Add GEFS regression test suite from EP5r2 configuration/case

[NickSzapiro-NOAA]

Commit Queue Requirements:

• Fill out all sections of this template.
• All sub component pull requests have been reviewed by their code managers.
• Run the full Intel+GNU RT suite (compared to current baselines) on either Hera/Derecho/Hercules
• Commit 'test_changes.list' from previous step

---

Description:

This PR updates the cpld_bmark_p8 tests to a prototype GEFS test case of fully coupled s2swa+IAU+stochastics physics, with configuration and warm starts from restarts of EP5r2 ensemble member 1 for 2021-03-25 06Z.

The EP5r2 test case was kindly provided by @bingfu-NOAA via @junwang-noaa with aerosol input data and configurations from @lipan-NOAA.

A separate INPUTDATA_ROOT_BMIC is no longer needed and is removed.

This suite should pass some basic reproducibility/quality checks, particularly:

• control reproduces itself
• restart reproduces control
• changing number of tasks reproduces control
• Intel debug version reproduces itself
• GNU and GNU debug versions run
  • GNU debug on hera fails with likely openmpi error:
    140: The OSC pt2pt component does not support MPI_THREAD_MULTIPLE in this release.
    140: Workarounds are to run on a single node, or to use a system with an RDMA
    140: capable network such as Infiniband.
  • GNU and GNU debug on hercules fail with NetCDF HDF error
    Error in handle_err: get_var3_r4 get_vara_real delp_inc NetCDF: HDF error
• Runs on supported platforms
  • Hera (intel)
  • Hercules (intel)
  • Gaea (intel)
  • Derecho (intel)
    With increased WAV_tasks, hangs 30 minutes into simulation
  • Larger issue of GNU support
• No major diffs from GEFS workflow configuration
  GOCART .rc files and ExtData directory structure to be revised for consistency with global-workflow
  Configuration/case may be updated

These failures seem to require library/platform support and work will continue in follow up issues.

Input data is currently in user space on hera:
/scratch1/NCEPDEV/nems/Nick.Szapiro/tasks/input_data/gefs.v13/RT_GEFS/
Scripts need updating once filepaths are in shared space.

Commit Message:

* UFSWM - Add GEFS regression test suite from EP5r2 configuration/case

Priority:

• Normal

Git Tracking

UFSWM:

• Closes Update cpld_bmark_p8 with GEFSv13 EP5 configuration #1987
• Closes Add RT test for gocart_on, gccpp_on, nasa_on #1818

Sub component Pull Requests:

• None

UFSWM Blocking Dependencies:

• Update inline post #2489
  Need to update UPP hash to include UPP PRs already committed (Add aerosol fields in the gefs UPP control files NOAA-EMC/UPP#1052, Add gefs inline post itag file NOAA-EMC/UPP#1060, and Reduce the printouts for GEFS processing. NOAA-EMC/UPP#1075)

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Changes

Regression Test Changes (Please commit test_changes.list):

• PR Adds New Tests/Baselines.

Input data Changes:

• New input data.

Library Changes/Upgrades:

• No Updates

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Testing Log:

• RDHPCS
  • Hera
  • Orion
  • Hercules
  • Jet
  • Gaea
  • Derecho
• WCOSS2
  • Dogwood/Cactus
  • Acorn
• CI
• opnReqTest (complete task if unnecessary)

[NeilBarton-NOAA]

@bbakernoaa Could you make these consistent with the monthly data?

[WenMeng-NOAA]

@NickSzapiro-NOAA The UPP develop recently had a commit (a6c1a38c) thst includes aerosol fields in the UPP control files for GEFS. Could you add changes to link postxconfig-NT-gefs.txt and postxconfig-NT-gefs_FH00.txt to the files postxconfig-NT-gefs.txt and postxconfig-NT-gefs-f00.txt under parm/gefs from UPP repository? Thanks!

[NickSzapiro-NOAA]

@WenMeng-NOAA Should there be an fv3atm PR first to update the UPP hash?

[WenMeng-NOAA]

@WenMeng-NOAA Should there be an fv3atm PR first to update the UPP hash?

@NickSzapiro-NOAA That's right.

[NickSzapiro-NOAA]

@WenMeng-NOAA Can we reduce the number of times lines like these get logged?

 820:  GEFS env var            0           0           0
 820:  Processing for GEFS and default setting is tmpl4_1 and tmpl4_11
 820:  After g2sec1 call we need to set listsec1(2) =            2
 820:  After g2sec1 call we need to set listsec1(13) =            1

They may be for development and double the size of the log file

[WenMeng-NOAA]

@WenMeng-NOAA Can we reduce the number of times lines like these get logged?

 820:  GEFS env var            0           0           0
 820:  Processing for GEFS and default setting is tmpl4_1 and tmpl4_11
 820:  After g2sec1 call we need to set listsec1(2) =            2
 820:  After g2sec1 call we need to set listsec1(13) =            1

They may be for development and double the size of the log file

@NickSzapiro-NOAA Could you open an issue at https://github.com/NOAA-EMC/UPP/issues, so we will work on that?

[NickSzapiro-NOAA]

@WenMeng-NOAA Can we reduce the number of times lines like these get logged?

 820:  GEFS env var            0           0           0
 820:  Processing for GEFS and default setting is tmpl4_1 and tmpl4_11
 820:  After g2sec1 call we need to set listsec1(2) =            2
 820:  After g2sec1 call we need to set listsec1(13) =            1

They may be for development and double the size of the log file

@NickSzapiro-NOAA Could you open an issue at https://github.com/NOAA-EMC/UPP/issues, so we will work on that?

NOAA-EMC/UPP#1074

[NickSzapiro-NOAA]

fyi, this error on derecho goes away when increasing WAV_tasks (80 to 120)

cxil_map: write error
...
libmpi_intel.so.1  000015539CBE3611  PMPI_File_write_a     Unknown  Unknown
libpnetcdf.so.4.0  0000155393BBA048  ncmpio_read_write     Unknown  Unknown
libpnetcdf.so.4.0  0000155393BB4DA9  Unknown               Unknown  Unknown
libpnetcdf.so.4.0  0000155393BB2319  Unknown               Unknown  Unknown
libpnetcdf.so.4.0  0000155393BAFA5B  Unknown               Unknown  Unknown
libpnetcdf.so.4.0  0000155393AFA1A2  ncmpi_wait_all        Unknown  Unknown
libpioc.so         0000155399FE9E05  flush_output_buff     Unknown  Unknown
libpioc.so         0000155399FE3746  PIOc_write_darray     Unknown  Unknown
libpioc.so         0000155399FEA085  flush_buffer          Unknown  Unknown
libpioc.so         0000155399FB3955  PIOc_sync             Unknown  Unknown
libpiof.so         0000155399900160  piolib_mod_mp_fre     Unknown  Unknown
fv3.exe            0000000005B4880F  ice_history_write        1237  ice_history_write.F90
fv3.exe            000000000589BC2A  ice_history_mp_ac        4134  ice_history.F90
fv3.exe            00000000057F47B7  ice_comp_nuopc_mp         888  ice_comp_nuopc.F90
...
libmpi_intel.so.1  000014E4701213A5  PMPI_Alltoallw        Unknown  Unknown
libpioc.so         000014E46F8CE5EF  pio_swapm             Unknown  Unknown
libpioc.so         000014E46F8D0EBA  rearrange_io2comp     Unknown  Unknown
libpioc.so         000014E46F8F20BA  PIOc_read_darray      Unknown  Unknown
fv3.exe            00000000018D148B  Unknown               Unknown  Unknown
fv3.exe            0000000001610043  Unknown               Unknown  Unknown
fv3.exe            000000000160F20D  Unknown               Unknown  Unknown
fv3.exe            0000000000CC4D85  Unknown               Unknown  Unknown
fv3.exe            0000000000CBF971  Unknown               Unknown  Unknown
fv3.exe            000000000059B5B3  Unknown               Unknown  Unknown
fv3.exe            0000000001C48B10  wav_comp_nuopc_mp         823  wav_comp_nuopc.F90

This wav line calls ESMF_MeshCreate

[NickSzapiro-NOAA]

Hi @jkbk2004 . If there are no input data changes coming up, can we stage input data for new test cases? Maybe @[INPUTDATA_ROOT]/GEFS/ is a good place.

It's on hera at /scratch1/NCEPDEV/nems/Nick.Szapiro/tasks/input_data/gefs.v13/RT_GEFS/ . The contents of WW3 subdirectory probably belong under INPUTDATA_ROOT_WW3 instead