Update FV3 (Thompson MP and RRTMGP), CMEPS, documentation and CI

[MinsukJi-NOAA]

PR Checklist

• Ths 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. Please consult the ufs-weather-model wiki if you are unsure how to do this.

• This PR has been tested using a branch which is up-to-date with the top of all sub-component repositories except for those sub-components which are the subject of this PR

• An Issue describing the work contained in this PR has been created either in the subcomponent(s) or in the ufs-weather-model. The Issue should be created in the repository that is most relevant to the changes in contained in the PR. The Issue and the dependent sub-component PR
  are specified below.

• If new or updated input data is required by this PR, it is clearly stated in the text of the PR.

Description

• This PR combines several PR's:
  • Add extended diagnostic output from Thompson MP + regression test, includes "Add optional scaling to RRTMGP flux adjustment" (#605), bug fix in several suite definition files #658 from @climbfuji for FV3 update
  • Update CMEPS #665 from @DeniseWorthen for CMEPS update
  • Build and RT/UT documentation for user's guide #593 from @MinsukJi-NOAA for documentation update
  • CI update which includes:
    • Add L127 control tests to CI; INLINE_POST now working
    • Add cpld_dbg test to CI
    • Update the ubuntu-hpc container to the latest g2, g2tmpl, upp libraries (see Update UPP control files for GFS, RRFS and HAFS #646)

Issue(s) addressed

• Extended diagnostic output from Thompson MP NCAR/ccpp-physics#680
• Update CMEPS from ESCOMP NOAA-EMC/CMEPS#50
• Add build information to UFS weather model guide #465 RT documentation in Users Guide #466 Update RT documentation with utest documentation #467

Testing

Initial tests on Hera against BL of 20210616

Failed tests for Intel:

cpld_control 001 (only RESTART/ufs.cpld.cpl.r.2016-10-04-00000.nc, expected)
cpld_decomp 003 (only RESTART/ufs.cpld.cpl.r.2016-10-04-00000.nc, expected)
cpld_ca 004 (only RESTART/ufs.cpld.cpl.r.2016-10-04-00000.nc, expected)
cpld_control_c192 005 (only RESTART/ufs.cpld.cpl.r.2016-10-05-00000.nc, expected)
cpld_control_c384 007 (only RESTART/ufs.cpld.cpl.r.2016-10-03-43200.nc, expected)
cpld_bmark_v16 009 (only RESTART/ufs.cpld.cpl.r.2013-04-01-21600.nc, expected)
cpld_bmark_v16_nsst 011 (only RESTART/ufs.cpld.cpl.r.2013-04-01-21600.nc, expected)
cpld_bmark_wave_v16 012 (only RESTART/ufs.cpld.cpl.r.2013-04-01-21600.nc, expected)
cpld_bmark_wave_v16_noahmp 013 (also in Dom's testing)
cpld_control_wave 014 (only RESTART/ufs.cpld.cpl.r.2016-10-04-00000.nc, expected)
cpld_debug 015 (only RESTART/ufs.cpld.cpl.r.2016-10-03-21600.nc, expected)

control_rrtmgp 030 (also in Dom's testing)
control_thompson 036 (also in Dom's testing)
control_thompson_no_aero 037 (also in Dom's testing)

regional_quilt_RRTMGP 045 (also in Dom's testing)

fv3_gsd 046 (also in Dom's testing)
fv3_rrfs_v1alpha 047 (also in Dom's testing)
fv3_HAFS_v0_hwrf_thompson 051 (also in Dom's testing)
fv3_esg_HAFS_v0_hwrf_thompson 052 (also in Dom's testing)

control_rrtmgp_debug 061 (also in Dom's testing)
control_thompson_extdiag_debug 068 (MISSING baseline)
fv3_rrfs_v1alpha_debug 073 (also in Dom's testing)

datm_control_cfsr 076 (only RESTART/DATM_CFSR.cpl.r.2011-10-02-00000.nc, expected)
datm_control_gefs 078 (only RESTART/DATM_GEFS.cpl.r.2011-10-02-00000.nc, expected)
datm_bulk_cfsr 079 (only RESTART/DATM_CFSR.cpl.r.2011-10-02-00000.nc, expected)
datm_bulk_gefs 080 (only RESTART/DATM_GEFS.cpl.r.2011-10-02-00000.nc, expected)
datm_mx025_cfsr 081 (only RESTART/DATM_CFSR.cpl.r.2011-10-02-00000.nc, expected)
datm_mx025_gefs 082 (only RESTART/DATM_GEFS.cpl.r.2011-10-02-00000.nc, expected)
datm_debug_cfsr 083 (only RESTART/DATM_CFSR.cpl.r.2011-10-01-21600.nc, expected)
datm_cdeps_control_cfsr 084 (only RESTART/DATM_CFSR.cpl.r.2011-10-02-00000.nc, expected)
datm_cdeps_control_gefs 086 (only RESTART/DATM_GEFS.cpl.r.2011-10-02-00000.nc, expected)
datm_cdeps_bulk_cfsr 087 (only RESTART/DATM_CFSR.cpl.r.2011-10-02-00000.nc, expected)
datm_cdeps_bulk_gefs 088 (only RESTART/DATM_GEFS.cpl.r.2011-10-02-00000.nc, expected)
datm_cdeps_mx025_cfsr 089 (only RESTART/DATM_CFSR.cpl.r.2011-10-02-00000.nc, expected)
datm_cdeps_mx025_gefs 090 (only RESTART/DATM_GEFS.cpl.r.2011-10-02-00000.nc, expected)
datm_cdeps_multiple_files_cfsr 091 (only RESTART/DATM_CFSR.cpl.r.2011-10-02-00000.nc, expected)
datm_cdeps_debug_cfsr 092 (only RESTART/DATM_CFSR.cpl.r.2011-10-01-21600.nc, expected)

Failed tests for Gnu:

control_rrtmgp 005 (also in Dom's testing)
fv3_rrfs_v1alpha 011
fv3_rrfs_v1alpha_debug 017
control_thompson_extdiag_debug 022 (MISSING baseline)
control_rrtmgp_debug 023 (also in Dom's testing)

cpld_control 028 (only RESTART/ufs.cpld.cpl.r.2016-10-04-00000.nc, expected)
cpld_debug 029 (only RESTART/ufs.cpld.cpl.r.2016-10-03-21600.nc, expected)

Initial CI tests

All passed: https://github.com/ufs-community/ufs-weather-model/actions/runs/1005274763

Final tests

• hera.intel
• hera.gnu
• orion.intel
• cheyenne.intel
• cheyenne.gnu
• gaea.intel
• jet.intel
• wcoss_cray
• wcoss_dell_p3
• CI: https://github.com/ufs-community/ufs-weather-model/runs/3020204994

Dependencies

• Add extended diagnostic output from Thompson MP, includes "Add optional scaling to RRTMGP flux adjustment" (#319), bug fix in several suite definition files NOAA-EMC/fv3atm#331
• Add extended diagnostic output from Thompson MP, includes "Add optional scaling to RRTMGP flux adjustment" (#668), fix index bug in m_micro.F90 NCAR/ccpp-physics#679
• Update CMEPS NOAA-EMC/CMEPS#51

[climbfuji]

Just to confirm, you reverted my temporary change in tests/fv3_conf/control_run.IN and added the new diag table diag_table_gfsv16_thompson_extdiag to the current input data set? If so, thanks for catching that from the notes in my PR!

[DeniseWorthen]

@climbfuji The diag_table fix was was done at 2b0ae64

[climbfuji]

Thanks for incorporating all my changes and testing them while I was on leave.