Link both global-nest fix files and non-nest ones at the same time #2632

guoqing-noaa · 2024-05-27T16:58:39Z

Description

This PR enables linking both global-nest fix files and non-nest ones at the same time and users can run both nesting and non-nesting experiments at the same time without worries about what fix files to be linked.

Resolves #2631

Type of change

New feature (adds functionality)

Change characteristics

Is this a breaking change (a change in existing functionality)? NO
Does this change require a documentation update? NO

How has this been tested?

Clone and build on Hera/Jet
Forecast-only on Hera/Jet

Checklist

Any dependent changes have been merged and published
My code follows the style guidelines of this project
I have performed a self-review of my own code
I have commented my code, particularly in hard-to-understand areas
My changes generate no new warnings
New and existing tests pass with my changes
I have made corresponding changes to the documentation if necessary

sorc/link_workflow.sh

guoqing-noaa · 2024-05-28T22:37:23Z

@aerorahul and @WalterKolczynski-NOAA Thanks a lot for the discussion in today's meeting!
I found that there are many more files involved regarding changing ${FIXgfs}/orog to ${FIXorog}. 11 files (from scripts/, parm/, ush/) will be affected:

scripts/exgdas_enkf_sfc.sh               
scripts/exglobal_atmos_sfcanl.sh         
scripts/exglobal_forecast.sh             
parm/config/gfs/config.base              
parm/ufs/fix/gfs/atmos.fixed_files.yaml  
parm/ufs/fix/gfs/land.fixed_files.yaml   
parm/ufs/fix/gfs/ocean.fixed_files.yaml  
ush/forecast_predet.sh                   
ush/gaussian_sfcanl.sh                   
ush/global_cycle.sh                      
ush/global_cycle_driver.sh

Where ush/global_cycle.sh and ush/global_cycle_driver.sh are linked from another repository ufs_utils.
I am hesitant to make changes to so many files. However, I can update them if you agree that this is the goal we should go.

FYI, here are the output from grep '\/orog' -ir scripts/* parm/* ush/*:

scripts/exgdas_enkf_sfc.sh:            ${NLN} "${FIXgfs}/orog/${CASE}/${CASE}_grid.tile${n}.nc"     "${DATA}/fngrid.${cmem}"                                           
scripts/exgdas_enkf_sfc.sh:            ${NLN} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile${n}.nc" "${DATA}/fnorog.${cmem}"                               
scripts/exgdas_enkf_sfc.sh:            ${NLN} "${FIXgfs}/orog/${CASE}/${CASE}_grid.tile${n}.nc"      "${DATA}/fngrid.${cmem}"                                          
scripts/exgdas_enkf_sfc.sh:            ${NLN} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile${n}.nc" "${DATA}/fnorog.${cmem}"                               
scripts/exglobal_atmos_sfcanl.sh:        ${NLN} "${FIXgfs}/orog/${CASE}/${CASE}_grid.tile${n}.nc"                         "${DATA}/fngrid.00${n}"                      
scripts/exglobal_atmos_sfcanl.sh:        ${NLN} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile${n}.nc"                     "${DATA}/fnorog.00${n}"          
scripts/exglobal_atmos_sfcanl.sh:    ${NLN} "${FIXgfs}/orog/${CASE}/${CASE}_grid.tile${n}.nc"                       "${DATA}/fngrid.00${n}"                            
scripts/exglobal_atmos_sfcanl.sh:    ${NLN} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile${n}.nc"                   "${DATA}/fnorog.00${n}"                
scripts/exglobal_forecast.sh:##         1. computing grid, ${FIXgfs}/orog/$CASE/${CASE}_grid.tile${n}.nc                                                               
scripts/exglobal_forecast.sh:##         2. orography data, ${FIXgfs}/orog/$CASE/${CASE}.mx${OCNRES}_oro_data.tile${n}.nc                                               
scripts/exglobal_forecast.sh:##         3. mosaic data, ${FIXgfs}/orog/$CASE/${CASE}_mosaic.nc                                                                         
parm/config/gfs/config.base:export FIXorog="${FIXgfs}/orog"                                                                                                            
parm/ufs/fix/gfs/atmos.fixed_files.yaml:  - [$(FIXgfs)/orog/$(CASE)/$(CASE)_mosaic.nc, $(DATA)/INPUT/grid_spec.nc]                                                     
parm/ufs/fix/gfs/atmos.fixed_files.yaml:  - [$(FIXgfs)/orog/$(CASE)/$(CASE)_grid.tile1.nc, $(DATA)/INPUT/]                                                             
parm/ufs/fix/gfs/atmos.fixed_files.yaml:  - [$(FIXgfs)/orog/$(CASE)/$(CASE)_grid.tile2.nc, $(DATA)/INPUT/]                                                             
parm/ufs/fix/gfs/atmos.fixed_files.yaml:  - [$(FIXgfs)/orog/$(CASE)/$(CASE)_grid.tile3.nc, $(DATA)/INPUT/]                                                             
parm/ufs/fix/gfs/atmos.fixed_files.yaml:  - [$(FIXgfs)/orog/$(CASE)/$(CASE)_grid.tile4.nc, $(DATA)/INPUT/]                                                             
parm/ufs/fix/gfs/atmos.fixed_files.yaml:  - [$(FIXgfs)/orog/$(CASE)/$(CASE)_grid.tile5.nc, $(DATA)/INPUT/]                                                             
parm/ufs/fix/gfs/atmos.fixed_files.yaml:  - [$(FIXgfs)/orog/$(CASE)/$(CASE)_grid.tile6.nc, $(DATA)/INPUT/]                                                             
parm/ufs/fix/gfs/land.fixed_files.yaml:     # Files from FIXgfs/orog/C??/sfc                                                                                           
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).facsf.tile1.nc, $(DATA)/]                                                
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).facsf.tile2.nc, $(DATA)/]                                                
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).facsf.tile3.nc, $(DATA)/]                                                
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).facsf.tile4.nc, $(DATA)/]                                                
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).facsf.tile5.nc, $(DATA)/]                                                
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).facsf.tile6.nc, $(DATA)/]                                                
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).maximum_snow_albedo.tile1.nc, $(DATA)/]                                  
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).maximum_snow_albedo.tile2.nc, $(DATA)/]                                  
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).maximum_snow_albedo.tile3.nc, $(DATA)/]                                  
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).maximum_snow_albedo.tile4.nc, $(DATA)/]                                  
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).maximum_snow_albedo.tile5.nc, $(DATA)/]                                  
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).maximum_snow_albedo.tile6.nc, $(DATA)/]                                  
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).slope_type.tile1.nc, $(DATA)/]                                           
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).slope_type.tile2.nc, $(DATA)/]                                           
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).slope_type.tile3.nc, $(DATA)/]                                           
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).slope_type.tile4.nc, $(DATA)/]                                           
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).slope_type.tile5.nc, $(DATA)/]                                           
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).slope_type.tile6.nc, $(DATA)/]                                           
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).snowfree_albedo.tile1.nc, $(DATA)/]                                      
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).snowfree_albedo.tile2.nc, $(DATA)/]                                      
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).snowfree_albedo.tile3.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).maximum_snow_albedo.tile4.nc, $(DATA)/]                         [50/4604]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).maximum_snow_albedo.tile5.nc, $(DATA)/]                                  
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).maximum_snow_albedo.tile6.nc, $(DATA)/]                                  
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).slope_type.tile1.nc, $(DATA)/]                                           
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).slope_type.tile2.nc, $(DATA)/]                                           
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).slope_type.tile3.nc, $(DATA)/]                                           
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).slope_type.tile4.nc, $(DATA)/]                                           
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).slope_type.tile5.nc, $(DATA)/]                                           
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).slope_type.tile6.nc, $(DATA)/]                                           
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).snowfree_albedo.tile1.nc, $(DATA)/]                                      
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).snowfree_albedo.tile2.nc, $(DATA)/]                                      
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).snowfree_albedo.tile3.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).snowfree_albedo.tile4.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).snowfree_albedo.tile5.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).snowfree_albedo.tile6.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).soil_type.tile1.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).soil_type.tile2.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).soil_type.tile3.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).soil_type.tile4.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).soil_type.tile5.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).soil_type.tile6.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).substrate_temperature.tile1.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).substrate_temperature.tile2.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).substrate_temperature.tile3.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).substrate_temperature.tile4.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).substrate_temperature.tile5.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).substrate_temperature.tile6.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).vegetation_greenness.tile1.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).vegetation_greenness.tile2.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).vegetation_greenness.tile3.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).vegetation_greenness.tile4.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).vegetation_greenness.tile5.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).vegetation_greenness.tile6.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).vegetation_type.tile1.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).vegetation_type.tile2.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).vegetation_type.tile3.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).vegetation_type.tile4.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).vegetation_type.tile5.nc, $(DATA)/]
parm/ufs/fix/gfs/land.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/sfc/$(CASE).mx$(OCNRES).vegetation_type.tile6.nc, $(DATA)/]
parm/ufs/fix/gfs/ocean.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/$(CASE).mx$(OCNRES)_oro_data.tile1.nc, $(DATA)/INPUT/oro_data.tile1.nc]
parm/ufs/fix/gfs/ocean.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/$(CASE).mx$(OCNRES)_oro_data.tile2.nc, $(DATA)/INPUT/oro_data.tile2.nc]
parm/ufs/fix/gfs/ocean.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/$(CASE).mx$(OCNRES)_oro_data.tile3.nc, $(DATA)/INPUT/oro_data.tile3.nc]
parm/ufs/fix/gfs/ocean.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/$(CASE).mx$(OCNRES)_oro_data.tile4.nc, $(DATA)/INPUT/oro_data.tile4.nc]                 [8/4604]
parm/ufs/fix/gfs/ocean.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/$(CASE).mx$(OCNRES)_oro_data.tile5.nc, $(DATA)/INPUT/oro_data.tile5.nc]
parm/ufs/fix/gfs/ocean.fixed_files.yaml:     - [$(FIXgfs)/orog/$(CASE)/$(CASE).mx$(OCNRES)_oro_data.tile6.nc, $(DATA)/INPUT/oro_data.tile6.nc]
ush/forecast_predet.sh:  FNALBC2=${FNALBC2:-"${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.facsf.tileX.nc"}
ush/forecast_predet.sh:  FNTG3C=${FNTG3C:-"${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.substrate_temperature.tileX.nc"}
ush/forecast_predet.sh:  FNVEGC=${FNVEGC:-"${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.vegetation_greenness.tileX.nc"}
ush/forecast_predet.sh:  FNVMNC=${FNVMNC:-"${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.vegetation_greenness.tileX.nc"}
ush/forecast_predet.sh:  FNVMXC=${FNVMXC:-"${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.vegetation_greenness.tileX.nc"}
ush/forecast_predet.sh:  FNSLPC=${FNSLPC:-"${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.slope_type.tileX.nc"}
ush/forecast_predet.sh:  FNALBC=${FNALBC:-"${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.snowfree_albedo.tileX.nc"}
ush/forecast_predet.sh:  FNVETC=${FNVETC:-"${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.vegetation_type.tileX.nc"}
ush/forecast_predet.sh:  FNSOTC=${FNSOTC:-"${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.soil_type.tileX.nc"}
ush/forecast_predet.sh:  FNSOCC=${FNSOCC:-"${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.soil_color.tileX.nc"}
ush/forecast_predet.sh:  FNABSC=${FNABSC:-"${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.maximum_snow_albedo.tileX.nc"}
ush/forecast_predet.sh:    ${NCP} "${FIXgfs}/orog/${CASE}/${CASE}_mosaic.nc" "${DATA}/INPUT/grid_spec.nc"
ush/forecast_predet.sh:    ${NCP} "${FIXgfs}/orog/${CASE}/${CASE}_mosaic.nc" "${DATA}/INPUT/${CASE}_mosaic.nc"
ush/forecast_predet.sh:    ${NCP} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile${tt}.nc" "${DATA}/INPUT/oro_data.tile${tt}.nc"
ush/forecast_predet.sh:    ${NCP} "${FIXgfs}/orog/${CASE}/${CASE}_grid.tile${tt}.nc"                 "${DATA}/INPUT/${CASE}_grid.tile${tt}.nc"
ush/gaussian_sfcanl.sh:#     fixed data : ${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile*.nc
ush/gaussian_sfcanl.sh:FIXWGTS=${FIXWGTS:-${FIXgfs}/orog/${CASE}/fv3_SCRIP_${CASE}_GRIDSPEC_lon${LONB_SFC}_lat${LATB_SFC}.gaussian.neareststod.nc}
ush/gaussian_sfcanl.sh:${NLN} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile1.nc" "./orog.tile1.nc"
ush/gaussian_sfcanl.sh:${NLN} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile2.nc" "./orog.tile2.nc"
ush/gaussian_sfcanl.sh:${NLN} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile3.nc" "./orog.tile3.nc"
ush/gaussian_sfcanl.sh:${NLN} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile4.nc" "./orog.tile4.nc"
ush/gaussian_sfcanl.sh:${NLN} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile5.nc" "./orog.tile5.nc"
ush/gaussian_sfcanl.sh:${NLN} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile6.nc" "./orog.tile6.nc"
ush/global_cycle.sh:#                   defaults to ${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.snowfree_albedo.tileX.nc
ush/global_cycle.sh:#                   Defaults to ${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.facsf.tileX.nc
ush/global_cycle.sh:#                   Defaults to ${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.substrate_temperature.tileX.nc
ush/global_cycle.sh:#                   Defaults to ${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.vegetation_greenness.tileX.nc
ush/global_cycle.sh:#                   Defaults to ${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.vegetation_type.tileX.nc
ush/global_cycle.sh:#                   Defaults to ${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.soil_type.tileX.nc
ush/global_cycle.sh:#                   Defaults to ${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.vegetation_greenness.tileX.nc
ush/global_cycle.sh:#                   Defaults to ${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.vegetation_greenness.tileX.nc
ush/global_cycle.sh:#                   Defaults to ${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.slope_type.tileX.nc
ush/global_cycle.sh:#                   Defaults to ${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.maximum_snow_albedo.tileX.nc
ush/global_cycle.sh:FNALBC2=${FNALBC2:-${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.facsf.tileX.nc}
ush/global_cycle.sh:FNTG3C=${FNTG3C:-${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.substrate_temperature.tileX.nc}
ush/global_cycle.sh:FNVEGC=${FNVEGC:-${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.vegetation_greenness.tileX.nc}
ush/global_cycle.sh:FNALBC=${FNALBC:-${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.snowfree_albedo.tileX.nc}
ush/global_cycle.sh:FNVETC=${FNVETC:-${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.vegetation_type.tileX.nc}
ush/global_cycle.sh:FNSOTC=${FNSOTC:-${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.soil_type.tileX.nc}
ush/global_cycle.sh:FNABSC=${FNABSC:-${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.maximum_snow_albedo.tileX.nc}
ush/global_cycle.sh:FNVMNC=${FNVMNC:-${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.vegetation_greenness.tileX.nc}
ush/global_cycle.sh:FNVMXC=${FNVMXC:-${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.vegetation_greenness.tileX.nc}
ush/global_cycle.sh:FNSLPC=${FNSLPC:-${FIXgfs}/orog/${CASE}/sfc/${CASE}.mx${OCNRES}.slope_type.tileX.nc}
ush/global_cycle_driver.sh:  ln -fs $FIXgfs/orog/${CASE}/C${CRES}_grid.tile${n}.nc       $DATA/fngrid.00$n
ush/global_cycle_driver.sh:    ln -fs $FIXgfs/orog/${CASE}/C${CRES}_oro_data.tile${n}.nc   $DATA/fnorog.00$n
ush/global_cycle_driver.sh:    ln -fs $FIXgfs/orog/${CASE}/C${CRES}.mx${OCNRES}_oro_data.tile${n}.nc   $DATA/fnorog.00$n

WalterKolczynski-NOAA · 2024-05-30T07:47:28Z

@guoqing-noaa I think changing it is still the way to go. Changing UFS Utils may require additional changes beyond scripts we use. @GeorgeGayno-NOAA will know for sure

@GeorgeGayno-NOAA Short version: We're looking to go back to using ${FIXorog} in place of ${FIXgfs}/orog as the best way to support running with a nest for the AR project, which needs a different set of orog and ugwd fix files. I know we only recently changed it, so apologies.

GeorgeGayno-NOAA · 2024-05-30T12:35:25Z

@guoqing-noaa I think changing it is still the way to go. Changing UFS Utils may require additional changes beyond scripts we use. @GeorgeGayno-NOAA will know for sure

@GeorgeGayno-NOAA Short version: We're looking to go back to using ${FIXorog} in place of ${FIXgfs}/orog as the best way to support running with a nest for the AR project, which needs a different set of orog and ugwd fix files. I know we only recently changed it, so apologies.

That change was done in this PR: ufs-community/UFS_UTILS#899. Does the entire PR need to be reverted or just the $FIXorog part?

guoqing-noaa · 2024-05-30T16:40:32Z

Thanks, @WalterKolczynski-NOAA and @GeorgeGayno-NOAA

Currently, the idea is to revert $FIXorog and $FIXugwd only

I will work on this.

GeorgeGayno-NOAA · 2024-05-30T16:54:24Z

Thanks, @WalterKolczynski-NOAA and @GeorgeGayno-NOAA

Currently, the idea is to revert $FIXorog and $FIXugwd only

I will work on this.

I will open a UFS_UTILS issue? Should I assign it to you or myself?

guoqing-noaa · 2024-05-30T19:02:09Z

I will open a UFS_UTILS issue? Should I assign it to you or myself?

Thanks, @GeorgeGayno-NOAA! It will be great if you can make changes for UFS_UTILS. And I can focus on making changes to the global workflow.

aerorahul · 2024-05-31T13:47:47Z

@guoqing-noaa @GeorgeGayno-NOAA
I agree w/ @WalterKolczynski-NOAA.
We should define FIXorog and FIXugwd depending on DO_NEST where applicable and use those 2 variables instead of $FIXgfs/orog and $FIXgfs/ugwd. The variables FIXorog and FIXugwd could be defined in config files or in the j-job that needs this information.
@GeorgeGayno-NOAA
Someone from the workflow team can make that change in the ufs-utils.
@guoqing-noaa
If you can make the update for the nest in the global-workflow in this PR, we could update the hash of ufs-utils included in this PR.
Please let me know if we need to coordinate/clarify offline.

GeorgeGayno-NOAA · 2024-05-31T14:12:09Z

@guoqing-noaa @GeorgeGayno-NOAA I agree w/ @WalterKolczynski-NOAA. We should define FIXorog and FIXugwd depending on DO_NEST where applicable and use those 2 variables instead of $FIXgfs/orog and $FIXgfs/ugwd. The variables FIXorog and FIXugwd could be defined in config files or in the j-job that needs this information. @GeorgeGayno-NOAA Someone from the workflow team can make that change in the ufs-utils.

Great. I opened this issue: ufs-community/UFS_UTILS#955

@guoqing-noaa If you can make the update for the nest in the global-workflow in this PR, we could update the hash of ufs-utils included in this PR. Please let me know if we need to coordinate/clarify offline.

guoqing-noaa · 2024-05-31T18:34:15Z

Thanks, @aerorahul. I will update this PR sometime today and get ready for a review.

aerorahul · 2024-05-31T18:56:54Z

@guoqing-noaa
Please see ufs-community/UFS_UTILS#956
You should be able to define and export FIXorog in the config files or in the script where global_cycle.sh is called to realize the change.

- link nest fix files when needed, i.e. keep the --nest option - change $FIXgfs/orog to $FIXorog - change $FIXgfs/ugwd to $FIXugwd

guoqing-noaa · 2024-05-31T19:45:42Z

@guoqing-noaa Please see ufs-community/UFS_UTILS#956 You should be able to define and export FIXorog in the config files or in the script where global_cycle.sh is called to realize the change.
Thanks! @aerorahul

guoqing-noaa · 2024-06-06T00:47:30Z

@aerorahul @WalterKolczynski-NOAA This PR is ready for review. Let me know if you have any comments. Thanks!

WalterKolczynski-NOAA

Looks good except the UFS_UTILS version needs to be updated. Let us know if you need guidance on how to update a submodule hash.

guoqing-noaa · 2024-06-11T01:16:16Z

Looks good except the UFS_UTILS version needs to be updated. Let us know if you need guidance on how to update a submodule hash.

@WalterKolczynski-NOAA Thanks for the feedback. I just updated the UFS_UTILS hash.

WalterKolczynski-NOAA

Conditionally approved pending successful completion of CI tests.

emcbot · 2024-06-11T08:08:00Z

CI Passed Hercules at
Built and ran in directory /work2/noaa/stmp/CI/HERCULES/2632

emcbot · 2024-06-11T20:48:11Z

CI Update on Wcoss2 at 06/11/24 08:48:10 PM
============================================
Cloning and Building global-workflow PR: 2632
with PID: 238626 on host: clogin05

emcbot · 2024-06-11T21:36:52Z

Automated global-workflow Testing Results:

Machine: Wcoss2
Start: Tue Jun 11 20:58:32 UTC 2024 on clogin05
---------------------------------------------------
Build: Completed at 06/11/24 09:36:38 PM
Case setup: Completed for experiment C48_ATM_49dcee8b
Case setup: Skipped for experiment C48mx500_3DVarAOWCDA_49dcee8b
Case setup: Skipped for experiment C48_S2SWA_gefs_49dcee8b
Case setup: Completed for experiment C48_S2SW_49dcee8b
Case setup: Completed for experiment C96_atm3DVar_extended_49dcee8b
Case setup: Skipped for experiment C96_atm3DVar_49dcee8b
Case setup: Skipped for experiment C96_atmaerosnowDA_49dcee8b
Case setup: Completed for experiment C96C48_hybatmDA_49dcee8b
Case setup: Completed for experiment C96C48_ufs_hybatmDA_49dcee8b

emcbot · 2024-06-11T22:48:11Z

Experiment C48_ATM_49dcee8b SUCCESS on Wcoss2 at 06/11/24 10:48:11 PM

emcbot · 2024-06-11T23:06:10Z

Experiment C48_S2SW_49dcee8b SUCCESS on Wcoss2 at 06/11/24 11:06:09 PM

emcbot · 2024-06-11T23:57:12Z

Experiment C96C48_ufs_hybatmDA_49dcee8b SUCCESS on Wcoss2 at 06/11/24 11:57:11 PM

emcbot · 2024-06-12T00:03:24Z

Experiment C96C48_hybatmDA_49dcee8b SUCCESS on Wcoss2 at 06/12/24 12:03:23 AM

emcbot · 2024-06-12T02:06:04Z

CI Passed Hera at
Built and ran in directory /scratch1/NCEPDEV/global/CI/2632

emcbot · 2024-06-12T05:42:30Z

Experiment C96_atm3DVar_extended_49dcee8b SUCCESS on Wcoss2 at 06/12/24 05:42:29 AM

emcbot · 2024-06-12T05:45:12Z

All CI Test Cases Passed on Wcoss2:

Experiment C48_ATM_49dcee8b *** SUCCESS *** at 06/11/24 10:48:11 PM
Experiment C48_S2SW_49dcee8b *** SUCCESS *** at 06/11/24 11:06:09 PM
Experiment C96C48_ufs_hybatmDA_49dcee8b *** SUCCESS *** at 06/11/24 11:57:11 PM
Experiment C96C48_hybatmDA_49dcee8b *** SUCCESS *** at 06/12/24 12:03:23 AM
Experiment C96_atm3DVar_extended_49dcee8b *** SUCCESS *** at 06/12/24 05:42:29 AM

…bal-workflow into feature/move_jcb * 'feature/move_jcb' of https://github.com/danholdaway/global-workflow: Add COM template for JEDI obs (NOAA-EMC#2678) Link both global-nest fix files and non-nest ones at the same time (NOAA-EMC#2632) Update ufs-weather-model (NOAA-EMC#2663) Add ability to process ocean/ice products specific to GEFS (NOAA-EMC#2561) Update cleanup job to use COMIN/COMOUT (NOAA-EMC#2649) Add overwrite to creat experiment in BASH CI (NOAA-EMC#2676) Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (NOAA-EMC#2645) Update RDHPCS Hera resource for `eupd` task (NOAA-EMC#2636)

* origin/develop: Add observation preparation job for aerosols DA to workflow (NOAA-EMC#2624) Remove ocean daily files (NOAA-EMC#2689) Update Jenkinsfile Add Hercules-EMC to the Jenkins configurable parameter list (NOAA-EMC#2685) Update gdas.cd and gsi_utils hashes (NOAA-EMC#2641) Add ability to use GEFS replay ICs (NOAA-EMC#2559) Replace `sleep` with `wait_for_file` (NOAA-EMC#2586) Add COM template for JEDI obs (NOAA-EMC#2678) Link both global-nest fix files and non-nest ones at the same time (NOAA-EMC#2632) Update ufs-weather-model (NOAA-EMC#2663) Add ability to process ocean/ice products specific to GEFS (NOAA-EMC#2561) Update cleanup job to use COMIN/COMOUT (NOAA-EMC#2649) Add overwrite to creat experiment in BASH CI (NOAA-EMC#2676) Add handling to select CRTM cloud optical table based on cloud scheme and update calcanal_gfs.py (NOAA-EMC#2645) Refs NOAA-EMC#2475

…2632) This PR enables linking both global-nest fix files and non-nest ones at the same time and users can run both nesting and non-nesting experiments at the same time without worries about what fix files to be linked. Resolves #2631

Link both global-nest fix files and non-nest ones at the same time

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github-advanced-security bot found potential problems May 27, 2024

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Merge branch 'develop' into pr_nest_fix_files

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GeorgeGayno-NOAA mentioned this pull request May 30, 2024

Replace script variables ${FIXorog} with $(FIXgfs}/orog ufs-community/UFS_UTILS#955

Closed

Merge branch 'develop' into pr_nest_fix_files

20d0921

guoqing-noaa added 2 commits May 31, 2024 13:38

Changes based on reviews

c9bdd93

- link nest fix files when needed, i.e. keep the --nest option - change $FIXgfs/orog to $FIXorog - change $FIXgfs/ugwd to $FIXugwd

update .gitignore

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Merge branch 'develop' into pr_nest_fix_files

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WalterKolczynski-NOAA requested changes Jun 6, 2024

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guoqing-noaa and others added 2 commits June 10, 2024 19:11

Merge branch 'develop' into pr_nest_fix_files

1af7fb4

update ufs_utils hash

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WalterKolczynski-NOAA approved these changes Jun 11, 2024

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WalterKolczynski-NOAA added the CI-Hercules-Ready **CM use only** PR is ready for CI testing on Hercules label Jun 11, 2024

emcbot added CI-Hercules-Building **Bot use only** CI testing is cloning/building on Hercules and removed CI-Hercules-Ready **CM use only** PR is ready for CI testing on Hercules labels Jun 11, 2024

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WalterKolczynski-NOAA requested a review from aerorahul June 12, 2024 15:04

WalterKolczynski-NOAA merged commit 2e6f1fc into NOAA-EMC:develop Jun 12, 2024
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Link both global-nest fix files and non-nest ones at the same time #2632

Link both global-nest fix files and non-nest ones at the same time #2632

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Link both global-nest fix files and non-nest ones at the same time #2632

Link both global-nest fix files and non-nest ones at the same time #2632

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