Error with CMIP6 file

[tessac2]

Name and Institution (Required)

Name: Tessa Clarizio
Institution: UIUC

Confirm you have reviewed the following documentation

• [y ] Support guidelines
• [ y] User manuals
• [y ] Debugging GEOS-Chem and HEMCO errors
• [y ] Current and past Github issues

Description of your issue or question

Hi GCSP! I am running GCHP v14.2.0 using Singularity with GEOSFP meteorology for 2019. I am running into an issue where I get an error "./HcoDir/CMIP6/v2020-03/2x2.5/CMIP6_GHG_surface_VMR_2019.2x25.nc [No such file or directory]". I am a bit confused why I am getting this error, because I was able to do a run successfully in the same time period in 2019 when I was using MERRA2 meteorology. I also got an error file I had not seen before, "PET000.ESMF_Logfile". So I am not sure if the reason I am getting this error is because of the different met fields or for other changes I made, and if there is a way to circumvent this error? I made the following modifications (which I did not do when I was testing out a run with MERRA2):

HEMCO_Config.rc

• Turned on QFED2
• Turned GFED off
• Turned GFED4 false

HEMCO_Diagn

• Changed all the 111 to 0 to indicate QFED for biomass burn, following the example of [QUESTION]HEMCO Diagnostic output when using QFED and GFAS geos-chem#579

ExtData.rc

• added in a QFED section (not confident I did correctly, but tried to follow examples given in Using a new inventory in ExtData.rc #412)

HISTORY.rc

• Turned on AerosolMass and Aerosols and set frequency and duration to 240000 to get daily output

gchp.20190701_0000z.log
HISTORY.txt
PET000.ESMF_LogFile.txt
slurm-11190673.txt
HEMCO_Diagn.txt
ExtData.txt
HEMCO_Config.txt

[yantosca]

Hi @tessac2, thanks for writing. I noticed in the slurm log there is this output:

nf90_open: returned error code (2) opening ./HcoDir/CMIP6/v2020-03/2x2.5/CMIP6_GHG_surface_VMR_2019.2x25.nc [No such file or directory]
pe=00014 FAIL at line=00280    NetCDF4_FileFormatter.F90                <status=2>
pe=00014 FAIL at line=00097    DataCollection.F90                       <status=2>
pe=00014 FAIL at line=02799    ExtDataGridCompMod.F90                   <status=2>
pe=00014 FAIL at line=02526    ExtDataGridCompMod.F90                   <status=2>
pe=00014 FAIL at line=01346    ExtDataGridCompMod.F90                   <status=2>
pe=00014 FAIL at line=01807    MAPL_Generic.F90                         <status=2>
pe=00014 FAIL at line=01337    MAPL_CapGridComp.F90                     <status=2>
pe=00014 FAIL at line=01300    MAPL_CapGridComp.F90                     <status=2>
pe=00014 FAIL at line=01260    MAPL_CapGridComp.F90                     <status=2>
pe=00014 FAIL at line=00837    MAPL_CapGridComp.F90                     <status=2>
pe=00014 FAIL at line=00977    MAPL_CapGridComp.F90                     <status=2>
pe=00014 FAIL at line=00301    MAPL_Cap.F90                             <status=2>
pe=00014 FAIL at line=00258    MAPL_Cap.F90                             <status=2>
pe=00014 FAIL at line=00192    MAPL_Cap.F90                             <status=2>
pe=00014 FAIL at line=00169    MAPL_Cap.F90                             <status=2>
pe=00014 FAIL at line=00031    GCHPctm.F90                              <status=2>

It looks like the file name specified in the out-of-the-box ExtData.rc is incorrect. A quick look in my HEMCO/CMIP6/v2020-03 shows that there isn't a resolution string in the file name:

$ cd /path/to/ExtData/HEMCO/CMIP6/v2020-03
$ ls *20*
CMIP6_GHG_surface_VMR_1820.nc  CMIP6_GHG_surface_VMR_2004.nc  CMIP6_GHG_surface_VMR_2010.nc
CMIP6_GHG_surface_VMR_1920.nc  CMIP6_GHG_surface_VMR_2005.nc  CMIP6_GHG_surface_VMR_2011.nc
CMIP6_GHG_surface_VMR_2000.nc  CMIP6_GHG_surface_VMR_2006.nc  CMIP6_GHG_surface_VMR_2012.nc
CMIP6_GHG_surface_VMR_2001.nc  CMIP6_GHG_surface_VMR_2007.nc  CMIP6_GHG_surface_VMR_2013.nc
CMIP6_GHG_surface_VMR_2002.nc  CMIP6_GHG_surface_VMR_2008.nc  CMIP6_GHG_surface_VMR_2014.nc
CMIP6_GHG_surface_VMR_2003.nc  CMIP6_GHG_surface_VMR_2009.nc

But in the default ExtData.rc.fullchem there are these entries with the .2x25.nc:

#
#==============================================================================
# --- Surface VMR (SfcVMR) ---
#==============================================================================
SfcVMR_CH3Cl  ppbv N Y F%y4-%m2-01T00:00:00 none none CH3Cl  ./HcoDir/CMIP6/v2020-03/2x2.5/CMIP6_GHG_surface_VMR_%y4.2x25.nc
SfcVMR_CH2Cl2 ppbv N Y F%y4-%m2-01T00:00:00 none none CH2Cl2 ./HcoDir/CMIP6/v2020-03/2x2.5/CMIP6_GHG_surface_VMR_%y4.2x25.nc
SfcVMR_CHCl3  ppbv N Y F%y4-%m2-01T00:00:00 none none CHCl3  ./HcoDir/CMIP6/v2020-03/2x2.5/CMIP6_GHG_surface_VMR_%y4.2x25.nc
SfcVMR_CH3Br  ppbv N Y F%y4-%m2-01T00:00:00 none none CH3Br  ./HcoDir/CMIP6/v2020-03/2x2.5/CMIP6_GHG_surface_VMR_%y4.2x25.nc
#

I believe that is the source of the error. Try removing the .2x25 from the above entries in ExtData.rc and see if that works. If so then that's a bug that we'll have to patch.

Tagging @msulprizio @lizziel

[tessac2]

Thanks Bob! My file path is slightly different than the one you showed /HEMCO/CMIP6/v2020-03/2x2.5 instead of /HEMCO/CMIP6/v2020-03. In the 2x2.5 folder I have files with the .2x25.nc extension (from http://geoschemdata.wustl.edu/ExtData/HEMCO/CMIP6/v2020-03/2x2.5/). Should the pathway instead be to /HEMCO/CMIP6/v2020-03?

I was also wondering if the error is because the simulation date is in 2019 and the most recent CMIP files is 2014? But I am unsure why I get this error when I previously was able to run a simulation successfully in 2019 when I had MERRA2 as the meteorology.

[yantosca]

Hi @tessac2. D'oh! I didn't see the 2x2.5 folder there, it was at the top of my screen and I was only looking at the bottom.

I also thought about the time cycling... that it the data only goes up to 2014. But I know that the ExtData time cycling isn't as sophisticated as HEMCO. @lizziel can correct me if I'm wrong, but I think it keeps searching backwards in time until it finds a file with a valid timestamp. So it the year being 2019 might not be the issue.

One thing you can try is to generate more debug output with by changingCAP.EXTDATA entries in logging.yml from WARNING to DEBUG. You'll get a list of the containers that are being read in. It'll generate a LOT more output, one line per core, so you may want to try running e.g. a c24 simulation with less cores so you don't get a huge allPEs.log file.

[tessac2]

Thanks @yantosca! When I ran the c24 simulation with the debug I got many PET*.ESMF_LogFiles (numbered 00 to 95). They all have a similar error message 20240520 164632.064 ERROR PET39 ESMF_Time.F90:815 ESMF_TimeGet() Object Set or SetDefault method not called - Object not Initialized . The slurm out file has a similar error as before, ./HcoDir/CMIP6/v2020-03/2x2.5/CMIP6_GHG_surface_VMR_2019.2x25.nc [No such file or directory]

slurm-11230222.txt
allPEs.zip
PET95.ESMF_LogFile.txt

[lizziel]

Hi @tessac2, the issue is you have a typo at the top of ExtData.rc:

fExt_AllowExtrap: .true.

Because there is an f it is not interpretting that line correctly and thus not extrapolating to closest year.

Regarding the PET files, these are ESMF error log files. We usually see ESMF time errors related to diagnostics in MAPL diagnostics and actually turned off ESMF error message generation by default in 14.3 since they are harmless. Try undoing the HISTORY.rc changes you made and see if the PET log files then go away. Report back on how that goes. This will give us more information to give to NASA GMAO (I have an open issue on their GitHub about ESMF logs files being created).

As an fyi, you do not need to print ExtData debug messages from all cores. You can limit it to root core only like this:

   CAP.EXTDATA:
       handlers: [mpi_shared]
       level: WARNING
       root_level: DEBUG
       propagate: false

I am updating the 14.4.0 docs to be more clear about this.

[yantosca]

Thanks @lizziel for catching that!

[lizziel]

@tessac2, let us know if the default ExtData.rc file had that typo. If yes, I'll create a general GitHub issue to alert users. 14.2.0 is pretty old at this point since we are about to release 14.4 so we will not go back and issue a patch.

[tessac2]

@lizziel Thank you so much for pointing that out! There was no typo in the default-- I (or my cat who loves to walk across the keyboard) must have accidentally hit a button when I was opening the ExtData.rc file and I did not notice. Thank you so much for catching it!

This solved the CMIP issue I am having, but I am still having a bit of trouble getting the code to run. I am now getting an error, where it says it cannot find variables like MEK, CH4, CO2, etc in the QFED files. My guess is that I labeled them wrong in the ExtData.rc when I was filling in the QFED section. I had tried to copy and paste from the HEMCO_Config.rc and rearrange accordingly to match the new formatting, and delete the lines that were just '-', but I still get errors. I am also a bit confused because the HEMCO_Config.rc has QFED emissions divided into PBL and FT, but I was not sure how to do that in ExtData (or if it is possible/necessary). I read through issue #412 and the links provided there but was still having a bit of trouble understanding. I was wondering if you could advise or if there is any example for QFED emissions? Thanks!

slurm-11272551.txt
ExtData.txt

[yantosca]

@tessac2, I have 2 cats so I understand exactly what you mean :-)

Also, in ExtData.rc I believe you don't have to read the same variable twice.

In the default HEMCO_Config.rc file e.g. ACET is written like this:

(((QFED2
0 QFED_ACET_PBL  $ROOT/QFED/v2018-07/$YYYY/$MM/qfed2.emis_acet.006.$YYYY$MM$DD.nc4 biomass 2000-2022/1-12/1-31/0/+12hour EFY xyL=1:PBL     kg/m2/s ACET 75/311        5 2
0 QFED_ACET_FT   $ROOT/QFED/v2018-07/$YYYY/$MM/qfed2.emis_acet.006.$YYYY$MM$DD.nc4 biomass 2000-2022/1-12/1-31/0/+12hour EFY xyL=PBL:5500m kg/m2/s ACET 75/312        5 2

But I think it could be written like this, so that the QFED_ACET_FT can be "piggybacked" onto the previous entry

0 QFED_ACET_PBL  $ROOT/QFED/v2018-07/$YYYY/$MM/qfed2.emis_acet.006.$YYYY$MM$DD.nc4 biomass 2000-2022/1-12/1-31/0/+12hour EFY xyL=1:PBL     kg/m2/s ACET 75/311        5 2
0 QFED_ACET_FT   -                                                                 -       -                             -   xyL=PBL:5500m kg/m2/s ACET 75/312        5 2

For "piggybacked" entries in GCHP, you only have to specify the entry where the file is read from disk (i.e. the one with the file name). HEMCO will figure out the rest.

So you would only need to add the QFED_*_PBL entries in ExtData.rc, I think.

[lizziel]

@yantosca is right on that! Putting the same filename/variable name pair in ExtData.rc more than once just slows down the model. If you use the dashes method in HEMCO_Config.rc then it reduces the GCHP I/O overhead.

As for the error of not finding ACET, I think it is because the variable name in the file is actually biomass. You need to put the file variable name rather than the GEOS-Chem species in ExtData.rc. MAPL will read that variable from file and assign it to the HEMCO variable name, e.g. QFED_ACET_PBL. Then HEMCO will assign it a GEOS-Chem species based on what is in HEMCO_Config.rc. Hopefully updating the ExtData.rc variable name name will fix the remaining issues.

[tessac2]

Thanks Bob!

For reference this was the error I was initially getting.

Then I deleted the FT entries in GCHP and changed the species name to biomass and got this error in the allPEs.log:

So I added the FT lines back in. It seems to be running now so I will update you on the results!

[lizziel]

Look like we commented at exactly the same time!

[tessac2]

Thanks @lizziel! It seems to be running now will follow up :)

[tessac2]

Just providing an update, I was able to get it to run temporarily, but the run keeps failing a few weeks in. I have been running for 1 week at a time. Initially I tried running in October 2020, running for 1 week at a time. Then, for the run starting 2020-10-22 I got the error KPP failed to converge. In line with other GCHP issues that had similar errors, I changed the restart file date and I started the simulation from another month, 2020-11-01. However, this also failed a couple weeks into the simulation with the same error.

gchp.20201022_0000z.log
gchp.20201115_0000z.log

[lizziel]

Hi @tessac2, are you able to reproduce this problem when running with the default emissions?

[tessac2]

Thanks @lizziel, I did not get the same error when I switched from QFED back to GFED. I wonder if I filled in the ExtData correctly when I had QFED emissions, and if this caused an error? (screenshot is shown in previous reply). Or if it has something else to do with QFED?

[lizziel]

Hi @tessac2, I am not sure if anyone in the community uses QFED with GCHP. You could try doing a run with frequent diagnostics and then look at the results to see if anything is going off the rails. You can also add in QFED emissions as diagnostics to see what they look like. These diagnostics use the vertical height injection feature of HEMCO (xyL=1:PBL) so I wonder if something is off there.

[tessac2]

Thanks @lizziel! I started another run using GFED and MERRA-2 for the meteorology, after discussion from IGC11 where GEOS-FP is not recommended after June 2020. However, now I am running into the same issue again. I was able to run the simulation for May 2021 but my June run fails on June 4, 2021.

gchp.20210601_0000z.log

[yantosca]

Hi @tessac2, thanks for the feedback. Looking at your output there are some rxn rates that really blow up. Also there are a lot of negative concentrations (probably a side effect of these). For example:

   9902850.5014838222      ClOO --> Cl + O2   5.9307137702429200      Cl2O2 --> 2 ClO
   5.9307137702429200      Cl2O2 --> 2 ClO
  0.20863623086246982      IONO --> I + NO2
   4.4691598926869987E-033 CH2OO + 2 H2O --> 0.06 PH2O2 + 0.4 HMHP + 0.06 H2O2 + 0.54 HCOOH + 0.06 CH2O
  0.41594861909815112      NO3 --> NO2 + O

Most of the rxn rates constants (1/s) are pretty small, of order 1e-5 to 1e-15 or less), so these stood out.

I also wonder if this is due to the dummy species being included in the KPP convergence. See geoschem/geos-chem#2359 and KineticPreProcessor/KPP#66. I've pulled the fix in the PR 2359 into the GEOS-Chem 14.5.0 branch, but you could try to implement the quick fix that @obin1 suggested in this comment. It's worth a shot.

[tessac2]

Thanks @yantosca! I am using Singularity to run GCHP however, so I am not sure if I am able to implement the quick fix since I cannot access the CodeDir (or at least I am not sure how to do that, there is no link in my run directory). I am not sure what is causing the reaction rates to blow up, perhaps like you said it is the dummy species?

[yantosca]

@tessac2: In the container, could you clone a new copy of GCHP? Then you can add the quick fix in and recompile it.

[lizziel]

@tessac2 I wonder if you are hitting integrator errors because of this bug in 14.2. Several users found instability in fullchem runs for GCHP. A fix was put into 14.3 for it. Could you try updating versions? 14.4.1 is the latest so we recommend that one.

[tessac2]

@yantosca I think I am only able to pull images from the Docker Hub. (https://hub.docker.com/r/geoschem/gchp/tags?page=1&ordering=last_updated). I run singularity pull gchp.sif docker://geoschem/gchp:14.2.0 to download the image then singularity exec -B $HOME:$HOME -B /projects/horowitz_group/GEOSChem_input_data/ExtData:/projects/horowitz_group/GEOSChem_input_data/ExtData -B /projects/horowitz_group/tessa/GCHP/rundirs:/workdir gchp.sif /bin/bash -c ". ~/.bashrc && /opt/geos-chem/bin/createRunDir.sh" to set up the run directory.

Thanks @lizziel! On versions past 14.2 there was an update where the openmpi version is no longer compatible with my campus cluster system, so I have been unable to test more recent versions. I know @yidant was looking into this.

@yidant I see you pushed v14.4.1 image yesterday, was the issue with the openmpi fixed in this version or will it be coming with the next version?

[yidant]

Hi @tessac2 , the v14.4.1 image only contains executable built from GCHP 14.4.1. The update will come with v14.5.0. Feel free to compile a new one!

The openmpi package is already updated in these versions.

[tessac2]

Thank @yidant. My NX and NY do not seem to be updating automatically? I have not had this issue with previous versions. It is saying my NX =4 and NY = 24 but according to my setCommonRunSettings my NX=2 and NY =48.

If I set the resolution to 48, I run into another error saying that libnetcdf.so.19 is missing from the gchp file. I had this error for v14.4.0 as well. This is not the gchp.sif file, but rather the gchp file that automatically populates in rundirs when creating a run directory.

[lizziel]

GCHP 14.4.1 has a bug where the error message you see for NX and NY is triggered if using certain combinations of grid resolution and cores. This will be fixed in 14.4.2. Commenting out the place where it errors out in setCommonRunSettings.sh fixes the issue. However, I think you would then run into the library issue you are seeing if you also hit it with 14.4.0. Using grid resolution that is a multiple of 24 would also fix the issue, but you are hitting the library problem with that too.

I think the best solution is to clone the code in your 14.1 environment and manually apply the HMS fix to see if that works.