Merge pull request #2258 from GEOS-ESM/develop

GitFlow: Merge develop into main

.circleci/config.yml

@@ -16,8 +16,8 @@ parameters:
 
 # Anchors to prevent forgetting to update a version
 os_version: &os_version ubuntu20
-baselibs_version: &baselibs_version v7.13.0
-bcs_version: &bcs_version v11.00.0
+baselibs_version: &baselibs_version v7.14.0
+bcs_version: &bcs_version v11.1.0
 tag_build_arg_name: &tag_build_arg_name maplversion
 
 orbs:
@@ -217,6 +217,7 @@ workflows:
           checkout_mapl_branch: true
           mepodevelop: false
           rebuild_procs: 1
+          extra_cmake_options: "-DBUILD_WITH_FLAP=ON"
 
   build-and-publish-docker:
     when:

.github/workflows/enforce-labels.yml

@@ -8,7 +8,7 @@ jobs:
   require-label:
     runs-on: ubuntu-latest
     steps:
-      - uses: mheap/github-action-required-labels@v4
+      - uses: mheap/github-action-required-labels@v5
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
@@ -21,7 +21,7 @@ jobs:
   blocking-label:
     runs-on: ubuntu-latest
     steps:
-      - uses: mheap/github-action-required-labels@v4
+      - uses: mheap/github-action-required-labels@v5
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:

.github/workflows/push-to-develop.yml

@@ -22,7 +22,10 @@ jobs:
           target_branch: release/MAPL-v3
           label: automatic,MAPL3,Skip Changelog
           template: .github/PULL_REQUEST_TEMPLATE/auto_pr_to_mapl3.md
-          get_diff: true
+          # Turning this to false until the action can get a fix for
+          # https://github.com/devops-infra/action-pull-request/issues/126
+          #get_diff: true
+          get_diff: false
           assignee: ${{ github.actor }}
           old_string: "<!-- Write your description here -->"
           new_string: ${{ github.event.commits[0].message }}

.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:v7.13.0-openmpi_4.1.4-gcc_12.1.0
+      image: gmao/ubuntu20-geos-env-mkl:v7.14.0-openmpi_4.1.4-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
@@ -77,7 +77,7 @@ jobs:
     name: Build and Test MAPL Intel
     runs-on: ubuntu-latest
     container:
-      image: gmao/ubuntu20-geos-env:v7.13.0-intelmpi_2021.6.0-intel_2022.1.0
+      image: gmao/ubuntu20-geos-env:v7.14.0-intelmpi_2021.6.0-intel_2022.1.0
       # 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

CHANGELOG.md

@@ -17,6 +17,71 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Deprecated
 
+## [2.40.0] - 2023-07-29
+
+### Added
+
+- Add ability of ExtData to fill variables on MAPL "tile" grids.
+- Added print of regrid method during History initialization
+- Added ability to use an `ESMF.rc` file to pass in pre-`ESMF_Initialize` options to ESMF (see [ESMF Docs](https://earthsystemmodeling.org/docs/release/latest/ESMF_refdoc/node4.html#SECTION04024000000000000000) for allowed flags.
+  - NOTE: File *must* be called `ESMF.rc`
+- Added ability to run ExtDataDriver.x on a MAPL "tile" grid
+- Add ability to introduce a time-step delay in ExtDataDriver.x to simulate the timestep latency of a real model
+- Added a MAPL\_Sleep function, equivalent to some vendor supplied but non-standard sleep function
+- sampling IODA file with trajectory sampler (step-1): make it run
+- Convert ExtData to use ESMF HConfig for YAML parsing rather than YaFYAML
+  - Set required ESMF version to 8.5.0
+- Add StationSamplerMod for station sampler
+- Added ReplaceMetadata message and method to replace oserver's metadata
+- Added field utilities to perform basic numeric operations on fields
+- Update arithemetic parser to work with any rank and type of ESMF fields
+- For ExtDataDriver.x only, added logging config to Tests/ExtDataDriverMod.F90 to enable Logger there
+- Added new fill option and run mode for ExtDataDriver.x
+
+### Changed
+
+- Updates to GFE library dependency
+  - Require gFTL v1.10.0
+  - Require gFTL-shared v1.6.1
+  - Require fArgParse v1.5.0
+  - Require pFlogger v1.9.5
+  - Removed yaFyaml as dependency
+- Updated programs using FLAP for command line parsing to use fArgParse instead
+- Updated `components.yaml` to use Baselibs 7.14.0
+  - ESMA_env v4.9.1 → v4.19.0
+    - Baselibs 7.14.0
+      - esmf v8.5.0
+      - GFE v1.11.0
+      - curl 8.2.1
+      - HDF5 1.10.10
+      - netCDF-C 4.9.2
+      - netCDF-Fortran 4.6.1
+      - CDO 2.2.1
+      - NCO 5.1.7
+    - Move to MPT 2.28 at NAS, and other various changes for TOSS4 at NAS
+    - Remove Haswell from `build.csh`
+  - ESMA_cmake v3.28.0 → v3.31.0
+    - Clean up for TOSS4 changes at NAS
+    - Add `QUIET_DEBUG` flag
+    - Suppress some common warnings with Intel Debug
+- Make the GEOSadas CI build separate as it often fails due to race conditions in GSI
+- Update CI to use BCs v11.1.0 and Baselibs 7.14.0
+- Updates to support building MAPL with spack instead of Baselibs
+  - Add `FindESMF.cmake` file to `cmake` directory (as it can't easily be found via spack)
+  - Move `CMAKE_MODULE_PATH` append statement up to find `FindESMF.cmake` before we `find_package(ESMF)`
+  - Default `BUILD_WITH_FLAP` to `OFF` as we don't build it in spack
+  - Explicitly build GEOSadas in CI with `-DBUILD_WITH_FLAP=ON` as GEOSadas is still behind in moving to use fArgParse
+
+### Fixed
+
+- Created cubed-sphere grid factory with files split by face
+- Removed unneeded and confusing default in History Grid Comp (see #2081)
+- Fixes in CMake for fArgParse transition
+
+### Deprecated
+
+- Deprecate the use of FLAP for command line parsing in favor of fArgParse. FLAP support will be removed in MAPL 3
+
 ## [2.39.7] - 2023-07-18
 
 ### Fixed

CMakeLists.txt

@@ -8,7 +8,7 @@ endif ()
 
 project (
   MAPL
-  VERSION 2.39.7
+  VERSION 2.40.0
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 # Set the possible values of build type for cmake-gui
@@ -58,6 +58,8 @@ if (NOT COMMAND esma)
 
 endif ()
 
+list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
+
 option (BUILD_SHARED_MAPL "Build shared MAPL libraries" ON)
 if (BUILD_SHARED_MAPL)
   set (MAPL_LIBRARY_TYPE SHARED)
@@ -71,38 +73,40 @@ message (STATUS "Building MAPL as ${MAPL_LIBRARY_TYPE} libraries")
 # This would then populate the target already leading to find_package()
 # errors.
 if(NOT TARGET GFTL::gftl)
-  # MAPL currently requires at least GFTL 1.5.1
-  find_package(GFTL 1.5.1 REQUIRED)
+  find_package(GFTL 1.10.0 REQUIRED)
 else()
-  if (GFTL_VERSION VERSION_LESS 1.5.1)
-    message(FATAL_ERROR "GFTL must be at least 1.5.1")
+  if (GFTL_VERSION VERSION_LESS 1.10.0)
+    message(FATAL_ERROR "gFTL must be at least 1.10.0")
   endif ()
 endif()
+message (STATUS "Found gFTL: ${GFTL_DIR} (found version ${GFTL_VERSION})")
+
 if(NOT TARGET GFTL_SHARED::gftl-shared)
-  find_package(GFTL_SHARED REQUIRED)
+  # MAPL currently requires at least gFTL-shared 1.6.1
+  find_package(GFTL_SHARED 1.6.1 REQUIRED)
+else ()
+  if (GFTL_SHARED_VERSION VERSION_LESS 1.6.1)
+    message(FATAL_ERROR "gFTL-shared must be at least 1.6.1")
+  endif ()
 endif()
+message (STATUS "Found gFTL-shared: ${GFTL_DIR} (found version ${GFTL_SHARED_VERSION})")
 
 option(BUILD_WITH_FARGPARSE "Use fArgParse for command line processing" ON)
 if(BUILD_WITH_FARGPARSE)
   if(NOT TARGET FARGPARSE::fargparse)
-    find_package(FARGPARSE 1.4.1 REQUIRED)
+    find_package(FARGPARSE 1.5.0 REQUIRED)
   else()
-    if (FARGPARSE_VERSION VERSION_LESS 1.4.1)
-      message(FATAL_ERROR "fArgParse must be at least 1.4.1")
+    if (FARGPARSE_VERSION VERSION_LESS 1.5.0)
+      message(FATAL_ERROR "fArgParse must be at least 1.5.0")
     endif ()
   endif()
+  message (STATUS "Building with fArgParse")
+  message (STATUS "Found fArgParse: ${FARGPARSE_DIR} (found version ${FARGPARSE_VERSION})")
 endif()
 
 option(USE_EXTDATA2G "Use ExtData2G" ON)
 if(USE_EXTDATA2G)
   set (EXTDATA2G_TARGET "MAPL.ExtData2G" CACHE STRING "ExtData2G Target")
-  if(NOT TARGET YAFYAML::yafyaml)
-    find_package(YAFYAML 1.0.4 REQUIRED)
-  else()
-    if (YAFYAML_VERSION VERSION_LESS 1.0.4)
-      message(FATAL_ERROR "yaFyaml must be at least 1.0.4")
-    endif ()
-  endif()
   message (STATUS "Building with ExtData2G")
 else()
   set (EXTDATA2G_TARGET "" CACHE STRING "ExtData2G Target")
@@ -111,15 +115,17 @@ endif()
 option(BUILD_WITH_PFLOGGER "Build MAPL with pFlogger library support" ON)
 if (BUILD_WITH_PFLOGGER)
   if(NOT TARGET PFLOGGER::pflogger)
-    find_package(PFLOGGER 1.9.1 REQUIRED)
+    find_package(PFLOGGER 1.9.5 REQUIRED)
   else()
-    if (PFLOGGER_VERSION VERSION_LESS 1.9.1)
-      message(FATAL_ERROR "pFlogger must be at least 1.9.1")
+    if (PFLOGGER_VERSION VERSION_LESS 1.9.5)
+      message(FATAL_ERROR "pFlogger must be at least 1.9.5")
     endif ()
   endif()
+  message (STATUS "Building with pFlogger")
+  message (STATUS "Found pFlogger: ${PFLOGGER_DIR} (found version ${PFLOGGER_VERSION})")
 endif()
 
-option(BUILD_WITH_FLAP "Use FLAP for command line processing" ON)
+option(BUILD_WITH_FLAP "Use FLAP for command line processing" OFF)
 if (BUILD_WITH_FLAP)
   find_package(FLAP REQUIRED)
 endif ()
@@ -142,7 +148,7 @@ if (NOT Baselibs_FOUND)
   endif()
 
   if (NOT TARGET esmf)
-    find_package(ESMF 8.4.0 MODULE REQUIRED)
+    find_package(ESMF 8.5.0 MODULE REQUIRED)
 
     # ESMF as used in MAPL requires MPI
     # NOTE: This looks odd because some versions of FindESMF.cmake out in the
@@ -157,6 +163,13 @@ if (NOT Baselibs_FOUND)
       add_library(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")
+  endif ()
 endif ()
 
 # We wish to add extra flags when compiling as Debug. We should only
@@ -209,7 +222,7 @@ add_subdirectory (base)
 add_subdirectory (MAPL)
 add_subdirectory (gridcomps)
 add_subdirectory (griddedio)
-if (BUILD_WITH_FLAP)
+if (BUILD_WITH_FARGPARSE)
    add_subdirectory (tutorial)
 endif()
 
@@ -219,7 +232,6 @@ if (PFUNIT_FOUND)
 endif ()
 
 # Support for automated code generation
-list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake")
 include(mapl_acg)
 include(mapl_create_stub_component)
 add_subdirectory (Apps)

Ford/docs-with-remote-esmf.md

@@ -21,7 +21,6 @@ exclude_dir: ../Ford
              ../build
              ../gFTL
              ../esmf
-             ../yaFyaml
              ../pFUnit
              ../fArgParse
              ../pFlogger

Ford/docs-with-remote-esmf.public_private_protected.md

@@ -22,7 +22,6 @@ exclude_dir: ../Ford
              ../build
              ../gFTL
              ../esmf
-             ../yaFyaml
              ../pFUnit
              ../fArgParse
              ../pFlogger

MAPL/CMakeLists.txt

@@ -3,7 +3,7 @@ esma_set_this()
 
 esma_add_library (${this}
   SRCS MAPL.F90
-  DEPENDENCIES MAPL.base MAPL.generic MAPL.pfio MAPL_cfio_r4 MAPL.gridcomps MAPL.orbit MAPL.griddedio ${EXTDATA_TARGET}
+  DEPENDENCIES MAPL.base MAPL.generic MAPL.pfio MAPL_cfio_r4 MAPL.gridcomps MAPL.orbit MAPL.griddedio MAPL.geom ${EXTDATA_TARGET}
                esmf NetCDF::NetCDF_Fortran MPI::MPI_Fortran
                $<$<BOOL:${BUILD_WITH_FLAP}>:FLAP::FLAP>
   TYPE ${MAPL_LIBRARY_TYPE}

MAPL/MAPL.F90

@@ -15,6 +15,7 @@ module MAPL
    use MAPL_OpenMP_Support, only : MAPL_find_bounds => find_bounds
    use MAPL_OpenMP_Support, only : MAPL_Interval => Interval
    use MAPL_Profiler, initialize_profiler =>initialize, finalize_profiler =>finalize
+   use MAPL_Geom
    implicit none
 end module MAPL
 

Tests/CMakeLists.txt

@@ -8,10 +8,10 @@ set (srcs
     VarspecDescription.F90
     )
 
-if (BUILD_WITH_FLAP)
+if (BUILD_WITH_FARGPARSE)
 
   ecbuild_add_executable (TARGET ExtDataDriver.x SOURCES ${srcs})
-  target_link_libraries (ExtDataDriver.x PRIVATE MAPL FLAP::FLAP esmf)
+  target_link_libraries (ExtDataDriver.x PRIVATE MAPL FARGPARSE::fargparse esmf)
   # 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(ExtDataDriver.x PRIVATE OpenMP::OpenMP_Fortran)
@@ -21,17 +21,12 @@ if (BUILD_WITH_FLAP)
   add_subdirectory(ExtData_Testing_Framework EXCLUDE_FROM_ALL)
 
   ecbuild_add_executable (TARGET pfio_MAPL_demo.x SOURCES pfio_MAPL_demo.F90)
-  target_link_libraries (pfio_MAPL_demo.x PRIVATE MAPL FLAP::FLAP esmf)
+  target_link_libraries (pfio_MAPL_demo.x PRIVATE MAPL FARGPARSE::fargparse esmf)
   # 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(pfio_MAPL_demo.x PRIVATE OpenMP::OpenMP_Fortran)
   endif ()
   set_target_properties(pfio_MAPL_demo.x PROPERTIES Fortran_MODULE_DIRECTORY ${MODULE_DIRECTORY})
-
-endif ()
-
-if (BUILD_WITH_FARGPARSE)
-
   ecbuild_add_executable (TARGET MAPL_demo_fargparse.x SOURCES MAPL_demo_fargparse.F90)
   target_link_libraries (MAPL_demo_fargparse.x PRIVATE MAPL FARGPARSE::fargparse esmf)
   # CMake has an OpenMP issue with NAG Fortran: https://gitlab.kitware.com/cmake/cmake/-/issues/21280

Tests/ExtDataDriver.F90

@@ -16,9 +16,9 @@ program ExtData_Driver
   character(len=*), parameter :: Iam="ExtData_Driver"
   type(ExtDataDriver) :: Driver
   type (MAPL_CapOptions) :: cap_options
-  type (MAPL_FlapCLI) :: cli
+  type (MAPL_FargparseCLI) :: cli
 
-  cli = MAPL_FlapCLI(description='extdata driver',authors='gmao')
+  cli = MAPL_FargparseCLI()
   cap_options=MAPL_CapOptions(cli)
 
   driver = ExtDataDriver('ExtDataApp',Root_SetServices,cap_options=cap_options,_RC)

Tests/ExtDataDriverMod.F90

@@ -58,7 +58,9 @@ function newExtDataDriver(name,set_services, unusable, cap_options, rc) result(d
          driver%cap_options = MAPL_CapOptions()
       endif
       call driver%initialize_mpi()
-      call MAPL_Initialize(comm=MPI_COMM_WORLD,rc=status)
+      call MAPL_Initialize(comm=MPI_COMM_WORLD, &
+           logging_config=driver%cap_options%logging_config, &
+           rc=status)
       _VERIFY(status)
       _RETURN(_SUCCESS)
    end function newExtDataDriver