Merge branch 'main' into add_badges

.github/workflows/documentation.yml

@@ -13,7 +13,8 @@ jobs:
       - uses: actions/setup-python@v3
       - name: Install dependencies
         run: |
-          pip install 'sphinx<=7.3.7' sphinx_rtd_theme myst_parser renku-sphinx-theme
+          pip install sphinx renku-sphinx-theme sphinx-rtd-theme          
+          pip install --upgrade sphinx-rtd-theme
       - name: Sphinx build
         run: |
           sphinx-build docs build

fre/make/tests/AM5_example/am5.yaml

@@ -0,0 +1,6 @@
+platformYaml: platforms.yaml
+compileYaml: compile.yaml
+release: f1a1r1
+INTEL: "intel-classic"
+FMSincludes: "-IFMS/fms2_io/include -IFMS/include -IFMS/mpp/include"
+momIncludes: "-Imom6/MOM6-examples/src/MOM6/pkg/CVMix-src/include" 

fre/make/tests/AM5_example/compile.yaml

@@ -0,0 +1,66 @@
+experiment: "am5"
+container_addlibs: 
+baremetal_linkerflags:  
+src:
+     - component: "FMS"
+       repo: "https://github.com/NOAA-GFDL/FMS.git"
+       cppdefs: "-DINTERNAL_FILE_NML -Duse_libMPI -Duse_netCDF" 
+       branch: "2022.01"
+       cppdefs: "-DHAVE_GETTID -Duse_libMPI -Duse_netCDF"
+       otherFlags: "$(FMSincludes)"
+     - component: "am5_phys"
+       requires: ["FMS"]
+       repo: "https://gitlab.gfdl.noaa.gov/FMS/am5_phys.git"
+       branch: "2022.01"
+       otherFlags: "$(FMSincludes)"
+     - component: "GFDL_atmos_cubed_sphere"
+       requires: ["FMS", "am5_phys"]
+       repo: "https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere.git"
+       cppdefs: "-DSPMD -DCLIMATE_NUDGE -DINTERNAL_FILE_NML"
+       branch: "2022.01"
+       paths: ["GFDL_atmos_cubed_sphere/driver/GFDL",
+              "GFDL_atmos_cubed_sphere/model",
+              "GFDL_atmos_cubed_sphere/driver/SHiELD/cloud_diagnosis.F90",
+              "GFDL_atmos_cubed_sphere/driver/SHiELD/gfdl_cloud_microphys.F90",
+              "GFDL_atmos_cubed_sphere/tools",
+              "GFDL_atmos_cubed_sphere/GFDL_tools"]
+       otherFlags: "$(FMSincludes)"
+     - component: "atmos_drivers"
+       requires: ["FMS", "am5_phys", "GFDL_atmos_cubed_sphere"]
+       repo: "https://github.com/NOAA-GFDL/atmos_drivers.git"
+       cppdefs: "-DSPMD -DCLIMATE_NUDGE"
+       branch: "2022.01"
+       paths: ["atmos_drivers/coupled"]
+       otherFlags: "$(FMSincludes)"
+     - component: "ice_sis"
+       requires: ["FMS", "ice_param", "mom6"]
+       repo: "https://gitlab.gfdl.noaa.gov/FMS/ice_sis.git"
+       branch: "2021.02"
+       otherFlags: "$(FMSincludes) $(momIncludes)"
+     - component: "ice_param"
+       repo: "https://github.com/NOAA-GFDL/ice_param.git"
+       cppdefs: "-Duse_yaml -Duse_libMPI -Duse_netCDF"
+       branch: "2021.02"
+       requires: ["FMS", "mom6"]
+       otherFlags: "$(FMSincludes) $(momIncludes)"
+     - component: "land_lad2"
+       requires: ["FMS"]
+       repo: "https://gitlab.gfdl.noaa.gov/FMS/land_lad2.git"
+       branch: "2022.01"
+       branch: "land_lad2_2021.02"
+       doF90Cpp: True
+       cppdefs: "-DINTERNAL_FILE_NML"
+       otherFlags: "$(FMSincludes)"
+     - component: "mom6"
+       requires: ["FMS"]
+       paths: ["mom6/MOM6-examples/src/MOM6/config_src/dynamic", "mom6/MOM6-examples/src/MOM6/config_src/coupled_driver", "mom6/MOM6-examples/src/MOM6/src/*/", "mom6/MOM6-examples/src/MOM6/src/*/*/", "mom6/ocean_BGC/generic_tracers", "mom6/ocean_BGC/mocsy/src"]
+       branch: ["2021.02","dev/gfdl/2018.04.06"]
+       repo: ["https://github.com/NOAA-GFDL/ocean_BGC.git","https://github.com/NOAA-GFDL/MOM6-examples.git"]
+       makeOverrides: 'OPENMP=""'
+       otherFlags: "$(FMSincludes) $(momIncludes)"
+     - component: "FMScoupler"
+       paths: ["FMScoupler/full", "FMScoupler/shared"]
+       repo: "https://github.com/NOAA-GFDL/FMScoupler.git"
+       branch: "2022.01"
+       requires: ["FMS", "atmos_drivers", "am5_phys", "land_lad2", "ice_sis", "ice_param", "mom6"]
+       otherFlags: "$(FMSincludes) $(momIncludes)"

fre/make/tests/AM5_example/platforms.yaml

@@ -0,0 +1,26 @@
+platforms:
+   - name: ncrc5.intel
+     compiler: intel
+     modulesInit: [" module use -a /ncrc/home2/fms/local/modulefiles \n","source $MODULESHOME/init/sh \n"]
+     modules: ["$(INTEL)/2022.2.1","fre/bronx-20",cray-hdf5/1.12.2.3, cray-netcdf/4.9.0.3]
+     fc: ftn
+     cc: cc
+     mkTemplate: "/ncrc/home2/fms/local/opt/fre-commands/bronx-20/site/ncrc5/$(INTEL).mk"
+     modelRoot: ${HOME}/fremake_canopy/test
+   - name: ncrc5.intel23
+     compiler: intel
+     modulesInit: [" module use -a /ncrc/home2/fms/local/modulefiles \n","source $MODULESHOME/init/sh \n"]
+     modules: ["$(INTEL)/2023.1.0","fre/bronx-20",cray-hdf5/1.12.2.3, cray-netcdf/4.9.0.3]
+     fc: ftn
+     cc: cc
+     mkTemplate: "/ncrc/home2/fms/local/opt/fre-commands/bronx-20/site/ncrc5/$(INTEL).mk"
+     modelRoot: ${HOME}/fremake_canopy/test
+   - name: hpcme.2023
+     compiler: intel
+     RUNenv: [". /spack/share/spack/setup-env.sh", "spack load libyaml", "spack load [email protected]", "spack load [email protected]"]
+     modelRoot: /apps
+     fc: mpiifort
+     cc: mpiicc
+     container: True
+     containerBuild: "podman"
+     containerRun: "apptainer" 

fre/make/tests/SHiELD_example/SHiELD.yaml

@@ -0,0 +1,10 @@
+platformYaml: platforms.yaml
+compileYaml: compile.yaml
+fv3_release: main
+phy_release: main
+fms_release: "2023.02"
+drivers_release: main
+coupler_release: "2023.02"
+FMSincludes: "-IFMS/fms2_io/include -IFMS/include -IFMS/mpp/include"
+momIncludes: "-Imom6/MOM6-examples/src/MOM6/pkg/CVMix-src/include"
+INTEL: intel-classic

fre/make/tests/SHiELD_example/compile.yaml

@@ -0,0 +1,38 @@
+experiment: shield_nh
+compileInclude: "-IFMS/fms2_io/include -IFMS/include -IFMS/mpp/include" 
+container_addlibs: ["bacio","sp","w3emc","w3nco"]
+baremetal_addlibs: ["-L/autofs/ncrc-svm1_proj/epic/spack-stack/spack-stack-1.6.0/envs/unified-env/install/intel/2023.1.0/bacio-2.4.1-wrykbu2/lib -lbacio_4", "-L/autofs/ncrc-svm1_proj/epic/spack-stack/spack-stack-1.6.0/envs/unified-env/install/intel/2023.1.0/bacio-2.4.1-wrykbu2/lib -lbacio_8", "-L/autofs/ncrc-svm1_proj/epic/spack-stack/spack-stack-1.6.0/envs/unified-env/install/intel/2023.1.0/sp-2.5.0-7bumbmx/lib64 -lsp_d", "-L/autofs/ncrc-svm1_proj/epic/spack-stack/spack-stack-1.6.0/envs/unified-env/install/intel/2023.1.0/w3emc-2.10.0-zmuykep/lib64 -lw3emc_d", "-L/autofs/ncrc-svm1_proj/epic/spack-stack/spack-stack-1.6.0/envs/unified-env/install/intel/2023.1.0/w3nco-2.4.1-76qm6h2/lib -lw3nco_d"]
+src:
+     - component: "FMS"
+       repo: "https://github.com/NOAA-GFDL/FMS.git"
+       cppdefs: "-Duse_libMPI -Duse_netCDF -Duse_LARGEFILE -DHAVE_SCHED_GETAFFINITY -DINTERNAL_FILE_NML -DGFS_PHYS -DGFS_CONSTANTS -DHAVE_GETTID" 
+       branch: "$(fms_release)"
+     - component: "SHiELD_physics"
+       requires: ["FMS"]
+       repo: "https://github.com/NOAA-GFDL/SHiELD_physics.git"
+       branch: "$(phy_release)"
+       paths: [SHiELD_physics/gsmphys,
+              SHiELD_physics/GFS_layer,
+              SHiELD_physics/IPD_layer]
+       cppdefs: "-Duse_libMPI -Duse_netCDF -DHAVE_SCHED_GETAFFINITY -DSPMD -Duse_LARGEFILE -DGFS_PHYS -DUSE_GFSL63 -DNEW_TAUCTMAX -DNEMS_GSM -DINTERNAL_FILE_NML -DMOIST_CAPPA -DUSE_COND"
+       otherFlags: "$(FMSincludes)"
+     - component: "fv3"
+       requires: ["FMS", "SHiELD_physics"]
+       repo: ["https://github.com/NOAA-GFDL/GFDL_atmos_cubed_sphere.git",
+             "https://github.com/NOAA-GFDL/atmos_drivers.git"]
+       cppdefs: "-Duse_libMPI -Duse_netCDF -DHAVE_SCHED_GETAFFINITY -DSPMD -Duse_LARGEFILE -DGFS_PHYS -DUSE_GFSL63 -DNEW_TAUCTMAX -DNEMS_GSM -DINTERNAL_FILE_NML -DMOIST_CAPPA -DUSE_COND"
+       branch: ["$(fv3_release)","$(drivers_release)"]
+       paths: [SHiELD_physics/FV3GFS/,
+              fv3/atmos_drivers/SHiELD/atmos_model.F90,
+              fv3/GFDL_atmos_cubed_sphere/driver/SHiELD/atmosphere.F90,
+              fv3/GFDL_atmos_cubed_sphere/tools/,
+              fv3/GFDL_atmos_cubed_sphere/model/,
+              fv3/GFDL_atmos_cubed_sphere/GFDL_tools/fv_diag_column.F90]
+       otherFlags: "$(FMSincludes)"
+     - component: "FMScoupler"
+       requires: ["FMS", "SHiELD_physics", "fv3"]
+       repo: "https://github.com/NOAA-GFDL/FMScoupler.git"
+       cppdefs: "-Duse_libMPI -Duse_netCDF -DHAVE_SCHED_GETAFFINITY -DSPMD -Duse_LARGEFILE -DGFS_PHYS -DUSE_GFSL63 -DNEW_TAUCTMAX -DNEMS_GSM -DINTERNAL_FILE_NML -DMOIST_CAPPA -DUSE_COND"
+       branch: "$(coupler_release)"
+       paths: ["FMScoupler/SHiELD/coupler_main.F90"]
+       otherFlags: "$(FMSincludes)"

fre/make/tests/SHiELD_example/platforms.yaml

@@ -0,0 +1,26 @@
+platforms:
+   - name: ncrc5.intel
+     compiler: intel
+     modulesInit: [" module use -a /ncrc/home2/fms/local/modulefiles \n","source $MODULESHOME/init/sh \n"]
+     modules: ["$(INTEL)/2022.2.1","fre/bronx-20",cray-hdf5/1.12.2.3, cray-netcdf/4.9.0.3]
+     fc: ftn
+     cc: cc
+     mkTemplate: "/ncrc/home2/fms/local/opt/fre-commands/bronx-20/site/ncrc5/$(INTEL).mk"
+     modelRoot: ${HOME}/fremake_canopy/SHiELDtest
+   - name: ncrc5.intel23
+     compiler: intel
+     modulesInit: [" module use -a /ncrc/home2/fms/local/modulefiles \n","source $MODULESHOME/init/sh \n"]
+     modules: ["$(INTEL)/2023.1.0","fre/bronx-20",cray-hdf5/1.12.2.3, cray-netcdf/4.9.0.3]
+     fc: ftn
+     cc: cc
+     mkTemplate: "/ncrc/home2/fms/local/opt/fre-commands/bronx-20/site/ncrc5/$(INTEL).mk"
+     modelRoot: ${HOME}/fremake_canopy/SHiELDtest
+   - name: hpcme.2023
+     compiler: intel
+     RUNenv: [". /spack/share/spack/setup-env.sh", "spack load libyaml", "spack load [email protected]", "spack load [email protected]"]
+     modelRoot: /apps
+     fc: mpiifort
+     cc: mpiicc
+     container: True
+     containerBuild: "podman"
+     containerRun: "apptainer"