update for dev2 realtime run by haiqinli · Pull Request #1498 · NOAA-EMC/rrfs-workflow

haiqinli · 2026-05-18T15:56:46Z

DESCRIPTION OF CHANGES:

Update the workflow to run with 4 aerosol tracers: smoke-fine, dust-fine, dust-coarse, and unspc-fine (anthropogenic emission);
Use regrid submodule;
Use namelist option of "config_mp_aero_emission" to turn on/off aerosol emission for TEMPO MP.

TESTS CONDUCTED:

CONUS12km test run: /scratch4/BMC/acomp/Haiqin.Li/OPSROOT/smoke_12km

Machines/Platforms:

WCOSS2
- Cactus/Dogwood
- Acorn
RDHPCS
- Hera
- Ursa
- Orion
- Hercules

Test cases:

ISSUE:

Fixes the issue(s) mentioned in #9999

CONTRIBUTORS (optional):

Jordan Schnell

guoqing-noaa · 2026-05-18T16:00:43Z

@@ -0,0 +1,19 @@
+prepend_path("MODULEPATH", "/gpfs/f6/bil-fire8/world-shared/Benjamin.Koziol/mpas-aerosols/spack-stack/envs/mpas-aerosols/modules/Core")


We usually don't do this way. Let's discuss this first.

guoqing-noaa · 2026-05-18T16:03:35Z

    config_gfl_sub3d = 1/" namelist.atmosphere
 fi

+if [[ "${MESH_NAME^^}" == "FWX1.25km" ]]; then


We don't use if switches based on MESH_NAME inside j-jobs and ex-scripts.

Also config_lbc_w = 'zero' should be a standard option now, right?

guoqing-noaa · 2026-05-18T16:04:33Z

    -e "${mpasout_replacement}"  "${PARMrrfs}"/streams.atmosphere  > streams.atmosphere
 #
-if [[ "${mpasout_interval,,}" == "none" ]]; then  # remove the da_state stream for coldstart only forecasts
+#if [[ "${mpasout_interval,,}" == "none" ]]; then  # remove the da_state stream for coldstart only forecasts


We cannot comment out this part. Let us talk about a better way to address the Chem needs.

I agree. When I run with rrfsx/MPAS-Model, we don't need to comment out this part. However, we have to comment out this when run with ufs-community/MPAS-Model

Fixed as suggested. Thanks!

guoqing-noaa · 2026-05-18T16:05:03Z

 # 3. CHEM_INPUT             -- location of interpolated files, ready to be used
-# 4. MESH_NAME                -- name of the MPAS domain, required to know if we have weights or data intepolated to the domain 
+# 4. MESH_NAME                -- name of the MPAS domain, required to know if we have weights or data intepolated to the domain
+# TEST COMMIT


Line 18 can be removed

Will remove line 18. Thanks!

Removed as suggested.

guoqing-noaa · 2026-05-18T16:07:45Z

We cannot use the ufs-community/MPAS-Model directly as it misses the output_timelevels and output_done_marker

I have a pending PR (ufs-community/MPAS-Model#240). Should I update the PR with output_timelevels and output_done_marker? Thanks!

We have two routes:
(1) We get ufs-community/MPAS-Model#240 merged first; then merge the changes to rrfsx/MPAS-Model which already has output_timelevels and output_done_marker
(2) If you need the above PR #240 change earlier, you can create a PR to rrfsx/MPAS-Model.

I just submitted a PR (RRFSx/MPAS-Model#25) to rrfsx/MPAS-Model. Thanks!

guoqing-noaa · 2026-05-18T16:08:42Z

 if [[ "${CHEM_GROUPS,,}" == *pollen* ]]; then
   if [[ -s "${UMBRELLA_PREP_CHEM_DATA}/bio.init.nc" ]]; then
-      sed -i "\${e} cat ${PARMrrfs}/chemistry/streams.atmosphere.pollen" streams.atmosphere # append before the last line (i.e. </stream>)
+      sed -i "\$e cat ${PARMrrfs}/chemistry/streams.atmosphere.pollen" streams.atmosphere # append before the last line (i.e. </stream>)


why change ${e} to $e?

Will change $e back to ${e}. Thanks!

for some reason the brackets cause this command to fail

I cannot remember exactly, but I think I manually tested ${e} in this command and it worked.
I will double check this. If it fails, we are fine to use $e. Thanks!

I misunderstood here. $e is actually $ and then e. So changing it to $ e still works but is more readable. Thanks!

guoqing-noaa · 2026-05-18T16:10:39Z

+#   if [[ "${CHEM_GROUPS,,}" == *ssalt* ]]; then
+#     ncap2 -O -s "ssalt_fine=1.e-12*qv" init.nc init.nc
+#     ncap2 -O -s "ssalt_coarse=1.e-12*qv" init.nc init.nc
+#   fi


Lines 35-61: Are they still needed? If not, we can remove them

jordanschnell · 2026-05-20T16:33:24Z

+fi # Is GRA2PES listed as one of the anthro inventories?
+
+
+# Now for NEMO emissions


there are additional helper scripts needed for the NEMO implemetnation
chem_create_merge_dates_ann.py
chem_get_merge_date.py
chem_merge_emissions.py
chem_merge_pt_emissions.py

jordanschnell · 2026-05-20T16:36:49Z

+  source "${USHrrfs}"/chem_prep_goes_aod.sh
+fi
+
 if [[ "${CHEM_GROUP}" == "dust" ]]; then


we will need to update the FIX files for dust based on the name changes in MPAS-Model

jordanschnell · 2026-05-20T16:37:54Z

      err_exit
    fi
  fi
+  ncap2 -O -s 'frp_in=frp_in.ttl($nkwildfire)' -s 'fre_in=fre_in.ttl($nkwildfire)' "${EMISFILE}" "${EMISFILE}"


please see latest commits - this dimension summing should only occur for the actual RAVE files, the dummy files will already have the correct dimensions

guoqing-noaa · 2026-05-26T18:52:38Z

-	url = https://github.com/RRFSx/MPAS-Model
-        branch = gsl/develop
+	url = https://github.com/haiqinli/MPAS-Model
+        branch = gsl/develop-mp-emission


@haiqinli Could you merge the latest rrfs-mpas-jedi branch and then revert changes in lines 8-9? Thanks!

Updated as suggested. Thanks!

guoqing-noaa · 2026-06-02T17:22:28Z

+  export MPASSIT_DX=1000.0
+  export MPASSIT_REF_LAT=37.0
+  export MPASSIT_REF_LON=-119.0
+


Lines 100-111: remove the "garnetSm1km" section

Removed as suggested. Thanks!

guoqing-noaa · 2026-06-02T17:23:52Z

-  }
-  trap cleanup SIGINT SIGTERM
+else
+  echo "Info: Not slurm nor PBS"


merge the latest rrfs-mpas-jedi branch so that the changes on the left side are not overwritten accidentally.

Merged the latest rrfs-mpas-jedi branch.

guoqing-noaa · 2026-06-02T17:24:50Z

+#!/usr/bin/env python3
+import argparse
+import numpy as np
+


Add some documentation here about what this is.

guoqing-noaa · 2026-06-02T17:43:23Z

 	url = https://github.com/pyDAmonitor/pyDAmonitor.git
        ignore = all
+[submodule "sorc/regrid-wrapper"]
+	path = sorc/regrid-wrapper


sorc/chem-regrid-wrapper

guoqing-noaa · 2026-06-26T22:03:15Z

+    config_apply_lbcs = true\n\
+    config_lbc_w = 'zero'/" namelist.atmosphere
+fi
+


@haiqinli and @sudheer-bh
As discussed, we would like to remove lines 66 to line 71, right?

Yes, you are correct. Will remove lines 66 to line 71 in the next commit. Thanks!

guoqing-noaa · 2026-06-27T04:07:52Z

+[submodule "sorc/chem-regrid-wrapper"]
+	path = sorc/chem-regrid-wrapper
+	url = https://github.com/RRFSx/regrid-wrapper.git
+	branch = mpas_aero_v0


@haiqinli I am working on a patch PR to your branch to resolve the remain PR issues.
I will add comments for reference purpose, you don't need to address them immediately. I will talk with you offline.

Line 49: if possible, the main branch will be preferred here as mpas_aero_v0 does not look like a permanent branch.

guoqing-noaa · 2026-06-27T04:11:02Z

@@ -0,0 +1,64 @@
+NH4SO4_IF


All txt files under workflow/tools/prep_for_optics have been moved to fix/chemistry as discussed.
So we will remove them here.

guoqing-noaa · 2026-06-27T04:17:57Z


-    dcTaskEnv['KEEPDATA'] = get_cascade_env(f"KEEPDATA_{task_id}".upper()).upper()
+    if "anthro" in chem_groups:
+       dcTaskEnv['KEEPDATA'] = 'YES'


Why do we always keep data for the anthropogenic group?

guoqing-noaa · 2026-06-27T04:19:13Z

-    dcTaskEnv['ANTHRO_EMISINV'] = 'GRA2PES'
+    dcTaskEnv['EXTRA_CHEMICAL_TRACERS'] = os.getenv('EXTRA_CHEMICAL_TRACERS','')
+    dcTaskEnv['ANTHRO_EMISINV'] = os.getenv('ANTHRO_EMISINV','GRA2PES')
+    dcTaskEnv['EBB_DCYCLE'] = os.getenv('EBB_DCYCLE', 0)


Lines 34-36 can be put inside the lines 23-28 block directly.

…_UTILS, pyDAmonitor and launch.sh

guoqing-noaa · 2026-06-27T05:39:56Z

 #
 fcst_len_hrs_cycles=${FCST_LEN_HRS_CYCLES:-"01 01"}
 my_fcst_length=$("${USHrrfs}/find_fcst_length.sh" "${fcst_len_hrs_cycles}" "${cyc}" )
+export FCST_LENGTH="${my_fcst_length}"


It looks like FCST_LENGTH is not used anywhere. Did I miss anything?

patch to PR1498

haiqinli added 2 commits May 12, 2026 16:00

"update for chemistry"

98bae88

"update to use GRA2PES anthropogenic emission"

a46ffc1

haiqinli requested review from BenjaminBlake-NOAA, MatthewPyle-NOAA and ShunLiu-NOAA as code owners May 18, 2026 15:56

github-advanced-security AI found potential problems May 18, 2026

View reviewed changes

guoqing-noaa reviewed May 18, 2026

View reviewed changes

Merge branch 'rrfs-mpas-jedi' into rrfs-mpas-jedi-smoke

7bb7357

jordanschnell reviewed May 20, 2026

View reviewed changes

guoqing-noaa mentioned this pull request May 21, 2026

add a new option 'chemrrfs' to build.all #1505

Merged

guoqing-noaa reviewed May 26, 2026

View reviewed changes

"update MPAS-Model and latest cheMPAS-fire configurations"

c633501

github-advanced-security AI found potential problems Jun 1, 2026

View reviewed changes

guoqing-noaa reviewed Jun 2, 2026

View reviewed changes

haiqinli added 2 commits June 4, 2026 19:42

Merge branch 'rrfs-mpas-jedi' into rrfs-mpas-jedi-smoke

53935fd

"sync from cheMPAS-Fire"

e26668a

github-advanced-security AI found potential problems Jun 4, 2026

View reviewed changes

Comment thread ush/chem_prep_anthro.sh Fixed

Comment thread ush/chem_prep_anthro.sh Fixed

haiqinli added 2 commits June 8, 2026 16:09

"update the chemistry namelists"

916142c

"update following reviewer's suggestions"

66d9e45

MatthewPyle-NOAA and others added 2 commits June 9, 2026 15:29

Merge branch 'rrfs-mpas-jedi' into rrfs-mpas-jedi-smoke

215d540

"rename sorc/regrid-wrapper -> sorc/chem-regrid-wrapper"

e5947aa

guoqing-noaa reviewed Jun 26, 2026

View reviewed changes

haiqinli added 2 commits June 26, 2026 23:22

Merge branch 'rrfs-mpas-jedi' into rrfs-mpas-jedi-smoke

2563176

"remove the config_lbc_w = 'zero' for 1.25km FWx run"

dc45b1f

guoqing-noaa reviewed Jun 27, 2026

View reviewed changes

guoqing-noaa added 10 commits June 26, 2026 22:46

sync with the lastest rrfs-mpas-jedi branch: MPASBlend, MPASSIT, RRFS…

e5e0257

…_UTILS, pyDAmonitor and launch.sh

use the main branch of regrid-wrapper in .gitmodules

4c49311

remove text fix files under workflow/tools/prep_for_optics

d120ce9

prep_for_optics/prep.optics.MPAS.py -> chem_prep_optics.py

e8f9389

address the Python Linter comments for chem* scripts under ush/

6ab7fe6

address the remaining python linter comments

773c7ad

update prep_chem.py

6c579db

remove tools/chem_prep_optics.py as it has been moved to ush/

29cc5ef

address the linter comment on config.chemistry

33a218e

sync with the latest rrfs-mpas-jedi branch for yaml_finalize

f43f7db

guoqing-noaa reviewed Jun 27, 2026

View reviewed changes

guoqing-noaa and others added 7 commits June 26, 2026 23:47

update exrrfs_prep_chem.sh

e567acc

update ush/chem_fcst.sh

b2de654

address the shellcheck linter comment for chem_prep_anthro.sh

ec624fa

address the shellcheck linter comment for chem_prep_geos_aod.sh

527ef5b

address the shellcheck linter comment for chem_prep_smoke.sh

44d3c67

more changes to be linter compliant

3bc79c1

Merge pull request #1 from guoqing-noaa/patch_1498

65cf56e

patch to PR1498

		@@ -0,0 +1,19 @@
		prepend_path("MODULEPATH", "/gpfs/f6/bil-fire8/world-shared/Benjamin.Koziol/mpas-aerosols/spack-stack/envs/mpas-aerosols/modules/Core")

		fi # Is GRA2PES listed as one of the anthro inventories?


		# Now for NEMO emissions

Uh oh!

Conversation

haiqinli commented May 18, 2026

DESCRIPTION OF CHANGES:

TESTS CONDUCTED:

Machines/Platforms:

Test cases:

ISSUE:

CONTRIBUTORS (optional):

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haiqinli May 19, 2026 •

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