Merge pull request #54 from GEOS-ESM/feature/mathomp4/update-components-ctm-2025Mar11

Update to match GEOSgcm main as of 2025-Mar-11

Author: mmanyin

.circleci/config.yml

@@ -1,82 +1,39 @@
 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
+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
+# Anchors to prevent forgetting to update a version
+os_version: &os_version ubuntu24
+baselibs_version: &baselibs_version v7.32.0
+bcs_version: &bcs_version v11.6.0
+tag_build_arg_name: &tag_build_arg_name gcmversion
+
+orbs:
+  ci: geos-esm/circleci-tools@4
 
 workflows:
   build-test:
     jobs:
-      - build-GEOSctm:
+      - ci/build:
           name: build-GEOSctm-on-<< matrix.compiler >>
-          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
-      - run:
-          name: "Compress artifacts"
-          command: |
-            gzip -9 /logfiles/*
-      - store_artifacts:
-          path: /logfiles
+          matrix:
+            parameters:
+              compiler: [gfortran, ifort, ifx]
+          baselibs_version: *baselibs_version
+          repo: GEOSctm
+          develop_repos: "GMAO_Shared GEOS_Util"
+          persist_workspace: false # Needs to be true to run fv3/gcm experiment, costs extra

.github/workflows/enforce-labels.yml

@@ -16,6 +16,8 @@ jobs:
           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,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:

.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/ubuntu24-geos-env:v7.32.0-intelmpi_2021.13-ifort_2021.13
+      # 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

@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.13)
+cmake_minimum_required (VERSION 3.24)
 cmake_policy (SET CMP0053 NEW)
 cmake_policy (SET CMP0054 NEW)
 
@@ -34,10 +34,58 @@ 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)
+
+  find_package(MAPL 2.54 QUIET)
+  if (MAPL_FOUND)
+    message(STATUS "Found MAPL: ${MAPL_BASE_DIR} (found version \"${MAPL_VERSION})\"")
+  endif ()
+
+endif ()
+
 ecbuild_declare_project()
 
 # Generic DFLAGS
@@ -63,5 +111,5 @@ install(
    DESTINATION ${CMAKE_INSTALL_PREFIX}
    )
 
-# Adds abiilty to tar source
+# Adds ability to tar source
 include (esma_cpack)

CMakePresets.json

@@ -1,23 +1,14 @@
 {
-  "version": 3,
+  "version": 7,
   "cmakeMinimumRequired": {
     "major": 3,
-    "minor": 21,
+    "minor": 27,
     "patch": 0
   },
+  "include": [
+    "presets/CMake$penv{CMAKE_PRESET_NAME}Presets.json"
+  ],
   "configurePresets": [
-    {
-      "name": "base-configure",
-      "hidden": true,
-      "displayName": "Base Configure Settings",
-      "description": "Sets build and install directories",
-      "binaryDir": "${sourceDir}/build-${presetName}",
-      "cacheVariables": {
-        "BASEDIR": "$env{BASEDIR}",
-        "CMAKE_INSTALL_PREFIX": "${sourceDir}/install-${presetName}",
-        "CMAKE_BUILD_TYPE": "${presetName}"
-      }
-    },
     {
       "name": "base-gnu",
       "hidden": true,