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.

[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.