add component defaults, rename templates to .in, rename ufs.configure for application, cleanup tests

[DeniseWorthen]

PR Author Checklist:

• I have linked PR's from all sub-components involved in section below. N/A
• I am confirming reviews are completed in ALL sub-component PR's. N/A
• I have run the full RT suite on either Hera/Cheyenne AND have attached the log to this PR below this line:
  • LOG: RegressionTests_hera.log
• I have added the list of all failed regression tests to "Anticipated changes" section.
• I have filled out all sections of the template.

Description

• Renames various template files for the coupled model to be .IN files

• Provides component defaults for cice, mom6, cmeps and ww3 that can be re-used among applications instead of repeating the same defaults for each application

• Renames ufs.configure files using the application (ie, s2s, s2swa) which uses them

• Adds CICE_, MOM6_ and WW3_ prefixes to many, but not all, configurable variables

• Adds additional configuration settings for CICE,MOM6,CMEPS restart and output directories

• Moves use_coldstart and use_mommesh from the ALLComp to the OCN attributes, since these are used only by MOM6

• Moves eps_imesh from the ALLComp to the ICE attributes since this is used only by ICE. Note MOM6 has a similar setting (eps_omesh) which is configured w/ a default value via MOM_input.

• gives MOM6 and CICE their own mesh file setting instead of meshiceocn since in upcoming configurations (regional MOM6, FVCOM etc) the ocean will not run with the ice model present

• Uses INPUT as input directory for all tests using CDEPS instead of various combinations of INPUT_DATM, DATM_INPUT, INPUT_DOCN etc

• removes unnecessary quotes in tests

• turns off control_wrtGauss_netcdf_parallel_intel test on hercules. See Issue multiple netcdf_parallel tests fail on hercules #2015

Linked Issues and Pull Requests

Associated UFSWM Issue to close

• closes rename "template" files as ".IN" files. #2000
• closes export component defaults instead of application defaults for coupled configs #1999
• closes rename various ufs.configure files according to application #2018
• needed by Consistent variables in UFS WM RT global test namelist templates and global workflow namelists #1664
• supercedes Additional template variables for CICE namelist #1998

Subcomponent Pull Requests

Blocking Dependencies

Subcomponents involved:

• AQM
• CDEPS
• CICE
• CMEPS
• CMakeModules
• FV3
• GOCART
• HYCOM
• MOM6
• NOAHMP
• WW3
• stochastic_physics
• none

Anticipated Changes

Input data

• No changes are expected to input data.
• Changes are expected to input data:
  • New input data.
  • Updated input data.

Regression Tests:

• No changes are expected to any regression test.
• Changes are expected to the following tests:

Three tests fail but run to completion:

7831:FAILED TESTS:
7832:147 hafs_regional_docn_intel failed in check_result
7833:hafs_regional_docn_intel 147 failed in run_test
7834:148 hafs_regional_docn_oisst_intel failed in check_result
7835:hafs_regional_docn_oisst_intel 148 failed in run_test
7836:149 hafs_regional_datm_cdeps_intel failed in check_result
7837:hafs_regional_datm_cdeps_intel 149 failed in run_test

These tests fail only because the filename stored in a file has a changed directory name, ie INPUT/sst.day.mean.2019.nc vs INPUT_DOCN/sst.day.mean.2019.nc. All other files for each of the failed tests is B4B:

grep NOT RegressionTests_hera.log
5125: Comparing ufs.hafs.docn.r.2019-08-29-21600.nc ............ALT CHECK......NOT OK
5140: Comparing ufs.hafs.docn.r.2019-08-29-21600.nc ............ALT CHECK......NOT OK
5153: Comparing ufs.hafs.datm.r.2019-08-30-00000.nc ............ALT CHECK......NOT OK

Hera RTs were re-run at 86415ba with identical results.

Tests effected by changes in this PR:

Libraries

• Not Needed
• Needed
  • Create separate issue in JCSDA/spack-stack asking for update to library. Include library name, library version.
  • Add issue link from JCSDA/spack-stack following this item

Code Managers Log

• This PR is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR.
• Move new/updated input data on RDHPCS Hera and propagate input data changes to all supported systems.
  • N/A

Testing Log:

• RDHPCS
  • Hera
  • Orion
  • Hercules
  • Jet
  • Gaea
  • Cheyenne
• WCOSS2
  • Dogwood/Cactus
  • Acorn
• CI
  • Completed
• opnReqTest
  • N/A
  • Log attached to comment

[aerorahul]

Thanks for the additional templating of the configuration files.
The changes look good.

[MatthewMasarik-NOAA]

WW3 updates look good to me.

[DeniseWorthen]

OK, I think we're good. The only files that I had to modify from the previous PR were to add the new MOM6 variables to the mom6 default export section and add them to the (renamed) MOM .IN files.

export MOM6_DIAG_COORD_DEF_Z_FILE=interpolate_zgrid_40L.nc
export MOM6_DIAG_MISVAL='-1e34'

[zach1221]

OK, I think we're good. The only files that I had to modify from the previous PR were to add the new MOM6 variables to the mom6 default export section and add them to the (renamed) MOM .IN files.

export MOM6_DIAG_COORD_DEF_Z_FILE=interpolate_zgrid_40L.nc
export MOM6_DIAG_MISVAL='-1e34'

Sounds good. I'll get everything started then.

[epic-cicd-jenkins]

Jenkins-ci ORTs passed

[DeniseWorthen]

Just noting that the hercules log shows a clean test because I turned off the troublesome control_wrtGauss_netcdf_parallel_intel test in this PR.

[zach1221]

Testing is complete, sending out final reviews.