Merge branch 'develop' into feature/wjiang/no_done

.circleci/config.yml

@@ -49,7 +49,7 @@ workflows:
             - docker-hub-creds
           matrix:
             parameters:
-              compiler: [ifort]
+              compiler: [gfortran, ifort]
           baselibs_version: *baselibs_version
           repo: MAPL
           mepodevelop: false

CHANGELOG.md

@@ -9,25 +9,36 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- Add GNU UFS-like CI test
+
 ### Changed
 
 - pFIO Clients don't send "Done" message when there is no request
 - Update `components.yaml`
   - ESMA_cmake v3.45.1
     - Fix bug in meson detection
+- Updated `checkpoint_simulator` to not create and close file if not writing
 
 ### Fixed
 
 ### Removed
 
 ### Deprecated
 
+## [2.46.1] - 2024-05-10
+
+## Fixed
+
+- Update `components.yaml` to avoid f2py error with python 3.11
+  - ESMA_cmake v3.45.1
+    - Fix bug in meson detection
+
 ## [2.46.0] - 2024-05-02
 
 ### Added
 
 - Update `FindESMF.cmake` to match that in ESMF 8.6.1
-
+- Add timer to the sampler code
 ### Changed
 
 - Set required version of ESMF to 8.6.1

CMakeLists.txt

@@ -8,7 +8,7 @@ endif ()
 
 project (
   MAPL
-  VERSION 2.45.0
+  VERSION 2.46.1
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 # Set the possible values of build type for cmake-gui

benchmarks/io/checkpoint_simulator/README.md

@@ -5,15 +5,15 @@ The code has the following options and needs an ESMF rc file named checkpoint\_b
 - "NX:" the x distribution for each face
 - "NY:" the y distribution for each face
 - "IM\_WORLD:" the cube resolution
-- "LM:" the nubmer of levels
+- "LM:" the number of levels
 - "NUM\_WRITERS:" the number of writing processes either to a single or independent files
 - "NUM\_ARRAYS:" the number of 3D variables to write to the file
 - "CHUNK:" whether to chunk, default true
 - "GATHER\_3D:" gather all levels at once (default is false which means a level at a time is gathered)
 - "SPLIT\_FILE:" default false, if true, each writer writes to and independent file
 - "WRITE\_BARRIER:" default false, add a barrier before each write to for synchronization
 - "DO\_WRITES:" default true, if false skips writing (so just an mpi test at that point)
-- "NTRIAL:" default 1, the number of trials to make writing
+- "NTRIALS:" default 1, the number of trials to make writing
 - "RANDOM\_DATA:" default true, if true will arrays with random data, if false sets the array to the rank of the process
 
-Note that whatever you set NX and NY to the program must be run on 6*NY*NY processors and the number of writers must evenly divide 6*NY
+Note that whatever you set NX and NY to the program must be run on `6*NX*NY` processors and the number of writers must evenly divide `6*NY`

benchmarks/io/checkpoint_simulator/checkpoint_simulator.F90

@@ -55,7 +55,7 @@ module mapl_checkpoint_support_mod
          procedure :: write_level
          procedure :: write_variable
          procedure :: reset
-   end type 
+   end type
 
 contains
 
@@ -98,7 +98,7 @@ subroutine set_parameters(this,config_file)
       this%mpi_time = 0.0
       call MPI_COMM_SIZE(MPI_COMM_WORLD,comm_size,status)
       if (comm_size /= (this%nx*this%ny*6)) call MPI_Abort(mpi_comm_world,error_code,status)
-      
+
       contains
 
       function get_logical_key(config,label,default_val) result(val)
@@ -115,7 +115,7 @@ function get_logical_key(config,label,default_val) result(val)
             val = default_val
          end if
       end function
-      
+
       function get_integer_key(config,label,default_val) result(val)
          integer :: val
          type(ESMF_Config), intent(Inout)  :: config
@@ -130,7 +130,7 @@ function get_integer_key(config,label,default_val) result(val)
             val = default_val
          end if
       end function
-      
+
    end subroutine
 
    subroutine reset(this)
@@ -144,7 +144,7 @@ subroutine reset(this)
       this%time_writing = 0.d0
       this%mpi_time = 0.0
    end subroutine
-      
+
    function compute_decomposition(this,axis) result(decomp)
       integer, allocatable :: decomp(:)
       class(test_support), intent(inout) :: this
@@ -172,7 +172,7 @@ subroutine allocate_n_arrays(this,im,jm)
       class(test_support), intent(inout) :: this
       integer, intent(in) :: im
       integer, intent(in) :: jm
-      
+
       integer :: n,rank,status
       character(len=3) :: formatted_int
       integer :: seed_size
@@ -201,7 +201,7 @@ subroutine create_arrays(this)
       integer, allocatable :: ims(:),jms(:)
       integer :: rank, status,comm_size,n,i,j,rank_counter,offset,index_offset
 
-      call MPI_Comm_Rank(MPI_COMM_WORLD,rank,status) 
+      call MPI_Comm_Rank(MPI_COMM_WORLD,rank,status)
       call MPI_Comm_Size(MPI_COMM_WORLD,comm_size,status)
       allocate(this%bundle(this%num_arrays))
       ims = this%compute_decomposition(axis=1)
@@ -244,13 +244,13 @@ subroutine create_arrays(this)
                rank_counter = rank_counter + 1
            enddo
         enddo
-     enddo 
-      
+     enddo
+
   end subroutine
 
   subroutine create_communicators(this)
      class(test_support), intent(inout) :: this
- 
+
      integer :: myid,status,nx0,ny0,color,j,ny_by_writers,local_ny,key
 
      local_ny = this%ny*6
@@ -280,7 +280,7 @@ subroutine create_communicators(this)
 
      call MPI_BARRIER(mpi_comm_world,status)
 
-     
+
   end subroutine
 
   subroutine close_file(this)
@@ -344,7 +344,7 @@ subroutine create_file(this)
            status = nf90_def_dim(this%ncid,"lon",this%im_world,xdim)
            if (this%split_file) then
               y_size = this%im_world*6/this%num_writers
-           else 
+           else
               y_size = this%im_world*6
            end if
            status = nf90_def_dim(this%ncid,"lat",y_size,ydim)
@@ -384,7 +384,7 @@ subroutine create_file(this)
   subroutine write_file(this)
      class(test_support), intent(inout) :: this
      integer :: status,i,l
-    
+
      integer(kind=INT64) :: sub_start,sub_end
 
      call MPI_BARRIER(MPI_COMM_WORLD,status)
@@ -619,7 +619,7 @@ subroutine write_level(this,var_name,local_var,z_index)
           io_time = end_time-start_time
           this%data_volume = this%data_volume+byte_to_mega*4.d0*size(var,kind=INT64)
           this%time_writing = this%time_writing + real(io_time,kind=REAL64)/real(count_rate,kind=REAL64)
-          
+
           deallocate(VAR, stat=status)
 
        endif ! myiorank
@@ -676,13 +676,13 @@ program checkpoint_tester
 
       call system_clock(count=start_write)
       call MPI_Barrier(MPI_COMM_WORLD,status)
-      call support%create_file()
+      if (support%do_writes) call support%create_file()
       call MPI_Barrier(MPI_COMM_WORLD,status)
 
       call support%write_file()
       call MPI_Barrier(MPI_COMM_WORLD,status)
 
-      call support%close_file()
+      if (support%do_writes) call support%close_file()
       call MPI_Barrier(MPI_COMM_WORLD,status)
 
       call system_clock(count=end_time)
@@ -707,7 +707,7 @@ program checkpoint_tester
          all_proc_throughput(i) = real(support%num_writers,kind=REAL32)*average_volume/average_time
       end if
    enddo
-       
+
    call system_clock(count=end_app)
    application_time = real(end_app - start_app,kind=REAL64)/real(count_rate,kind=REAL64)
    if (rank == 0) then
@@ -741,7 +741,7 @@ program checkpoint_tester
       std_fs_throughput = sqrt(std_fs_throughput/real(support%n_trials,kind=REAL64))
       write(*,'(G16.8,G16.8,G16.8,G16.8)')mean_throughput,std_throughput,mean_fs_throughput,std_fs_throughput
    end if
-   
-     
+
+
    call MPI_Finalize(status)
 end program

gridcomps/History/MAPL_HistoryCollection.F90

@@ -9,7 +9,7 @@ module MAPL_HistoryCollectionMod
   use MAPL_VerticalDataMod
   use MAPL_TimeDataMod
   use HistoryTrajectoryMod
-  use MaskSamplerGeosatMod  
+  use MaskSamplerGeosatMod
   use StationSamplerMod
   use gFTL_StringStringMap
   use MAPL_EpochSwathMod

gridcomps/History/MAPL_HistoryGridComp.F90

@@ -2422,7 +2422,7 @@ subroutine Initialize ( gc, import, dumexport, clock, rc )
              list(n)%timeInfo = TimeData(clock,tm,MAPL_nsecf(list(n)%frequency),IntState%stampoffset(n),integer_time=intstate%integer_time)
           end if
           if (list(n)%timeseries_output) then
-             list(n)%trajectory = HistoryTrajectory(cfg,string,clock,_RC)
+             list(n)%trajectory = HistoryTrajectory(cfg,string,clock,genstate=GENSTATE,_RC)
              call list(n)%trajectory%initialize(items=list(n)%items,bundle=list(n)%bundle,timeinfo=list(n)%timeInfo,vdata=list(n)%vdata,_RC)
              IntState%stampoffset(n) = list(n)%trajectory%epoch_frequency
           elseif (list(n)%sampler_spec == 'mask') then
@@ -3451,11 +3451,14 @@ subroutine Run ( gc, import, export, clock, rc )
   ! swath only
    epoch_swath_grid_case: do n=1,nlist
       call MAPL_TimerOn(GENSTATE,trim(list(n)%collection))
-      call MAPL_TimerOn(GENSTATE,"SwathGen")
       if (index(trim(list(n)%output_grid_label), 'SwathGrid') > 0) then
+         call MAPL_TimerOn(GENSTATE,"Swath")
+         call MAPL_TimerOn(GENSTATE,"RegridAccum")
          call Hsampler%regrid_accumulate(list(n)%xsampler,_RC)
+         call MAPL_TimerOff(GENSTATE,"RegridAccum")
 
          if( ESMF_AlarmIsRinging ( Hsampler%alarm ) ) then
+            call MAPL_TimerOn(GENSTATE,"RegenGriddedio")
             create_mode = PFIO_NOCLOBBER ! defaut no overwrite
             if (intState%allow_overwrite) create_mode = PFIO_CLOBBER
             ! add time to items
@@ -3473,12 +3476,13 @@ subroutine Run ( gc, import, export, clock, rc )
             call list(n)%mGriddedIO%destroy(_RC)
             call list(n)%mGriddedIO%CreateFileMetaData(list(n)%items,list(n)%xsampler%acc_bundle,timeinfo_uninit,vdata=list(n)%vdata,global_attributes=global_attributes,_RC)
             call list(n)%items%pop_back()
-
             collection_id = o_Clients%add_hist_collection(list(n)%mGriddedIO%metadata, mode = create_mode)
             call list(n)%mGriddedIO%set_param(write_collection_id=collection_id)
+            call MAPL_TimerOff(GENSTATE,"RegenGriddedio")
          endif
+         call MAPL_TimerOff(GENSTATE,"Swath")
       end if
-      call MAPL_TimerOff(GENSTATE,"SwathGen")
+
       call MAPL_TimerOff(GENSTATE,trim(list(n)%collection))
    end do epoch_swath_grid_case
 
@@ -3525,7 +3529,7 @@ subroutine Run ( gc, import, export, clock, rc )
                ! it's tempting to use the variable "oneMonth" but it does not work
                ! instead we compute the differece between
                ! thisMonth and lastMonth and as a new timeInterval
-
+               !
                call ESMF_ClockGet(clock,currTime=current_time,_RC)
                call ESMF_TimeIntervalSet( oneMonth, MM=1, _RC)
                lastMonth = current_time - oneMonth
@@ -3645,6 +3649,7 @@ subroutine Run ( gc, import, export, clock, rc )
          if (.not.list(n)%timeseries_output .AND. &
               list(n)%sampler_spec /= 'station' .AND. &
               list(n)%sampler_spec /= 'mask') then
+
             IOTYPE: if (list(n)%unit < 0) then    ! CFIO
                call list(n)%mGriddedIO%bundlepost(list(n)%currentFile,oClients=o_Clients,_RC)
             else
@@ -3691,14 +3696,24 @@ subroutine Run ( gc, import, export, clock, rc )
             end if IOTYPE
          end if
 
+
          if (list(n)%sampler_spec == 'station') then
             call ESMF_ClockGet(clock,currTime=current_time,_RC)
+            call MAPL_TimerOn(GENSTATE,"Station")
+            call MAPL_TimerOn(GENSTATE,"AppendFile")
             call list(n)%station_sampler%append_file(current_time,_RC)
+            call MAPL_TimerOff(GENSTATE,"AppendFile")
+            call MAPL_TimerOff(GENSTATE,"Station")
          elseif (list(n)%sampler_spec == 'mask') then
             call ESMF_ClockGet(clock,currTime=current_time,_RC)
+            call MAPL_TimerOn(GENSTATE,"Mask")
+            call MAPL_TimerOn(GENSTATE,"AppendFile")
             call list(n)%mask_sampler%append_file(current_time,_RC)
+            call MAPL_TimerOff(GENSTATE,"AppendFile")
+            call MAPL_TimerOff(GENSTATE,"Mask")
          endif
 
+
       endif OUTTIME
 
       if( NewSeg(n) .and. list(n)%unit /= 0 .and. list(n)%duration /= 0 ) then
@@ -3724,20 +3739,20 @@ subroutine Run ( gc, import, export, clock, rc )
   ! swath only
    epoch_swath_regen_grid: do n=1,nlist
       call MAPL_TimerOn(GENSTATE,trim(list(n)%collection))
-      call MAPL_TimerOn(GENSTATE,"Swath regen")
       if (index(trim(list(n)%output_grid_label), 'SwathGrid') > 0) then
+         call MAPL_TimerOn(GENSTATE,"Swath")
          if( ESMF_AlarmIsRinging ( Hsampler%alarm ) .and. .not. ESMF_AlarmIsRinging(list(n)%end_alarm) ) then
-
+            call MAPL_TimerOn(GENSTATE,"RegenGrid")
             key_grid_label = list(n)%output_grid_label
             call Hsampler%destroy_rh_regen_ogrid ( key_grid_label, IntState%output_grids, list(n)%xsampler, _RC )
-
             pgrid => IntState%output_grids%at(trim(list(n)%output_grid_label))
             call list(n)%xsampler%Create_bundle_RH(list(n)%items,list(n)%bundle,Hsampler%tunit, &
                  ogrid=pgrid,vdata=list(n)%vdata,_RC)
             if( MAPL_AM_I_ROOT() )  write(6,'(//)')
+            call MAPL_TimerOff(GENSTATE,"RegenGrid")
          endif
+         call MAPL_TimerOff(GENSTATE,"Swath")
       end if
-      call MAPL_TimerOff(GENSTATE,"Swath regen")
       call MAPL_TimerOff(GENSTATE,trim(list(n)%collection))
    end do epoch_swath_regen_grid
 
@@ -3754,16 +3769,24 @@ subroutine Run ( gc, import, export, clock, rc )
    WRITELOOP: do n=1,nlist
 
       call MAPL_TimerOn(GENSTATE,trim(list(n)%collection))
-      call MAPL_TimerOn(GENSTATE,"Write Timeseries")
+
       if (list(n)%timeseries_output) then
+         call MAPL_TimerOn(GENSTATE,"Trajectory")
+         call MAPL_TimerOn(GENSTATE,"RegridAccum")
          call list(n)%trajectory%regrid_accumulate(_RC)
+         call MAPL_TimerOff(GENSTATE,"RegridAccum")
          if( ESMF_AlarmIsRinging ( list(n)%trajectory%alarm ) ) then
+            call MAPL_TimerOn(GENSTATE,"AppendFile")
             call list(n)%trajectory%append_file(current_time,_RC)
             call list(n)%trajectory%close_file_handle(_RC)
+            call MAPL_TimerOff(GENSTATE,"AppendFile")
             if ( .not. ESMF_AlarmIsRinging(list(n)%end_alarm) ) then
+               call MAPL_TimerOn(GENSTATE,"RegenLS")
                call list(n)%trajectory%destroy_rh_regen_LS (_RC)
+               call MAPL_TimerOff(GENSTATE,"RegenLS")
             end if
          end if
+         call MAPL_TimerOff(GENSTATE,"Trajectory")
       end if
 
       if( Writing(n) .and. list(n)%unit < 0) then
@@ -3772,7 +3795,6 @@ subroutine Run ( gc, import, export, clock, rc )
 
       end if
 
-      call MAPL_TimerOff(GENSTATE,"Write Timeseries")
       call MAPL_TimerOff(GENSTATE,trim(list(n)%collection))
    enddo WRITELOOP