Refine PM2.5 DA for the RRFS_SD model #609

hongli-wang · 2023-08-11T20:34:50Z

Description

Refine the PM2.5 DA for the RRFS_SD model by use of veg_type, which is used to decide whether the obs is in urban area or not. Different thresholds for innovations outside/inside urban areas will be used. Add new namelist parameters, such as threshold for innovations, anowbufr type
Read in station terrain height, PM10 et al if extended BUFR format for anow air quality data is used

Fixes #606

Type of change

Please delete options that are not relevant.

Bug fix (non-breaking change which fixes an issue)
[X ] New feature (non-breaking change which adds functionality)
Breaking change (fix or feature that would cause existing functionality to not work as expected)
This change requires a documentation update

How Has This Been Tested?

Checklist

[X ] My code follows the style guidelines of this project
I have performed a self-review of my own code
I have commented my code, particularly in hard-to-understand areas
New and existing tests pass with my changes
Any dependent changes have been merged and published

DUE DATE for this PR is 9/22/2023. If this PR is not merged into develop by this date, the PR will be closed and returned to the developer.

hu5970 · 2023-08-25T14:53:34Z

@hongli-wang Could you suggest two reviewers for this PR?

hongli-wang · 2023-08-25T14:57:15Z

@hongli-wang Could you suggest two reviewers for this PR?

@hu5970 Previously, Ting and Cory reviewed the initial development of PM2.5 DA for RRFS_SD. They are the best to review this update.

RussTreadon-NOAA · 2023-08-25T15:00:11Z

Cory is not available as a peer reviewer. Cory is a member of the Handling Review team. Handling Review team members process PRs. We need two peer reviewers not from the Handling Review team.

hongli-wang · 2023-08-25T21:24:43Z

Cory is not available as a peer reviewer. Cory is a member of the Handling Review team. Handling Review team members process PRs. We need two peer reviewers not from the Handling Review team.

@RussTreadon-NOAA Thanks for letting me know. Guoqing @guoqing-noaa can help to review the code. Thanks.

CoryMartin-NOAA · 2023-08-28T17:03:35Z

@hongli-wang can you start by running the GSI regression tests on Hera? I will also run them on WCOSS2 once we know the all pass on Hera. Thanks!

hongli-wang · 2023-08-28T18:15:13Z

Cory is not available as a peer reviewer. Cory is a member of the Handling Review team. Handling Review team members process PRs. We need two peer reviewers not from the Handling Review team.

@RussTreadon-NOAA Thanks for letting me know. Guoqing @guoqing-noaa can help to review the code. Thanks.

hongli-wang · 2023-08-28T18:16:29Z

Cory is not available as a peer reviewer. Cory is a member of the Handling Review team. Handling Review team members process PRs. We need two peer reviewers not from the Handling Review team.

@RussTreadon-NOAA Thanks for letting me know. Guoqing @guoqing-noaa can help to review the code. Thanks.

Youhua ([email protected]) can also review the code. Thanks.

TingLei-NOAA · 2023-08-29T17:47:08Z

src/gsi/chemmod.f90

@@ -287,7 +292,9 @@ subroutine init_chem

    berror_chem=.false.
    berror_fv3_cmaq_regional=.false.  ! Set .true. to use berror for fv3_cmaq_regional, whose cv has 10 characters
+    berror_fv3_sd_regional=.false.    ! Set .true. to use berror for rrfs_sd model, whose cv has 10 characters


Would add an explanation for =.false.?

Would add an explanation for =.false.?

Thanks for the comments. I will revise soon.

TingLei-NOAA · 2023-08-29T17:47:38Z

src/gsi/chemmod.f90

    oneobtest_chem=.false.
+    anowbufr_ext=.false.


documentation for this variable

TingLei-NOAA · 2023-08-29T17:56:38Z

src/gsi/read_anowbufr.f90

        if ( iret > 0 .and. (conc < conc_missing ) .and. &
               (conc >= zero)) then
+           if(indata(nxob) > r360)cycle 
+           if(indata(nyob) > 0.5_r_kind*r360)cycle


why don't directly use r180 (if r180 is not defined, it could be defined along with r360). The extra r180 will avoid the multiplication for 0.5*r360 for each obs.

hongli-wang · 2023-08-30T14:36:05Z

@hongli-wang can you start by running the GSI regression tests on Hera? I will also run them on WCOSS2 once we know the all pass on Hera. Thanks!

A bit busy this week. I will do it as soon as I can.

CoryMartin-NOAA · 2023-08-30T14:38:21Z

@hongli-wang no big rush, we have a few weeks.

guoqing-noaa · 2023-08-31T17:25:12Z

src/gsi/chemmod.f90

@@ -103,7 +108,7 @@ module chemmod
  real(r_kind),parameter :: pm2_5_teom_max=900.0_r_kind !ug/m3
 !some parameters need to be put here since convinfo file won't
 !accomodate, stands for maximum realistic value of surface pm2.5
-  real(r_kind),parameter :: pm10_teom_max=150.0_r_kind !ug/m3
+  real(r_kind),parameter :: pm10_teom_max=3000.0_r_kind !ug/m3


This comment is not related to the code. But just curious whey bumping the max value from 150 to 3000?

This comment is not related to the code. But just curious whey bumping the max value from 150 to 3000?

@guoqing-noaa The default value may not consider the heavy fire event. The value of 3000 is a reasonable PM10 value when a heavy fire event or dust storm takes place.

guoqing-noaa · 2023-08-31T18:49:15Z

src/gsi/read_anowbufr.f90

+              obstr='TPHR QCIND COPOPM ELV COPOPM10 COPOCO'
+              anowbufr=.true.
+              write(6,*)'READ_PM2_5:  AIRNOW data type, subset=',subset
+           end if


Suggest reverse the if and else block, i.e: if anowbufr_ext then; else ... (although they function the same, the latter reads more straightforward :) )

Accepted. Thanks.

src/gsi/read_anowbufr.f90

guoqing-noaa · 2023-08-31T18:50:49Z

src/gsi/read_anowbufr.f90

+              obstr='TPHR QCIND COPOPM ELV COPOPM10 COPOCO'
+              anowbufr=.true.
+              write(6,*)'READ_PM10:  AIRNOW data type, subset=',subset
+           end if


same comments as the above

Accepted. Thanks.

guoqing-noaa · 2023-08-31T18:54:11Z

src/gsi/read_anowbufr.f90

+              if (trim(obstype)=='pm2_5') indata(ncopopm)=indata_b(3)
+              if (trim(obstype)=='pm10')  indata(ncopopm)=indata_b(5)
+              site_elev = indata_b(4)
+           end if


remove two spaces to align the indentation

guoqing-noaa · 2023-08-31T19:06:24Z

src/gsi/setuppm2_5.f90

          end if
-          if (pm25wc_ges(2) >= 1.0_r_kind) then
+          if (pm25wc_ges(2) >= 2.0_r_kind) then


Is the change from 1.0 to 2.0 a bug fix or a threshold change? For the latter, will it be better to use a parameter to control this?

src/gsi/setuppm2_5.f90

guoqing-noaa · 2023-08-31T19:13:37Z

src/gsi/chemmod.f90

@@ -90,7 +93,9 @@ module chemmod

  logical :: aero_ratios

-  logical :: oneobtest_chem,diag_incr,berror_chem,berror_fv3_cmaq_regional
+  logical :: oneobtest_chem,diag_incr,berror_chem
+  logical :: berror_fv3_cmaq_regional,berror_fv3_sd_regional


I searched this PR, it looks like we don't need separate berror_fv3_sd_regional and berror_fv3_cmaq_regional?

berror_fv3_sd_regional is only used at Line 460 of src/gsi/m_berror_stats_reg.f90 and there is no difference if we use berror_fv3_cmaq_regional instead. Is it possible to just use berror_fv3_cmaq_regional, or combine them to one logical variable, such as berror_fv3_aero_regional?

The current ones make it more clear to know which B file will be used, and the previous retros runs can repeat without any changes of GSI namelist parameter. This is good to users.
Your suggestion will make the changes be general and good in code development.
So what do you think?

Do you plan to use different BEC for cmaq and sd? Or will they be the same as they are right now?

@guoqing-noaa
Different B files are used. The one for CMAQ has 70 aerosol species whereas
rrfs-ad only has 3 tracers. I think a separate parameter is good for users. I have no problem in combining then if that is the way you prefer. Thanks.

Got it. Thanks for the explanation!

guoqing-noaa · 2023-08-31T19:16:48Z

src/gsi/chemmod.f90


  character(len=max_varname_length), dimension(naero_smoke_fv3), parameter :: &
-        aeronames_smoke_fv3=[character(len=max_varname_length) ::  'smoke','dust' ]
+        aeronames_smoke_fv3=[character(len=max_varname_length) ::  'smoke','dust','coarsepm']


"coarsepm" is added here. However it is never used. And we have to modify Line 282 of src/gsi/setuppm2_5.f90
to remove the "coarsepm" contribution

Yes, you are correct. This was done by -1 in the do loop. For example,
do i=2,naero_smoke_fv3-1 ! remove contribution from coarsepm

Right, if we will remove coarsepm in src/gsi/setuppm2_5.f90 (line 281), why would we add it here?

@guoqing-noaa
This is because the dust PM10/AOD DA is not included in this PR. But we do consider EnVar to update the coarsepm, possibly in a next PR with FED DA.

guoqing-noaa · 2023-08-31T19:24:07Z

src/gsi/chemmod.f90

@@ -76,10 +78,11 @@ module chemmod
  logical :: luse_deepblue
  character(len=max_varname_length) :: crtm_aerosol_model,crtm_aerosolcoeff_format,crtm_aerosolcoeff_file
  integer(i_kind) :: aod_qa_limit  ! qa >=  aod_qa_limit will be retained
-  integer(i_kind) :: icvt_cmaq_fv3
+  integer(i_kind) :: icvt_cmaq_fv3,pm10_da_scheme


pm10_da_scheme is not used anywhere in this PR.

hongli-wang · 2023-09-08T17:09:36Z

@TingLei-NOAA @guoqing-noaa
Hi Ting and Guoqing,
Thanks for your comments. I have taken almost all of your suggestions and modified the codes. Please review the code again. Thanks. Hongli

TingLei-NOAA · 2023-09-08T18:06:49Z

@hongli-wang just maybe last two question: did you run your test for this PR with GSI at debug mode? :). and did you finish the regression tests?

hongli-wang · 2023-09-08T20:33:28Z

@hongli-wang just maybe last two question: did you run your test for this PR with GSI at debug mode? :). and did you finish the regression tests?

@TingLei-NOAA yes tested my code on debug mode. Not finish regression test yet, and I will do it.

TingLei-NOAA · 2023-09-08T21:25:26Z

@hongli-wang Thanks. Then, the success of your regression tests are the only thing I need to know to give my approval for this PR. Thanks a lot for your efforts for keeping improving the codes.

hongli-wang · 2023-09-19T15:18:57Z

@hongli-wang can you update to the head of GSI develop? I think the regression test issues I'm seeing on both Hera and Orion are related to issues with changes from #571 not being included here

@CoryMartin-NOAA yes, just rebased my code, will have some tests and run a regression test.

hongli-wang · 2023-09-19T16:03:55Z

@hongli-wang can you update to the head of GSI develop? I think the regression test issues I'm seeing on both Hera and Orion are related to issues with changes from #571 not being included here

@CoryMartin-NOAA yes, just rebased my code, will have some tests and run a regression test.

@CoryMartin-NOAA @TingLei-NOAA

Regression tests failed due to GSI can't find correct intel lib, for example:
/scratch1/BMC/wrfruc/hwang/ctest/tmpreg_rrfs_3denvar_glbens/rrfs_3denvar_glbens_loproc_updat/gsi.x: error while loading shared libraries: libmkl_intel_lp64.so.2
Dir on Hera:
/scratch1/BMC/wrfruc/hwang/ctest

Any suggestions?

CoryMartin-NOAA · 2023-09-19T16:07:19Z

@hongli-wang that's because the modulefiles changes in develop recently. Make sure your develop build is also up to date now that you've pulled in the recent updates.

I'm running the tests on Orion and Cactus now.

hongli-wang · 2023-09-19T16:26:21Z

@hongli-wang that's because the modulefiles changes in develop recently. Make sure your develop build is also up to date now that you've pulled in the recent updates.

I'm running the tests on Orion and Cactus now.

@CoryMartin-NOAA
Both develop and my branch are up to date and recompiled. Is there anything else I can do to keep the build to to date?
Thanks for performing regression tests on Orion and Cactus.

CoryMartin-NOAA · 2023-09-19T19:22:57Z

Rerunning on Cactus:
All tests pass except hwrf_nmm_d3 which fails the scalability test and rtma which fails the runtime maximum for a couple of the cases.

On Orion:

The following tests FAILED:
	  2 - [=[global_4dvar]=] (Failed)
	  5 - [=[hwrf_nmm_d3]=] (Failed)
	  6 - [=[rtma]=] (Failed)
	  7 - [=[rrfs_3denvar_glbens]=] (Failed)
	  8 - [=[netcdf_fv3_regional]=] (Failed)

The 4DVar test failed the scalability test.
The HWRF test barely failed the scalability test.
The RTMA test also failed the scalability test.
The RRFS test exceeded the runtime for one test by 3 seconds.
Finally, the FV3 regional test also failed for scalability.

I think given these results, the tests "pass"

hongli-wang · 2023-09-19T19:43:00Z

Rerunning on Cactus: All tests pass except hwrf_nmm_d3 which fails the scalability test and rtma which fails the runtime maximum for a couple of the cases.

On Orion:
The following tests FAILED:
	  2 - [=[global_4dvar]=] (Failed)
	  5 - [=[hwrf_nmm_d3]=] (Failed)
	  6 - [=[rtma]=] (Failed)
	  7 - [=[rrfs_3denvar_glbens]=] (Failed)
	  8 - [=[netcdf_fv3_regional]=] (Failed)
The 4DVar test failed the scalability test. The HWRF test barely failed the scalability test. The RTMA test also failed the scalability test. The RRFS test exceeded the runtime for one test by 3 seconds. Finally, the FV3 regional test also failed for scalability.

I think given these results, the tests "pass"

@CoryMartin-NOAA
That is a good news. Thanks!
I have the issue that GSI can't find the lib to run on Hera. The same issue if I ran GSI on Jet new.

Do you think we can move forward, ask Ting and Guoqing to review and approve this PR?

Thank again!
Hongli

CoryMartin-NOAA · 2023-09-19T19:44:25Z

@guoqing-noaa @TingLei-NOAA can you re-review this? We can double check the regression tests at the end but I think all we are seeing here is machine instability. Thanks @hongli-wang for your work on this so far!

CoryMartin-NOAA · 2023-09-25T18:29:30Z

GitHub says 76 files changed, I think this needs updated to the head of develop again before it can be accurately reviewed.

hongli-wang · 2023-09-25T19:04:07Z

GitHub says 76 files changed, I think this needs updated to the head of develop again before it can be accurately reviewed.

@CoryMartin-NOAA
I noticed this too. It was caused my last rebase (not sure why it happened). I will rebase/merge the code again.

hongli-wang · 2023-09-25T20:57:10Z

GitHub says 76 files changed, I think this needs updated to the head of develop again before it can be accurately reviewed.

@CoryMartin-NOAA I noticed this too. It was caused my last rebase (not sure why it happened). I will rebase/merge the code again.

@CoryMartin-NOAA
Remerged code to EMC develop branch and delete a unused namelist variable. Could you please help to run regression tests if it is required? I can try if the reg tests work on Hera tomorrow. Thanks.

hongli-wang · 2023-09-26T22:44:26Z

Please see my reply in the previous email.

…

On Tue, Sep 26, 2023 at 4:23 PM Guoqing Ge ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In src/gsi/chemmod.f90 <#609 (comment)>: > character(len=max_varname_length), dimension(naero_smoke_fv3), parameter :: & - aeronames_smoke_fv3=[character(len=max_varname_length) :: 'smoke','dust' ] + aeronames_smoke_fv3=[character(len=max_varname_length) :: 'smoke','dust','coarsepm'] Right, if we will remove coarsepm in src/gsi/setuppm2_5.f90 (line 281), why would we add it here? — Reply to this email directly, view it on GitHub <#609 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMXB44VENS3HDJOFU4SXIB3X4NIWFANCNFSM6AAAAAA3NMH3YY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

hongli-wang · 2023-09-26T22:47:17Z

Different B files are used. The one for CMAQ has 70 aerosol species whereas rrfs-ad only has 3 tracers.

…

On Tue, Sep 26, 2023 at 4:21 PM Guoqing Ge ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In src/gsi/chemmod.f90 <#609 (comment)>: > @@ -90,7 +93,9 @@ module chemmod logical :: aero_ratios - logical :: oneobtest_chem,diag_incr,berror_chem,berror_fv3_cmaq_regional + logical :: oneobtest_chem,diag_incr,berror_chem + logical :: berror_fv3_cmaq_regional,berror_fv3_sd_regional Do you plan to use different BEC for cmaq and sd? Or will they be the same as they are right now? — Reply to this email directly, view it on GitHub <#609 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMXB44W5FBEGYHKMTETVYQTX4NIP3ANCNFSM6AAAAAA3NMH3YY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

CoryMartin-NOAA · 2023-09-27T13:38:32Z

@hongli-wang at this point, I'll re-run the regression tests on WCOSS once we have approvals from the reviewers.

guoqing-noaa

LGTM. Thanks for the discussions and changes!

hongli-wang · 2023-09-29T13:30:02Z

@hongli-wang at this point, I'll re-run the regression tests on WCOSS once we have approvals from the reviewers.

@CoryMartin-NOAA
Ting and Guoqing has approved this PR. Could you please run the regression test again?

Thanks,
Hongli

CoryMartin-NOAA · 2023-09-29T14:20:55Z

@hongli-wang already submitted them this morning on Cactus. I'll post when they are finished.

CoryMartin-NOAA · 2023-09-29T17:24:55Z

Only 2 regression tests fail on Cactus, and they are due to scalability, which are nonfatal. I think this is good to go now.

hongli-wang · 2023-09-29T17:28:31Z

Only 2 regression tests fail on Cactus, and they are due to scalability, which are nonfatal. I think this is good to go now.

@CoryMartin-NOAA
Thank you!

hongli-wang added 2 commits August 11, 2023 20:06

add anowbufr_ext into gsimod namelist

c4d84a9

cleanup print sentencce

e66c837

RussTreadon-NOAA assigned hongli-wang Aug 14, 2023

CoryMartin-NOAA self-assigned this Aug 28, 2023

CoryMartin-NOAA requested review from guoqing-noaa and TingLei-NOAA August 28, 2023 14:11

hongli-wang closed this Aug 28, 2023

hongli-wang reopened this Aug 28, 2023

RussTreadon-NOAA mentioned this pull request Aug 29, 2023

Adding GLM Flash Extent Density to GSI Observer #588

Closed

TingLei-NOAA reviewed Aug 29, 2023

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guoqing-noaa reviewed Aug 31, 2023

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Cleanup and refine code for PR.

f02b817

hongli-wang added 3 commits September 8, 2023 22:26

add anowbufr_ext into gsimod namelist

181b8b8

cleanup print sentencce

f274e81

Cleanup and refine code for PR.

addbb6e

hongli-wang added 4 commits September 19, 2023 14:46

Cleanup and refine code for PR.

9714cc5

add anowbufr_ext into gsimod namelist

126ba88

Cleanup and refine code for PR.

3d4a21c

Merge branch 'GSI_SD' of https://github.com/hongli-wang/GSI into GSI_SD

80fb69f

CoryMartin-NOAA requested review from guoqing-noaa and TingLei-NOAA September 19, 2023 19:43

hongli-wang added 2 commits September 25, 2023 19:39

Merge remote-tracking branch 'upstream/develop' into GSI_SD

a2a9de8

Remove pm10_da_scheme from namelist

f4bb476

TingLei-NOAA approved these changes Sep 25, 2023

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guoqing-noaa approved these changes Sep 27, 2023

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CoryMartin-NOAA approved these changes Sep 29, 2023

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CoryMartin-NOAA merged commit ba5a2ca into NOAA-EMC:develop Sep 29, 2023
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CoryMartin-NOAA deleted the GSI_SD branch September 29, 2023 17:51

Refine PM2.5 DA for the RRFS_SD model #609

Refine PM2.5 DA for the RRFS_SD model #609

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