Merge pull request #3226 from GEOS-ESM/develop

GitFlow: Merge develop into main for 2.51 release

.circleci/config.yml

@@ -33,7 +33,7 @@ workflows:
             - docker-hub-creds
           matrix:
             parameters:
-              compiler: [gfortran, ifort]
+              compiler: [gfortran, ifort, ifx]
               cmake_generator: ['Unix Makefiles','Ninja']
           baselibs_version: *baselibs_version
           repo: MAPL
@@ -49,7 +49,7 @@ workflows:
             - docker-hub-creds
           matrix:
             parameters:
-              compiler: [gfortran, ifort]
+              compiler: [gfortran, ifort, ifx]
           baselibs_version: *baselibs_version
           repo: MAPL
           mepodevelop: false
@@ -60,14 +60,29 @@ workflows:
           # ExtData1G tests were removed from ESSENTIAL, so we run them separately here as UFS might still use 1G?
           ctest_options: "-L 'ESSENTIAL|EXTDATA1G_SMALL_TESTS' --output-on-failure"
 
+      # Builds MAPL without pFUnit support
+      - ci/build:
+          name: build-MAPL-without-pFUnit-on-<< matrix.compiler >>
+          context:
+            - docker-hub-creds
+          matrix:
+            parameters:
+              compiler: [ifort, ifx]
+          baselibs_version: *baselibs_version
+          repo: MAPL
+          mepodevelop: false
+          remove_pfunit: true
+          run_unit_tests: true
+          ctest_options: "-L 'ESSENTIAL' --output-on-failure"
+
       # 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: [gfortran, ifort, ifx]
               tutorial_name:
                 - hello_world
                 - parent_no_children
@@ -89,7 +104,7 @@ workflows:
             - docker-hub-creds
           matrix:
             parameters:
-              compiler: [gfortran, ifort]
+              compiler: [gfortran, ifort, ifx]
           baselibs_version: *baselibs_version
           repo: GEOSgcm
           checkout_fixture: true
@@ -104,7 +119,7 @@ workflows:
             - docker-hub-creds
           matrix:
             parameters:
-              compiler: [gfortran, ifort]
+              compiler: [gfortran, ifort, ifx]
           requires:
             - build-GEOSgcm-on-<< matrix.compiler >>
           repo: GEOSgcm
@@ -185,23 +200,23 @@ workflows:
           compiler_version: "2021.13"
           image_name: geos-env
           tag_build_arg_name: *tag_build_arg_name
-      #- ci/publish_docker:
-          #filters:
-            #tags:
-              #only: /^v.*$/
-          #name: publish-ifx-docker-image
-          #context:
-            #- docker-hub-creds
-            #- ghcr-creds
-          #os_version: *os_version
-          #baselibs_version: *baselibs_version
-          #container_name: mapl
-          #mpi_name: intelmpi
-          #mpi_version: "2021.13"
-          #compiler_name: ifx
-          #compiler_version: "2024.2"
-          #image_name: geos-env
-          #tag_build_arg_name: *tag_build_arg_name
+      - ci/publish_docker:
+          filters:
+            tags:
+              only: /^v.*$/
+          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: "2021.14"
+          compiler_name: ifx
+          compiler_version: "2025.0"
+          image_name: geos-env
+          tag_build_arg_name: *tag_build_arg_name
       - ci/publish_docker:
           filters:
             tags:
@@ -214,8 +229,8 @@ workflows:
           baselibs_version: *baselibs_version
           container_name: mapl
           mpi_name: openmpi
-          mpi_version: 5.0.2
+          mpi_version: 5.0.5
           compiler_name: gcc
-          compiler_version: 13.2.0
+          compiler_version: 14.2.0
           image_name: geos-env-mkl
           tag_build_arg_name: *tag_build_arg_name

CHANGELOG.md

@@ -17,6 +17,59 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Deprecated
 
+## [2.51.0] - 2024-12-06
+
+### Added
+
+- Added macro `_RETURN(_SUCCESS)` to fetch_data
+- Allow update offsets of ±timestep in ExtData2G
+- Minor revision (and generalization) of grid-def for GSI purposes
+- Add ability to use an `ESMF_CONFIG_FILE` environment variable to specify name of 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.
+- Allow lat-lon grid factory to detect and use CF compliant lat-lon bounds in a file when making a grid
+- PFIO/Variable class, new procedures to retrieve string/reals/int attributes from a variable
+- Added a call in GenericRefresh to allow GC's refresh method to be called; in support
+  of CICE6 rewind
+
+### Changed
+
+- Change minimum CMake version to 3.24
+  - This is needed for f2py and meson support
+- Refactored tableEnd check
+- Added commandline options to `checkpoint_benchmark.x` and `restart_benchmark.x` to allow for easier testing of different configurations. Note that the old configuration file style of input is allowed via the `--config_file` option (which overrides any other command line options)
+- Update ESMF version for Baselibs to match that of Spack for consistency
+- Update `components.yaml`
+  - ESMA_env v4.32.0
+    - Baselibs 7.27.0
+      - ESMF 8.7.0
+      - curl 8.10.1
+      - NCO 5.2.8
+      - CDO 2.4.4
+      - GSL 2.8
+      - jpeg 9f
+      - Various build fixes
+  - ESMA_cmake v3.55.0
+    - Fixes for using MAPL as a library in spack builds of GEOSgcm
+    - Various backports from v4
+    - Code for capturing `mepo status` output
+    - Fixes for f2py and meson (NOTE: Requires CMake minimum version of 3.24 in project for complete functionality)
+    - Fixes for `MPI_STACK` code run multiple times
+- Updates to CI
+  - Use v7.27.0 Baselibs
+  - Use GCC 14 for GNU tests
+  - Add pFUnit-less build test
+  - Enable ifx tests
+- Improve some writes to be more informative
+  - In `base/MAPL_CFIO.F90`, added `Iam` to a print statement so that when a read fails we know which routine failed
+  - In `gridcomps/ExtData2G/ExtDataConfig.F90`, print out the name of the duplicate collection that causes model to fail
+
+### Fixed
+
+- Fixed issue of some Baselibs builds appearing to support zstandard. This is not possible due to Baselibs building HDF5 and netCDF as static libraries
+- Workaround ifx bug in `pfio/ArrayReference.F90` (NOTE: This currently targets all versions of ifx, but will need to be qualified or removed in the future)
+- Updates to support llvm-flang
+- Trajectory sampler: fix a bug when group_name does not exist in netCDF file and a bug that omitted the first time point
+- Fixed a bug where the periodicity around the earth of the lat-lon grid was not being set properly when grid did not span from pole to pole
+
 ## [2.50.3] - 2024-12-02
 
 ### Fixed

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required (VERSION 3.23)
+cmake_minimum_required (VERSION 3.24)
 
 get_property(is_multi_config GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
 if(NOT is_multi_config AND NOT (CMAKE_BUILD_TYPE OR DEFINED ENV{CMAKE_BUILD_TYPE}))
@@ -8,7 +8,7 @@ endif ()
 
 project (
   MAPL
-  VERSION 2.50.3
+  VERSION 2.51.0
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 # Set the possible values of build type for cmake-gui
@@ -156,8 +156,8 @@ 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 8.6.0)
-    message(FATAL_ERROR "ESMF must be at least 8.6.0")
+  if (ESMF_VERSION VERSION_LESS 8.6.1)
+    message(FATAL_ERROR "ESMF must be at least 8.6.1")
   endif ()
 endif ()
 

base/CMakeLists.txt

@@ -1,14 +1,5 @@
 esma_set_this (OVERRIDE MAPL.base)
 
-if(CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
-  if(CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 20)
-    if(CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER 17)
-      add_definitions(-D__ifort_18)
-    endif()
-  endif()
-endif()
-
-
 set (srcs
   MAPL_Profiler.F90
   CFIOCollection.F90                    MAPL_RegridderManager.F90

base/FileMetadataUtilities.F90

@@ -116,30 +116,15 @@ function get_var_attr_real32(this,var_name,attr_name,rc) result(attr_real32)
       character(len=*), intent(in) :: attr_name
       integer, optional, intent(out) :: rc
 
-      real(REAL32) :: tmp(1)
-      real(REAL64) :: tmpd(1)
       integer :: status
       character(:), allocatable :: fname
-      type(Attribute), pointer :: attr
       type(Variable), pointer :: var
-      class(*), pointer :: attr_val(:)
 
       fname = this%get_file_name(_RC)
       var => this%get_variable(var_name,_RC)
       _ASSERT(associated(var),"no variable named "//var_name//" in "//fname)
-      attr => var%get_attribute(attr_name,_RC)
-      _ASSERT(associated(attr),"no attribute named "//attr_name//" in "//var_name//" in "//fname)
-      attr_val => attr%get_values()
-      select type(attr_val)
-      type is(real(kind=REAL32))
-         tmp = attr_val
-         attr_real32 = tmp(1)
-      type is(real(kind=REAL64))
-         tmpd = attr_val
-         attr_real32 = REAL(tmpd(1))
-      class default
-         _FAIL('unsupported subclass (not real32) for units of attribute named '//attr_name//' in '//var_name//' in '//fname)
-      end select
+      attr_real32 = var%get_attribute_real32(attr_name, rc=status)
+      _ASSERT(status == _SUCCESS, 'failed to get attribute named '//attr_name//' in '//var_name//' in '//fname)
 
       _RETURN(_SUCCESS)
    end function get_var_attr_real32
@@ -151,28 +136,17 @@ function get_var_attr_real64(this,var_name,attr_name,rc) result(attr_real64)
       character(len=*), intent(in) :: attr_name
       integer, optional, intent(out) :: rc
 
-      real(REAL64) :: tmp(1)
       integer :: status
       character(:), allocatable :: fname
-      type(Attribute), pointer :: attr
       type(Variable), pointer :: var
-      class(*), pointer :: attr_val(:)
 
       fname = this%get_file_name(_RC)
       var => this%get_variable(var_name,_RC)
       _ASSERT(associated(var),"no variable named "//var_name//" in "//fname)
-      attr => var%get_attribute(attr_name,_RC)
-      _ASSERT(associated(attr),"no attribute named "//attr_name//" in "//var_name//" in "//fname)
-      attr_val => attr%get_values()
-      select type(attr_val)
-      type is(real(kind=REAL64))
-         tmp = attr_val
-         attr_real64 = tmp(1)
-      class default
-         _FAIL('unsupported subclass (not real64) for units of attribute named '//attr_name//' in '//var_name//' in '//fname)
-      end select
-
+      attr_real64 = var%get_attribute_real64(attr_name, rc=status)
+      _ASSERT(status == _SUCCESS, 'failed to get attribute named '//attr_name//' in '//var_name//' in '//fname)
       _RETURN(_SUCCESS)
+
    end function get_var_attr_real64
 
    function get_var_attr_int32(this,var_name,attr_name,rc) result(attr_int32)
@@ -182,26 +156,15 @@ function get_var_attr_int32(this,var_name,attr_name,rc) result(attr_int32)
       character(len=*), intent(in) :: attr_name
       integer, optional, intent(out) :: rc
 
-      integer(INT32) :: tmp(1)
       integer :: status
       character(:), allocatable :: fname
-      type(Attribute), pointer :: attr
       type(Variable), pointer :: var
-      class(*), pointer :: attr_val(:)
 
       fname = this%get_file_name(_RC)
       var => this%get_variable(var_name,_RC)
       _ASSERT(associated(var),"no variable named "//var_name//" in "//fname)
-      attr => var%get_attribute(attr_name,_RC)
-      _ASSERT(associated(attr),"no attribute named "//attr_name//" in "//var_name//" in "//fname)
-      attr_val => attr%get_values()
-      select type(attr_val)
-      type is(integer(kind=INT32))
-         tmp = attr_val
-         attr_int32 = tmp(1)
-      class default
-         _FAIL('unsupported subclass (not int32) for units of attribute named '//attr_name//' in '//var_name//' in '//fname)
-      end select
+      attr_int32 = var%get_attribute_int32(attr_name, rc=status)
+      _ASSERT(status == _SUCCESS, 'failed to get attribute named '//attr_name//' in '//var_name//' in '//fname)
 
       _RETURN(_SUCCESS)
    end function get_var_attr_int32
@@ -213,26 +176,15 @@ function get_var_attr_int64(this,var_name,attr_name,rc) result(attr_int64)
       character(len=*), intent(in) :: attr_name
       integer, optional, intent(out) :: rc
 
-      integer(INT64) :: tmp(1)
       integer :: status
       character(:), allocatable :: fname
-      type(Attribute), pointer :: attr
       type(Variable), pointer :: var
-      class(*), pointer :: attr_val(:)
 
       fname = this%get_file_name(_RC)
       var => this%get_variable(var_name,_RC)
       _ASSERT(associated(var),"no variable named "//var_name//" in "//fname)
-      attr => var%get_attribute(attr_name,_RC)
-      _ASSERT(associated(attr),"no attribute named "//attr_name//" in "//var_name//" in "//fname)
-      attr_val => attr%get_values()
-      select type(attr_val)
-      type is(integer(kind=INT64))
-         tmp = attr_val
-         attr_int64 = tmp(1)
-      class default
-         _FAIL('unsupported subclass (not int64) for units of attribute named '//attr_name//' in '//var_name//' in '//fname)
-      end select
+      attr_int64 = var%get_attribute_int64(attr_name, rc=status)
+      _ASSERT(status == _SUCCESS, 'failed to get attribute named '//attr_name//' in '//var_name//' in '//fname)
 
       _RETURN(_SUCCESS)
    end function get_var_attr_int64
@@ -246,22 +198,13 @@ function get_var_attr_string(this,var_name,attr_name,rc) result(attr_string)
 
       integer :: status
       character(:), allocatable :: fname
-      type(Attribute), pointer :: attr
       type(Variable), pointer :: var
-      class(*), pointer :: attr_val
 
       fname = this%get_file_name(_RC)
       var => this%get_variable(var_name,_RC)
       _ASSERT(associated(var),"no variable named "//var_name//" in "//fname)
-      attr => var%get_attribute(attr_name,_RC)
-      _ASSERT(associated(attr),"no attribute named "//attr_name//" in "//var_name//" in "//fname)
-      attr_val => attr%get_value()
-      select type(attr_val)
-      type is(character(*))
-         attr_string = attr_val
-      class default
-         _FAIL('unsupported subclass (not string) for units of attribute named '//attr_name//' in '//var_name//' in '//fname)
-      end select
+      attr_string = var%get_attribute_string(attr_name, rc=status)
+      _ASSERT(status == _SUCCESS, 'failed to get attribute named '//attr_name//' in '//var_name//' in '//fname)
 
       _RETURN(_SUCCESS)
    end function get_var_attr_string

base/MAPL_CFIO.F90

@@ -2840,8 +2840,8 @@ subroutine MAPL_CFIOReadBundle ( FILETMPL, TIME, BUNDLE, NOREAD, RC, &
     call fill_grads_template ( filename, filetmpl, &
                            experiment_id=EXPID, nymd=nymd, nhms=nhms, rc=status )
     _VERIFY(STATUS)
-    !call WRITE_PARALLEL("CFIO: Reading " // trim(filename))
-    if (mapl_am_i_root()) write(*,*)"CFIO: Reading ",trim(filename)," at ",nymd," ",nhms
+
+    if (mapl_am_i_root()) write(*,'(a, ": Reading ", a, " at ", i8, " ", i6)') Iam, trim(filename), nymd, nhms
 
 
     cfioIsCreated = .false.