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UFS-dev PR#184 #132

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UFS-dev PR#184 #132

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Identical to ufs-community#2213 (BL change)

Also contains:
ufs-community#2181 (BL change)
ufs-community#1147 (no BL change)
ufs-community#2194 (BL change)
ufs-community#2202 (no BL change)
ufs-community#2195 (no BL change, new INPUT data)
ufs-community#2193 (no BL change)
ufs-community#2175 (BL change)
ufs-community#2223 (no BL change)
ufs-community#2145 (BL change)
ufs-community#2201 (no BL change)
ufs-community#2234 (no BL change)
ufs-community#2160 (no BL change)
ufs-community#2225 (no BL change)

climbfuji and others added 15 commits March 18, 2024 14:44
…ure/capgen into main/20240308) Combined PR ufs-community#2190 (ufs-community#2181)

* FV3 - Update submodule pointers for ccpp-framework and ccpp-physics. Change units flashes 5 min-1 to flashes min-1 and update long name to make clear this is per 5 minutes.
    * ccpp-physics - In physics/Interstitials/UFS_SCM_NEPTUNE/maximum_hourly_diagnostics.meta: change units flashes 5 min-1 to flashes min-1 and update long name to make clear this is per 5 minutes.
    * ccpp-framework - Update main from feature/capgen as of 2024-03-08 (includes optional argument updates in feature/capgen). Only commit on top of the merge is NCAR/ccpp-framework@6cdd38a which is required to parse the metadata in the Unified Forecast System / ccpp-physics (underscores in units, e.g. degree_north).
…allow-argument-mismatch' flag (ufs-community#1147)

* UFSWM - Fix type mismatch compiler error when gfortran 10 is used without '-fallow-argument-mismatch' flag.
  * FV3 - Fix type mismatch compiler error when gfortran 10 is used without '-fallow-argument-mismatch' flag.
    * ccpp-physics - Resolve various subroutine argument mismatches.
    * ccpp-framework - Add support to use mpi_f08 MPI module .
  * stochastic_physics - Fix type mismatch compiler error when gfortran 10 is used without '-fallow-argument-mismatch' flag.
- update module paths in Hera intel/gnu lua files for Rocky8 OS spack-stack libraries.
…ity#2197), add xr_cnvcld flag to FV3 (ufs-community#2185) (ufs-community#2202)

* UFSWM - atparse.bash: correctly handle input that doesn't end with an end-of-line character. Fix some bugs in Rocoto support and clean up rt.sh.
  * FV3 - namelist flag xr_cnvcld to control if suspended grid-mean convective cloud condensate should be included in cloud fraction and optical depth calculation in radiation in the GFS suite
    * ccpp - physics-level changes to implement new namelist variable
  * MOM6 - update MOM6 code to eliminate all compiler warnings
…#2193)

* UFSWM - Update module_write_netcdf to avoid hangs in RRFS runs
  * FV3 - Update module_write_netcdf to avoid hangs in RRFS runs
…ommunity#2175)

  * CMEPS - allow additional dimension in cpl_scalars for CSG and regional ATM domains for use in mediator history files 
  * CMEPS - fix mapping mask for lnd->atm
  * FV3 - add export of cpl_scalars
  * NOAHMP - add export of cpl_scalars
…fs-community#2223)

cubed_sphere hash update: f060e85 for a bug- fix in the HAILCAST diagnostic code (units issue)
Update to CICE-Consortium/CICE aca8357. Adds implementation of namelist PIO options for CICE
…m wrong for nests (ufs-community#2201)

* UFSWM - None.
  * FV3 - Write component will use kchunk3d. Model init sends the right tile number to CCPP.
    * atmos_cubed_sphere - Initialize the hailwat variable. Pass global_tile index to model.
*doc/UserGuide
   *requirements.txt - updates inda version from 3.6 to 3.7
* UFSWM 
  * doc/Userguide
    * source
      * conf.py
      * Configurations.rst
      * FAQ.rst
      * InputsOutputs.rst
      * Introduction.rst
…Adds -v Verbose option. (ufs-community#2218)  Remove nowarn Intel compiler flag (ufs-community#2225)

* UFSWM
- Add bash linting to CI:
  - uses superlinter to check for consistent bash code writing
- Cleans up .sh scripts to comply with superlinter
- Cleans up .sh scripts to be more consistent, easier to read.
- Add's -v verbose option if debugging outputs needed, otherwise simplifies rt.sh run echo's.
- Addresses smaller bugs
  - quota/timeout search logic adjusted.
  - check for dirs existing (DISKNM, STMP, PTMP) before starting.
  - adjustments/cleanup to ecflow/rocoto sections
  - rt.sh will attempt to start ecflow, and only stop ecflow if it started from rt.sh.
  - fix for issue where run_dir will not delete properly.
* FV3: Address compiler warnings
  * atmos_cubed_sphere: Address compiler warnings.
* UFSWM - Update inline post
  * FV3 - Update upp submodule for inline post
@grantfirl
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grantfirl commented May 23, 2024

@mkavulich I've been trying to update the different version of rt.sh that you modified to work with our system as we catch up with ufs-dev, but the changes to rt.sh in this PR are too extensive to try to reconcile. I'm thinking that we probably need to rebase rt.sh off of this PR and re-implement the changes within to work within the NCAR system.

@grantfirl
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Expected Failed RTs:
2213
control_p8_atmlnd_sbs intel
control_p8_atmlnd intel
control_restart_p8_atmlnd intel
control_p8_atmlnd_debug intel

2145
cpld_control_gfsv17_iau intel
cpld_control_ciceC_p8 intel
cpld_control_c192_p8 intel
cpld_restart_c192_p8 intel
cpld_control_c48 intel
datm_cdeps_ciceC_cfsr intel
datm_cdeps_mx025_cfsr intel
datm_cdeps_mx025_gefs intel
cpld_control_nowave_noaero_p8 gnu

2175
hafs_regional_atm_ocn intel
hafs_regional_docn intel
hafs_regional_docn_oisst intel
control_p8_atmlnd intel
control_restart_p8_atmlnd intel

2194
all GNU tests

2181
conus13km_control intel
conus13km_2threads intel
conus13km_restart_mismatch intel
conus13km_debug intel
conus13km_debug_qr intel
conus13km_debug_2threads intel
conus13km_radar_tten_debug intel
conus13km_control gnu
conus13km_2threads gnu
conus13km_restart_mismatch gnu
conus13km_debug gnu
conus13km_debug_qr gnu
conus13km_debug_2threads gnu
conus13km_radar_tten_debug gnu

@mkavulich
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Thanks for the heads up. I probably won't be able to get to this for a while given how busy I am elsewhere, and a short week coming up. Is it all right if this waits for a week or two?

@grantfirl
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New WW3 input data copied to /scratch1/BMC/gmtb/CCPP_regression_testing/NCAR_ufs-weather-model/input_data/20230920

@grantfirl
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Thanks for the heads up. I probably won't be able to get to this for a while given how busy I am elsewhere, and a short week coming up. Is it all right if this waits for a week or two?

I guess that it's OK to wait on the UFS PR side, but the reason I'm adding this is to bring ccpp-physics up-to-date with ufs/dev for the release.

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