Merge pull request #3051 from GEOS-ESM/develop

GitFlow: Merge develop into main for 2.48 release

.circleci/config.yml

@@ -17,11 +17,11 @@ parameters:
 # 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
+bcs_version: &bcs_version v11.6.0
 tag_build_arg_name: &tag_build_arg_name maplversion
 
 orbs:
-  ci: geos-esm/circleci-tools@2
+  ci: geos-esm/circleci-tools@4
 
 workflows:
   build-and-test-MAPL:
@@ -136,7 +136,7 @@ workflows:
             - docker-hub-creds
           matrix:
             parameters:
-              compiler: [gfortran,ifort]
+              compiler: [gfortran, ifort]
           baselibs_version: *baselibs_version
           repo: GEOSldas
           mepodevelop: false
@@ -171,7 +171,7 @@ workflows:
           filters:
             tags:
               only: /^v.*$/
-          name: publish-intel-docker-image
+          name: publish-ifort-docker-image
           context:
             - docker-hub-creds
             - ghcr-creds
@@ -180,10 +180,27 @@ workflows:
           container_name: mapl
           mpi_name: intelmpi
           mpi_version: "2021.13"
-          compiler_name: intel
-          compiler_version: "2024.2"
+          compiler_name: ifort
+          compiler_version: "2021.13"
           image_name: geos-env
           tag_build_arg_name: *tag_build_arg_name
+      #- ci/publish_docker:
+          #filters:
+            #tags:
+              #only: /^v.*$/
+          #name: publish-ifx-docker-image
+          #context:
+            #- docker-hub-creds
+            #- ghcr-creds
+          #os_version: *os_version
+          #baselibs_version: *baselibs_version
+          #container_name: mapl
+          #mpi_name: intelmpi
+          #mpi_version: "2021.13"
+          #compiler_name: ifx
+          #compiler_version: "2024.2"
+          #image_name: geos-env
+          #tag_build_arg_name: *tag_build_arg_name
       - ci/publish_docker:
           filters:
             tags:

.github/CODEOWNERS

@@ -5,11 +5,3 @@
 
 # The MAPL Team owns all the files
 * @GEOS-ESM/mapl-team
-
-# The Python Transition Team will own Python files
-# until the Python 3 transition is completed
-*.py @GEOS-ESM/python-transition-team
-
-# The GEOS CMake Team is the CODEOWNER for the CMakeLists.txt files in this repository
-CMakeLists.txt @GEOS-ESM/cmake-team
-

.github/workflows/workflow.yml

@@ -86,7 +86,7 @@ jobs:
     name: Build and Test MAPL Intel
     runs-on: ubuntu-latest
     container:
-      image: gmao/ubuntu20-geos-env:v7.25.0-intelmpi_2021.13-intel_2024.2
+      image: gmao/ubuntu20-geos-env:v7.25.0-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

Apps/CMakeLists.txt

@@ -26,25 +26,13 @@ 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::ESMF)
+target_link_libraries (Regrid_Util.x PRIVATE MAPL MPI::MPI_Fortran ESMF::ESMF OpenMP::OpenMP_Fortran)
 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::ESMF)
+target_link_libraries (time_ave_util.x PRIVATE MAPL MPI::MPI_Fortran ESMF::ESMF OpenMP::OpenMP_Fortran)
 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::ESMF)
+target_link_libraries (Comp_Testing_Driver.x PRIVATE MAPL MPI::MPI_Fortran ESMF::ESMF OpenMP::OpenMP_Fortran)
 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")
-  target_link_libraries(Comp_Testing_Driver.x PRIVATE OpenMP::OpenMP_Fortran)
-endif ()

Apps/Regrid_Util.F90

@@ -96,7 +96,7 @@ subroutine process_command_line(this,rc)
     this%lat_range=uninit
     this%shave=64
     this%deflate=0
-    this%quantize_algorithm=1
+    this%quantize_algorithm=0
     this%quantize_level=0
     this%use_weights = .false.
     nargs = command_argument_count()
@@ -424,6 +424,7 @@ subroutine main()
          call t_prof%stop("Read")
 
          call MPI_BARRIER(MPI_COMM_WORLD,STATUS)
+         _VERIFY(status)
 
          call t_prof%start("write")
 

Apps/time_ave_util.F90

@@ -133,9 +133,13 @@ program  time_ave
 
 !call timebeg ('main')
 
-   call mpi_init                ( ierror ) ; comm = mpi_comm_world
+   call mpi_init                ( ierror ) 
+   _VERIFY(ierror)
+   comm = mpi_comm_world
    call mpi_comm_rank ( comm,myid,ierror )
+   _VERIFY(ierror)
    call mpi_comm_size ( comm,npes,ierror )
+   _VERIFY(ierror)
    call ESMF_Initialize(logKindFlag=ESMF_LOGKIND_NONE,mpiCommunicator=MPI_COMM_WORLD, _RC)
    call MAPL_Initialize(_RC)
    t_prof = DistributedProfiler('time_ave_util',MpiTImerGauge(),MPI_COMM_WORLD)
@@ -813,6 +817,7 @@ program  time_ave
       enddo    ! End ntime Loop within file
 
       call MPI_BARRIER(comm,status)
+      _VERIFY(status)
    enddo
 
    do k=0,ntods
@@ -1064,7 +1069,9 @@ program  time_ave
          endif
 
          call mpi_reduce( qmin(nloc(n)+L-1),qming,1,mpi_real,mpi_min,0,comm,ierror )
+         _VERIFY(ierror)
          call mpi_reduce( qmax(nloc(n)+L-1),qmaxg,1,mpi_real,mpi_max,0,comm,ierror )
+         _VERIFY(ierror)
          if( root ) then
             if(L.eq.1) then
                write(6,3101) trim(vname2(n)),plev,qming,qmaxg
@@ -1076,6 +1083,7 @@ program  time_ave
 3102     format(1x,'               ',a20,' Level: ',f9.3,'  Min: ',g15.8,'  Max: ',g15.8)
       enddo
       call MPI_BARRIER(comm,status)
+      _VERIFY(status)
       if( root ) print *
    enddo
    if( root ) print *
@@ -1676,7 +1684,7 @@ end function is_leap_year
 
    subroutine usage(root)
       logical, intent(in) :: root
-      integer :: status,errorcode
+      integer :: status,errorcode,rc
       if(root) then
          write(6,100)
 100      format(  "usage:  ",/,/ &
@@ -1710,6 +1718,7 @@ subroutine usage(root)
                )
       endif
       call MPI_Abort(MPI_COMM_WORLD,errorcode,status)
+      _VERIFY(status)
    end subroutine usage
 
     subroutine generate_report()

CHANGELOG.md

@@ -17,6 +17,67 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Deprecated
 
+## [2.48.0] - 2024-09-24
+
+### Added
+
+- Added 5 new ExtData tests to test compression, bit-shaving, and quantization
+
+### Changed
+
+- Rename all single-digit ExtData tests to have a leading zero (i.e., `case1` -> `case01`)
+- Add restart benchmark code `restart_simulator.x` in benchmark directory
+- Start implementing changes for vertical regridding in ExtData
+- Made the POSITIVE field attribute defaults to "down" in case it is not found
+- VLOCATION is not querried in MAPL_VerticalMethods.F90 for rank 2 fields
+- Fixed time print in Cap GC (from slashes to colons)
+- Added ability to read the attribute with explicit type "string" of a netcdf variable.
+- Add ability to connect export of the MAPL hierachy to ExtData via CAP.rc file
+- Added new driver, CapDriver.x, to excerise the MAPL_Cap with the configuratable component also used by ExtDataDriver.x
+- Added Fortran interface to UDUNITS2
+  - NOTE: This now means MAPL depends on UDUNITS2 (and transitively, expat)
+- Improve mask sampler by adding an MPI step and a LS_chunk (intermediate step)
+- CI Updates
+  - Update Baselibs in CI to 7.25.0
+  - Update to circleci-tools orb v4
+    - This adds the ability to do an `ifx` test along with the `ifort` test (though `ifx` is not yet enabled)
+- Update `components.yaml`
+  - ESMA_env v4.30.1
+    - Update to Baselibs 7.25.0
+      - ESMF 8.6.1
+      - GFE v1.16.0
+        - gFTL v1.14.0
+        - gFTL-shared v1.9.0
+        - fArgParse v1.8.0
+        - pFUnit v4.10.0
+        - yaFyaml v1.4.0
+      - curl 8.8.0
+      - NCO 5.2.6
+      - Other various fixes from the v8 branch
+    - Move to use Intel ifort 2021.13 at NCCS SLES15, NAS, and GMAO Desktops
+    - Move to use Intel MPI at NCCS SLES15 and GMAO Desktops
+    - Move to GEOSpyD Min24.4.4 Python 3.11
+    - Fix for csh at NAS
+  - ESMA_cmake v3.51.0
+    - Update `esma_add_fortran_submodules` function
+    - Move MPI detection out of FindBaselibs
+    - Add SMOD to submodule generator
+    - NAG OpenMP Workaround
+    - Support for Jemalloc and LLVM Flang
+- Add support for preliminary CF Conventions quantization properties
+  - Add new quantization keyword `granular_bitround` to History. This will be the preferred keyword for quantization in the future
+    replacing `GranularBR`
+
+### Fixed
+
+- Fix profiler PercentageColumn test for GCC 14
+- Fix bug in ExtData Tests. CMake was overwriting the `EXTDATA2G_SMALL_TESTS` LABEL with `ESSENTIAL`
+
+### Deprecated
+
+- Deprecate `GranularBR` as a quantization method keyword in History. We will prefer `granular_bitround` in the future to match
+  draft CF conventions. This will be removed in MAPL 3.
+
 ## [2.47.2] - 2024-08-16
 
 ### Fixed

CMakeLists.txt

@@ -8,7 +8,7 @@ endif ()
 
 project (
   MAPL
-  VERSION 2.47.2
+  VERSION 2.48.0
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 # Set the possible values of build type for cmake-gui
@@ -218,6 +218,7 @@ if (APPLE)
   add_compile_definitions("-D__DARWIN")
 endif()
 
+add_subdirectory (udunits2f)
 add_subdirectory (pfio)
 add_subdirectory (profiler)
 add_subdirectory (generic)

Tests/CMakeLists.txt

@@ -1,38 +1,32 @@
+esma_set_this (OVERRIDE MAPL.test_utilities)
+
 set(MODULE_DIRECTORY "${esma_include}/Tests")
 
 set (srcs
-    ExtDataDriverGridComp.F90
     ExtDataRoot_GridComp.F90
-    ExtDataDriver.F90
-    ExtDataDriverMod.F90
     VarspecDescription.F90
     )
 
+esma_add_library (${this} SRCS ${srcs} DEPENDENCIES MAPL NetCDF::NetCDF_Fortran NetCDF::NetCDF_C TYPE ${MAPL_LIBRARY_TYPE})
+
 if (BUILD_WITH_FARGPARSE)
 
-  ecbuild_add_executable (TARGET ExtDataDriver.x SOURCES ${srcs})
-  target_link_libraries (ExtDataDriver.x PRIVATE MAPL FARGPARSE::fargparse ESMF::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)
-  endif ()
+  ecbuild_add_executable (TARGET ExtDataDriver.x SOURCES ExtDataDriver.F90 ExtDataDriverGridComp.F90 ExtDataDriverMod.F90)
+  target_link_libraries (ExtDataDriver.x PRIVATE MAPL MAPL.test_utilities FARGPARSE::fargparse ESMF::ESMF OpenMP::OpenMP_Fortran)
   set_target_properties(ExtDataDriver.x PROPERTIES Fortran_MODULE_DIRECTORY ${MODULE_DIRECTORY})
   target_compile_definitions (ExtDataDriver.x PRIVATE $<$<BOOL:${USE_EXTDATA2G}>:BUILD_WITH_EXTDATA2G>)
   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 FARGPARSE::fargparse ESMF::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 ()
+  target_link_libraries (pfio_MAPL_demo.x PRIVATE MAPL FARGPARSE::fargparse ESMF::ESMF OpenMP::OpenMP_Fortran)
   set_target_properties(pfio_MAPL_demo.x PROPERTIES Fortran_MODULE_DIRECTORY ${MODULE_DIRECTORY})
+
   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::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(MAPL_demo_fargparse.x PRIVATE OpenMP::OpenMP_Fortran)
-  endif ()
+  target_link_libraries (MAPL_demo_fargparse.x PRIVATE MAPL FARGPARSE::fargparse ESMF::ESMF OpenMP::OpenMP_Fortran)
   set_target_properties(MAPL_demo_fargparse.x PROPERTIES Fortran_MODULE_DIRECTORY ${MODULE_DIRECTORY})
 
+  ecbuild_add_executable (TARGET CapDriver.x SOURCES CapDriver.F90)
+  target_link_libraries (CapDriver.x PRIVATE MAPL MAPL.test_utilities FARGPARSE::fargparse ESMF::ESMF OpenMP::OpenMP_Fortran)
+  set_target_properties(CapDriver.x PROPERTIES Fortran_MODULE_DIRECTORY ${MODULE_DIRECTORY})
+
 endif ()

Tests/CapDriver.F90

@@ -0,0 +1,24 @@
+#define I_AM_MAIN
+
+#include "MAPL_Generic.h"
+
+program CapDriver_Main
+   use MPI
+   use MAPL
+   use ExtDataUtRoot_GridCompMod, only:  ROOT_SetServices => SetServices
+   implicit none
+
+   character(len=*), parameter :: Iam="CapDriver_Main"
+   type (MAPL_Cap) :: cap
+   type (MAPL_FargparseCLI) :: cli
+   type (MAPL_CapOptions) :: cap_options
+   integer :: status
+
+   cli = MAPL_FargparseCLI()
+   cap_options = MAPL_CapOptions(cli)
+   cap = MAPL_Cap('Root', ROOT_SetServices, cap_options = cap_options)
+
+   call cap%run(_RC)
+
+end program CapDriver_Main
+

Tests/ExtDataDriverMod.F90

@@ -217,6 +217,7 @@ subroutine initialize_mpi(this, unusable, rc)
       _UNUSED_DUMMY(unusable)
 
       call MPI_Init(ierror)
+      _VERIFY(ierror)
 
       this%comm_world=MPI_COMM_WORLD
       call MPI_Comm_rank(this%comm_world, this%rank, ierror); _VERIFY(ierror)