Jgfouca/scream downstream 04 11 24 #6343

jgfouca · 2024-04-11T15:54:21Z

Bring latest EAMxx and other changes from scream repo.

Non-eamxx changes:

Change GitHub CI to skip E3SM CI for eamxx (for now)
Add an eamxx-specific workflow in the CI to ensure default input files for SCREAM are available and downloadable
ELM config changes: new namelist defaults added for ne256pg2 and ne1024pg2 land configurations to support F20TR compsets with these resolutions
EAM changes: scream/micro_p3.F90 updates/fixes. Should only impact SCREAM stuff. Also, there's a fix for DP SCREAM output coordinate issue where x-coordinates should be assocated with spherep lon values and y-coordinates should be associated with lat values
Change kokkos build to ensure cxx17 standard

[non-BFB] for HOMMExx cases.

On mappy, this PR is non-BFB for these cases, which I think is expected:

DIFF ERS_D.ne4pg2_oQU480.F2010.mappy_gnu.eam-hommexx (phase BASELINE)
DIFF SMS_Ln9_P24x1.ne4_ne4.FDPSCREAM-ARM97.mappy_gnu (phase BASELINE)
DIFF SMS_R_Ld5.ne4_ne4.FSCM-ARM97.mappy_gnu.eam-scm (phase BASELINE)

… sees

…-SCREAMv1 Automatically Merged using E3SM Pull Request AutoTester PR Title: Add F20TR-SCREAMv1 compset PR Author: brhillman PR LABELS: AT: AUTOMERGE

…fig/20240227 Automatically Merged using E3SM Pull Request AutoTester PR Title: Update machine config for Livermore Computing machines PR Author: AaronDonahue PR LABELS: BFB, Machine File, AT: AUTOMERGE, AT: Skip Stand-Alone Testing, AT: Skip v1 Testing

…-units Automatically Merged using E3SM Pull Request AutoTester PR Title: set_string for some radiation diagnostics PR Author: mahf708 PR LABELS: radiation, AT: AUTOMERGE, diagnostic

Use standard script format. Some minor fixes. Make sure it will work with py3.6.

Adds MAM4xx: Aerosol optics

…rge_2024_04_04 * origin/master: (122 commits) aerosol_optics - fixing name of variable: from tau_g_sw to tau_ssa_g_sw. add doc for namelist variables for MAM4 optics input files aerosol_optics - remove code. aerosol_optics - fixing run time error; we need to use get_field_out("qc") instead of get_field_in("qc"). aerosol_optics - remove old comment. aerosol_optics - remove aero_tau_forward from field manager. aerosol_optics - remove old comment. aerosol_optics - remove temporal variables from field manager. aerosol_optics - fix typo. aerosol_optics - rename: aero_tau_forward -> tau_f_lw . aerosol_optics - remove aero from aero_tau_sw. aerosol_optics - remove aero from aero_tau_ssa_sw. aerosol_optics - remove aero from variable name. aerosol_optics - removed duplicate variable. aerosol_optics - from Updated to Required. aerosol_optics - update comments. aerosol_optics - update comments. aerosol_optics - comment. aerosol_optics - update comment. aerosol_optics - rename layout. ...

…4_04_04 Jgfouca/upstream merge 2024 04 04

…stream_04_11_24 * scream/master: (539 commits) aerosol_optics - fixing name of variable: from tau_g_sw to tau_ssa_g_sw. add doc for namelist variables for MAM4 optics input files aerosol_optics - remove code. aerosol_optics - fixing run time error; we need to use get_field_out("qc") instead of get_field_in("qc"). aerosol_optics - remove old comment. aerosol_optics - remove aero_tau_forward from field manager. Add fallow-arg-mismatch to mappy aerosol_optics - remove old comment. aerosol_optics - remove temporal variables from field manager. aerosol_optics - fix typo. aerosol_optics - rename: aero_tau_forward -> tau_f_lw . aerosol_optics - remove aero from aero_tau_sw. aerosol_optics - remove aero from aero_tau_ssa_sw. aerosol_optics - remove aero from variable name. Switch mappy over to new toolchain aerosol_optics - removed duplicate variable. aerosol_optics - from Updated to Required. aerosol_optics - update comments. aerosol_optics - update comments. aerosol_optics - comment. ...

github-actions · 2024-04-11T15:56:22Z

PR Preview Action v1.4.7
🚀 Deployed preview to https://E3SM-Project.github.io/E3SM/pr-preview/pr-6343/
on branch `gh-pages` at 2024-04-11 15:56 UTC

rljacob · 2024-04-11T19:15:08Z

.github/workflows/eamxx_default_files.yml

@@ -0,0 +1,62 @@
+name: inputdata


what does this do?

I think it checks that certain inputs are downloaded.

Yep, that's right. It checkes that eamxx default files in the xml are actually present on the server, and if they are not present, it will open an issue. It runs periodically behind the scenes.

We can disable it for now if this is an issue (or have it run only on the scream side downstream).

This should be harmless for E3SM, right?

Yes, it is harmless. In fact, it should be a good addition (early notification for server/user errors). It won't try to figure out what's wrong with E3SM inputfiles at all, but we can extend that later if desired.

rljacob

PR description should describe all changes outside of components/eamxx.

rljacob · 2024-04-11T19:15:39Z

cime_config/config_grids.xml

@@ -4480,6 +4480,11 @@
      <map name="ROF2LND_FMAPNAME">lnd/clm2/mappingdata/maps/ne240np4/map_0.1x0.1_nomask_to_ne240np4_nomask_aave_da_c120706.nc</map>
    </gridmap>

+    <gridmap lnd_grid="ne256np4.pg2" rof_grid="r0125">
+      <map name="LND2ROF_FMAPNAME">cpl/gridmaps/ne256pg2/map_ne256pg2_to_r0125_mono.200212.nc</map>
+      <map name="ROF2LND_FMAPNAME">cpl/gridmaps/ne256pg2/map_r0125_to_ne256pg2_mono.200212.nc</map>


"mono" is no longer a valid key in a map name.

@brhillman , can you chime in here? Looks like you added this on the eamxx side with this commit:

commit b23a4b48fe0fe967a3f3442a4fb52a0ecd9267d5 Author: Benjamin Hillman <[email protected]> Date: Fri Feb 2 17:10:48 2024 -0500 Add grid maps for ne256 with MOSART r0125 diff --git a/cime_config/config_grids.xml b/cime_config/config_grids.xml index 614eaf0..f877867 100755 --- a/cime_config/config_grids.xml +++ b/cime_config/config_grids.xml @@ -4385,6 +4385,11 @@ <map name="ROF2LND_FMAPNAME">lnd/clm2/mappingdata/maps/ne240np4/map_0.1x0.1_nomask_to_ne240np4_nomask_aave_da_c120706.nc</map> </gridmap> + <gridmap lnd_grid="ne256np4.pg2" rof_grid="r0125"> + <map name="LND2ROF_FMAPNAME">cpl/gridmaps/ne256pg2/map_ne256pg2_to_r0125_mono.200212.nc</map> + <map name="ROF2LND_FMAPNAME">cpl/gridmaps/ne256pg2/map_r0125_to_ne256pg2_mono.200212.nc</map> + </gridmap>

@rljacob what are we calling the conservative monotonic tempest remap algorithm now?

See https://acme-climate.atlassian.net/wiki/spaces/DOC/pages/1217757434/Mapping+file+algorithms+and+naming+convention

Its traave since its a pg2 grid.

@brhillman , @rljacob , so should this be changed to:
map_ne256pg2_to_r0125_traave.200212.nc
map_r0125_to_ne256pg2_traave.200212.nc

jgfouca · 2024-04-11T19:48:33Z

components/elm/bld/namelist_files/namelist_defaults.xml

@@ -274,10 +274,13 @@ ic_tod="0" sim_year="2000" glc_nec="0" use_crop=".true." irrigate=".true." nu_co
 <!-- Initial conditions for DYAMOND1, DYAMOND2 and for seasons of ENSO neutral year 2013 -->
 <finidat hgrid="ne1024np4.pg2" mask="ICOS10" ic_ymd="20160801">lnd/clm2/initdata/20220928.I2010CRUELM.ne1024pg2_ICOS10.elm.r.2016-08-01-00000.nc</finidat>
 <finidat hgrid="ne1024np4.pg2" mask="ICOS10" ic_ymd="20200120">lnd/clm2/initdata/20221218.F2010-CICE.ne30pg2_ne1024pg2.elm.r.2020-01-20-00000.nc</finidat>
+<finidat hgrid="ne1024np4.pg2" mask="ICOS10" ic_ymd="19941001">lnd/clm2/initdata/20231226.I2010CRUELM.ne1024pg2_ICOS10.elm.r.1994-10-01-00000.nc</finidat>


@brhillman , looks like you made these changes to ELM too. Can you give a quick explanation? The commit was:

commit f8e9303e7fcc7867883300b52df3c0bd44f7f593 Author: Benjamin Hillman <[email protected]> Date: Thu Feb 22 13:51:09 2024 -0500 Fix finidat for elm ne1024

Additional inputfiles for different start dates for decadal runs. Only affect ne1024 and ne256, I don't see a problem here.

jgfouca · 2024-04-11T19:49:50Z

components/elm/bld/namelist_files/use_cases/20thC_CMIP6_transient.xml

@@ -45,6 +45,10 @@

 <fsurdat hgrid="r05">lnd/clm2/surfdata_map/surfdata_0.5x0.5_simyr1850_c200609_with_TOP.nc</fsurdat>

+<!-- Hack to override files for ne1024 for SCREAM, even though the sim years do not match up -->


@brhillman , same here:

commit 3e74f881fa314a16c8c8d97a066f29b06fe511e3 Author: Benjamin Hillman <[email protected]> Date: Tue Jan 16 02:30:15 2024 -0600 Add hacks to elm use cases to use correct ne1024 land data

These were added to get the decadal run to configure. Only affects ne1024.

rljacob · 2024-04-17T02:03:37Z

components/eam/src/dynamics/se/stepon.F90

@@ -585,8 +585,8 @@ subroutine stepon_run3(dtime, cam_out, phys_state, dyn_in, dyn_out)
   if (dp_crm) then

     do ie=1,nelemd
-       out_gridx(:,:) = dyn_in%elem(ie)%spherep(:,:)%lat
-       out_gridy(:,:) = dyn_in%elem(ie)%spherep(:,:)%lon
+       out_gridx(:,:) = dyn_in%elem(ie)%spherep(:,:)%lon


This looks like it fixed a bug.

Yep:

commit 4802bc8aed0ecb2f32dbeaa5405e9192e8aad4d6 Author: Peter Bogenschutz <[email protected]> Date: Tue Jan 9 13:47:55 2024 -0800 fixes DP SCREAM output coordinate issue where x-coordinates should be assocated with spherep lon values and y-coordinates should be associated with lat values diff --git a/components/eam/src/dynamics/se/stepon.F90 b/components/eam/src/dynamics/se/stepon.F90 index 831fd6d..38a3769 100644 --- a/components/eam/src/dynamics/se/stepon.F90 +++ b/components/eam/src/dynamics/se/stepon.F90 @@ -585,8 +585,8 @@ subroutine stepon_run3(dtime, cam_out, phys_state, dyn_in, dyn_out) if (dp_crm) then do ie=1,nelemd - out_gridx(:,:) = dyn_in%elem(ie)%spherep(:,:)%lat - out_gridy(:,:) = dyn_in%elem(ie)%spherep(:,:)%lon + out_gridx(:,:) = dyn_in%elem(ie)%spherep(:,:)%lon + out_gridy(:,:) = dyn_in%elem(ie)%spherep(:,:)%lat call outfld('crm_grid_x', out_gridx, npsq, ie)

I've updated the description.

rljacob · 2024-04-17T02:07:37Z

PR description is better but still needs some words about the changes to eam code.

jgfouca · 2024-04-17T16:38:02Z

@rljacob , done.

rljacob · 2024-04-17T17:15:49Z

Also, can you describe what cases this in non-BFB for?

rljacob · 2024-04-17T17:16:12Z

Oh I see you did. Nevermind.

Bring latest EAMxx and other changes from scream repo. Non-eamxx changes: 1) Change GitHub CI to skip E3SM CI for eamxx (for now) 2) Add an eamxx-specific workflow in the CI to ensure default input files for SCREAM are available and downloadable 3) ELM config changes: new namelist defaults added for ne256pg2 and ne1024pg2 land configurations to support F20TR compsets with these resolutions 4) EAM changes: scream/micro_p3.F90 updates/fixes. Should only impact SCREAM stuff. Also, there's a fix for DP SCREAM output coordinate issue where x-coordinates should be assocated with spherep lon values and y-coordinates should be associated with lat values 5) Change kokkos build to ensure cxx17 standard On mappy, this PR is non-BFB for these cases, which I think is expected: DIFF ERS_D.ne4pg2_oQU480.F2010.mappy_gnu.eam-hommexx (phase BASELINE) DIFF SMS_Ln9_P24x1.ne4_ne4.FDPSCREAM-ARM97.mappy_gnu (phase BASELINE) DIFF SMS_R_Ld5.ne4_ne4.FSCM-ARM97.mappy_gnu.eam-scm (phase BASELINE) [non-BFB] for HOMMExx cases.

jgfouca · 2024-04-17T17:20:57Z

Merged to next.

rljacob · 2024-04-25T16:59:45Z

@jgfouca this caused some diffs in integration tests that use SCREAM. Please make bless requests.

jgfouca · 2024-04-25T17:18:13Z

@rljacob , done

mahf708 and others added 30 commits February 28, 2024 07:16

setting something to a value actually needs an equal sign

569aa3f

aerosol_optics - remove coupled test.

c683b81

aerosol_optics - add coupled test-physics_only

e536515

no const because we are setting string

ba5fcf0

aerosol_optics - update output file.

fac5cf4

Scale optical depth before converting to emissivity

68b28e9

Add cldfrac_rad to always be consistent with cloud fraction radiation…

9673691

… sees

Expose cosp::do_subcol_sampling as namelist option

228af1d

Default to no cosp subcolumns for ne256 and above

4a98092

Add doc for cosp_subcolumns

9d9249c

Add finidat default for ne256

ffbb9df

aerosol_optics - add coupled test.

c3df5b4

aerosol-optics - upate mam4xx to get fix in water uptake.

fb06895

aerosol_optics - fix label in uncouple test.

d9b1b78

Add doc string for do_subcol_sampling

dfea194

aerosol_optics - remove hard-coded variables.

7ecad1a

aerosol_optics - remove old comment.

85b0ee5

Clean up condition and add documentation about unset fields

e51c21b

aerosol_optics - switch mam4xx to main branch.

28da5a0

Merge Pull Request #2730 from E3SM-Project/scream/brhillman/add-F20TR…

8fceb48

…-SCREAMv1 Automatically Merged using E3SM Pull Request AutoTester PR Title: Add F20TR-SCREAMv1 compset PR Author: brhillman PR LABELS: AT: AUTOMERGE

Delete cmake files for 2 machines we don't support on LC.

3c91e26

Merge Pull Request #2735 from E3SM-Project/scream/mahf708/eamxx/diags…

a3f9f4a

…-units Automatically Merged using E3SM Pull Request AutoTester PR Title: set_string for some radiation diagnostics PR Author: mahf708 PR LABELS: radiation, AT: AUTOMERGE, diagnostic

check-hashes-ers: Bring in to eamxx/scripts ecosystem

054d574

Use standard script format. Some minor fixes. Make sure it will work with py3.6.

EAMxx: add possibility of querying whether a PIO file has an attribute

9c03432

EAMxx: read timestamp's nsteps only if present on file

bbb6627

EAMxx: change default value for TimeStamp::m_num_steps to very neg value

9997253

EAMxx: read/write timestamp's nstep only if asked to do so

56e30f3

EAMxx: better format logging in scorpio input/output

7928a27

EAMxx: allow to set a logger in the time interp utility

bf0d107

AaronDonahue and others added 4 commits April 10, 2024 16:18

Merge pull request #2718 from eagles-project/oscar/aerosol_optics_rebase

10dad56

Adds MAM4xx: Aerosol optics

Merge pull request #2784 from E3SM-Project/jgfouca/upstream_merge_202…

d60caf6

…4_04_04 Jgfouca/upstream merge 2024 04 04

jgfouca added the EAMxx PRs focused on capabilities for EAMxx label Apr 11, 2024

jgfouca requested a review from rljacob April 11, 2024 15:54

jgfouca assigned jgfouca and AaronDonahue Apr 11, 2024

rljacob reviewed Apr 11, 2024

View reviewed changes

rljacob requested changes Apr 11, 2024

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jgfouca added the non-BFB PR makes roundoff changes to answers. label Apr 11, 2024

jgfouca commented Apr 11, 2024

View reviewed changes

rljacob assigned AaronDonahue and unassigned AaronDonahue Apr 17, 2024

rljacob requested a review from AaronDonahue April 17, 2024 02:01

rljacob reviewed Apr 17, 2024

View reviewed changes

rljacob approved these changes Apr 17, 2024

View reviewed changes

jgfouca merged commit baef174 into master Apr 18, 2024
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jgfouca deleted the jgfouca/scream_downstream_04_11_24 branch April 18, 2024 15:03

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Jgfouca/scream downstream 04 11 24 #6343

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edited by rljacob

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jgfouca commented Apr 25, 2024

		@@ -45,6 +45,10 @@

		<fsurdat hgrid="r05">lnd/clm2/surfdata_map/surfdata_0.5x0.5_simyr1850_c200609_with_TOP.nc</fsurdat>

		<!-- Hack to override files for ne1024 for SCREAM, even though the sim years do not match up -->

Jgfouca/scream downstream 04 11 24 #6343

Jgfouca/scream downstream 04 11 24 #6343

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jgfouca commented Apr 11, 2024 • edited by rljacob Loading

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