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Merged
DomHeinzeller merged 7 commits into from
Dec 8, 2020
Merged

Update gsl/develop from develop 2020/12/08 #50

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bbc3771
Updates to stochastic_physics_wrapper (#280)
pjpegion Nov 30, 2020
63591b6
Update for Jet, bug fixes in running with frac_grid=T and GFDL MP, an…
climbfuji Dec 2, 2020
81c7e25
Merge branch 'develop' of https://github.com/ufs-community/ufs-weathe…
climbfuji Dec 3, 2020
125c442
Feature/update mom6 and retain b4b results for 025x025 resolution (#290)
jiandewang Dec 4, 2020
0cf031e
Update CICE, Move regression test input outside baseline directory (#…
DeniseWorthen Dec 7, 2020
43bd803
Merge branch 'develop' of https://github.com/ufs-community/ufs-weathe…
climbfuji Dec 8, 2020
d321f99
Revert change to .gitmodules and update submodule pointer for fv3atm
climbfuji Dec 8, 2020
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2 changes: 1 addition & 1 deletion CICE-interface/CICE
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Submodule CICE updated 45 files
+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
1 change: 1 addition & 0 deletions CICE-interface/cice_files.cmake
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Original file line number Diff line number Diff line change
Expand Up @@ -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

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2 changes: 1 addition & 1 deletion FV3
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Submodule FV3 updated 4 files
+5 −3 atmos_model.F90
+1 −1 ccpp/physics
+27 −18 io/FV3GFS_io.F90
+64 −47 stochastic_physics/stochastic_physics_wrapper.F90
2 changes: 1 addition & 1 deletion MOM6-interface/MOM6
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Submodule MOM6 updated 205 files
19 changes: 12 additions & 7 deletions MOM6-interface/mom6_files.cmake
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
)
3 changes: 2 additions & 1 deletion cmake/configure_jet.intel.cmake
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Original file line number Diff line number Diff line change
@@ -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)
1 change: 1 addition & 0 deletions fms_files.cmake
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Original file line number Diff line number Diff line change
@@ -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
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72 changes: 31 additions & 41 deletions modulefiles/jet.intel/fv3
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Original file line number Diff line number Diff line change
@@ -1,53 +1,43 @@
#%Module######################################################################
##
## nems prerequisites
##
#%Module

proc ModulesHelp {} {
puts stderr "The prerequisites for compiling or running FV3 on Jet/Intel"
puts stderr "\tcit - loads modules required for building and running UFS Model on Jet/Intel"
}

module purge
module-whatis "loads UFS Model prerequisites for Jet/Intel"

##
## load contrib environment
## load slurm utils (arbitrary.pl layout.pl)
##
module use -a /contrib/sutils/modulefiles
module use /contrib/sutils/modulefiles
module load sutils

module load intel/18.0.5.274
module load impi/2018.4.274

##
## use pre-compiled PNG, NetCDF, ESMF and NCEP libraries for above compiler / MPI combination
##
module use -a /lfs4/HFIP/hfv3gfs/software/ufs-stack-20200909/intel-18.0.5.274/impi-2018.4.274/modules

module load libpng/1.6.35
module load netcdf/4.7.4
module load esmf/8.1.0bs27

module load bacio/2.4.0
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

##
## load cmake
##
module load cmake/3.16.1
setenv CMAKE_C_COMPILER mpiicc
setenv CMAKE_CXX_COMPILER mpiicpc
setenv CMAKE_Fortran_COMPILER mpiifort
setenv CMAKE_Platform jet.intel

module use /lfs4/HFIP/hfv3gfs/nwprod/hpc-stack/libs/modulefiles/stack

# At this time (2020/11/30), this is the pre-release version 1.0.0
module load hpc/1.1.0
module load hpc-intel/18.0.5.274
module load hpc-impi/2018.4.274

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

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
2 changes: 1 addition & 1 deletion stochastic_physics
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Submodule stochastic_physics updated from 6eac84 to e4913c
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