JustinPerket · JustinPerket · Nov 13, 2020 · Nov 17, 2020 · Nov 19, 2020 · Nov 23, 2020
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -68,7 +68,7 @@ jobs:
     - name: Free up disk space
       run: |
         sudo docker rmi $(sudo docker image ls | grep -E -m1 '<none>' | awk '{ print $3 }')
-        sudo docker rmi $(sudo docker image ls | awk '/ci-test-base/ { print $3 }')
+        sudo docker rmi $(sudo docker image ls | awk '/ubuntu-hpc/ { print $3 }')
 
     - name: Prepare artifacts
       run: |

diff --git a/.github/workflows/manage.yml b/.github/workflows/manage.yml
@@ -22,15 +22,15 @@ jobs:
           tr_id=$(cat ${GITHUB_EVENT_PATH} | ./json_helper.py get_trigger_id)
           tr_br=$(cat ${GITHUB_EVENT_PATH} | ./json_helper.py get_trigger_br)
           check=$(cat ${GITHUB_EVENT_PATH} | ./json_helper.py check_skip)
-          echo "::set-env name=TRIGGER_ID::${tr_id}"
-          echo "::set-env name=TRIGGER_BR::${tr_br}"
+          echo "TRIGGER_ID=${tr_id}" >> $GITHUB_ENV
+          echo "TRIGGER_BR=${tr_br}" >> $GITHUB_ENV
           echo "skip-ci: ${check}"
           if [[ $check == yes ]]; then
             echo "skip-ci is requested"
-            echo '::set-env name=CURR_JOB::cancelled'
+            echo "CURR_JOB=cancelled" >> $GITHUB_ENV
             curl -X POST -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -H "Accept: application/vnd.github.v3+json" ${repo}/$tr_id/cancel
           else
-            echo '::set-env name=CURR_JOB::running'
+            echo "CURR_JOB=running" >> $GITHUB_ENV
           fi
 
       - name: Cancel redundant jobs

diff --git a/CICE-interface/CICE b/CICE-interface/CICE
diff --git a/CICE-interface/cice_files.cmake b/CICE-interface/cice_files.cmake
@@ -28,6 +28,7 @@ list(APPEND cice_shared_files
   CICE/cicecore/cicedynB/dynamics/ice_dyn_evp.F90
   CICE/cicecore/cicedynB/dynamics/ice_dyn_evp_1d.F90
   CICE/cicecore/cicedynB/dynamics/ice_dyn_shared.F90
+  CICE/cicecore/cicedynB/dynamics/ice_dyn_vp.F90
   CICE/cicecore/cicedynB/dynamics/ice_transport_driver.F90
   CICE/cicecore/cicedynB/dynamics/ice_transport_remap.F90
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -103,7 +103,7 @@ find_package(sp REQUIRED)
 find_package(w3emc REQUIRED)
 find_package(w3nco REQUIRED)
 if(INLINE_POST)
-  find_package(nceppost REQUIRED)
+  find_package(upp REQUIRED)
 endif()
 
 # See https://github.com/NOAA-EMC/NCEPLIBS-nemsio/pull/22

diff --git a/FV3 b/FV3
diff --git a/MOM6-interface/MOM6 b/MOM6-interface/MOM6
diff --git a/MOM6-interface/mom6_files.cmake b/MOM6-interface/mom6_files.cmake
@@ -24,12 +24,13 @@ list(APPEND mom6_src_files
   MOM6/src/core/MOM_CoriolisAdv.F90
   MOM6/src/core/MOM_PressureForce.F90
   MOM6/src/core/MOM_PressureForce_Montgomery.F90
-  MOM6/src/core/MOM_PressureForce_analytic_FV.F90
+  MOM6/src/core/MOM_PressureForce_FV.F90
   MOM6/src/core/MOM_barotropic.F90
   MOM6/src/core/MOM_boundary_update.F90
   MOM6/src/core/MOM_checksum_packages.F90
   MOM6/src/core/MOM_continuity.F90
   MOM6/src/core/MOM_continuity_PPM.F90
+  MOM6/src/core/MOM_density_integrals.F90
   MOM6/src/core/MOM_dynamics_split_RK2.F90
   MOM6/src/core/MOM_dynamics_unsplit.F90
   MOM6/src/core/MOM_dynamics_unsplit_RK2.F90
@@ -214,12 +215,13 @@ list(APPEND mom6_src_files
   MOM6/src/user/Kelvin_initialization.F90
   MOM6/src/user/MOM_controlled_forcing.F90
   MOM6/src/user/MOM_wave_interface.F90
-  MOM6/src/user/Neverland_initialization.F90
+  MOM6/src/user/Neverworld_initialization.F90
   MOM6/src/user/Phillips_initialization.F90
   MOM6/src/user/RGC_initialization.F90
   MOM6/src/user/Rossby_front_2d_initialization.F90
   MOM6/src/user/SCM_CVMix_tests.F90
   MOM6/src/user/adjustment_initialization.F90
+  MOM6/src/user/basin_builder.F90
   MOM6/src/user/baroclinic_zone_initialization.F90
   MOM6/src/user/benchmark_initialization.F90
   MOM6/src/user/circle_obcs_initialization.F90
@@ -241,11 +243,15 @@ list(APPEND mom6_src_files
   MOM6/src/user/user_revise_forcing.F90
 
   MOM6/src/ocean_data_assim/MOM_oda_driver.F90
-  MOM6/src/ocean_data_assim/core/ocean_da_core.F90
-  MOM6/src/ocean_data_assim/core/ocean_da_types.F90
-  MOM6/src/ocean_data_assim/core/write_ocean_obs.F90
 
-  MOM6/src/ocean_data_assim/geoKdTree/kdtree.f90
+  MOM6/config_src/external/GFDL_ocean_BGC/FMS_coupler_util.F90
+  MOM6/config_src/external/GFDL_ocean_BGC/generic_tracer.F90
+  MOM6/config_src/external/GFDL_ocean_BGC/generic_tracer_utils.F90
+  MOM6/config_src/external/ODA_hooks/kdtree.f90
+  MOM6/config_src/external/ODA_hooks/ocean_da_core.F90
+  MOM6/config_src/external/ODA_hooks/ocean_da_types.F90
+  MOM6/config_src/external/ODA_hooks/write_ocean_obs.F90
+
 )
 
 list(APPEND mom6_nuopc_src_files
@@ -261,7 +267,6 @@ list(APPEND mom6_solo_src_files
   MOM6/config_src/solo_driver/MESO_surface_forcing.F90
   MOM6/config_src/solo_driver/MOM_driver.F90
   MOM6/config_src/solo_driver/MOM_surface_forcing.F90
-  MOM6/config_src/solo_driver/Neverland_surface_forcing.F90
   MOM6/config_src/solo_driver/atmos_ocean_fluxes.F90
   MOM6/config_src/solo_driver/user_surface_forcing.F90
 )
diff --git a/cmake/configure_cheyenne.intel.cmake b/cmake/configure_cheyenne.intel.cmake
@@ -1,2 +1,3 @@
-set(INLINE_POST     ON CACHE BOOL "Enable inline post" FORCE)
+set(INLINE_POST     ON  CACHE BOOL "Enable inline post" FORCE)
+set(PARALLEL_NETCDF ON  CACHE BOOL "Enable parallel NetCDF" FORCE)
 set(DEBUG_LINKMPI   OFF CACHE BOOL "Enable linkmpi option when DEBUG mode is on" FORCE)
diff --git a/cmake/configure_gaea.intel.cmake b/cmake/configure_gaea.intel.cmake
@@ -1,2 +1,3 @@
-set(INLINE_POST     ON CACHE BOOL "Enable inline post" FORCE)
+set(INLINE_POST     ON  CACHE BOOL "Enable inline post" FORCE)
+set(PARALLEL_NETCDF ON  CACHE BOOL "Enable parallel NetCDF" FORCE)
 set(DEBUG_LINKMPI   OFF CACHE BOOL "Enable linkmpi option when DEBUG mode is on" FORCE)
diff --git a/cmake/configure_jet.intel.cmake b/cmake/configure_jet.intel.cmake
@@ -1,3 +1,4 @@
-set(INLINE_POST     ON  CACHE BOOL "Enable inline post" FORCE)
+set(INLINE_POST     ON CACHE BOOL "Enable inline post" FORCE)
+set(PARALLEL_NETCDF ON CACHE BOOL "Enable parallel NetCDF" FORCE)
 set(AVX2            OFF CACHE BOOL "Enable AVX2 instruction set" FORCE)
 set(SIMDMULTIARCH   ON  CACHE BOOL "Enable multi-target SIMD instruction sets" FORCE)
diff --git a/fms_files.cmake b/fms_files.cmake
@@ -1,4 +1,5 @@
 list(APPEND fms_src_files
+    FMS/affinity/fms_affinity.F90
     FMS/amip_interp/amip_interp.F90
     FMS/astronomy/astronomy.F90
     FMS/axis_utils/axis_utils.F90

diff --git a/modulefiles/cheyenne.gnu/fv3 b/modulefiles/cheyenne.gnu/fv3
@@ -1,60 +1,45 @@
-#%Module######################################################################
-##
-##    NEMS FV3 Prerequisites: Cheyenne/GNU
+#%Module
 
 proc ModulesHelp {} {
-  puts stderr "\tcit - loads modules required for building and running FV3 under NEMS on Cheyenne/GNU"
+  puts stderr "\tcit - loads modules required for building and running UFS Model on Cheyenne/GNU"
 }
 
-module-whatis "loads NEMS FV3 prerequisites for Cheyenne/GNU"
+module-whatis "loads UFS Model prerequisites for Cheyenne/GNU"
 
-# NOTE: the "module purge" and loading of the module command are
-# handled by the module-setup.sh (or .csh) script.
+module load cmake/3.16.4
+setenv CMAKE_C_COMPILER mpicc
+setenv CMAKE_CXX_COMPILER mpicxx
+setenv CMAKE_Fortran_COMPILER mpif90
+setenv CMAKE_Platform cheyenne.gnu
 
-##
-## load programming environment
-## this typically includes compiler, MPI and job scheduler
-##
+# load programming environment
 module load ncarenv/1.3
 module load gnu/9.1.0
-module load mpt/2.19
+module load mpt/2.22
 module load ncarcompilers/0.5.0
+module unload netcdf
+
+module use /glade/p/ral/jntp/GMTB/tools/hpc-stack-nco-20201113/modulefiles/stack
+module load hpc/1.0.0-beta1
+module load hpc-gnu/9.1.0
+module load hpc-mpt/2.22
 
-##
-## use pre-compiled PNG, NetCDF, ESMF and NCEP libraries for above compiler / MPI combination
-##
-module use -a /glade/p/ral/jntp/GMTB/tools/ufs-stack-20200909/gnu-9.1.0/mpt-2.19/modules
+module load jasper/2.0.22
+module load zlib/1.2.11
+module load png/1.6.35
 
-module load libpng/1.6.35
+module load hdf5/1.10.6
 module load netcdf/4.7.4
-module load esmf/8.1.0bs27
+module load pio/2.5.1
+module load esmf/8_1_0_beta_snapshot_27
 
-module load bacio/2.4.0
+module load bacio/2.4.1
 module load crtm/2.3.0
-module load g2/3.4.0
-module load g2tmpl/1.9.0
-module load ip/3.3.0
-module load nceppost/dceca26
-module load nemsio/2.5.1
-module load sp/2.3.0
-module load w3emc/2.7.0
-module load w3nco/2.4.0
-
-module load gfsio/1.4.0
-module load sfcio/1.4.0
-module load sigio/2.3.0
-
-##
-## SIONlib library
-##
-module use -a /glade/p/ral/jntp/GMTB/tools/modulefiles/gnu-9.1.0/mpt-2.19
-module load SIONlib/1.7.4
-
-##
-## load cmake
-##
-module load cmake/3.16.4
-setenv CMAKE_C_COMPILER mpicc
-setenv CMAKE_CXX_COMPILER mpicxx
-setenv CMAKE_Fortran_COMPILER mpif90
-setenv CMAKE_Platform cheyenne.gnu
+module load g2/3.4.1
+module load g2tmpl/1.9.1
+module load ip/3.3.3
+module load nemsio/2.5.2
+module load sp/2.3.3
+module load w3emc/2.7.3
+module load w3nco/2.4.1
+module load upp/10.0.0
diff --git a/modulefiles/cheyenne.gnu/fv3_debug b/modulefiles/cheyenne.gnu/fv3_debug
@@ -0,0 +1,45 @@
+#%Module
+
+proc ModulesHelp {} {
+  puts stderr "\tcit - loads modules required for building and running UFS Model on Cheyenne/GNU"
+}
+
+module-whatis "loads UFS Model prerequisites for Cheyenne/GNU"
+
+module load cmake/3.16.4
+setenv CMAKE_C_COMPILER mpicc
+setenv CMAKE_CXX_COMPILER mpicxx
+setenv CMAKE_Fortran_COMPILER mpif90
+setenv CMAKE_Platform cheyenne.gnu
+
+# load programming environment
+module load ncarenv/1.3
+module load gnu/9.1.0
+module load mpt/2.22
+module load ncarcompilers/0.5.0
+module unload netcdf
+
+module use /glade/p/ral/jntp/GMTB/tools/hpc-stack-nco-20201113/modulefiles/stack
+module load hpc/1.0.0-beta1
+module load hpc-gnu/9.1.0
+module load hpc-mpt/2.22
+
+module load jasper/2.0.22
+module load zlib/1.2.11
+module load png/1.6.35
+
+module load hdf5/1.10.6
+module load netcdf/4.7.4
+module load pio/2.5.1
+module load esmf/8_1_0_beta_snapshot_27-debug
+
+module load bacio/2.4.1
+module load crtm/2.3.0
+module load g2/3.4.1
+module load g2tmpl/1.9.1
+module load ip/3.3.3
+module load nemsio/2.5.2
+module load sp/2.3.3
+module load w3emc/2.7.3
+module load w3nco/2.4.1
+module load upp/10.0.0
diff --git a/modulefiles/cheyenne.intel/fv3 b/modulefiles/cheyenne.intel/fv3
@@ -1,60 +1,45 @@
-#%Module######################################################################
-##
-##    NEMS FV3 Prerequisites: Cheyenne/Intel
+#%Module
 
 proc ModulesHelp {} {
-  puts stderr "\tcit - loads modules required for building and running FV3 under NEMS on Cheyenne/Intel"
+  puts stderr "\tcit - loads modules required for building and running UFS Model on Cheyenne/Intel"
 }
 
-module-whatis "loads NEMS FV3 prerequisites for Cheyenne/Intel"
+module-whatis "loads UFS Model prerequisites for Cheyenne/Intel"
 
-# NOTE: the "module purge" and loading of the module command are
-# handled by the module-setup.sh (or .csh) script.
+module load cmake/3.16.4
+setenv CMAKE_C_COMPILER mpicc
+setenv CMAKE_CXX_COMPILER mpicxx
+setenv CMAKE_Fortran_COMPILER mpif90
+setenv CMAKE_Platform cheyenne.intel
 
-##
-## load programming environment
-## this typically includes compiler, MPI and job scheduler
-##
+# load programming environment
 module load ncarenv/1.3
 module load intel/19.1.1
-module load mpt/2.19
+module load mpt/2.22
 module load ncarcompilers/0.5.0
+module unload netcdf
+
+module use /glade/p/ral/jntp/GMTB/tools/hpc-stack-nco-20201113/modulefiles/stack
+module load hpc/1.0.0-beta1
+module load hpc-intel/19.1.1
+module load hpc-mpt/2.22
 
-##
-## use pre-compiled PNG, NetCDF, ESMF and NCEP libraries for above compiler / MPI combination
-##
-module use -a /glade/p/ral/jntp/GMTB/tools/ufs-stack-20200909/intel-19.1.1/mpt-2.19/modules
+module load jasper/2.0.22
+module load zlib/1.2.11
+module load png/1.6.35
 
-module load libpng/1.6.35
+module load hdf5/1.10.6
 module load netcdf/4.7.4
-module load esmf/8.1.0bs27
+module load pio/2.5.1
+module load esmf/8_1_0_beta_snapshot_27
 
-module load bacio/2.4.0
+module load bacio/2.4.1
 module load crtm/2.3.0
-module load g2/3.4.0
-module load g2tmpl/1.9.0
-module load ip/3.3.0
-module load nceppost/dceca26
-module load nemsio/2.5.1
-module load sp/2.3.0
-module load w3emc/2.7.0
-module load w3nco/2.4.0
-
-module load gfsio/1.4.0
-module load sfcio/1.4.0
-module load sigio/2.3.0
-
-##
-## SIONlib library
-##
-module use -a /glade/p/ral/jntp/GMTB/tools/modulefiles/intel-19.1.1/mpt-2.19
-module load SIONlib/1.7.4
-
-##
-## load cmake
-##
-module load cmake/3.16.4
-setenv CMAKE_C_COMPILER mpicc
-setenv CMAKE_CXX_COMPILER mpicxx
-setenv CMAKE_Fortran_COMPILER mpif90
-setenv CMAKE_Platform cheyenne.intel
+module load g2/3.4.1
+module load g2tmpl/1.9.1
+module load ip/3.3.3
+module load nemsio/2.5.2
+module load sp/2.3.3
+module load w3emc/2.7.3
+module load w3nco/2.4.1
+module load upp/10.0.0
+9 −35		cicecore/cicedynB/dynamics/ice_dyn_eap.F90
+38 −77		cicecore/cicedynB/dynamics/ice_dyn_evp.F90
+2 −2		cicecore/cicedynB/dynamics/ice_dyn_evp_1d.F90
+267 −13		cicecore/cicedynB/dynamics/ice_dyn_shared.F90
+3,689 −0		cicecore/cicedynB/dynamics/ice_dyn_vp.F90
+11 −3		cicecore/cicedynB/general/ice_forcing.F90
+133 −17		cicecore/cicedynB/general/ice_init.F90
+3 −1		cicecore/cicedynB/general/ice_step_mod.F90
+71 −1		cicecore/cicedynB/infrastructure/comm/mpi/ice_global_reductions.F90
+71 −1		cicecore/cicedynB/infrastructure/comm/serial/ice_global_reductions.F90
+1 −0		cicecore/cicedynB/infrastructure/ice_grid.F90
+6 −4		cicecore/drivers/direct/hadgem3/CICE_InitMod.F90
+5 −0		cicecore/drivers/direct/hadgem3/CICE_RunMod.F90
+6 −4		cicecore/drivers/mct/cesm1/CICE_InitMod.F90
+5 −0		cicecore/drivers/mct/cesm1/CICE_RunMod.F90
+20 −18		cicecore/drivers/nuopc/cmeps/CICE_InitMod.F90
+5 −4		cicecore/drivers/nuopc/dmi/CICE_InitMod.F90
+5 −0		cicecore/drivers/nuopc/dmi/CICE_RunMod.F90
+6 −4		cicecore/drivers/standalone/cice/CICE_InitMod.F90
+1 −2		cicecore/drivers/standalone/cice/CICE_RunMod.F90
+5 −0		cicecore/drivers/standalone/cice/CICE_RunMod.F90_debug
+0 −1		cicecore/shared/ice_fileunits.F90
+15 −0		configuration/scripts/ice_in
+1 −1		configuration/scripts/machines/Macros.banting_intel
+2 −2		configuration/scripts/machines/Macros.cesium_intel
+1 −1		configuration/scripts/machines/Macros.conda_linux
+1 −1		configuration/scripts/machines/Macros.conda_macos
+1 −1		configuration/scripts/machines/Macros.daley_intel
+1 −1		configuration/scripts/machines/Macros.fram_intel
+1 −1		configuration/scripts/machines/Macros.millikan_intel
+1 −0		configuration/scripts/machines/environment.yml
+1 −0		configuration/scripts/options/set_env.lapack
+3 −0		configuration/scripts/options/set_nml.diagimp
+3 −0		configuration/scripts/options/set_nml.dynanderson
+3 −0		configuration/scripts/options/set_nml.dynpicard
+1 −0		configuration/scripts/options/set_nml.nonlin5000
+6 −0		configuration/scripts/options/set_nml.run3dt
+1 −0		configuration/scripts/tests/base_suite.ts
+1 −1		doc/source/cice_index.rst
+4 −3		doc/source/developer_guide/dg_driver.rst
+5 −5		doc/source/developer_guide/dg_dynamics.rst
+27 −0		doc/source/master_list.bib
+164 −64		doc/source/science_guide/sg_dynamics.rst
+19 −0		doc/source/user_guide/ug_case_settings.rst
+1 −1		icepack
+8 −3		CMakeLists.txt
+1 −1		atmos_cubed_sphere
+5 −3		atmos_model.F90
+3 −0		ccpp/config/ccpp_prebuild_config.py
+1 −1		ccpp/framework
+1 −1		ccpp/physics
+93 −0		ccpp/suites/suite_FV3_GFS_v16beta_coupled.xml
+1 −0		ccpp/suites/suite_FV3_GSD_noah.xml
+1 −0		ccpp/suites/suite_FV3_GSD_v0.xml
+93 −0		ccpp/suites/suite_FV3_GSD_v0_unified_ugwp_suite.xml
+91 −0		ccpp/suites/suite_FV3_GSD_v0_unified_ugwp_suite_noah.xml
+160 −65		gfsphysics/GFS_layer/GFS_typedefs.F90
+166 −17		gfsphysics/GFS_layer/GFS_typedefs.meta
+1 −1		io/CMakeLists.txt
+47 −31		io/FV3GFS_io.F90
+2 −2		io/makefile
+4 −0		io/module_wrt_grid_comp.F90
+6 −0		module_fcst_grid_comp.F90
+64 −47		stochastic_physics/stochastic_physics_wrapper.F90