Thanks @JianpingHuang-NOAA for reporting this.

It looks like the issue is that those diagnostics were removed for HEMCO v3.9.2 release. We need to specify them in the HEMCO_Diagn.rcs instead.

@zmoon Let me know if it is ready for a test. Thanks !

@JianpingHuang-NOAA we're still figuring out what we should do. Our first idea didn't work (Patrick tested). Will let you know.

@zmoon Dogwood was down today. I will test it when the machine is up.

@zmoon The job still failed with the same error message after adding the following three lines in the "HEMCO_sa_Diagn.rc" at
~/parm/nexus_config/cmaq_nei2019

InvMEGAN_AAXX AAXX 108 -1 -1 2 kg/m2/s
InvMEGAN_FAXX FAXX 108 -1 -1 2 kg/m2/s
InvMEGAN_APIN APIN 108 -1 -1 2 kg/m2/s

Hi @JianpingHuang-NOAA, we're still working out how to get those outputs working with HEMCO 3.10. In the meantime could you try #71, which reverts HEMCO to 3.9.1? Note that git submodule update --recursive or such will be needed after switching to that branch.

@zmoon I did :git submodule update" and then recompiled the nexus code, and still got the following error message,

PROGRAM: combine_ant_bio.py
Starting...

mapping species AACD
Traceback (most recent call last):
File "/lfs/h2/emc/physics/noscrub/jianping.huang/nwdev/packages/aqm.v8.0.0h/sorc/arl_nexus/utils/combine_ant_bio.py", line 201, in
raise SystemExit(main(**parse_args()))
File "/lfs/h2/emc/physics/noscrub/jianping.huang/nwdev/packages/aqm.v8.0.0h/sorc/arl_nexus/utils/combine_ant_bio.py", line 116, in main
ds_new[spc][:] = ds["InvMEGAN_AAXX"][:]
File "src/netCDF4/_netCDF4.pyx", line 2386, in netCDF4._netCDF4.Dataset.getitem
IndexError: InvMEGAN_AAXX not found in /
PBS: Running epilogue on parent mom node: nid002735...

Job 6547999.dbqs01 - PBS Job Script:

(Note: Duplicate #PBS entries are a function how PBS interprets and caches the original job script.)
"

Can you check what HEMCO commit you have? I did a test run and did get those outputs using #71

I checked out a fresh develop branch from https://github.com/noaa-oar-arl/NEXUS
, and still seeing

commit deaa1923f3d3e06e264c4ccbe0e3b7dc32edcc20
Merge: 41605bd b88ff92
Author: Bob Yantosca [email protected]
Date: Fri Nov 8 12:31:27 2024 -0500

**HEMCO 3.10.0 release**

#71 hasn't been merged to the develop branch yet (waiting for Patrick to check if it fixes the issue). You'd have to check out the corresponding branch.

It works with HEMCO 3.9.1

Yes confirmed that it works on WCOSS2, closing this issue.