Update v3 SSP compsets/configurations/tests and use_case files #6335

wlin7 · 2024-04-08T02:11:27Z

Add/update SSP compsets with standard v3 configurations. The changes include:

SSP245, SSP370, SSP585
atm and land configurations
atm and land use_case files
wcprodssp testmod (replacing workaround that are based on hybrid v2/v3 configurations)

[non-BFB] only for SSP tests
[NML] changes only for SSP tests

Checklist and Notes

E90 emission for SSP scenarios need to be inspected. The one specified was created in 2017 and uses variable emis_e90, while emis_anthro is used for piControl/historical and F compsets (updated with the one created for all v3 SSP scenarios) (done)
E90 emission file scenario independent (confirmed)
LULC (landuse.timeseries) file at r05 are needed for SSP245 and SSP585 (done, note that LULC files are independent of land/ocean mask)
Volcanic SO2 emission file for SSP245 needs to be relocated (currently put on the directory for SSP370 forcings) (done)
DMS flux file scenario independent?
fsurdat, 1850 or 2015 more appropriate? If 2015, could be made scenario dependent.
use new prescribed oxidant file oxid_SSP370_1.9x2.5_L70_1849-2101_c20240228.nc (replacing oxid_SSP370_1.9x2.5_L70_2015-2100_c20211006.nc)
Also use oxidant files c20240228 for SSP245 and SSP585
linv3 file, which version to use, c20230705 or c20231207? piControl and historical have been using the c20230705 version.
SSP370, SSP245, SSP585 as is run ok.
SS
Available test runs for comparing nml files (atm_in and lnd_in) if they are helpful for your review
historical: /lcrc/group/e3sm2/ac.wlin/E3SMv3/v3.LR.historical_0051/run
SSP245: /lcrc/group/e3sm2/ac.wlin/E3SMv3/SSP/v3.LR.ssp245_0051/tests/S_1x2_nmonths/run
SSP370: /lcrc/group/e3sm2/ac.wlin/E3SMv3/SSP/v3.LR.ssp370_0051/tests/S_1x2_nmonths/run
SSP585: /lcrc/group/e3sm2/ac.wlin/E3SMv3/SSP/v3.LR.ssp585_0051/tests/S_1x2_nmonths/run

github-actions · 2024-04-08T02:13:20Z

PR Preview Action v1.4.7
🚀 Deployed preview to https://E3SM-Project.github.io/E3SM/pr-preview/pr-6335/
on branch `gh-pages` at 2024-05-03 14:11 UTC

tangq · 2024-04-08T20:01:05Z

Hi @wlin7 , regarding your E90 checklist and notes below,

I assume the file created in 2017 refers to this file /lcrc/group/e3sm/data/inputdata/atm/cam/chem/emis/CMIP6_emissions_1750_2015/emissions_E90global_surface_1750-2100_0.9x1.25_c20170322.nc, which was before E90 was implemented for E3SMv3. We certainly do NOT want to use this file in E3SM.

For E3SMv3, we should use this E90 file for ALL SSP scenarios because E90 is an artificial tracer which doesn't change with SSPs.
/lcrc/group/acme/public_html/inputdata/atm/cam/chem/trop_mozart/ub/emissions_E90_surface_1750-2101_1.9x2.5_c20231222.nc, which was created by Jinbo a couple months ago. (@jinboxie can provide details if needed.)

Checklist and Notes

E90 emission for SSP scenarios need to be inspected. The one specified was created in 2017 and uses variable emis_e90, while emis_anthro is used for piControl/historical and F compsets

wlin7 · 2024-04-08T22:34:46Z

Thank you @tangq and @jinboxie . It is great you have already created one for all v3 SSP scenarios.

wlin7 · 2024-04-15T23:08:15Z

Hi @hwangacme @mingxuanwupnnl @tangq @keziming @jinboxie , @keziming @bishtgautam
This SSP PRs involve many files you helped create. Please help review if the settings are all good.

You may start with the checklist and notes in the PR message. Available historical and SSP tests may be helpful for comparing the settings.

tangq

The PR looks good to me except the prescribed methane settings pointing to the 1990s climatology. These settings are likely not used and should be deleted to avoid confusions.

tangq · 2024-04-16T00:23:10Z

components/eam/bld/namelist_files/use_cases/SSP245_eam_CMIP6_chemUCI-Linoz-mam5-vbs.xml

+<!-- prescribed methane  -->
+<prescribed_ghg_file      >ch4_oxid_1.9x2.5_L26_1990-1999clim.c090804.nc</prescribed_ghg_file>
+<prescribed_ghg_datapath  >atm/cam/chem/methane</prescribed_ghg_datapath>
+<prescribed_ghg_type      >CYCLICAL</prescribed_ghg_type>
+<prescribed_ghg_cycle_yr  >1995</prescribed_ghg_cycle_yr>
+<prescribed_ghg_filelist  >''</prescribed_ghg_filelist>
+<prescribed_ghg_specifier>'prsd_ch4:CH4'</prescribed_ghg_specifier>


I am not sure why we need this prescribed methane file, which appears to be the seasonal cycle climatology of 1990-1999, for the SSPs. I confirmed that "prsd_ch4" is not defined in chem_mech.in, so it is highly likely these settings are not used in the simulation. Shall we delete it here and in other two SSP use case files too?

Nice catch, @tangq . We did have discussion on this (#5781, #5823). It is not needed.

tangq · 2024-04-16T00:24:27Z

components/eam/bld/namelist_files/use_cases/SSP370_eam_CMIP6_chemUCI-Linoz-mam5-vbs.xml

+<!-- prescribed methane  -->
+<prescribed_ghg_file      >ch4_oxid_1.9x2.5_L26_1990-1999clim.c090804.nc</prescribed_ghg_file>
+<prescribed_ghg_datapath  >atm/cam/chem/methane</prescribed_ghg_datapath>
+<prescribed_ghg_type      >CYCLICAL</prescribed_ghg_type>
+<prescribed_ghg_cycle_yr  >1995</prescribed_ghg_cycle_yr>
+<prescribed_ghg_filelist  >''</prescribed_ghg_filelist>
+<prescribed_ghg_specifier>'prsd_ch4:CH4'</prescribed_ghg_specifier>


See comments above.

tangq · 2024-04-16T00:24:55Z

components/eam/bld/namelist_files/use_cases/SSP585_eam_CMIP6_chemUCI-Linoz-mam5-vbs.xml

+<!-- prescribed methane  -->
+<prescribed_ghg_file      >ch4_oxid_1.9x2.5_L26_1990-1999clim.c090804.nc</prescribed_ghg_file>
+<prescribed_ghg_datapath  >atm/cam/chem/methane</prescribed_ghg_datapath>
+<prescribed_ghg_type      >CYCLICAL</prescribed_ghg_type>
+<prescribed_ghg_cycle_yr  >1995</prescribed_ghg_cycle_yr>
+<prescribed_ghg_filelist  >''</prescribed_ghg_filelist>
+<prescribed_ghg_specifier>'prsd_ch4:CH4'</prescribed_ghg_specifier>


see comments above.

mingxuanwupnnl

Thank you @wlin7 Emission files and oxidant files look good to me.

bishtgautam · 2024-04-16T04:22:00Z

components/elm/bld/namelist_files/use_cases/2015-2100_SSP245_transient.xml

+<!-- *** NOT USED FOR SATELLITE PHENOLOGY ***
+<stream_year_first_ndep phys="elm" use_cn=".true."   >1850</stream_year_first_ndep>
+<stream_year_last_ndep  phys="elm" use_cn=".true."   >2005</stream_year_last_ndep>
+<model_year_align_ndep  phys="elm" use_cn=".true."   >1850</model_year_align_ndep>
+
+<stream_year_first_pdep phys="elm" use_cn=".true."   >2000</stream_year_first_pdep>
+<stream_year_last_pdep  phys="elm" use_cn=".true."   >2000</stream_year_last_pdep>
+<model_year_align_pdep  phys="elm" use_cn=".true."   >2000</model_year_align_pdep>
+
+<stream_year_first_popdens phys="elm" use_cn=".true."   >1850</stream_year_first_popdens>
+<stream_year_last_popdens  phys="elm" use_cn=".true."   >2010</stream_year_last_popdens>
+<model_year_align_popdens  phys="elm" use_cn=".true."   >1850</model_year_align_popdens>
+-->


These might need to be uncommented, and @acme-y9s might know more about these BGC settings.

Thanks for careful review, @bishtgautam . I didn't realize the whole block was commented out.
The settings, if uncommented, would be the same as for historical (CMIP6_transient). Are they suitable for SSPs?

Currently, with the blocked commented out, stream_year values for *_pdep, *_ndep, and *_popdens are all using 2000.

Going with the transient settings as for the historical use_case for now.

wlin7 · 2024-04-16T16:09:44Z

Hi @tangq , the settings for the prescribed methane section has been all removed from the SSP use_case files via
9a0ab28 . Note that similar settings still exist in other use_case _files (e.g., 1850, 2010, 20TR). Related settings still show up in atm_in. Complete removal requires removal from namelist_defaults_eam.xml and changes of logics in build-namelist (and probably configure). This is not done.

hwangacme

No problems found. Just identified some minor naming issues.

hwangacme · 2024-04-16T20:09:45Z

cime_config/allactive/config_compsets.xml

@@ -113,12 +113,17 @@

 <compset>
  <alias>WCYCLSSP585</alias>
-  <lname>SSP585SOI_EAM%CMIP6_ELM%SPBC_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
+  <lname>SSP585SOI_EAM%CMIP6_ELM%CNPRDCTCBCTOP_MPASSI_MPASO_MOSART_SGLC_SWAV</lname>
 </compset>


Is there any particular consideration to name these SSPs under WCYCL? These compsets are now being created for different groups.

@hwangacme , that is more of continuing the naming convention we have been having. We will have still a distinction of WCYCLSSP, CRYOSSP, BGCSSP. The WCYCL ones come first.

hwangacme · 2024-04-16T20:12:34Z

components/eam/bld/namelist_files/use_cases/SSP245_eam_CMIP6_chemUCI-Linoz-mam5-vbs.xml

+<so2_ext_file         >atm/cam/chem/trop_mozart_aero/emis/CMIP6_SSP245_ne30/cmip6_ssp245_mam4_so2_volc_elev_2015-2100_c240331.nc </so2_ext_file>
+<soag0_ext_file       >atm/cam/chem/trop_mozart_aero/emis/CMIP6_SSP245_ne30/emissions-cmip6_ssp245_e3sm_SOAG0_elev_2015-2100_1.9x2.5_c20240219.nc </soag0_ext_file>
+<bc_a4_ext_file       >atm/cam/chem/trop_mozart_aero/emis/CMIP6_SSP245_ne30/cmip6_ssp245_mam4_bc_a4_elev_2015-2100_c200716.nc </bc_a4_ext_file>
+<mam7_num_a1_ext_file >atm/cam/chem/trop_mozart_aero/emis/CMIP6_SSP245_ne30/cmip6_ssp245_mam4_num_a1_elev_2015-2100_c200716.nc </mam7_num_a1_ext_file>


Shall we change these "mam7" pointers of input files to "mam4"? They look quite confusing here.

Indeed appear confusing. Does 'a1' refer to the same thing in mam7 and mam4?

num_a1 does refer to the same thing for both MAM4 and MAM7, but num_a3 for MAM7 below refers to num_a4 for MAM4.

Thanks, @hwangacme . Indeed in all the use_case files, there is a comment that mam7_num_a3 is to set num_a4 emission. If to change the pointers, need to update all use_case files and namelist_default, as well as build-namelist. These should be fine; but would also introduce NML diff for all standard tests (and make nml in ongoing production simulations look different). We can apply the changes at a later time.

rljacob · 2024-05-01T19:00:27Z

@wlin7 is this ready for merging?

wlin7 · 2024-05-01T20:47:20Z

@rljacob , the land settings need further review/input. @acme-y9s and @thorntonpe , can you please take a look? It is about the use_case settings to work with the BGC land.

acme-y9s · 2024-05-02T17:30:16Z

@wlin7 @bishtgautam For the nitrogen deposition (nden) and population density (popdens) files, we do have the transient files that we used for BGCv1 simulation (like SSP585). For the phosphorus deposition file (pden) we only one year. If you do not specify the those files in your use_case file, the model will have default setting files (maybe based on you simulation year ), but the default files may not what you need. There should be ndep and popdens files for each SSPs, you can specify thoses files in each SSP's use_case file. I did specify those files for our BGCv1 SSP585 case, you can have a look if you want. Or, if you need help, feel free to let me know.

rljacob · 2024-05-02T17:45:49Z

cime_config/testmods_dirs/allactive/wcprodssp/user_nl_elm

 hist_fincl2 = 'H2OSNO', 'FSNO', 'QRUNOFF', 'QSNOMELT', 'FSNO_EFF', 'SNORDSL', 'SNOW', 'FSDS', 'FSR', 'FLDS', 'FIRE', 'FIRA'
 hist_mfilt = 1,365
- hist_nhtfrq = -24,-24
+ hist_nhtfrq = 0,-24


should be -24 for testing.

Thanks for catching it. Done, for user_nl_eam as well.

wlin7 · 2024-05-02T22:43:17Z

@wlin7 @bishtgautam For the nitrogen deposition (nden) and population density (popdens) files, we do have the transient files that we used for BGCv1 simulation (like SSP585). For the phosphorus deposition file (pden) we only one year. If you do not specify the those files in your use_case file, the model will have default setting files (maybe based on you simulation year ), but the default files may not what you need. There should be ndep and popdens files for each SSPs, you can specify thoses files in each SSP's use_case file. I did specify those files for our BGCv1 SSP585 case, you can have a look if you want. Or, if you need help, feel free to let me know.

Thanks, @acme-y9s definitely need more help from you on this. Can you please provide the files (the path if ready on our machine) and the proper year-align settings? We can update the specification in a next PR.

Update v3 SSP compsets/configurations/tests and use_case files Add/update SSP compsets with standard v3 configurations. The changes include: . SSP245, SSP370, SSP585 . atm and land configurations . atm and land use_case files . wcprodssp testmod (replacing workaround that are based on hybrid v2/v3 configurations) [non-BFB] only for SSP tests [NML] changes only for SSP tests * origin/wlin/update_v3ssp_compsets: Change h0 tapes output frequency for the SSP testmod Set SSP245 default STARTDATE Update SSP use_case files with transient BGC land mode settings Update the SSP testmod Remove prescribed methane section from use_case files for SSPs Update v3 SSP585 use_case files Add v3 SSP245 compsets and use_case files Update SSP370 prescribed oxidant file Rename v3 SSP370 LULC file Replace old E90 file with one for all v3 SSP scenarios Update SSP370 compset/configuration and use_case files

wlin7 · 2024-05-03T02:20:56Z

Merged to next.

Update v3 SSP compsets/configurations/tests and use_case files Add/update SSP compsets with standard v3 configurations. The changes include: . SSP245, SSP370, SSP585 . atm and land configurations . atm and land use_case files . wcprodssp testmod (replacing workaround that are based on hybrid v2/v3 configurations) [non-BFB] only for SSP tests [NML] changes only for SSP tests

wlin7 · 2024-05-03T14:18:57Z

Remerged to next after restoring the config settings for 4xCO2 and 1pctCO2 compset. Pattern _EAM%CMIP6_ can not match the CO2 compset longname, which uses - in place of _ following the string CMIP6.

wlin7 · 2024-05-04T21:59:15Z

Only expected SSP test diffs with this PR on next (and compy's SSP370 FAIL due to permission to download additional forcing files).

The PR is merged to master (to create a master repo with SSP compsets). Requests for bless SSP test DIFFs are submitted but before they are blessed, both next and master will see diff on Monday.

peterdschwartz · 2024-05-13T16:54:47Z

@wlin7 Maybe due to machine issues at the time, but this PR may still have DIFFs on pm-cpu that need to be blessed(for example https://my.cdash.org/viewTest.php?onlyfailed&buildid=2561805).

Update SSP370 compset/configuration and use_case files

e8a6bfd

wlin7 added 5 commits April 8, 2024 17:37

Replace old E90 file with one for all v3 SSP scenarios

6f91d15

Rename v3 SSP370 LULC file

643dae0

Update SSP370 prescribed oxidant file

8600d43

Add v3 SSP245 compsets and use_case files

7bcc0a7

Update v3 SSP585 use_case files

feb3eaf

rljacob added this to the v3.0.1 milestone Apr 10, 2024

wlin7 changed the title ~~WIP: Update v3 SSP compsets/configurations/tests and use_case files~~ Update v3 SSP compsets/configurations/tests and use_case files Apr 15, 2024

wlin7 requested review from hwangacme, tangq, mingxuanwupnnl, jinboxie, keziming and bishtgautam April 15, 2024 22:55

keziming approved these changes Apr 15, 2024

View reviewed changes

tangq approved these changes Apr 16, 2024

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mingxuanwupnnl approved these changes Apr 16, 2024

View reviewed changes

rljacob assigned wlin7 Apr 16, 2024

rljacob added Coupled Model Atmosphere Land labels Apr 16, 2024

bishtgautam reviewed Apr 16, 2024

View reviewed changes

Remove prescribed methane section from use_case files for SSPs

9a0ab28

hwangacme approved these changes Apr 16, 2024

View reviewed changes

Update the SSP testmod

3238b7b

wlin7 mentioned this pull request May 2, 2024

Solve gas_ac=NAN issue #6385

Merged

wlin7 added 2 commits May 1, 2024 20:54

Update SSP use_case files with transient BGC land mode settings

f535848

Set SSP245 default STARTDATE

9311a73

rljacob reviewed May 2, 2024

View reviewed changes

Change h0 tapes output frequency for the SSP testmod

a592963

Restore config settings for idealized CO2 compsets

cdc1f48

wlin7 mentioned this pull request May 3, 2024

Add documentation for running coupled e3sm #6391

Closed

wlin7 merged commit 2f10b6c into master May 4, 2024
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wlin7 deleted the wlin/update_v3ssp_compsets branch May 4, 2024 21:55

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Update v3 SSP compsets/configurations/tests and use_case files #6335

Update v3 SSP compsets/configurations/tests and use_case files #6335

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Update v3 SSP compsets/configurations/tests and use_case files #6335

Update v3 SSP compsets/configurations/tests and use_case files #6335

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