HEMCO error: Cannot get field FLASH_DENS

[madhumitamahant]

Your name

Madhumita Mahant

Your affiliation

phD student

What happened? What did you expect to happen?

HEMCO ERROR: Cannot find file for current simulation time: /home/IITB/india-aqpogc/24d1274/ExtData//HEMCO/OFFLINE_LIGHTNING/v2020-03/MERRA2/0001/FLASH_CTH_MERRA2_0.5x0.625_0001_01.nc4 - Cannot get field FLASH_DENS. Please check file name and time (incl. time range flag) in the config. file
 
HEMCO ERROR: Error encountered in routine HCOIO_Read!
 
HEMCO ERROR: Error in HCOIO_DATAREAD called from HEMCO ReadList_Fill: FLASH_DENS
 --> LOCATION: ReadList_Fill (HCO_ReadList_Mod.F90)
 
HEMCO ERROR: Error in ReadList_Fill (6) called from HEMCO ReadList_Read
 --> LOCATION: ReadList_Read (HCO_ReadList_Mod.F90)
 Error in ReadList_Read called from hco_run
===============================================================================
GEOS-Chem ERROR: Error encountered in "HCO_Run"!
 -> at HCOI_GC_Run (in module GeosCore/hco_interface_gc_mod.F90)

THIS ERROR ORIGINATED IN HEMCO!  Please check the HEMCO log file for 
additional error messages!
===============================================================================


Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7f18dbccd171 in ???
#1  0x7f18dbccc313 in ???
#2  0x7f18dacf35af in ???
#3  0x7f18dbecad4d in ???
#4  0x48ab03 in __hco_interface_gc_mod_MOD_hcoi_gc_run
	at /home/IITB/india-aqpogc/24d1274/gc_2x25_47L_merra2_fullchem/CodeDir/src/GEOS-Chem/GeosCore/hco_interface_gc_mod.F90:1163
#5  0x453cef in __emissions_mod_MOD_emissions_run
	at /home/IITB/india-aqpogc/24d1274/gc_2x25_47L_merra2_fullchem/CodeDir/src/GEOS-Chem/GeosCore/emissions_mod.F90:185
#6  0x405d92 in geos_chem
	at /home/IITB/india-aqpogc/24d1274/gc_2x25_47L_merra2_fullchem/CodeDir/src/GEOS-Chem/Interfaces/GCClassic/main.F90:702
#7  0x4045e6 in main
	at /home/IITB/india-aqpogc/24d1274/gc_2x25_47L_merra2_fullchem/CodeDir/src/GEOS-Chem/Interfaces/GCClassic/main.F90:32

What are the steps to reproduce the bug?

i have tried creating a directory for offline lightening ( lightening climatology file) inside ExtData and downloaded it.

Please attach any relevant configuration and log files.

HEMCO ERROR: Error encountered in routine HCOIO_Read!

HEMCO ERROR: Error in HCOIO_DATAREAD called from HEMCO ReadList_Fill: FLASH_DENS
 --> LOCATION: ReadList_Fill (HCO_ReadList_Mod.F90)

HEMCO ERROR: Error in ReadList_Fill (6) called from HEMCO ReadList_Read
 --> LOCATION: ReadList_Read (HCO_ReadList_Mod.F90)
 Error in ReadList_Read called from hco_run
===============================================================================
GEOS-Chem ERROR: Error encountered in "HCO_Run"!
 -> at HCOI_GC_Run (in module GeosCore/hco_interface_gc_mod.F90)

THIS ERROR ORIGINATED IN HEMCO!  Please check the HEMCO log file for
additional error messages!
===============================================================================


Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7f18dbccd171 in ???
#1  0x7f18dbccc313 in ???
#2  0x7f18dacf35af in ???
#3  0x7f18dbecad4d in ???
#4  0x48ab03 in __hco_interface_gc_mod_MOD_hcoi_gc_run
        at /home/IITB/india-aqpogc/24d1274/gc_2x25_47L_merra2_fullchem/CodeDir/src/GEOS-Chem/GeosCore/hco_interface_gc_mod.F90:1163
#5  0x453cef in __emissions_mod_MOD_emissions_run
        at /home/IITB/india-aqpogc/24d1274/gc_2x25_47L_merra2_fullchem/CodeDir/src/GEOS-Chem/GeosCore/emissions_mod.F90:185
#6  0x405d92 in geos_chem
        at /home/IITB/india-aqpogc/24d1274/gc_2x25_47L_merra2_fullchem/CodeDir/src/GEOS-Chem/Interfaces/GCClassic/main.F90:702
#7  0x4045e6 in main
        at /home/IITB/india-aqpogc/24d1274/gc_2x25_47L_merra2_fullchem/CodeDir/src/GEOS-Chem/Interfaces/GCClassic/main.F90:32

What GEOS-Chem version were you using?

14.2.2

What environment were you running GEOS-Chem on?

Other (please explain below)

What compiler and version were you using?

Compiler: GNU Fortran (GCC) Version: 8.5.0, Build system: CMake MPI: OpenMPI 5.0.5

Will you be addressing this bug yourself?

Yes

In what configuration were you running GEOS-Chem?

GCClassic

What simulation were you running?

Full chemistry

As what resolution were you running GEOS-Chem?

2*2.5 global

What meterology fields did you use?

MERRA-2

Additional information

i am using HPC cluster ( Paramrudra)

[yantosca]

Thanks for writing @madhumitamahant. This error is of the type described here on ReadTheDocs. In particular, I believe that your simulation lies outside of the available time range for which the OFFLINE_LIGHTNING data is available.

To fix this you can select the lightning climatology (which is a monthly mean based on several years of lightning data). In your HEMCO_Config.rc file, change:

103     LightNOx               : on    NO
    --> LightningClimatology   :       false
    --> CDF table              :       $ROOT/LIGHTNOX/v2014-07/light_dist.ott2010.dat

to

103     LightNOx               : on    NO
    --> LightningClimatology   :       true
    --> CDF table              :       $ROOT/LIGHTNOX/v2014-07/light_dist.ott2010.dat

and then re-run your simulation.

[yantosca]

@madhumitamahant: I added a section to ReadTheDocs describing this error and the fix. This will go live with GEOS-Chem 14.8.0 but in the meantime you can see it here: https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/error-guide.html#hemco-error-cannot-get-field-flash-dens

[madhumitamahant]

i tried different approach by changing the data source from washu to AWS and this issue got resolved but now the new issue for final run arrived is this

HEMCO: Opening ./Restarts/GEOSChem.Restart.20220101_0000z.nc4
===============================================================================
GEOS-CHEM ERROR: Could not find FRLAKE in HEMCO data list!
STOP at GET_MET_2D (get_met_mod.F90)" . Is it because i changed from washu to AWS for downloading the data?\

[madhumitamahant]

"#553" i had taken the reference of this issue553, but in my case the master switches already true and the downloaded files are not currupted. What could be the possible cause?

[yantosca]

Thanks for the update @madhumitamahant. Constant fields like PHIS, FRLAKE, FRLAND are stored in the "CN" file. Download this file to your GEOS_2x.25/MERRA2/2015/01 folder:

• https://geos-chem.s3-us-west-2.amazonaws.com/GEOS_2x2.5/MERRA2/2015/01/MERRA2.20150101.CN.2x25.nc4

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