Mac ci

.github/actions/macos-setup/action.yml

@@ -0,0 +1,23 @@
+# This file is part of MOM6, the Modular Ocean Model version 6.
+# See the LICENSE file for licensing information.
+# SPDX-License-Identifier: Apache-2.
+
+name: 'install-macos-prerequisites'
+
+description: 'Install prerequisites for Mac OS compilation'
+
+runs:
+  using: 'composite'
+
+  steps:
+    - name: Install macOS packages
+      shell: bash
+      run: |
+        echo "::group::Install packages"
+        brew reinstall gcc
+        brew install automake
+        brew install netcdf
+        brew install netcdf-fortran
+        brew install openmpi
+        brew install libyaml
+        echo "::endgroup::"

.github/workflows/github_cmake_macos.yml

@@ -0,0 +1,33 @@
+name: CMake build and unit tests on MacOS
+
+on:
+  push:
+    branches:
+    - main
+
+jobs:
+  build:
+    runs-on: macOS-latest
+    strategy:
+      matrix:
+        libyaml-flag: [ "", -DWITH_YAML=on ]
+        build-type: [ "-DCMAKE_BUILD_TYPE=Release", "-DCMAKE_BUILD_TYPE=Debug" ]
+    env:
+      CMAKE_FLAGS: "${{ matrix.build-type }} ${{ matrix.libyaml-flag }}"
+      EXCLUDE_TESTS: "test_mpp_nesting|test_mpp_clock_begin_end_id|test_time_*"
+      CC: gcc-15
+      FC: gfortran
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ./.github/actions/macos-setup/
+      - name: Generate makefiles with CMake
+        run: |
+          mkdir build
+          cd build
+          brew shellenv
+          cmake $CMAKE_FLAGS ..
+      - name: Build the library
+        run: |
+          brew shellenv
+          make -j -C build
+

CMakeLists.txt

@@ -314,6 +314,10 @@ foreach(kind ${kinds})
     target_link_libraries(${libTgt}_c PRIVATE OpenMP::OpenMP_C)
   endif()
 
+  if(YAML_FOUND)
+    target_link_libraries(${libTgt}_c PRIVATE PkgConfig::YAML)
+  endif()
+
   # Fortran
   add_library(${libTgt}_f OBJECT ${fms_fortran_src_files})
 
@@ -459,6 +463,10 @@ if(NOT kinds)
       target_link_libraries(${libTgt}_c PRIVATE OpenMP::OpenMP_C)
     endif()
 
+    if(YAML_FOUND)
+      target_link_libraries(${libTgt}_c PRIVATE PkgConfig::YAML)
+    endif()
+
     # Fortran
     add_library(${libTgt}_f OBJECT ${fms_fortran_src_files})
 
@@ -717,6 +725,7 @@ if(UNIT_TESTS)
     test_fms/fms/test_fms.F90
     test_fms/interpolator/test_interpolator.F90
     test_fms/mpp/test_clock_init.F90
+    test_fms/mpp/test_corner_mosaic.F90
     test_fms/mpp/test_domains_simple.F90
     test_fms/mpp/test_domains_utility_mod.F90
     test_fms/mpp/test_global_arrays.F90

diag_manager/diag_output.F90

@@ -48,7 +48,6 @@ MODULE diag_output_mod
   use mpp_domains_mod, only: mpp_get_UG_io_domain
   use mpp_domains_mod, only: mpp_get_UG_domain_npes
   use mpp_domains_mod, only: mpp_get_UG_domain_pelist
-  use mpp_mod,         only: mpp_gather
   use mpp_mod,         only: uppercase,lowercase
   use fms2_io_mod
 

diag_manager/fms_diag_axis_object.F90

@@ -458,7 +458,13 @@ subroutine write_axis_data(this, fms2io_fileobj, parent_axis)
       if (present(parent_axis)) then
         select type(parent_axis)
         type is (fmsDiagFullAxis_type)
-          call write_data(fms2io_fileobj, this%subaxis_name, parent_axis%axis_data(i:j))
+          ! Added this select type so the the data is indexed correctly
+          select type (vardata => parent_axis%axis_data)
+          type is (real(kind=r8_kind))
+              call write_data(fms2io_fileobj, this%subaxis_name, vardata(i:j))
+          type is (real(kind=r4_kind))
+              call write_data(fms2io_fileobj, this%subaxis_name, vardata(i:j))
+          end select
         end select
       endif
     type is (fmsDiagDiurnalAxis_type)
@@ -881,8 +887,10 @@ subroutine fill_subaxis(this, starting_index, ending_index, axis_id, parent_id,
     if (present(nz_subaxis)) nsubaxis = nz_subaxis
 
     this%axis_id = axis_id
-    this%starting_index = starting_index
-    this%ending_index = ending_index
+
+    ! The min and max were added here to support axis that are both increasing and decreasing
+    this%starting_index = min(starting_index, ending_index)
+    this%ending_index = max(starting_index, ending_index)
     this%parent_axis_id = parent_id
     write(nsubaxis_char, '(i2.2)')  nsubaxis
     this%subaxis_name = trim(parent_axis_name)//"_sub"//nsubaxis_char

fms2_io/include/compressed_write.inc

@@ -137,7 +137,7 @@ subroutine compressed_write_1d(fileobj, variable_name, cdata, unlim_dim_level, &
         call error("unsupported variable type: "//trim(append_error_msg))
      end select
   else
-     select type(cdata)
+    select type(cdata)
       type is (integer(kind=i4_kind))
         allocate(buf_i4_kind(1))
       type is (integer(kind=i8_kind))
@@ -148,7 +148,7 @@ subroutine compressed_write_1d(fileobj, variable_name, cdata, unlim_dim_level, &
         allocate(buf_r8_kind(1))
       class default
         call error("unsupported variable type: "//trim(append_error_msg))
-     end select
+    end select
   endif
 
   !Gather the data onto the I/O root and write it out.
@@ -253,6 +253,19 @@ subroutine compressed_write_2d(fileobj, variable_name, cdata, unlim_dim_level, &
       class default
         call error("unsupported variable type: "//trim(append_error_msg))
      end select
+  else
+    select type(cdata)
+      type is (integer(kind=i4_kind))
+        allocate(buf_i4_kind(1, 1))
+      type is (integer(kind=i8_kind))
+        allocate(buf_i8_kind(1, 1))
+      type is (real(kind=r4_kind))
+        allocate(buf_r4_kind(1, 1))
+      type is (real(kind=r8_kind))
+        allocate(buf_r8_kind(1, 1))
+      class default
+        call error("unsupported variable type: "//trim(append_error_msg))
+    end select
   endif
 
   c(:) = 1
@@ -376,7 +389,20 @@ subroutine compressed_write_3d(fileobj, variable_name, cdata, unlim_dim_level, &
         call allocate_array(buf_r8_kind, e)
       class default
         call error("unsupported variable type: "//trim(append_error_msg))
-     end select
+    end select
+  else
+    select type(cdata)
+      type is (integer(kind=i4_kind))
+        allocate(buf_i4_kind(1, 1, 1))
+      type is (integer(kind=i8_kind))
+        allocate(buf_i8_kind(1, 1, 1))
+      type is (real(kind=r4_kind))
+        allocate(buf_r4_kind(1, 1, 1))
+      type is (real(kind=r8_kind))
+        allocate(buf_r8_kind(1, 1, 1))
+      class default
+        call error("unsupported variable type: "//trim(append_error_msg))
+    end select
   endif
 
   c(:) = 1

fms2_io/include/domain_read.inc

@@ -119,6 +119,7 @@ subroutine domain_read_2d(fileobj, variable_name, vdata, unlim_dim_level, &
   integer                 :: xgsize                !< Size of global x io domain
   integer                 :: ygbegin               !< Starting y index of global io domain
   integer                 :: ygsize                !< Size of global y io domain
+  integer                 :: dim_order(2)          !< Order of the dimensions
   type(domain2d), pointer :: io_domain             !< pointer to the io_domain
 
   !< The global data is only allocated by the io root PEs
@@ -164,14 +165,6 @@ subroutine domain_read_2d(fileobj, variable_name, vdata, unlim_dim_level, &
     return
   endif
 
-  if (xdim_index .ne. 1 .or. ydim_index .ne. 2) then
-    ! This is a KLUDGE
-    ! mpp_scatter assumes that the variable is (x,y), if that is not the case it remaps the data
-    ! to a 4D array and calls domain_read_4d which does not use mpp_scatter yet
-    vdata_dummy(1:size(vdata,1),1:size(vdata,2), 1:1, 1:1) => vdata(:,:)
-    call domain_read_4d(fileobj, variable_name, vdata_dummy, unlim_dim_level)
-    return
-  endif
   io_domain => mpp_get_io_domain(fileobj%domain)
   c(:) = 1
   e(:) = shape(vdata)
@@ -240,29 +233,32 @@ subroutine domain_read_2d(fileobj, variable_name, vdata, unlim_dim_level, &
   e(xdim_index) = xc_size
   e(ydim_index) = yc_size
 
+  dim_order(xdim_index) = 1
+  dim_order(ydim_index) = 2
+
   select type(vdata)
   type is (integer(kind=i4_kind))
     call allocate_array(buf_i4_kind_pe, e)
     call mpp_scatter(isc-xgbegin+1, isc+xc_size-xgbegin, jsc-ygbegin+1, jsc+yc_size-ygbegin, fileobj%pelist, &
-                     buf_i4_kind_pe, buf_i4_kind, fileobj%is_root)
+                     buf_i4_kind_pe, buf_i4_kind, dim_order, fileobj%is_root)
     call put_array_section(buf_i4_kind_pe, vdata, c, e)
     deallocate(buf_i4_kind_pe)
   type is (integer(kind=i8_kind))
     call allocate_array(buf_i8_kind_pe, e)
     call mpp_scatter(isc-xgbegin+1, isc+xc_size-xgbegin, jsc-ygbegin+1, jsc+yc_size-ygbegin, fileobj%pelist, &
-                     buf_i8_kind_pe, buf_i8_kind, fileobj%is_root)
+                     buf_i8_kind_pe, buf_i8_kind, dim_order, fileobj%is_root)
     call put_array_section(buf_i8_kind_pe, vdata, c, e)
     deallocate(buf_i8_kind_pe)
   type is (real(kind=r4_kind))
     call allocate_array(buf_r4_kind_pe, e)
     call mpp_scatter(isc-xgbegin+1, isc+xc_size-xgbegin, jsc-ygbegin+1, jsc+yc_size-ygbegin, fileobj%pelist, &
-                     buf_r4_kind_pe, buf_r4_kind, fileobj%is_root)
+                     buf_r4_kind_pe, buf_r4_kind, dim_order, fileobj%is_root)
     call put_array_section(buf_r4_kind_pe, vdata, c, e)
     deallocate(buf_r4_kind_pe)
   type is (real(kind=r8_kind))
     call allocate_array(buf_r8_kind_pe, e)
     call mpp_scatter(isc-xgbegin+1, isc+xc_size-xgbegin, jsc-ygbegin+1, jsc+yc_size-ygbegin, fileobj%pelist, &
-                     buf_r8_kind_pe, buf_r8_kind, fileobj%is_root)
+                     buf_r8_kind_pe, buf_r8_kind, dim_order, fileobj%is_root)
     call put_array_section(buf_r8_kind_pe, vdata, c, e)
     deallocate(buf_r8_kind_pe)
   class default
@@ -304,6 +300,7 @@ subroutine domain_read_3d(fileobj, variable_name, vdata, unlim_dim_level, &
 
   integer                 :: xdim_index            !< The index of the variable that is the x dimension
   integer                 :: ydim_index            !< The index of the variable that is the y dimension
+  integer                 :: zdim_index            !< The index of the variable that is the z dimension
   integer                 :: xpos                  !< The position of the x axis
   integer                 :: ypos                  !< The position of the y axis
   integer                 :: i                     !< For do loops
@@ -320,6 +317,7 @@ subroutine domain_read_3d(fileobj, variable_name, vdata, unlim_dim_level, &
   integer                 :: xgsize                !< Size of global x io domain
   integer                 :: ygbegin               !< Starting y index of global io domain
   integer                 :: ygsize                !< Size of global y io domain
+  integer                 :: dim_order(3)          !< Order of the dimensions
   type(domain2d), pointer :: io_domain             !< pointer to the io_domain
 
   !< The global data is only allocated by the io root PEs
@@ -365,14 +363,6 @@ subroutine domain_read_3d(fileobj, variable_name, vdata, unlim_dim_level, &
     return
   endif
 
-  if (xdim_index .ne. 1 .or. ydim_index .ne. 2) then
-    ! This is a KLUDGE
-    ! mpp_scatter assumes that the variable is (x,y), if that is not the case it remaps the data
-    ! to a 4D array and calls domain_read_4d which does not use mpp_scatter yet
-    vdata_dummy(1:size(vdata,1),1:size(vdata,2), 1:size(vdata,3), 1:1) => vdata(:,:,:)
-    call domain_read_4d(fileobj, variable_name, vdata_dummy, unlim_dim_level)
-    return
-  endif
   io_domain => mpp_get_io_domain(fileobj%domain)
   c(:) = 1
   if (present(corner)) c = corner
@@ -444,29 +434,36 @@ subroutine domain_read_3d(fileobj, variable_name, vdata, unlim_dim_level, &
   e(xdim_index) = xc_size
   e(ydim_index) = yc_size
 
+  ! Calculate the index of the z dimension
+  zdim_index = 6 - xdim_index - ydim_index
+
+  dim_order(xdim_index) = 1
+  dim_order(ydim_index) = 2
+  dim_order(zdim_index) = 3
+
   select type(vdata)
   type is (integer(kind=i4_kind))
     call allocate_array(buf_i4_kind_pe, e)
-    call mpp_scatter(isc-xgbegin+1, isc+xc_size-xgbegin, jsc-ygbegin+1, jsc+yc_size-ygbegin, e(3), fileobj%pelist, &
-                     buf_i4_kind_pe, buf_i4_kind, fileobj%is_root)
+    call mpp_scatter(isc-xgbegin+1, isc+xc_size-xgbegin, jsc-ygbegin+1, jsc+yc_size-ygbegin, e(zdim_index), &
+                     fileobj%pelist, buf_i4_kind_pe, buf_i4_kind, dim_order, fileobj%is_root)
     call put_array_section(buf_i4_kind_pe, vdata, c, e)
     deallocate(buf_i4_kind_pe)
   type is (integer(kind=i8_kind))
     call allocate_array(buf_i8_kind_pe, e)
-    call mpp_scatter(isc-xgbegin+1, isc+xc_size-xgbegin, jsc-ygbegin+1, jsc+yc_size-ygbegin, e(3), fileobj%pelist, &
-                     buf_i8_kind_pe, buf_i8_kind, fileobj%is_root)
+    call mpp_scatter(isc-xgbegin+1, isc+xc_size-xgbegin, jsc-ygbegin+1, jsc+yc_size-ygbegin, e(zdim_index), &
+                     fileobj%pelist, buf_i8_kind_pe, buf_i8_kind, dim_order, fileobj%is_root)
     call put_array_section(buf_i8_kind_pe, vdata, c, e)
     deallocate(buf_i8_kind_pe)
   type is (real(kind=r4_kind))
     call allocate_array(buf_r4_kind_pe, e)
-    call mpp_scatter(isc-xgbegin+1, isc+xc_size-xgbegin, jsc-ygbegin+1, jsc+yc_size-ygbegin, e(3), fileobj%pelist, &
-                     buf_r4_kind_pe, buf_r4_kind, fileobj%is_root)
+    call mpp_scatter(isc-xgbegin+1, isc+xc_size-xgbegin, jsc-ygbegin+1, jsc+yc_size-ygbegin, e(zdim_index), &
+                     fileobj%pelist, buf_r4_kind_pe, buf_r4_kind, dim_order, fileobj%is_root)
     call put_array_section(buf_r4_kind_pe, vdata, c, e)
     deallocate(buf_r4_kind_pe)
   type is (real(kind=r8_kind))
     call allocate_array(buf_r8_kind_pe, e)
-    call mpp_scatter(isc-xgbegin+1, isc+xc_size-xgbegin, jsc-ygbegin+1, jsc+yc_size-ygbegin, e(3), fileobj%pelist, &
-                     buf_r8_kind_pe, buf_r8_kind, fileobj%is_root)
+    call mpp_scatter(isc-xgbegin+1, isc+xc_size-xgbegin, jsc-ygbegin+1, jsc+yc_size-ygbegin, e(zdim_index), &
+                     fileobj%pelist, buf_r8_kind_pe, buf_r8_kind, dim_order, fileobj%is_root)
     call put_array_section(buf_r8_kind_pe, vdata, c, e)
     deallocate(buf_r8_kind_pe)
   class default