Convert GFS DDTs from blocked data structures to contiguous arrays (now also includes https://github.com/NOAA-EMC/fv3atm/pull/752)

.github/pull_request_template.md

@@ -35,3 +35,8 @@ Do PRs in upstream repositories need to be merged first?
 If so add the "waiting for other repos" label and list the upstream PRs
 - waiting on noaa-emc/nems/pull/<pr_number>
 - waiting on noaa-emc/fv3atm/pull/<pr_number>
+
+# Requirements before merging
+- [ ] All new code in this PR is tested by at least one unit test
+- [ ] All new code in this PR includes Doxygen documentation
+- [ ] All new code in this PR does not add new compilation warnings (check CI output)

.github/workflows/GCC.yml

@@ -24,7 +24,7 @@ jobs:
         mpi: ["mpich", "openmpi"]
 
     steps:
-
+        
     - name: checkout-fv3atm
       uses: actions/checkout@v4
       with:
@@ -59,6 +59,7 @@ jobs:
         spack config add "packages:mpi:require:'${{ matrix.mpi }}'"
         spack concretize |& tee ${SPACK_ENV}/log.concretize
         spack install -j2 --fail-fast
+        echo "spackrc=$?" >> ${GITHUB_ENV}
         spack clean --all
 
   build_fv3atm:
@@ -73,9 +74,20 @@ jobs:
 
     steps:
 
-    - name: install-doxygen
+    # Only do Doxygen and gcovr build for one job
+    - name: decide-doc-gcovr-build
+      run: |
+        if [[ "${{ matrix.cmake_opts }}" == "-D32BIT=ON" && "${{ matrix.gcc_ver }}" == 12 && "${{ matrix.mpi }}" == mpich ]]; then
+          echo 'devbuild=ON' | tee -a ${GITHUB_ENV}
+          echo 'gcov_cmake="-DCMAKE_Fortran_FLAGS=-fprofile-abs-path -fprofile-arcs -ftest-coverage -O0"' | tee -a ${GITHUB_ENV}
+        else
+          echo 'devbuild=OFF' | tee -a ${GITHUB_ENV}
+        fi
+
+    - name: install-utilities
       run: |
         sudo apt-get install doxygen graphviz
+        python3 -m pip install gcovr
 
     - name: install-cmake
       run: |
@@ -109,14 +121,34 @@ jobs:
         export CC=mpicc
         export CXX=mpicxx
         export FC=mpif90
-        cat /home/runner/work/fv3atm/fv3atm/spack-develop/opt/spack/linux-ubuntu22.04-zen2/gcc-12.3.0/fms-2023.04-*/lib/cmake/fms/fms-config.cmake
-        cmake ${GITHUB_WORKSPACE}/fv3atm -DBUILD_TESTING=ON ${{ matrix.cmake_opts }} -DENABLE_DOCS=ON
+        cmake ${GITHUB_WORKSPACE}/fv3atm -DBUILD_TESTING=ON ${{ matrix.cmake_opts }} -DENABLE_DOCS=ON ${{ env.gcov_cmake }}
         make -j2
-        ls -l /home/runner/work/fv3atm/fv3atm/fv3atm/io
 
-    - uses: actions/upload-artifact@v4
+    - name: run-tests
+      run: |
+        cd $GITHUB_WORKSPACE/build
+        ctest -j2 --output-on-failure --rerun-failed
+
+    - name: get-test-coverage
+      if: ${{ env.devbuild == 'ON' }}
+      run: |
+        cd $GITHUB_WORKSPACE/build
+        gcovr -r .. -v --html-details --gcov-executable gcov-12 --exclude $GITHUB_WORKSPACE/fv3atm/tests --exclude $GITHUB_WORKSPACE/fv3atm/stochastic_physics_repo --exclude $GITHUB_WORKSPACE/fv3atm/build/ccpp --exclude $GITHUB_WORKSPACE/fv3atm/ccpp/physics --exclude $GITHUB_WORKSPACE/fv3atm/ccpp/framework --exclude $GITHUB_WORKSPACE/fv3atm/atmos_cubed_sphere  --exclude CMakeFiles --print-summary -o test-coverage.html
+
+    - name: upload-test-coverage
+      uses: actions/upload-artifact@v4
+      if: ${{ env.devbuild == 'ON' }}
+      with:
+        name: test-coverage-fv3atm-${{ github.sha }}
+        path: |
+              ${{ github.workspace }}/build/*.html 
+              ${{ github.workspace }}/build/*.css
+
+    - name: upload-docs
+      uses: actions/upload-artifact@v4
+      if: ${{ env.devbuild == 'ON' }}
       with:
-        name: docs-gcc${{ matrix.gcc_ver }}-${{ matrix.mpi }}-${{ matrix.cmake_opts }}
+        name: docs-fv3atm
         path: |
           build/docs/html
 
@@ -126,4 +158,3 @@ jobs:
       with:
         name: ccpp_prebuild_logs-gcc${{ matrix.gcc_ver }}-${{ matrix.mpi }}-${{ matrix.cmake_opts }}
         path: ${{ github.workspace }}/build/ccpp/ccpp_prebuild.*
-

CMakeLists.txt

@@ -164,6 +164,11 @@ if(OPENMP)
   target_link_libraries(fv3atm PUBLIC OpenMP::OpenMP_Fortran)
 endif()
 
+if(BUILD_TESTING)
+  include(CTest)
+  add_subdirectory(tests)
+endif()
+
 ###############################################################################
 ### Install
 ###############################################################################

ccpp/config/ccpp_prebuild_config.py

@@ -55,16 +55,15 @@
         },
     'GFS_typedefs' : {
         'GFS_control_type'      : 'GFS_Control',
-        'GFS_data_type'         : 'GFS_Data(cdata%blk_no)',
-        'GFS_diag_type'         : 'GFS_Data(cdata%blk_no)%Intdiag',
-        'GFS_tbd_type'          : 'GFS_Data(cdata%blk_no)%Tbd',
-        'GFS_sfcprop_type'      : 'GFS_Data(cdata%blk_no)%Sfcprop',
-        'GFS_coupling_type'     : 'GFS_Data(cdata%blk_no)%Coupling',
-        'GFS_statein_type'      : 'GFS_Data(cdata%blk_no)%Statein',
-        'GFS_cldprop_type'      : 'GFS_Data(cdata%blk_no)%Cldprop',
-        'GFS_radtend_type'      : 'GFS_Data(cdata%blk_no)%Radtend',
-        'GFS_grid_type'         : 'GFS_Data(cdata%blk_no)%Grid',
-        'GFS_stateout_type'     : 'GFS_Data(cdata%blk_no)%Stateout',
+        'GFS_statein_type'      : 'GFS_Statein',
+        'GFS_stateout_type'     : 'GFS_Stateout',
+        'GFS_grid_type'         : 'GFS_Grid',
+        'GFS_tbd_type'          : 'GFS_Tbd',
+        'GFS_cldprop_type'      : 'GFS_Cldprop',
+        'GFS_sfcprop_type'      : 'GFS_Sfcprop',
+        'GFS_radtend_type'      : 'GFS_Radtend',
+        'GFS_coupling_type'     : 'GFS_Coupling',
+        'GFS_diag_type'         : 'GFS_Intdiag',
         'GFS_typedefs' : '',
         },
     }

ccpp/data/CCPP_data.F90

@@ -8,7 +8,15 @@ module CCPP_data
     use CCPP_typedefs, only: GFS_interstitial_type,  &
                              GFDL_interstitial_type
     use GFS_typedefs,  only: GFS_control_type,       &
-                             GFS_data_type
+                             GFS_statein_type,       &
+                             GFS_stateout_type,      &
+                             GFS_grid_type,          &
+                             GFS_tbd_type,           &
+                             GFS_cldprop_type,       &
+                             GFS_sfcprop_type,       &
+                             GFS_radtend_type,       &
+                             GFS_coupling_type,      &
+                             GFS_diag_type
 
     implicit none
 
@@ -20,15 +28,31 @@ module CCPP_data
            ccpp_suite,             &
            GFDL_interstitial,      &
            GFS_control,            &
-           GFS_data,               &
+           GFS_statein,            &
+           GFS_stateout,           &
+           GFS_grid,               &
+           GFS_tbd,                &
+           GFS_cldprop,            &
+           GFS_sfcprop,            &
+           GFS_radtend,            &
+           GFS_coupling,           &
+           GFS_intdiag,            &
            GFS_interstitial
 
     !-------------------------------------------------------!
-    !  GFS data containers, GFS_Data has dimension nblocks  !
-    !  and GFS_Interstitial has dimension nthreads          !
+    !  GFS data containers;                                 !
+    !  GFS_Interstitial has dimension nthreads              !
     !-------------------------------------------------------!
     type(GFS_control_type),                                    save, target :: GFS_control
-    type(GFS_data_type),          dimension(:),   allocatable, save, target :: GFS_data
+    type(GFS_statein_type),                                    save, target :: GFS_statein
+    type(GFS_stateout_type),                                   save, target :: GFS_stateout
+    type(GFS_grid_type),                                       save, target :: GFS_grid
+    type(GFS_tbd_type),                                        save, target :: GFS_tbd
+    type(GFS_cldprop_type),                                    save, target :: GFS_cldprop
+    type(GFS_sfcprop_type),                                    save, target :: GFS_sfcprop
+    type(GFS_radtend_type),                                    save, target :: GFS_radtend
+    type(GFS_coupling_type),                                   save, target :: GFS_coupling
+    type(GFS_diag_type),                                       save, target :: GFS_intdiag
     type(GFS_interstitial_type),  dimension(:),   allocatable, save, target :: GFS_interstitial
 
     !------------------------------------------------------!

ccpp/data/CCPP_data.meta

@@ -24,24 +24,66 @@
   units = DDT
   dimensions = ()
   type = GFS_control_type
-[GFS_Data(ccpp_block_number)]
-  standard_name = GFS_data_type_instance
-  long_name = instance of derived type GFS_data_type
+[GFS_Statein]
+  standard_name = GFS_statein_type_instance
+  long_name = prognostic state data in from dycore
   units = DDT
   dimensions = ()
-  type = GFS_data_type
+  type = GFS_statein_type
+[GFS_Stateout]
+  standard_name = GFS_stateout_type_instance
+  long_name = prognostic state or tendencies return to dycore
+  units = DDT
+  dimensions = ()
+  type = GFS_stateout_type
+[GFS_Grid]
+  standard_name = GFS_grid_type_instance
+  long_name = instance of derived type GFS_grid_type
+  units = DDT
+  dimensions = ()
+  type = GFS_grid_type
+[GFS_Tbd]
+  standard_name = GFS_tbd_type_instance
+  long_name = instance of derived type GFS_tbd_type
+  units = DDT
+  dimensions = ()
+  type = GFS_tbd_type
+[GFS_Cldprop]
+  standard_name = GFS_cldprop_type_instance
+  long_name = instance of derived type GFS_cldprop_type
+  units = DDT
+  dimensions = ()
+  type = GFS_cldprop_type
+[GFS_Sfcprop]
+  standard_name = GFS_sfcprop_type_instance
+  long_name = instance of derived type GFS_sfcprop_type
+  units = DDT
+  dimensions = ()
+  type = GFS_sfcprop_type
+[GFS_Radtend]
+  standard_name = GFS_radtend_type_instance
+  long_name = instance of derived type GFS_radtend_type
+  units = DDT
+  dimensions = ()
+  type = GFS_radtend_type
+[GFS_Coupling]
+  standard_name = GFS_coupling_type_instance
+  long_name = instance of derived type GFS_coupling_type
+  units = DDT
+  dimensions = ()
+  type = GFS_coupling_type
+[GFS_Intdiag]
+  standard_name = GFS_diag_type_instance
+  long_name = instance of derived type GFS_diag_type
+  units = DDT
+  dimensions = ()
+  type = GFS_diag_type
 [GFS_Interstitial(ccpp_thread_number)]
   standard_name = GFS_interstitial_type_instance
   long_name = instance of derived type GFS_interstitial_type
   units = DDT
   dimensions = ()
   type = GFS_interstitial_type
-[GFS_Data]
-  standard_name = GFS_data_type_instance_all_blocks
-  long_name = instance of derived type GFS_data_type
-  units = DDT
-  dimensions = (ccpp_block_count)
-  type = GFS_data_type
 [GFS_Interstitial]
   standard_name = GFS_interstitial_type_instance_all_threads
   long_name = instance of derived type GFS_interstitial_type