Add sub-regioan diag output example in 1D case

.github/workflows/mom6_cobalt_1D.yaml

@@ -28,9 +28,8 @@ jobs:
     - name: Build mom6-sis2-cobalt
       working-directory: ./builds
       run: |
-        apt update; apt install -y wget
         echo "build mom6-sis2-cobalt ..."
-        ./linux-build.bash -m docker -p linux-gnu -t debug -f mom6sis2
+        ./linux-build.bash -m docker -p linux-gnu -t debug -f mom6sis2_yaml
 
     - name: Download 1d model dataset
       working-directory: ./exps
@@ -42,6 +41,11 @@ jobs:
       run: | 
        ./driver.sh 
 
+    - name: Run mppnccombine to combine sub-region diag outputs 
+      working-directory: ./exps/OM4.single_column.COBALT
+      run: |
+       /opt/bin/mppnccombine -64 -h 16384 -m -k 100 20040102.ocean_daily_subset.nc 20040102.ocean_daily_subset.nc.00*
+
     - name: Check ref
       working-directory: ./exps/OM4.single_column.COBALT
       run: | 

.gitmodules

@@ -30,14 +30,14 @@
 	path = src/libyaml
 	url = https://github.com/yaml/libyaml.git
 	branch = master
-[submodule "src/MOM6"]
-	path = src/MOM6
-	url = https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/MOM6.git
-	branch = dev/cefi
 [submodule "src/FMS"]
 	path = src/FMS
 	url = https://github.com/NOAA-GFDL/FMS.git
 	branch = 2024.01.02
+[submodule "src/MOM6"]
+	path = src/MOM6
+	url = https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/MOM6.git
+	branch = dev/cefi
 [submodule "src/coupler"]
 	path = src/coupler
 	url = https://github.com/NOAA-GFDL/FMScoupler.git

builds/linux-build.bash

@@ -102,6 +102,56 @@ fi
 
     make $makeflags MOM6SIS2
 
+elif [[ $flavor == "mom6sis2_yaml" ]]; then
+
+    echo "build mom6sis2 with FMS2 cap and yaml"
+
+[[ -d build/$machine_name-$platform/libyaml/$target ]] && rm -rf build/$machine_name-$platform/libyaml/$target
+mkdir -p build/$machine_name-$platform/libyaml/$target
+pushd $srcdir/libyaml
+$srcdir/libyaml/bootstrap
+$srcdir/libyaml/configure --prefix=$abs_rootdir/build/$machine_name-$platform/libyaml/$target 
+make 
+make install
+
+if [ $? -ne 0 ]; then
+   echo "Could not build the libyaml library!"
+   exit 1
+fi
+popd
+
+mkdir -p build/$machine_name-$platform/shared/$target
+pushd build/$machine_name-$platform/shared/$target
+rm -f path_names
+$srcdir/mkmf/bin/list_paths $srcdir/FMS/{affinity,amip_interp,column_diagnostics,diag_integral,drifters,horiz_interp,memutils,sat_vapor_pres,topography,astronomy,constants,diag_manager,field_manager,include,monin_obukhov,platform,tracer_manager,axis_utils,coupler,fms,fms2_io,interpolator,mosaic,mosaic2,random_numbers,time_interp,tridiagonal,block_control,data_override,exchange,mpp,time_manager,string_utils,parser}/ $srcdir/FMS/libFMS.F90
+$srcdir/mkmf/bin/mkmf -t $abs_rootdir/$machine_name/$platform.mk -o "-I../../libyaml/$target/include" -p libfms.a -l "-L../../libyaml/$target/lib -lyaml $linker_options" -c "-Duse_libMPI -Duse_yaml -Duse_netCDF -DMAXFIELDMETHODS_=800" path_names
+
+make $makeflags libfms.a
+
+if [ $? -ne 0 ]; then
+   echo "Could not build the FMS library!"
+   exit 1
+fi
+
+popd
+
+    mkdir -p build/$machine_name-$platform/ocean_ice/$target
+    pushd build/$machine_name-$platform/ocean_ice/$target
+    rm -f path_names
+    $srcdir/mkmf/bin/list_paths $srcdir/MOM6/{config_src/infra/FMS2,config_src/memory/dynamic_symmetric,config_src/drivers/FMS_cap,config_src/external/ODA_hooks,config_src/external/database_comms,config_src/external/drifters,config_src/external/stochastic_physics,pkg/GSW-Fortran/{modules,toolbox}/,src/{*,*/*}/} $srcdir/SIS2/{config_src/dynamic_symmetric,config_src/external/Icepack_interfaces,src} $srcdir/icebergs/src $srcdir/FMS/{coupler,include}/ $srcdir/{ocean_BGC/generic_tracers,ocean_BGC/mocsy/src}/ $srcdir/{atmos_null,ice_param,land_null,coupler/shared/,coupler/full/}/
+
+
+compiler_options='-DINTERNAL_FILE_NML -DUSE_FMS2_IO -Duse_yaml -DMAX_FIELDS_=600 -DNOT_SET_AFFINITY -D_USE_MOM6_DIAG -D_USE_GENERIC_TRACER -DUSE_PRECISION=2 -D_USE_LEGACY_LAND_ -Duse_AM3_physics'
+linker_options=''
+if [[ "$target" =~ "stdpar" ]] ; then
+    compiler_options="$compiler_options -stdpar -Minfo=accel"
+    linker_options="$linker_options -stdpar "
+fi
+
+    $srcdir/mkmf/bin/mkmf -t $abs_rootdir/$machine_name/$platform.mk -o "-I../../shared/$target -I../../libyaml/$target/include" -p MOM6SIS2 -l "-L../../shared/$target -lfms -L../../libyaml/$target/lib -lyaml $linker_options" -c "$compiler_options" path_names
+
+    make $makeflags MOM6SIS2
+
 elif [[ $flavor == "fms1_mom6sis2" ]]; then
 
     echo "build mom6sis2 with FMS1 cap" 

docs/source/InputsOutputs.rst

@@ -186,6 +186,8 @@ Model output is controlled via the FMS diag_manager using the ``diag_table``.
 
 The diag_table file has three kinds of section: Title, File and Field. The title section is mandatory and always the first. There can be multiple file and field sections typically either in pairs or grouped in to all files and all fields, but always with the file section preceding the corresponding field section.
 
+The new FMS2 comes with a new rewritten diag manager. The old diag_manager code has been kept intact and will be used by default. The rewritten diag manager can be enabled via ``use_modern_diag = .true.`` to your ``diag_manager_nml``. Keep in mind that the rewritten diag manager only supports the YAML format of diag_Table (this requires the additional third-party libyaml when building FMS2). Users can refer to `this page <https://github.com/NOAA-GFDL/FMS/blob/main/diag_manager/diag_yaml_format.md>`__ for more details of the diag_table yaml format. An example diag_table.yaml can be found in our 1D case: ``exps/OM4.single_column.COBALT/diag_table.yaml``.
+
 .. _TitleSec:
 
 ---------------------------

exps/OM4.single_column.COBALT/diag_table.yaml

@@ -0,0 +1,21 @@
+title: test_diag_manager
+base_date: 1993 1 1 0 0 0
+diag_files:
+- file_name: ocean_daily_subset
+  time_units: days
+  unlimdim: time
+  is_ocean: true
+  freq: 1 days
+  varlist:
+  - module: ocean_model
+    var_name: thetao
+    reduction: average
+    kind: r4
+  sub_region:
+  - grid_type: index
+    tile: 1
+    corner1: 2,2 
+    corner2: 3,2
+    corner3: 2,3 
+    corner4: 3,3
+

exps/OM4.single_column.COBALT/driver.sh

@@ -1,6 +1,7 @@
 #!/bin/bash
 
 #
+export LD_LIBRARY_PATH=../../builds/build/docker-linux-gnu/libyaml/debug/lib:$LD_LIBRARY_PATH
 rm -rf RESTART*
 
 #
@@ -11,6 +12,7 @@ echo "run 48hrs test ..."
 ln -fs input.nml_48hr input.nml
 mpirun --allow-run-as-root -np 1 ../../builds/build/docker-linux-gnu/ocean_ice/debug/MOM6SIS2 > out1 2>err1
 tail out1
+tail err1
 mv RESTART RESTART_48hrs
 mv ocean.stats* RESTART_48hrs
 
@@ -19,6 +21,7 @@ echo "run 24hrs test ..."
 ln -fs input.nml_24hr input.nml
 mpirun --allow-run-as-root -np 1 ../../builds/build/docker-linux-gnu/ocean_ice/debug/MOM6SIS2 > out2 2>err2
 tail out2
+tail err2
 mv RESTART RESTART_24hrs
 mv ocean.stats* RESTART_24hrs
 
@@ -33,8 +36,10 @@ echo "run 24hrs rst test ..."
 ln -fs input.nml_24hr_rst input.nml
 mpirun --allow-run-as-root -np 1 ../../builds/build/docker-linux-gnu/ocean_ice/debug/MOM6SIS2 > out3 2>err3
 tail out3
+tail err3
 mv RESTART RESTART_24hrs_rst
 mv ocean.stats* RESTART_24hrs_rst
+[[ ! -f 20040102.ocean_daily_subset.nc.0000 ]] && echo "Can not find sub-region diag output! Exit!" && exit 1
 
 # Define the directories containing the files
 DIR1="RESTART_24hrs_rst/"

exps/OM4.single_column.COBALT/input.nml_24hr_rst

@@ -57,6 +57,7 @@
             max_input_fields = 2000
             max_output_fields = 5000
             mix_snapshot_average_fields=.false.
+            use_modern_diag=.true.
 /
 
  &flux_exchange_nml