Merge pull request #2593 from GEOS-ESM/develop

GitFlow: Merge develop into main for release
GEOS-ESM · Feb 9, 2024 · b09ae30 · b09ae30
2 parents 70d50bc + 1a2f909
commit b09ae30
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -24,9 +24,8 @@ orbs:
   ci: geos-esm/circleci-tools@2
 
 workflows:
-  build-and-test:
+  build-and-test-MAPL:
     jobs:
-
       # Builds MAPL in a "default" way - Intel
       - ci/build:
           name: build-and-test-MAPL-on-<< matrix.compiler >>-using-<< matrix.cmake_generator >>
@@ -35,7 +34,7 @@ workflows:
           matrix:
             parameters:
               compiler: [ifort]
-              cmake_generator: ['Unix Makefiles']
+              cmake_generator: ['Unix Makefiles','Ninja']
           baselibs_version: *baselibs_version
           repo: MAPL
           mepodevelop: false
@@ -61,7 +60,7 @@ workflows:
           matrix:
             parameters:
               compiler: [gfortran]
-              cmake_generator: ['Unix Makefiles']
+              cmake_generator: ['Unix Makefiles','Ninja']
           baselibs_version: *baselibs_version
           repo: MAPL
           mepodevelop: false
@@ -86,65 +85,58 @@ workflows:
           run_unit_tests: true
           ctest_options: "-LE 'PERFORMANCE|EXTDATA1G_BIG_TESTS|EXTDATA2G_BIG_TESTS' --output-on-failure"
 
-      # Build GEOSgcm -- ifort
-      - ci/build:
-          name: build-GEOSgcm-on-<< matrix.compiler >>
+      # Run MAPL Tutorials
+      - ci/run_mapl_tutorial:
+          name: run-<< matrix.tutorial_name >>-Tutorial-with-<< matrix.compiler >>
           context:
             - docker-hub-creds
           matrix:
             parameters:
+              #compiler: [gfortran, ifort]
               compiler: [ifort]
+              tutorial_name:
+                - hello_world
+                - parent_no_children
+                - parent_one_child_import_via_extdata
+                - parent_one_child_no_imports
+                - parent_two_siblings_connect_import_export
+          # We will only run the tutorials with GNU make. No need to double up
+          # as Ninja is a build test only
+          requires:
+            - build-and-test-MAPL-on-<< matrix.compiler >>-using-Unix Makefiles
           baselibs_version: *baselibs_version
-          repo: GEOSgcm
-          checkout_fixture: true
-          mepodevelop: true
-          checkout_mapl_branch: true
-          persist_workspace: true # Needs to be true to run fv3/gcm experiment, costs extra, retained for one day
 
-      # Build GEOSgcm -- GCC
+  build-and-run-GEOSgcm:
+    jobs:
+      # Build GEOSgcm -- ifort
       - ci/build:
           name: build-GEOSgcm-on-<< matrix.compiler >>
           context:
             - docker-hub-creds
           matrix:
             parameters:
-              compiler: [gfortran]
+              compiler: [ifort]
           baselibs_version: *baselibs_version
           repo: GEOSgcm
           checkout_fixture: true
           mepodevelop: true
           checkout_mapl_branch: true
           persist_workspace: true # Needs to be true to run fv3/gcm experiment, costs extra, retained for one day
 
-      # Build GEOSldas on ifort
-      - ci/build:
-          name: build-GEOSldas-on-<< matrix.compiler >>
-          context:
-            - docker-hub-creds
-          matrix:
-            parameters:
-              compiler: [ifort]
-          baselibs_version: *baselibs_version
-          repo: GEOSldas
-          mepodevelop: false
-          checkout_fixture: true
-          fixture_branch: develop
-          checkout_mapl_branch: true
-
-      # Build GEOSldas on gfortran
+      # Build GEOSgcm -- GCC
       - ci/build:
-          name: build-GEOSldas-on-<< matrix.compiler >>
+          name: build-GEOSgcm-on-<< matrix.compiler >>
           context:
             - docker-hub-creds
           matrix:
             parameters:
               compiler: [gfortran]
           baselibs_version: *baselibs_version
-          repo: GEOSldas
-          mepodevelop: false
+          repo: GEOSgcm
           checkout_fixture: true
-          fixture_branch: develop
+          mepodevelop: true
           checkout_mapl_branch: true
+          persist_workspace: true # Needs to be true to run fv3/gcm experiment, costs extra, retained for one day
 
       # Run GCM (1 hour, no ExtData)
       - ci/run_gcm:
@@ -176,26 +168,37 @@ workflows:
           gcm_ocean_type: MOM6
           change_layout: false
 
-      # Run MAPL Tutorials
-      - ci/run_mapl_tutorial:
-          name: run-<< matrix.tutorial_name >>-Tutorial-with-<< matrix.compiler >>
+  build-GEOSldas:
+    jobs:
+      # Build GEOSldas on ifort
+      - ci/build:
+          name: build-GEOSldas-on-<< matrix.compiler >>
           context:
             - docker-hub-creds
           matrix:
             parameters:
-              #compiler: [gfortran, ifort]
               compiler: [ifort]
-              tutorial_name:
-                - hello_world
-                - parent_no_children
-                - parent_one_child_import_via_extdata
-                - parent_one_child_no_imports
-                - parent_two_siblings_connect_import_export
-          # We will only run the tutorials with GNU make. No need to double up
-          # as Ninja is a build test only
-          requires:
-            - build-and-test-MAPL-on-<< matrix.compiler >>-using-Unix Makefiles
           baselibs_version: *baselibs_version
+          repo: GEOSldas
+          mepodevelop: false
+          checkout_fixture: true
+          fixture_branch: develop
+          checkout_mapl_branch: true
+
+      # Build GEOSldas on gfortran
+      - ci/build:
+          name: build-GEOSldas-on-<< matrix.compiler >>
+          context:
+            - docker-hub-creds
+          matrix:
+            parameters:
+              compiler: [gfortran]
+          baselibs_version: *baselibs_version
+          repo: GEOSldas
+          mepodevelop: false
+          checkout_fixture: true
+          fixture_branch: develop
+          checkout_mapl_branch: true
 
   build-GEOSadas:
     jobs:
@@ -250,7 +253,7 @@ workflows:
           baselibs_version: *baselibs_version
           container_name: mapl
           mpi_name: openmpi
-          mpi_version: 4.1.4
+          mpi_version: 5.0.0
           compiler_name: gcc
           compiler_version: 12.1.0
           image_name: geos-env-mkl

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
@@ -17,7 +17,7 @@ jobs:
     name: Build and Test MAPL GNU
     runs-on: ubuntu-latest
     container:
-      image: gmao/ubuntu20-geos-env-mkl:v7.17.0-openmpi_4.1.4-gcc_12.1.0
+      image: gmao/ubuntu20-geos-env-mkl:v7.17.0-openmpi_5.0.0-gcc_12.1.0
       # 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
@@ -30,7 +30,7 @@ jobs:
       OMPI_MCA_btl_vader_single_copy_mechanism: none
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/[email protected].0
+        uses: styfle/[email protected].1
         with:
           access_token: ${{ github.token }}
       - name: Checkout
@@ -86,7 +86,7 @@ jobs:
         #password: ${{ secrets.DOCKERHUB_TOKEN }}
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/[email protected].0
+        uses: styfle/[email protected].1
         with:
           access_token: ${{ github.token }}
       - name: Checkout

diff --git a/.gitignore b/.gitignore
@@ -9,6 +9,10 @@
 *.py.bak
 CMakeUserPresets.json
 
+# Ignore possible symlinked build and install directories
+build-*
+install-*
+
 *.swp
 *.swo
 .DS_Store

diff --git a/Apps/CMakeLists.txt b/Apps/CMakeLists.txt
@@ -24,23 +24,23 @@ install(
   DESTINATION bin/forcing_converter)
 
 ecbuild_add_executable (TARGET Regrid_Util.x SOURCES Regrid_Util.F90)
-target_link_libraries (Regrid_Util.x PRIVATE MAPL MPI::MPI_Fortran esmf)
+target_link_libraries (Regrid_Util.x PRIVATE MAPL MPI::MPI_Fortran ESMF::ESMF)
 target_include_directories (Regrid_Util.x PRIVATE $<BUILD_INTERFACE:${MAPL_SOURCE_DIR}/include>)
 # CMake has an OpenMP issue with NAG Fortran: https://gitlab.kitware.com/cmake/cmake/-/issues/21280
 if (NOT CMAKE_Fortran_COMPILER_ID MATCHES "NAG")
   target_link_libraries(Regrid_Util.x PRIVATE OpenMP::OpenMP_Fortran)
 endif ()
 
 ecbuild_add_executable (TARGET time_ave_util.x SOURCES time_ave_util.F90)
-target_link_libraries (time_ave_util.x PRIVATE MAPL MPI::MPI_Fortran esmf)
+target_link_libraries (time_ave_util.x PRIVATE MAPL MPI::MPI_Fortran ESMF::ESMF)
 target_include_directories (time_ave_util.x PRIVATE $<BUILD_INTERFACE:${MAPL_SOURCE_DIR}/include>)
 # CMake has an OpenMP issue with NAG Fortran: https://gitlab.kitware.com/cmake/cmake/-/issues/21280
 if (NOT CMAKE_Fortran_COMPILER_ID MATCHES "NAG")
   target_link_libraries(time_ave_util.x PRIVATE OpenMP::OpenMP_Fortran)
 endif ()
 
 ecbuild_add_executable (TARGET Comp_Testing_Driver.x SOURCES Comp_Testing_Driver.F90)
-target_link_libraries (Comp_Testing_Driver.x PRIVATE MAPL MPI::MPI_Fortran esmf)
+target_link_libraries (Comp_Testing_Driver.x PRIVATE MAPL MPI::MPI_Fortran ESMF::ESMF)
 target_include_directories (Comp_Testing_Driver.x PRIVATE $<BUILD_INTERFACE:${MAPL_SOURCE_DIR}/include>)
 # CMake has an OpenMP issue with NAG Fortran: https://gitlab.kitware.com/cmake/cmake/-/issues/21280
 if (NOT CMAKE_Fortran_COMPILER_ID MATCHES "NAG")

diff --git a/Apps/Regrid_Util.F90 b/Apps/Regrid_Util.F90
@@ -338,7 +338,7 @@ Program Regrid_Util
 
     subroutine main()
 
-   type(regrid_support) :: support
+   type(regrid_support), target :: support
 
    type(ESMF_VM)       :: vm             ! ESMF Virtual Machine
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,6 +17,54 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Deprecated
 
+## [2.44.0] - 2024-02-08
+
+### Added
+
+- Added nf90 interface to read and write 1d string
+- Convert from ABI Fixed Grid to lon/lat coordinates used in MAPL_XYGridFactory (supporting geostationary GOES-R series)
+- Modify trajectory sampler for a collection with multiple platforms: P3B (air craft) + FIREX
+- Modify swath sampler to handle two Epoch swath grids
+- Handle regrid accumulate for time step (1 sec) during which no obs exists
+- Use IntState%stampoffset(n) to adjust filenames for an epoch time
+- parse "GOCART::CO2" from 'geovals_fields' entry in PLATFORM
+- Add call MAPL_InitializeShmem to ExtDataDriverGridComp.F90
+- Read swath data on root, call MAPL_CommsBcast [which sends data to Shmem (when Shmem initialized) or to MAPL_comm otherwise]. This approach avoids race in reading nc files [e.g. 37 files for 3 hr swath data]
+- Added memory utility, MAPL_MemReport that can be used in any code linking MAPL
+- Added capability in XY grid factory to add a mask to the grid any points are missing needed for geostationary input data
+- Added capability in the MAPL ESMF regridding wrapper to apply a destination mask if the destination grid contains a mask
+- Added `INSTALL.md` file to provide instructions on how to install MAPL
+
+### Changed
+
+- Updated ESMF required version to 8.6.0
+- Allocate gridded fields to use the pinflag option needed for the Single System Image  (SSI) capability.
+- Made changes to allocate fields to use farray instead of farrayPtr. This allows explicit specification of indexflag required by the new MAPL field split functionality. This functionality allows a clean way to create a new field from an exiting field where the new field is a 'slice' of the existing field with the slicing index being that of the trailing ungiridded dim of the existing field.
+- Replaced RC=STATUS plus `_VERIFY(RC)` in `Base_Base_implementation.F90` with just `_RC` in line with our new convention.
+- Updated CI to use Open MPI 5.0.0 for GNU
+- Enable Ninja for CI builds of MAPL
+- Removed use of `ESMF_HAS_ACHAR_BUG` CMake option and code use in `MAPL_Config.F90`. Testing has shown that with ESMF 8.6 (which is
+  now required), NAG no longer needs this workaround.
+- Refactor the CircleCI workflows for more flexibility
+- Fix field utils issue - add npes argument to test subroutine decorators.
+- Change MAPL CMake to use `ESMF::ESMF` target instead of `esmf` or `ESMF` as the imported target name
+  - Updated `FindESMF.cmake` to match that of ESMF `develop` as of commit `da8f410`. This will be in ESMF 8.6.1+
+  - Requires ESMA_cmake 3.40.0 or later as this adds the `ESMF::ESMF` target ALIAS for Baselibs and non-Baselibs builds
+- Changed `CMakePresets.json`
+  - Updated to version 7 and required CMake 3.27.0 (the minimum version that supports CMakePresets.json v7)
+  - Changed build style on NCCS machines to by default put build and install directories in a user-specified directory so as not to
+    pollute swdev
+
+### Fixed
+
+- Restore missing submodule interfaces
+- Explictly `use` some `iso_c_binding` types previously pulled in through ESMF. This is fixed in future ESMF versions (8.7+) and so
+  we anticipate this here
+- Add explicit `Fortran_MODULE_DIRECTORY` to `CMakeLists.txt` in benchmarks to avoid race condition in Ninja builds
+- Add check to make sure ESMF was not built as `mpiuni`
+- Fixed failing tests for `field_utils`.
+- Various fixes for NVHPC work
+
 ## [2.43.2] - 2024-02-06
 
 ### Fixed

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -8,7 +8,7 @@ endif ()
 
 project (
   MAPL
-  VERSION 2.43.2
+  VERSION 2.44.0
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 # Set the possible values of build type for cmake-gui
@@ -147,28 +147,29 @@ if (NOT Baselibs_FOUND)
      add_definitions(-DH5_HAVE_PARALLEL)
   endif()
 
-  if (NOT TARGET esmf)
-    find_package(ESMF 8.5.0 MODULE REQUIRED)
+  if (NOT TARGET ESMF::ESMF)
+    find_package(ESMF 8.6.0 MODULE REQUIRED)
 
     # ESMF as used in MAPL requires MPI
     # NOTE: This looks odd because some versions of FindESMF.cmake out in the
     #       world provide an "esmf" target while others provide "ESMF". So we
     #       need this ugliness to support both.
-    if (TARGET esmf)
-      target_link_libraries(esmf INTERFACE MPI::MPI_Fortran)
+    if (TARGET ESMF::ESMF)
+      target_link_libraries(ESMF::ESMF INTERFACE MPI::MPI_Fortran)
     else()
-      target_link_libraries(ESMF INTERFACE MPI::MPI_Fortran)
+      target_link_libraries(ESMF::ESMF INTERFACE MPI::MPI_Fortran)
       # MAPL and GEOS use lowercase target due to historical reasons but
       # the latest FindESMF.cmake file from ESMF produces an ESMF target.
-      add_library(esmf ALIAS ESMF)
+      add_library(ESMF::ESMF ALIAS ESMF)
+      add_library(ESMF::ESMF ALIAS esmf)
     endif()
   endif ()
 else ()
   # This is an ESMF version test when using Baselibs which doesn't use the
   # same find_package internally in ESMA_cmake as used above (with a version
   # number) so this lets us at least trap use of old Baselibs here.
-  if (ESMF_VERSION VERSION_LESS 8.5.0)
-    message(FATAL_ERROR "ESMF must be at least 8.5.0")
+  if (ESMF_VERSION VERSION_LESS 8.6.0)
+    message(FATAL_ERROR "ESMF must be at least 8.6.0")
   endif ()
 endif ()
 

diff --git a/CMakePresets.json b/CMakePresets.json
@@ -1,22 +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}"
-      }
-    },
     {
       "name": "base-gnu",
       "hidden": true,