Merge branch 'main' into release/v2.46

GEOS-ESM · Aug 16, 2024 · e0087ba · e0087ba
2 parents e8b8e5e + d444793
commit e0087ba
Show file tree

Hide file tree

Showing 25 changed files with 1,074 additions and 548 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -49,15 +49,16 @@ workflows:
             - docker-hub-creds
           matrix:
             parameters:
-              compiler: [ifort]
+              compiler: [gfortran, ifort]
           baselibs_version: *baselibs_version
           repo: MAPL
           mepodevelop: false
           remove_flap: true
           remove_pflogger: true
           extra_cmake_options: "-DBUILD_WITH_FLAP=OFF -DBUILD_WITH_PFLOGGER=OFF -DBUILD_WITH_FARGPARSE=OFF -DUSE_EXTDATA2G=OFF -DBUILD_SHARED_MAPL=OFF"
           run_unit_tests: true
-          ctest_options: "-L 'ESSENTIAL' --output-on-failure"
+          # 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"
 
       # Run MAPL Tutorials
       - ci/run_mapl_tutorial:

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -3,6 +3,7 @@
 - [ ] New feature (non-breaking change which adds functionality)
 - [ ] Breaking change (fix or feature that would cause existing functionality to change)
 - [ ] Trivial change (affects only documentation or cleanup)
+- [ ] Refactor (no functional changes, no api changes)
 
 ## Checklist
 - [ ] Tested this change with a run of GEOSgcm

diff --git a/Apps/MAPL_GridCompSpecs_ACG.py b/Apps/MAPL_GridCompSpecs_ACG.py
diff --git a/Apps/Regrid_Util.F90 b/Apps/Regrid_Util.F90
@@ -26,6 +26,7 @@ module regrid_util_support_mod
       integer :: deflate, shave
       integer :: quantize_algorithm
       integer :: quantize_level
+      logical :: use_weights
    contains
       procedure :: create_grid
       procedure :: process_command_line
@@ -97,6 +98,7 @@ subroutine process_command_line(this,rc)
     this%deflate=0
     this%quantize_algorithm=1
     this%quantize_level=0
+    this%use_weights = .false.
     nargs = command_argument_count()
     do i=1,nargs
       call get_command_argument(i,str)
@@ -159,6 +161,8 @@ subroutine process_command_line(this,rc)
       case('-quantize_level')
          call get_command_argument(i+1,astr)
          read(astr,*)this%quantize_level
+      case('-file_weights')
+         this%use_weights = .true.
       case('--help')
          if (mapl_am_I_root()) then
 
@@ -413,9 +417,9 @@ subroutine main()
          if (mapl_am_i_root()) write(*,*)'processing timestep from '//trim(filename)
          time = tSeries(i)
          if (support%onlyvars) then
-            call MAPL_Read_bundle(bundle,trim(filename),time=time,regrid_method=support%regridMethod,only_vars=support%vars,_RC)
+            call MAPL_Read_bundle(bundle,trim(filename),time=time,regrid_method=support%regridMethod,only_vars=support%vars,file_weights=support%use_weights, _RC)
          else
-            call MAPL_Read_bundle(bundle,trim(filename),time=time,regrid_method=support%regridMethod,_RC)
+            call MAPL_Read_bundle(bundle,trim(filename),time=time,regrid_method=support%regridMethod,file_weights=support%use_weights, _RC)
          end if
          call t_prof%stop("Read")
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,12 +17,48 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Deprecated
 
-## [2.46.3] - 2024-08-16
+## [2.47.2] - 2024-08-16
 
 ### Fixed
 
 - Fix bug in supporting externally initialized MPI
 
+## [2.47.1] - 2024-07-17
+
+### Fixed
+
+- Fixed bug in FieldSet routines when passing R8 ESMF fields
+
+## [2.47.0] - 2024-06-24
+
+### Added
+
+- Add new option to `Regrid_Util.x` to write and re-use ESMF pregenerated weights
+- If file path length exceeds `ESMF_MAXSTR`, add `_FAIL` in subroutine fglob
+- Add GNU UFS-like CI test
+- Add capability to mangle `LONG_NAME` in ACG with a different prefix
+
+### Changed
+
+- pFIO Clients don't send "Done" message when there is no request
+- Update `components.yaml`
+  - ESMA_cmake v3.46.0
+    - Fix bugs in meson detection
+    - Fix for building on older macOS
+    - Add `esma_add_fortran_submodules` function
+- Updated `checkpoint_simulator` to not create and close file if not writing
+- Update ExtData tests
+  - Add new category of `SLOW` tests that take 10-30 seconds and remove them from the `ESSENTIAL`
+    label run in CI
+  - Remove ExtData1G tests from `ESSENTIAL` label, but run them in the UFS-like CI test
+- Improved timing for station sampler with GHCNd input: used LocStream with CS background, LS with uniform distributed points, and `MPI_GatherV`
+
+### Fixed
+
+- Fixed a bug in `generate_newnxy` in `MAPL_SwathGridFactory.F90` (`NX*NY=Ncore`)
+- Fixes for NVHPC 24.5
+  - Convert `MAPL_GeosatMaskMod` to "interface-in-both-files" submodule style
+
 ## [2.46.2] - 2024-05-31
 
 ### Removed
@@ -42,9 +78,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - Update `FindESMF.cmake` to match that in ESMF 8.6.1
-
-### Changed
-
+- Add timer to the sampler code
 - Set required version of ESMF to 8.6.1
 - Update `components.yaml`
   - ESMA_cmake v3.45.0

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -8,7 +8,7 @@ endif ()
 
 project (
   MAPL
-  VERSION 2.46.3
+  VERSION 2.47.2
   LANGUAGES Fortran CXX C)  # Note - CXX is required for ESMF
 
 # Set the possible values of build type for cmake-gui

diff --git a/Tests/ExtData_Testing_Framework/CMakeLists.txt b/Tests/ExtData_Testing_Framework/CMakeLists.txt
@@ -2,63 +2,78 @@
 string(REPLACE " " ";" MPI_Fortran_LIBRARY_VERSION_LIST ${MPI_Fortran_LIBRARY_VERSION_STRING})
 list(GET MPI_Fortran_LIBRARY_VERSION_LIST 0 MPI_Fortran_LIBRARY_VERSION_FIRSTWORD)
 if(MPI_Fortran_LIBRARY_VERSION_FIRSTWORD MATCHES "Open")
-   list(APPEND MPIEXEC_PREFLAGS "-oversubscribe")
+  list(APPEND MPIEXEC_PREFLAGS "-oversubscribe")
 endif()
 
 file(STRINGS "test_cases/extdata_1g_cases.txt" TEST_CASES_1G)
 
 set(cutoff "7")
 
+# We want to make a list of tests that are slow and can
+# be skipped for ESSENTIAL testing. Most ExtData tests
+# take 1-2 seconds at most, but some take 20-30 seconds.
+set(SLOW_TESTS
+  "case6"
+  "case14"
+  "case15"
+  "case16"
+  "case20"
+  "case22"
+  "case23"
+)
+
 foreach(TEST_CASE ${TEST_CASES_1G})
   if (EXISTS ${CMAKE_CURRENT_LIST_DIR}/test_cases/${TEST_CASE}/nproc.rc)
-     file(READ ${CMAKE_CURRENT_LIST_DIR}/test_cases/${TEST_CASE}/nproc.rc num_procs)
+    file(READ ${CMAKE_CURRENT_LIST_DIR}/test_cases/${TEST_CASE}/nproc.rc num_procs)
   else()
-     set(num_procs "1")
+    set(num_procs "1")
   endif()
   add_test(
-     NAME "ExtData1G_${TEST_CASE}"
-     COMMAND ${CMAKE_COMMAND}
-       -DTEST_CASE=${TEST_CASE}
-       -DMPIEXEC_EXECUTABLE=${MPIEXEC_EXECUTABLE}
-       -DMPIEXEC_NUMPROC_FLAG=${MPIEXEC_NUMPROC_FLAG}
-       -DMY_BINARY_DIR=${CMAKE_BINARY_DIR}/bin
-       -DMPIEXEC_PREFLAGS=${MPIEXEC_PREFLAGS}
-       -DIS_EXTDATA2G=NO
-       -P ${CMAKE_CURRENT_SOURCE_DIR}/run_extdata.cmake
-       )
-  if (${num_procs} LESS ${cutoff})
-     set_tests_properties ("ExtData1G_${TEST_CASE}" PROPERTIES LABELS "EXTDATA1G_SMALL_TESTS")
-     set_tests_properties ("ExtData1G_${TEST_CASE}" PROPERTIES LABELS "ESSENTIAL")
+    NAME "ExtData1G_${TEST_CASE}"
+    COMMAND ${CMAKE_COMMAND}
+      -DTEST_CASE=${TEST_CASE}
+      -DMPIEXEC_EXECUTABLE=${MPIEXEC_EXECUTABLE}
+      -DMPIEXEC_NUMPROC_FLAG=${MPIEXEC_NUMPROC_FLAG}
+      -DMY_BINARY_DIR=${CMAKE_BINARY_DIR}/bin
+      -DMPIEXEC_PREFLAGS=${MPIEXEC_PREFLAGS}
+      -DIS_EXTDATA2G=NO
+      -P ${CMAKE_CURRENT_SOURCE_DIR}/run_extdata.cmake
+  )
+  if (${num_procs} GREATER ${cutoff})
+    set_tests_properties ("ExtData1G_${TEST_CASE}" PROPERTIES LABELS "EXTDATA1G_BIG_TESTS")
+  elseif (${TEST_CASE} IN_LIST SLOW_TESTS)
+    set_tests_properties ("ExtData1G_${TEST_CASE}" PROPERTIES LABELS "EXTDATA1G_SLOW_TESTS")
   else()
-     set_tests_properties ("ExtData1G_${TEST_CASE}" PROPERTIES LABELS "EXTDATA1G_BIG_TESTS")
+    set_tests_properties ("ExtData1G_${TEST_CASE}" PROPERTIES LABELS "EXTDATA1G_SMALL_TESTS")
   endif()
-
 endforeach()
 
 file(STRINGS "test_cases/extdata_2g_cases.txt" TEST_CASES_2G)
 
 foreach(TEST_CASE ${TEST_CASES_2G})
 
   if (EXISTS ${CMAKE_CURRENT_LIST_DIR}/test_cases/${TEST_CASE}/nproc.rc)
-     file(READ ${CMAKE_CURRENT_LIST_DIR}/test_cases/${TEST_CASE}/nproc.rc num_procs)
+    file(READ ${CMAKE_CURRENT_LIST_DIR}/test_cases/${TEST_CASE}/nproc.rc num_procs)
   else()
-     set(num_procs "1")
+    set(num_procs "1")
   endif()
   add_test(
-     NAME "ExtData2G_${TEST_CASE}"
-     COMMAND ${CMAKE_COMMAND}
-       -DTEST_CASE=${TEST_CASE}
-       -DMPIEXEC_EXECUTABLE=${MPIEXEC_EXECUTABLE}
-       -DMPIEXEC_NUMPROC_FLAG=${MPIEXEC_NUMPROC_FLAG}
-       -DMY_BINARY_DIR=${CMAKE_BINARY_DIR}/bin
-       -DMPIEXEC_PREFLAGS=${MPIEXEC_PREFLAGS}
-       -DIS_EXTDATA2G=YES
-       -P ${CMAKE_CURRENT_SOURCE_DIR}/run_extdata.cmake
-     )
-  if (${num_procs} LESS ${cutoff})
-     set_tests_properties ("ExtData2G_${TEST_CASE}" PROPERTIES LABELS "EXTDATA2G_SMALL_TESTS")
-     set_tests_properties ("ExtData2G_${TEST_CASE}" PROPERTIES LABELS "ESSENTIAL")
+    NAME "ExtData2G_${TEST_CASE}"
+    COMMAND ${CMAKE_COMMAND}
+      -DTEST_CASE=${TEST_CASE}
+      -DMPIEXEC_EXECUTABLE=${MPIEXEC_EXECUTABLE}
+      -DMPIEXEC_NUMPROC_FLAG=${MPIEXEC_NUMPROC_FLAG}
+      -DMY_BINARY_DIR=${CMAKE_BINARY_DIR}/bin
+      -DMPIEXEC_PREFLAGS=${MPIEXEC_PREFLAGS}
+      -DIS_EXTDATA2G=YES
+      -P ${CMAKE_CURRENT_SOURCE_DIR}/run_extdata.cmake
+  )
+  if (${num_procs} GREATER ${cutoff})
+    set_tests_properties ("ExtData2G_${TEST_CASE}" PROPERTIES LABELS "EXTDATA2G_BIG_TESTS")
+  elseif (${TEST_CASE} IN_LIST SLOW_TESTS)
+    set_tests_properties ("ExtData2G_${TEST_CASE}" PROPERTIES LABELS "EXTDATA2G_SLOW_TESTS")
   else()
-     set_tests_properties ("ExtData2G_${TEST_CASE}" PROPERTIES LABELS "EXTDATA2G_BIG_TESTS")
+    set_tests_properties ("ExtData2G_${TEST_CASE}" PROPERTIES LABELS "EXTDATA2G_SMALL_TESTS")
+    set_tests_properties ("ExtData2G_${TEST_CASE}" PROPERTIES LABELS "ESSENTIAL")
   endif()
 endforeach()
diff --git a/base/MAPL_ObsUtil.F90 b/base/MAPL_ObsUtil.F90
@@ -941,11 +941,16 @@ subroutine fglob(search_name, filename, rc)     ! give the last name
 
     character(kind=C_CHAR, len=:), allocatable :: c_search_name
     character(kind=C_CHAR, len=512) :: c_filename
-    integer slen
+    integer :: slen, lenmax
 
     c_search_name = trim(search_name)//C_NULL_CHAR
     rc = f_call_c_glob(c_search_name, c_filename, slen)
     filename=""
+    lenmax = len(filename)
+    if (lenmax < slen) then
+       if (MAPL_AM_I_ROOT())  write(6,*) 'pathlen vs filename_max_char_len: ', slen, lenmax
+       _FAIL ('PATHLEN is greater than filename_max_char_len')
+    end if
     if (slen>0) filename(1:slen)=c_filename(1:slen)
 
     return

diff --git a/base/MAPL_SwathGridFactory.F90 b/base/MAPL_SwathGridFactory.F90
@@ -169,12 +169,8 @@ function make_new_grid(this, unusable, rc) result(grid)
 
       _UNUSED_DUMMY(unusable)
 
-      !!if (mapl_am_I_root()) write(6,*) 'MAPL_SwathGridFactory.F90:  bf this%create_basic_grid'
       grid = this%create_basic_grid(_RC)
-      !!if (mapl_am_I_root()) write(6,*) 'MAPL_SwathGridFactory.F90:  af this%create_basic_grid'
       call this%add_horz_coordinates_from_file(grid,_RC)
-      !!if (mapl_am_I_root()) write(6,*) 'MAPL_SwathGridFactory.F90:  af this%add_horz_coordinates_from_file'
-
       _RETURN(_SUCCESS)
    end function make_new_grid
 
@@ -483,6 +479,7 @@ subroutine initialize_from_config_with_prefix(this, config, prefix, unusable, rc
 
       call lgr%debug(' %a  %a', 'CurrTime =', trim(tmp))
 
+
       if ( index(tmp, 'T') /= 0 .OR. index(tmp, '-') /= 0 ) then
          call ESMF_TimeSet(currTime, timeString=tmp, _RC)
       else
@@ -718,6 +715,7 @@ subroutine initialize_from_config_with_prefix(this, config, prefix, unusable, rc
       endif
       ! ims is set at here
       call this%check_and_fill_consistency(_RC)
+      call lgr%debug(' %a  %i5  %i5', 'nx, ny (check_and_fill_consistency) = ', this%nx, this%ny)
 
       _RETURN(_SUCCESS)
 
@@ -864,7 +862,6 @@ subroutine check_and_fill_consistency(this, unusable, rc)
             call this%generate_newnxy(_RC)
          end if
       end if
-
       _RETURN(_SUCCESS)
 
    contains
@@ -1145,43 +1142,48 @@ subroutine generate_newnxy(this,unusable,rc)
       class (KeywordEnforcer), optional, intent(in) :: unusable
       integer, optional, intent(out) :: rc
       integer :: n
+      integer :: j, pet_count
 
       _UNUSED_DUMMY(unusable)
 
+      pet_count = this%nx * this%ny
       n = this%im_world/this%nx
       if (n < 2) then
-         this%nx = generate_new_decomp(this%im_world,this%nx)
-         deallocate(this%ims)
-         allocate(this%ims(0:this%nx-1))
-         call MAPL_DecomposeDim(this%im_world, this%ims, this%nx)
+         do j = this%im_world/2, 1, -1
+            if ( mod(pet_count, j) == 0 .and. this%im_world/j >= 2 ) then
+               exit  ! found a decomposition
+            end if
+         end do
+         this%nx = j
+         this%ny = pet_count/j
       end if
+
       n = this%jm_world/this%ny
       if (n < 2) then
-         this%ny = generate_new_decomp(this%jm_world,this%ny)
-         deallocate(this%jms)
-         allocate(this%jms(0:this%ny-1))
-         call MAPL_DecomposeDim(this%jm_world, this%jms, this%ny)
+         do j = this%jm_world/2, 1, -1
+            if ( mod(pet_count, j) == 0 .and. this%jm_world/j >=2 ) then
+               exit  ! found a decomposition
+            end if
+         end do
+         this%ny = j
+         this%nx = pet_count/j
       end if
 
+      if ( this%im_world/this%nx < 2 .OR. this%jm_world/this%ny < 2 ) then
+         _FAIL ('Algorithm failed')
+      end if
+
+      if (allocated(this%ims)) deallocate(this%ims)
+      allocate(this%ims(0:this%nx-1))
+      call MAPL_DecomposeDim(this%im_world, this%ims, this%nx)
+      if (allocated(this%jms)) deallocate(this%jms)
+      allocate(this%jms(0:this%ny-1))
+      call MAPL_DecomposeDim(this%jm_world, this%jms, this%ny)
+
       _RETURN(_SUCCESS)
 
    end subroutine generate_newnxy
 
-   function generate_new_decomp(im,nd) result(n)
-      integer, intent(in) :: im, nd
-      integer :: n
-      logical :: canNotDecomp
-
-      canNotDecomp = .true.
-      n = nd
-      do while(canNotDecomp)
-         if ( (im/n) < 2) then
-            n = n/2
-         else
-            canNotDecomp = .false.
-         end if
-      enddo
-   end function generate_new_decomp
 
    subroutine init_halo(this, unusable, rc)
       class (SwathGridFactory), target, intent(inout) :: this

diff --git a/benchmarks/io/checkpoint_simulator/README.md b/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`