_request.labels.*.name, '0 diff trivial')"
     runs-on: ubuntu-latest
     container:
-      image: gmao/ubuntu20-geos-env-mkl:v6.2.4-openmpi_4.0.5-gcc_10.3.0
-      credentials:
-        username: ${{ secrets.DOCKERHUB_USERNAME }}
-        password: ${{ secrets.DOCKERHUB_TOKEN }}
+      image: gmao/ubuntu20-geos-env:v7.25.0-intelmpi_2021.13-intel_2024.2
+      # Per https://github.com/actions/virtual-environments/issues/1445#issuecomment-713861495
+      # It seems like we might not need secrets on GitHub Actions which is good for forked
+      # pull requests
+      #credentials:
+        #username: ${{ secrets.DOCKERHUB_USERNAME }}
+        #password: ${{ secrets.DOCKERHUB_TOKEN }}
     env:
       OMPI_ALLOW_RUN_AS_ROOT: 1
       OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
       OMPI_MCA_btl_vader_single_copy_mechanism: none
     steps:
+      # https://github.com/orgs/community/discussions/25678#discussioncomment-5242449
+      - name: Delete huge unnecessary tools folder
+        run: rm -rf /opt/hostedtoolcache
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.5.0
+        uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
       - name: Checkout CTM
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 1
+      - name: Set all directories as git safe
+        run: |
+          git config --global --add safe.directory '*'
       - name: Versions etc.
         run: |
-          gfortran --version
+          ifort --version
           mpirun --version
           echo $BASEDIR
       - name: Mepo clone external repos
         run: |
           mepo clone
           mepo status
-          mepo status
       - name: Update other branches
         if:
           "!contains('refs/heads/main,refs/heads/develop', github.ref)"
@@ -54,7 +64,7 @@ jobs:
         run: |
           mkdir build
           cd build
-          cmake .. -DBASEDIR=$BASEDIR/Linux -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_BUILD_TYPE=Debug -DMPIEXEC_PREFLAGS='--oversubscribe' -DUSE_F2PY=OFF
+          cmake .. -DBASEDIR=$BASEDIR/Linux -DCMAKE_Fortran_COMPILER=ifort -DCMAKE_BUILD_TYPE=Debug -DMPIEXEC_PREFLAGS='--oversubscribe' -DUSE_F2PY=OFF
       - name: Build
         run: |
           cd build

.gitignore

@@ -9,3 +9,14 @@
 parallel_build.o*
 log.*
 CMakeUserPresets.json
+
+# Ignore possible symlinked directories
+build-*
+install-*
+
+*.swp
+*.swo
+.DS_Store
+*#
+.#*
+**/CVS/

CMakeLists.txt

@@ -1,10 +1,10 @@
-cmake_minimum_required (VERSION 3.13)
+cmake_minimum_required (VERSION 3.17)
 cmake_policy (SET CMP0053 NEW)
 cmake_policy (SET CMP0054 NEW)
 
 project (
   GEOSctm
-  VERSION 2.0.1
+  VERSION 2.3.0
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 if ("${PROJECT_SOURCE_DIR}" STREQUAL "${PROJECT_BINARY_DIR}")
@@ -34,10 +34,64 @@ set (FV_PRECISION "R8" CACHE STRING "Precision of FV3 core (R4, R4R8, R8)")
 foreach (dir cmake @cmake cmake@)
   if (EXISTS ${CMAKE_CURRENT_LIST_DIR}/${dir})
     list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/${dir}")
+    set (ESMA_CMAKE_PATH "${CMAKE_CURRENT_LIST_DIR}/${dir}" CACHE PATH "Path to ESMA_cmake code")
   endif ()
 endforeach ()
+
+# We need to find MPI before we go into esma
+# for the MPI stack detection to work
+set(MPI_DETERMINE_LIBRARY_VERSION TRUE)
+find_package(MPI)
+
 include (esma)
 
+# Add CMake for when not using Baselibs
+if (NOT Baselibs_FOUND)
+
+  find_package(NetCDF REQUIRED C Fortran)
+  add_definitions(-DHAS_NETCDF4)
+  add_definitions(-DHAS_NETCDF3)
+  add_definitions(-DNETCDF_NEED_NF_MPIIO)
+  add_definitions(-DHAS_NETCDF3)
+
+  find_package(HDF5 REQUIRED)
+  if(HDF5_IS_PARALLEL)
+     add_definitions(-DH5_HAVE_PARALLEL)
+  endif()
+
+  if (NOT TARGET ESMF::ESMF)
+    find_package(ESMF 8.6.1 MODULE REQUIRED)
+    target_link_libraries(ESMF::ESMF INTERFACE MPI::MPI_Fortran)
+
+    # GEOS uses lowercase target due to historical reasons but
+    # the latest FindESMF.cmake file from ESMF produces an ESMF::ESMF target.
+    if (NOT TARGET esmf)
+      add_library(esmf ALIAS ESMF::ESMF)
+    endif ()
+    if (NOT TARGET ESMF)
+      add_library(ESMF ALIAS ESMF::ESMF)
+    endif ()
+  endif ()
+
+  find_package(GFTL_SHARED REQUIRED)
+
+  find_package(ZLIB REQUIRED)
+  # Another issue with historical reasons, old/wrong zlib target used in GEOS
+  add_library(ZLIB::zlib ALIAS ZLIB::ZLIB)
+
+  # Using FMS from spack requires updates to fvdycore due to interface changes
+  # in FMS 2022. This is commented for now until this transition can occur.
+  #################################################
+  # find_package(FMS QUIET COMPONENTS R4 R8)      #
+  # if (FMS_FOUND)                                #
+  #   # We need aliases due to historical reasons #
+  #   add_library(fms_r4 ALIAS FMS::fms_r4)       #
+  #   add_library(fms_r8 ALIAS FMS::fms_r8)       #
+  # endif ()                                      #
+  #################################################
+
+endif ()
+
 ecbuild_declare_project()
 
 # Generic DFLAGS
@@ -63,5 +117,14 @@ install(
    DESTINATION ${CMAKE_INSTALL_PREFIX}
    )
 
-# Adds abiilty to tar source
+# Adds ability to tar source
 include (esma_cpack)
+
+# This installs a tarball of the source code
+# in the installation directory.
+# MUST BE THE LAST CODE IN THIS FILE
+option(INSTALL_SOURCE_TARFILE "Create and install source tarfile" OFF)
+if(INSTALL_SOURCE_TARFILE)
+  install(CODE "set(CMAKE_PROJECT_NAME \"${CMAKE_PROJECT_NAME}\")")
+  install(SCRIPT "${ESMA_CMAKE_PATH}/esma_postinstall.cmake")
+endif()