BGC update #497

apcraig · 2024-08-09T18:57:38Z

PR checklist

This is a significant update in the BGC including refactoring Icepack interfaces.

Deprecate skl BGC but leave code alone for now hoping we get help from the community to validate the latest code.
Add BGC parameters to icepack_parameters.F90
Update BGC physics, consistent with Adds icepack BGC E3SM-Project/E3SM#6457. Remove redundant arguments in BGC interfaces.
- icepack_aerosol.F90
  - revised subroutine update_snow_bgc
- icepack_algae.F90
  - revised subroutine zbio
  - revised subroutine z_biogeochemistry
  - revised subroutine algal_dyn
  - add subroutine bgc_carbon_sum
- icepack_brine.F90
  - revise subroutine prepare_hbrine
  - revise subroutine update_hbrine
- icepack_mechred.F90
  - add mbio calculation to subroutine ridge_shift
  - add flux_bio calculation to subroutine ridge_ice
- icepack_therm_itd.F90
  - update calculation of dvssl and dvint in subroutine lateral_melt
- icepack_zbgc.F90
  - lots of stuff
- icepack_zbgc_shared.F90
  - lots of stuff
Remove redundant arguments in non-BGC interfaces.
- icepack_atmo.F90
- icepack_fsd.F90
- icepack_isotope.F90
- icepack_itd.F90
- icepack_meltpond_topo.F90
- icepack_mushy_physics.F90
- icepack_snow.F90
- icepack_therm_bl99.F90
- icepack_therm_mushy.F90
- icepack_therm_shared.F90
- icepack_therm_vertical.F90
- icepack_tracers.F90
- icepack_wavefracspec.F90
Generalize merge_fluxes to make all arguments optional
Fix bug in subroutine snow_redist computation of hsn_new when nslyr=1
Update the Icepack driver consistent with Icepack interface changes
Update zbgc initialization in the Icepack driver, move bgc parameter intiialization to icepack_init_parameters, update icepack_init_zbgc call.
Update some calls to icepack_warnings_setabort to add file and line number.
Update warning package to improve OpenMP robustness. Fixes potential race conditions that show up when lots of output is produced.
Modified congel implementation in subroutine thickness_changes in icepack_therm_vertical.F90 to recover bit-for-bit results. New congel and new bgc implementation were bit-for-bit independently, but when combining the changes, the intel compiler (with -O2) introduces non bit-for-bit changes (roundoff).
Update bgc namelist defaults and settings in icepack_in
Update bgc tracer sizing in set_env files
Update testing, remove skl tests, add zaero tests.

We still need to

Closes #180

… standard dEdd config

Update to Consortium Main Aug 17, 2022

…o snicar

clean up trailing blanks

…ested

Add calls to icepack_init_radiation to icepack driver

Add some SNICAR SSP table checks, aborts, etc

new namelist variables and options. Add new namelist to icepack_in. Add snicar and snicartest options. Minor updates to namelist output

Update snow table implementation and add SNICAR SSP Tables

Update ssp data for dEdd_snicar

… cell

…ata for use_snicar

Add additional SNICAR SSP fields for aerosols, BGC

-Corrects typos -Improves the notation for the iron equations -Corrects the DIC equation. BFB

Corrections to bgc documentation

-Updates bgc environment variables -Corrects and updates BGC namelist parameter table -Corrects and updates BGC parameter arrays table BFB

BFB

BFB.

BFB

Updates bgc case settings documentation take 2

eclare108213

This is looking good. A few notes on the documentation (one not directly related to this PR):

Could the reference to CICE.v5 in the second sentence of section 2.9.1.1 be updated to the current doc? Those equation numbers in the v5 documentation don’t make sense — something didn’t get translated correctly. The problem is that the equations being referenced are in the CICE docs, not the Icepack docs (equations 4 and 5 in section 2.3 Tracers). I recommend removing the parenthetical “(eq. 15 and 16…)”. Section 2.4 Tracers in the Icepack doc should probably reference section 2.3 Tracers in the CICE doc, and vice versa.
also add the notice that skl is being deprecated at the beginning of section 2.9.4
There’s a space after the hyphen in brine-volume, in the 4th paragraph of section 2.9.4.2
The Johnson95 and Edwards2012 citations aren’t being rendered correctly in the doc
The Nquota math variables look weird, but I guess they’re what’s intended.

What is the status with respect to the to-do list at the top of this PR?

eclare108213 · 2024-08-14T16:47:12Z

columnphysics/icepack_snow.F90

                                        zqsn(:,n))
                  if (icepack_warnings_aborted(subname)) return
               else
-                  hsn_new(1) = hsn_new(1) + dhsn
+                  hsn_new(n) = hsn_new(n) + dhsn


Note that this is a bug fix (which I thought we had already fixed!).

This has always been a fix on this branch. It hasn't been checked in to the trunk yet, but will with the bgc.

eclare108213 · 2024-08-14T16:52:07Z

columnphysics/icepack_warnings.F90

@@ -1,16 +1,28 @@

 module icepack_warnings

-      use icepack_kinds
+! Provides a logging and abort package for Icepack.


why are the icepack_warnings.F90 changes included in the BGC PR?

There were some openmp issues when lots of output was being written (ie. icepack bgc debugging). This was causing problems so I worked on it as part of the bgc branch and it was pulled into the E3SM version. In particular, this is not related to bgc, but it became part of the bgc work.

apcraig · 2024-09-12T00:56:40Z

I have updated the three bgc parameters and fixed some of the documentation problems. With regard to the boxes on the PR page, I think most are done. I will do some final testing as we approach the merge, but testing is now working well. Will we want a new validation run, three bgc parameters have changed values? Finally, while skl is currently deprecated on the branch, do we want to continue to work on that?

apcraig · 2024-09-12T16:27:47Z

I ran a full test suite last night on Derecho with 5 or 6 compilers for Icepack and CICE. The test results look good. So, I think we're close and this is where we are

Testing is looking good
Documentation has been updated. I think it's ready or at least close?
We are going to deprecate skl with the possibly to revive later
We have done a long validation and had a very cursory look, it seems OK. This was done before the latest updates of three namelist settings. Do we want to redo the 8 year bgc gx1 test?
The zaerosol test is generating conservation errors and has NOT been added to the tested configurations. Do we need to do more debugging/testing? Do we want to add the test even if it's not working perfectly with the hope that it might be fixed in the future? Do we want to defer on the zaerosol test? Ideally, someone would debug the results before we merge, but if we don't do that, then I still favor adding that test to the test suite to keep it on the radar. I would also add an issue.

njeffery · 2024-09-12T16:40:03Z

@apcraig & @eclare108213 : I'll do some testing of the zaerosol only case from the E3SM side and see if I can reproduce the conservation errors. chrysalis is slow, though. I don't know that this PR should wait.

apcraig · 2024-09-12T17:14:11Z

Thanks @njeffery. With the zaerosol test, does the snow need to be on or off or maybe either?

njeffery · 2024-09-12T17:24:21Z

Both should work. I'm testing with the snow on.

apcraig · 2024-09-13T15:20:22Z

I have added zaero configuration and tests. I ran with both snow on and off, both run to completion in Icepack and CICE but all zaero tests generate conservation errors. But the new tests are running and have been added which I think is good.

njeffery · 2024-09-13T15:32:53Z

@apcraig : Great! thanks for adding those tests.

My E3SM ocean-ice test case with zaeros active but no sea ice bgc has gone 4 years without any error messages. When do the error messages first appear in Icepack? I'm wondering if there is an initial condition problem for the Icepack test cases.

apcraig · 2024-09-13T16:00:15Z

OK, I think this could be ready to merge.

I have read thru the bgc documentation quickly and fixed a couple final formatting things.
The skl is deprecated with hopes of revival in the future.
The zaero tests have been added to Icepack and CICE with and without snow turned on. All zaero tests run to completion with conservation errors. Those conservation errors will need to be addressed at some point, we can create an Issue for it.
A full test suite was run on Derecho with 5 and 6 compilers for CICE and Icepack respectively on Sept 12. Test results are as expected. All tests are bit-for-bit except bgc and congel. A small number of tests do fail but that's consistent with what is happening on the main trunk. These failed tests are understood (mostly hdf5 and nvhpc compiler).

@njeffery, @eclare108213, please approve this and the CICE PR if you think they are ready to merge.

apcraig · 2024-09-13T16:05:57Z

@njeffery. The conservation errors appear at every timestep in Icepack and CICE with the zaero configuration. I did a test last week where I set the zaero forcing to 0 by changing

    faero_atm(:,:,1,:) = 1.e-12_dbl_kind ! kg/m^2 s                                                                             
    faero_atm(:,:,2,:) = 1.e-13_dbl_kind
faero_atm(:,:,3,:) = 1.e-14_dbl_kind
    faero_atm(:,:,4,:) = 1.e-14_dbl_kind
    faero_atm(:,:,5,:) = 1.e-14_dbl_kind
    faero_atm(:,:,6,:) = 1.e-14_dbl_kind

to

    faero_atm = 0.0_dbl_kind

The conservation errors went away. Of coarse, the aerosol tracer remained identically zero throughout as well, so maybe not very useful.

Could it be that something about HOW I'm running the cases is incorrect. I will send output from those cases via email separately.

njeffery

Approved based on ocean-ice multiyear testing of Icepack bgc and zaerosols in E3SM and reading of the documentation changes.

…tests.

apcraig · 2024-09-13T18:23:31Z

The conservation errors have been fixed. I needed to run nblyr=7 instead of 1. That has been checked in and the zaero cases are now running with NO conservation errors.

njeffery · 2024-09-13T18:30:54Z

Awesome!

eclare108213

Awesome, thanks for all the work on this, @njeffery @apcraig

This is a significant update in the BGC including refactoring Icepack interfaces. Deprecate skl BGC but leave code alone for now hoping we get help from the community to validate the latest code. Add BGC parameters to icepack_parameters.F90 Update BGC physics, consistent with E3SM-Project/E3SM#6457. Remove redundant arguments in BGC interfaces. icepack_aerosol.F90 revised subroutine update_snow_bgc icepack_algae.F90 revised subroutine zbio revised subroutine z_biogeochemistry revised subroutine algal_dyn add subroutine bgc_carbon_sum icepack_brine.F90 revise subroutine prepare_hbrine revise subroutine update_hbrine icepack_mechred.F90 add mbio calculation to subroutine ridge_shift add flux_bio calculation to subroutine ridge_ice icepack_therm_itd.F90 update calculation of dvssl and dvint in subroutine lateral_melt icepack_zbgc.F90 lots of stuff icepack_zbgc_shared.F90 lots of stuff Remove redundant arguments in non-BGC interfaces. icepack_atmo.F90 icepack_fsd.F90 icepack_isotope.F90 icepack_itd.F90 icepack_meltpond_topo.F90 icepack_mushy_physics.F90 icepack_snow.F90 icepack_therm_bl99.F90 icepack_therm_mushy.F90 icepack_therm_shared.F90 icepack_therm_vertical.F90 icepack_tracers.F90 icepack_wavefracspec.F90 Generalize merge_fluxes to make all arguments optional Fix bug in subroutine snow_redist computation of hsn_new when nslyr=1 Update the Icepack driver consistent with Icepack interface changes Update zbgc initialization in the Icepack driver, move bgc parameter intiialization to icepack_init_parameters, update icepack_init_zbgc call. Update some calls to icepack_warnings_setabort to add file and line number. Update warning package to improve OpenMP robustness. Fixes potential race conditions that show up when lots of output is produced. Modified congel implementation in subroutine thickness_changes in icepack_therm_vertical.F90 to recover bit-for-bit results. New congel and new bgc implementation were bit-for-bit independently, but when combining the changes, the intel compiler (with -O2) introduces non bit-for-bit changes (roundoff). Update bgc namelist defaults and settings in icepack_in Update bgc tracer sizing in set_env files Update testing, remove skl tests, add zaero tests. --------- Co-authored-by: Elizabeth Hunke <eclare@lanl.gov> Co-authored-by: David Bailey <dbailey@ucar.edu> Co-authored-by: Nicole Jeffery <njeffery@lanl.gov>

eclare108213 and others added 30 commits August 4, 2022 13:56

initial implementation of SNICAR-AD in Icepack, not tested but BFB in…

604d0ad

… standard dEdd config

adding use_snicar flag (true if shortwave=dEdd_snicar)

60fc58d

initializing use_snicar based on shortwave namelist value

e264065

adding a few more arguments to the calling tree

8109ebf

Merge pull request CICE-Consortium#5 from CICE-Consortium/main

4ff4e28

Update to Consortium Main Aug 17, 2022

Merge branch 'main' of https://github.com/cice-consortium/icepack int…

49d1294

…o snicar

remove repeat ridging warnings for niter=1

3c65376

use 5-band wghtns for snicar

2bd3504

basic initialization for snicar tables

56a2ccd

clean up trailing blanks

d2f3870

Merge pull request #4 from apcraig/snicar-clean01

f03e228

clean up trailing blanks

interim commit with some snicar initialization, unconnected and not t…

cd31ec2

…ested

Add data_dEdd_3band to icepack_init_radiation

a2bbd1d

Add calls to icepack_init_radiation to icepack driver

Add ability to set SNICAR SSP data via icepack_parameters

d2ea5ed

Add some SNICAR SSP table checks, aborts, etc

Add reading of SNICAR SSP file in Icepack driver including

4bf19c6

new namelist variables and options. Add new namelist to icepack_in. Add snicar and snicartest options. Minor updates to namelist output

rebase, update, and test

8cb547a

Merge pull request CICE-Consortium#5 from apcraig/snwtable

258f623

Update snow table implementation and add SNICAR SSP Tables

Update ssp output

4e2d90b

Reorder SNICAR SSP test data arrays to be consistent with source code

e569c4c

Merge pull request CICE-Consortium#6 from apcraig/sspoutput

1d6eaa6

Update ssp data for dEdd_snicar

move 5band data to subroutine; enable snicar testing on 1 no-ice grid…

f88b03c

… cell

move more data to 3- and 5-band initialization routines, use module d…

6d68ee9

…ata for use_snicar

change snicar coefficient names and use module data for them

b3ca79c

cleaning up argument lists

8ad73dd

Add additional SNICAR SSP fields

89e0d9a

Merge pull request CICE-Consortium#7 from apcraig/moresspio

93f9f3c

Add additional SNICAR SSP fields for aerosols, BGC

set tmask=0 only for land cell

ef37585

interim compute_dEdd_5bd subroutine (runs)

3e636b2

separate 3-band and 5-band compute_dEdd routines

914130b

Fix errors in calls to compute_dEdd. Some cleanup.

0fabd24

njeffery and others added 8 commits September 10, 2024 10:10

Corrections to bgc documentation

a72c11d

-Corrects typos -Improves the notation for the iron equations -Corrects the DIC equation. BFB

Merge pull request #2 from njeffery/update-bgc-doc

88cc351

Corrections to bgc documentation

Updates bgc case settings documentation

763bef2

-Updates bgc environment variables -Corrects and updates BGC namelist parameter table -Corrects and updates BGC parameter arrays table BFB

Removed redundancy in bgc documentation

894e289

BFB

Corrected removal of redundancy

6ad5b0d

BFB.

Removed extra space.

492cb27

BFB

Merge pull request #4 from njeffery/bgcpr1-nj

43c81a0

Updates bgc case settings documentation take 2

Merge branch 'bgcpr1' of https://github.com/apcraig/icepack into bgcpr1

9971d2d

eclare108213 reviewed Sep 11, 2024

View reviewed changes

update documentation and update 3 bgc parameter defaults

e06d076

Add zaero tests

af708e1

Update Documentation

4ae7b62

apcraig marked this pull request as ready for review September 13, 2024 16:00

njeffery approved these changes Sep 13, 2024

View reviewed changes

Update zaero test, using nblyr=7. Fixes conservation errors in zaero …

4046323

…tests.

eclare108213 added the Type: Bug label Sep 15, 2024

eclare108213 approved these changes Sep 15, 2024

View reviewed changes

apcraig merged commit 05ac0ec into CICE-Consortium:main Sep 15, 2024
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BGC update #497

BGC update #497

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BGC update #497

BGC update #497

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