Merge pull request #2116 from GEOS-ESM/develop

GitFlow: Merge Develop into Main for release
GEOS-ESM · May 1, 2023 · a78c1ce · a78c1ce
2 parents d6b49c8 + 99cd6cc
commit a78c1ce
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -101,12 +101,8 @@ workflows:
           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 -- only to main
+      # Build GEOSgcm -- GCC
       - ci/build:
-          filters:
-            branches:
-              only:
-                - main
           name: build-GEOSgcm-on-<< matrix.compiler >>
           context:
             - docker-hub-creds
@@ -135,12 +131,8 @@ workflows:
           fixture_branch: develop
           checkout_mapl_branch: true
 
-      # Build GEOSldas on gfortran -- only to main
+      # Build GEOSldas on gfortran
       - ci/build:
-          filters:
-            branches:
-              only:
-                - main
           name: build-GEOSldas-on-<< matrix.compiler >>
           context:
             - docker-hub-creds
@@ -154,12 +146,8 @@ workflows:
           fixture_branch: develop
           checkout_mapl_branch: true
 
-      # Build GEOSadas (ifort only, needs a couple develop branches) -- only to main
+      # Build GEOSadas (ifort only, needs a couple develop branches)
       - ci/build:
-          filters:
-            branches:
-              only:
-                - main
           name: build-GEOSadas-on-<< matrix.compiler >>
           context:
             - docker-hub-creds
@@ -172,17 +160,13 @@ workflows:
           checkout_fixture: true
           # This branch on GEOSadas will be used to track subrepos needed
           # for GEOSadas + MAPL develop much like how we do with MAPL 3
-          fixture_branch: feature/mathomp4/mapldevelop
+          #fixture_branch: feature/mathomp4/mapldevelop
           checkout_mapl_branch: true
           mepodevelop: false
           rebuild_procs: 1
 
-      # Run GCM (1 hour, no ExtData) -- only to main
+      # Run GCM (1 hour, no ExtData)
       - ci/run_gcm:
-          filters:
-            branches:
-              only:
-                - main
           name: run-GCM-on-<< matrix.compiler >>
           context:
             - docker-hub-creds
@@ -195,18 +179,14 @@ workflows:
           baselibs_version: *baselibs_version
           bcs_version: *bcs_version
 
-      # Run Coupled GCM (1 hour, no ExtData) -- only to main
+      # Run Coupled GCM (1 hour, no ExtData)
       - ci/run_gcm:
-          filters:
-            branches:
-              only:
-                - main
           name: run-coupled-GCM-on-<< matrix.compiler >>
           context:
             - docker-hub-creds
           matrix:
             parameters:
-              compiler: [ifort]
+              compiler: [gfortran, ifort]
           requires:
             - build-GEOSgcm-on-<< matrix.compiler >>
           repo: GEOSgcm
@@ -215,12 +195,8 @@ workflows:
           gcm_ocean_type: MOM6
           change_layout: false
 
-      # Run MAPL Tutorials -- only to main
+      # Run MAPL Tutorials
       - ci/run_mapl_tutorial:
-          filters:
-            branches:
-              only:
-                - main
           name: run-<< matrix.tutorial_name >>-Tutorial-with-<< matrix.compiler >>
           context:
             - docker-hub-creds

diff --git a/.github/workflows/enforce-labels.yml b/.github/workflows/enforce-labels.yml
@@ -8,7 +8,7 @@ jobs:
   require-label:
     runs-on: ubuntu-latest
     steps:
-      - uses: mheap/github-action-required-labels@v3
+      - uses: mheap/github-action-required-labels@v4
         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@v3
+      - uses: mheap/github-action-required-labels@v4
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:

diff --git a/.github/workflows/trigger-circleci-pipeline-on-release.yml b/.github/workflows/trigger-circleci-pipeline-on-release.yml
@@ -7,6 +7,6 @@ jobs:
     steps:
       - name: CircleCI Trigger on Release
         id: docker-build
-        uses: CircleCI-Public/trigger-circleci-pipeline-action@v1.0.7
+        uses: CircleCI-Public/trigger-circleci-pipeline-action@v1.1.0
         env:
           CCI_TOKEN: ${{ secrets.CCI_TOKEN }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,6 +17,30 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Deprecated
 
+## [2.38.0] - 2023-05-01
+
+### Added
+
+- Printed time to write files to the disk in MultiGroupServer
+- Added merge function to Filemetadata to merge two meta objects
+- Added support for "DEPENDS_ON" and "DEPENDS_ON_CHILDREN" for export_specs. The typical usage on this feature is when the calculation of a variable involves other export variables, either from the same component (DEPENDS_ON specifies the list on such variables), or in the children (in this case the expectation is that all of the children have the SAME export). In both cases MAPL performs automatic allocation of these export variables.
+- Added support for use of pFlogger simTime in logging (only if `-DBUILD_WITH_PFLOGGER=ON`)
+  - Note: Due to bug in pFlogger v1.9.3 and older, you *must* specify a `dateFmt` in your logging configuration file in the
+    formatter when using `simTime` (see [pFlogger issue #90](https://github.com/Goddard-Fortran-Ecosystem/pFlogger/issues/90)).
+    This is fixed in pFlogger v1.10.0
+- Add geom subdirectory and contents for MAPL Geom framework
+
+### Changed
+
+- Add logic to GriddedIO class so that if an uninitialized time object is passed, the resulting file will not depend on time
+- Make sure the pfio files are closed when the time and speed appear in logfile
+- Enable more tests in CircleCI
+
+### Fixed
+
+- Move ioserver_profiler%stop call to the right place
+- Caught an untrapped error condition when writing to NetCDF
+
 ## [2.37.3] - 2023-04-25
 
 ### Fixed
@@ -46,6 +70,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- Fixed message in _ASSERT statement in ESMFL_Mod.F90
 - Fixed bug in CubedSphereGridFactory when constructing a grid from a file
 - Cleaned up cubed-sphere grid factory and NCIO to produce files with consistent capitalization and types for the stretching factor
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -4,7 +4,7 @@ cmake_policy (SET CMP0054 NEW)
 
 project (
   MAPL
-  VERSION 2.37.3
+  VERSION 2.38.0
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 # Set the default build type to release
@@ -202,6 +202,7 @@ add_subdirectory (MAPL_cfio MAPL_cfio_r8)
 add_subdirectory (pfio)
 add_subdirectory (profiler)
 add_subdirectory (generic)
+add_subdirectory (geom)
 add_subdirectory (oomph) # temporary - will rename to generic when done
 add_subdirectory (shared)
 add_subdirectory (include)

diff --git a/base/ApplicationSupport.F90 b/base/ApplicationSupport.F90
@@ -80,6 +80,8 @@ subroutine initialize_pflogger(unusable,comm,logging_config,rc)
       use pflogger, only: StreamHandler, FileHandler, HandlerVector
       use pflogger, only: MpiLock, MpiFormatter
       use pflogger, only: INFO, WARNING
+      use PFL_Formatter, only: get_sim_time
+      use mapl_SimulationTime, only: fill_time_dict
 
       use, intrinsic :: iso_fortran_env, only: OUTPUT_UNIT
 
@@ -109,6 +111,7 @@ subroutine initialize_pflogger(unusable,comm,logging_config,rc)
       end if
 
       call pfl_initialize()
+      get_sim_time => fill_time_dict
 
       if (logging_configuration_file /= '') then
          call logging%load_file(logging_configuration_file)

diff --git a/base/CMakeLists.txt b/base/CMakeLists.txt
@@ -59,10 +59,14 @@ set (srcs
   # tstqsat.F90
   )
 
+# Add SimulationTime.F90 to srcs if we are building with pflogger
+if (BUILD_WITH_PFLOGGER)
+  list(APPEND srcs SimulationTime.F90)
+endif()
 
 esma_add_library(
   ${this} SRCS ${srcs}
-  DEPENDENCIES MAPL.shared MAPL.constants MAPL.profiler MAPL.pfio MAPL_cfio_r4 PFLOGGER::pflogger 
+  DEPENDENCIES MAPL.shared MAPL.constants MAPL.profiler MAPL.pfio MAPL_cfio_r4 PFLOGGER::pflogger
                GFTL_SHARED::gftl-shared-v2 GFTL_SHARED::gftl-shared-v1  GFTL::gftl-v2 GFTL::gftl-v1
                esmf NetCDF::NetCDF_Fortran MPI::MPI_Fortran
   TYPE ${MAPL_LIBRARY_TYPE})

diff --git a/base/ESMFL_Mod.F90 b/base/ESMFL_Mod.F90
@@ -256,7 +256,7 @@ subroutine ESMFL_StateGetField(State, FieldName, Bundle, FieldAlias, RC)
 
       call ESMF_FieldBundleGet(BUNDLE, FIELDNAME=NameInBundle, isPresent=isPresent, rc=STATUS)
       _VERIFY(STATUS)
-      _ASSERT(.not. isPresent, trim(NameInBundle) // ' not found in bundle.')
+      _ASSERT(.not. isPresent, trim(NameInBundle) // ' found in bundle.')
 
 ! Get Field from State
 

diff --git a/base/MAPL_TimeMethods.F90 b/base/MAPL_TimeMethods.F90
@@ -20,20 +20,28 @@ module MAPL_TimeDataMod
      type(ESMF_TimeInterval) :: offset
      character(len=:), allocatable :: funits
      logical :: integer_time
+     logical :: is_initialized = .false.
    contains
      procedure :: add_time_to_metadata
      procedure :: define_time_variable
      procedure :: compute_time_vector
      procedure :: get_start_time
      procedure :: get
      procedure :: setFrequency
+     procedure :: am_i_initialized
   end type timeData
 
   interface timeData
      module procedure new_time_data
   end interface timeData
 contains
 
+  function am_i_initialized(this) result(logical_temp)
+     logical  :: logical_temp
+     class(TimeData), intent(inout) :: this
+     logical_temp = this%is_initialized
+  end
+
   function new_time_data(clock,ntime,frequency,offset,funits,integer_time,rc) result(tData)
     type(timeData) :: tData
     type(ESMF_Clock),intent(inout) :: clock
@@ -44,6 +52,7 @@ function new_time_data(clock,ntime,frequency,offset,funits,integer_time,rc) resu
     logical, optional, intent(in) :: integer_time
     integer, optional, intent(Out) :: rc
 
+    tData%is_initialized = .true.
     tdata%clock=clock
     tdata%ntime=ntime
     tdata%frequency=frequency
@@ -230,16 +239,17 @@ subroutine add_time_to_metadata(this,metadata,rc)
     integer :: tdim
     integer :: status
 
-    if (this%ntime==-1) then
-       tdim = pFIO_UNLIMITED
-    else
-       tdim = this%ntime
+    if (this%is_initialized) then
+       if (this%ntime==-1) then
+          tdim = pFIO_UNLIMITED
+       else
+          tdim = this%ntime
+       end if
+       call metadata%add_dimension('time',tdim)
+       v = this%define_time_variable(_RC)
+       call metadata%add_variable('time',v,_RC)
     end if
-    call metadata%add_dimension('time',tdim)
-    v = this%define_time_variable(rc=status)
-    _VERIFY(status)
-    call metadata%add_variable('time',v,rc=status)
-    _VERIFY(status)
+    _RETURN(_SUCCESS)
 
   end subroutine add_time_to_metadata
 

diff --git a/base/ServerManager.F90 b/base/ServerManager.F90
@@ -282,15 +282,16 @@ end subroutine initialize
    subroutine finalize(this,rc)
       class(ServerManager), intent(inout) :: this
       integer, optional, intent(out) :: rc
+      integer :: status
       ! reporting here is for client_server in the same process which don't call start()
       ! problem here: all servers should coordinate to report one by one to avoid messy output
       if (associated(this%i_server)) then
-         call this%i_server%report_profile()
+         call this%i_server%report_profile(_RC)
          deallocate(this%i_server)
       endif
 
       if (associated(this%o_server)) then
-         call this%o_server%report_profile()
+         call this%o_server%report_profile(_RC)
          deallocate(this%o_server)
       endif
       call this%directory_service%free_directory_resources()

diff --git a/base/SimulationTime.F90 b/base/SimulationTime.F90
@@ -0,0 +1,52 @@
+! This module allows pFlogger to access the current simulation time in
+! MAPL and thereby annotate log entries with the current simulation
+! time.  To accomplish this, the module hold a (shallow) copy
+! of the clock in CapGridComp.
+
+module mapl_SimulationTime
+   use pflogger, only: StringUnlimitedMap
+   use ESMF
+   implicit none
+   private
+
+   public :: set_reference_clock
+   public :: fill_time_dict
+
+   type(ESMF_Clock), save :: reference_clock
+
+contains
+
+   subroutine set_reference_clock(clock)
+      type(ESMF_Clock), intent(in) :: clock
+      reference_clock = clock
+   end subroutine set_reference_clock
+
+   subroutine fill_time_dict(dict)
+      type (StringUnlimitedmap), intent(out) :: dict
+
+      integer :: status
+      type(ESMF_Time) :: time
+
+      integer :: yy, mm, dd, h, m, s
+
+      call ESMF_ClockValidate(reference_clock, rc=status)
+      if (status /= 0) error stop "Must pass reference via set_reference_clock() before use."
+
+      call ESMF_ClockGet(reference_clock, currTime=time, rc=status)
+      if (status /= 0) error stop "could not get current time in SimulationTime.F90"
+
+      call ESMF_TimeGet(time, yy=yy, mm=mm, dd=dd, h=h, m=m, s=s, rc=status)
+      if (status /= 0) error stop "Failed to get data from ESMF_TimeGet()."
+
+      call dict%insert('Y',yy)
+      call dict%insert('M',mm)
+      call dict%insert('D',dd)
+      call dict%insert('HH',h)
+      call dict%insert('MM',m)
+      call dict%insert('SS',s)
+      call dict%insert('MS',0)
+
+   end subroutine Fill_Time_Dict
+
+end module mapl_SimulationTime
+