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GEOS-Chem "Science Codebase" repository. Contains GEOS-Chem science routines, run directory generation scripts, and interface code. This repository is used as a submodule within the GCClassic and GCHP wrappers, as well as in other modeling contexts (external ESMs).
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[QUESTION] 12.9.3 to 13.0.2 error in reading restart file #712

Closed CharikleiaGRN closed 3 years ago

CharikleiaGRN commented 3 years ago

I am trying to run the same simulation on 12.9.3 and .13.0.2 and never works for the second one. I downloaded the HEMCO/GCClassic_Output/13.0.0/ and the GEOSCHEM_RESTARTS/GC_13.0.0/ and of course Updated Streets Hg emissions, Updated EDGAR 4.3 Hg emissions. I copied the ./GEOSChem.Restart.20150101_0000z.nc4 to the run directory as this is my start date. (Is it the right way?)

The simulation stops when it is going to read the restart file. Thank you

Output

HEMCO: Opening /media/data_03/gcgrid/data/ExtData/GEOS_2x2.5/GEOS_FP/2015/01/GEOSFP.20150101.A3mstE.2x25.nc
HEMCO: Opening /media/data_03/gcgrid/data/ExtData/GEOS_2x2.5/GEOS_FP/2015/01/GEOSFP.20150101.I3.2x25.nc
HEMCO: Opening /media/data_03/gcgrid/data/ExtData/GEOS_2x2.5/GEOS_FP/2015/01/GEOSFP.20150102.I3.2x25.nc
HEMCO: Opening /media/data_03/gcgrid/data/ExtData/HEMCO/Yuan_XLAI/v2019-03/Yuan_proc_MODIS_XLAI.025x025.2015.nc
HEMCO: Opening ./GEOSChem.Restart.20150101_0000z.nc4
 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!
===============================================================================

===============================================================================
GEOS-Chem ERROR: Error encountered in "HCOI_GC_Run"!
 -> at Emissions_Run (in module GeosCore/emissions_mod.F90)
===============================================================================

===============================================================================
GEOS-CHEM ERROR: Error encountered in "Emissions_Run", Phase 0

This error can indicate a missing file. Please check the HEMCO log file for 
additional error messages!

STOP at  -> at GEOS-Chem (in GeosCore/main.F90)
===============================================================================
     - CLEANUP: deallocating arrays now...

HEMCO.log

--> LOCATION: HCOIO_READ_STD (hcoio_read_std_mod.F90)
HEMCO WARNING: Data is treated as unitless, but file attribute suggests it is not: kg kg-1. File: /media/data_03/gcgrid/data/ExtData/GEOS_2x2.5/GEOS_FP/2015/01/GEOSFP.20150102.I3.2x25.nc
--> LOCATION: HCOIO_READ_STD (hcoio_read_std_mod.F90)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
HEMCO ERROR: Cannot find field SPC_Hg0. Please check variable name in the config. file
ERROR LOCATION: HCOIO_READ_STD (hcoio_read_std_mod.F90)
ERROR LOCATION: HCOIO_DataRead (hcoio_dataread_mod.F90)
ERROR LOCATION: ReadList_Fill (hco_readlist_mod.F90)
ERROR LOCATION: ReadList_Read (hco_readlist_mod.F90)
ERROR LOCATION: HCO_RUN (hco_driver_mod.F90)

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
HEMCO ERROR: Error encountered in routine HCOIO_Read_Std!
ERROR LOCATION: HCOIO_READ_STD (hcoio_read_std_mod.F90)
ERROR LOCATION: HCOIO_DataRead (hcoio_dataread_mod.F90)
ERROR LOCATION: ReadList_Fill (hco_readlist_mod.F90)
ERROR LOCATION: ReadList_Read (hco_readlist_mod.F90)
ERROR LOCATION: HCO_RUN (hco_driver_mod.F90)

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
HEMCO ERROR: Error in HCOIO_DATAREAD called from HEMCO ReadList_Fill: SPC_Hg0
ERROR LOCATION: ReadList_Fill (HCO_ReadList_Mod.F90)

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
HEMCO ERROR: Error in called ReadList_Fill (7) from HEMCO ReadList_Read
ERROR LOCATION: ReadList_Read (HCO_ReadList_Mod.F90)

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

input.geos

%%% SIMULATION MENU %%% :
Start YYYYMMDD, hhmmss  : 20150101 000000
End   YYYYMMDD, hhmmss  : 20150201 000000
Run directory           : ./
Root data directory     : /media/data_03/gcgrid/data/ExtData
Met field               : GEOSFP
Simulation name         : Hg
Species database file   : ./species_database.yml
Turn on debug printout? : F
Use GC classic timers?  : F
------------------------+------------------------------------------------------
%%% GRID MENU %%%       :
Grid resolution         : 2.0x2.5
Longitude min/max       : -180.0 180.0
Latitude  min/max       :  -90.0  90.0
 Half-sized polar boxes?: T
Number of levels        : 72
Nested grid simulation? : F
 Buffer zone (N S E W ) :  0  0  0  0
------------------------+------------------------------------------------------
%%% TIMESTEP MENU %%%   :
Tran/conv timestep [sec]: 600
Chem/emis timestep [sec]: 1200
------------------------+------------------------------------------------------
%%% ADVECTED SPECIES MENU %%%:
Species name            : Hg0
Species name            : Hg2
Species name            : HgP
------------------------+------------------------------------------------------
%%% TRANSPORT MENU %%%  :
Turn on Transport       : T
 => Fill Negative Values: T
 => IORD, JORD, KORD    : 3  3  7
------------------------+------------------------------------------------------
%%% CONVECTION MENU %%% :
Turn on Cloud Conv?     : T
Turn on PBL Mixing?     : T
 => Use non-local PBL?  : T
------------------------+------------------------------------------------------
%%% AEROSOL MENU %%%    :
Online SULFATE AEROSOLS : F
 => Metal cat. SO2 ox.? : F
Online CARBON  AEROSOLS : F
 => Use Brown Carbon?   : F
Online COMPLEX SOA      : F
 => Semivolatile POA?   : F
Online DUST    AEROSOLS : F
 => Acidic uptake ?     : F
Online SEASALT AEROSOLS : F
 => SALA radius bin [um]: 0.01 0.5
 => SALC radius bin [um]: 0.5  8.0
 => MARINE ORG AEROSOLS : F
Settle strat. aerosols  : F
Online PSC AEROSOLS     : F
Allow homogeneous NAT?  : F
NAT supercooling req.(K): 3.0
Ice supersaturation req.: 1.2
Perform PSC het. chem.? : F
Calc. strat. aero. OD?  : F
Enhance BC Absorption?  : F
 => hydrophilic BC      : 1.5
 => hydrophobic BC      : 1.0
Photolyse nitrate aer.? : F
 => NITs Jscale (JHNO3) : 0.0
 => NIT  Jscale (JHNO3) : 0.0
 => % channel A (HONO)  : 66.667
 => % channel B (NO2)   : 33.333
------------------------+------------------------------------------------------
%%% DEPOSITION MENU %%% :
Turn on Dry Deposition? : T
Turn on Wet Deposition? : T
Turn on CO2 Effect?     : F
CO2 level               : 600.0
Reference CO2 level     : 380.0
Diag alt above sfc [m]  : 10
------------------------+------------------------------------------------------
%%% CHEMISTRY MENU %%%  :
Turn on Chemistry?      : T
Use linear. strat. chem?: F
 => Use Linoz for O3?   : F
Use UCX strat. chem?    : F
Active strat. H2O?      : F
Overhead O3 for FAST-JX :---
 => Online O3 from model: F
 => O3 from met fields  : F
 => TOMS/SBUV O3        : F
Gamma HO2               : 0.2
------------------------+------------------------------------------------------
%%% PHOTOLYSIS MENU %%% :
FAST-JX directory       : /media/data_03/gcgrid/data/ExtData/CHEM_INPUTS/FAST_JX/v2020-02/
------------------------+------------------------------------------------------
%%% RADIATION MENU %%%  :
AOD Wavelength (nm)     : 550
Turn on RRTMG?          : F
Calculate LW fluxes?    : F
Calculate SW fluxes?    : F
Clear-sky flux?         : F
All-sky flux?           : F
Radiation Timestep [sec]: 10800
------------------------+------------------------------------------------------
%%% MERCURY MENU %%%    :
Error check tag/tot Hg? : F
Use dynamic ocean Hg?   : F
Preindustrial sim?      : F
Use GTMM soil model?    : F
GTMM Hg rst file (bpch) : GTM.totHg.YYYYMMDDhh
Use Arctic river Hg?    : T
Tie HgII(aq) red to UVB?: T
------------------------+------------------------------------------------------
%%% OBSPACK MENU %%%    :
Turn on ObsPack diag?   : F
Quiet logfile output    : F
ObsPack input file      : ./obspack_co2_1_OCO2MIP_2018-11-28.YYYYMMDD.nc
ObsPack output file     : ./OutputDir/GEOSChem.ObsPack.YYYYMMDD_hhmmz.nc4
ObsPack output species  : NO CO O3
------------------------+------------------------------------------------------
###############################################################################
#####  THE FOLLOWING MENUS ARE ONLY READ WHEN YOU COMPILE GEOS-Chem       #####
#####  WITH THE BPCH_DIAG=y OPTION.                                       #####
#####                                                                     #####
#####  BPCH_DIAG=y IS ALREADY TURNED ON BY DEFAULT FOR:                   #####
#####  (1) TOMAS simulations                                              #####
#####  (2) RRTMG simulations                                              #####
#####  (3) Hg simulations                                                 #####
#####  (4) POPs simulatons                                                #####
#####                                                                     #####
#####  FOR ALL OTHER SIMULATIONS, BPCH DIAGNOSTICS ARE TURNED OFF BY      #####
#####  DEFAULT (i.e. BPCH_DIAG=n IS USED UNLESS YOU SPECIFY OTHERWISE).   #####
###############################################################################
------------------------+------------------------------------------------------
%%% OUTPUT MENU %%%     : 123456789.123456789.123456789.1--1=ZERO+2=BPCH
Schedule output for JAN : 3000000000000000000000000000000
Schedule output for FEB : 30000000000000000000000000000
Schedule output for MAR : 3000000000000000000000000000000
Schedule output for APR : 300000000000000000000000000000
Schedule output for MAY : 3000000000000000000000000000000
Schedule output for JUN : 300000000000000000000000000000
Schedule output for JUL : 3000000000000000000000000000000
Schedule output for AUG : 3000000000000000000000000000000
Schedule output for SEP : 300000000000000000000000000000
Schedule output for OCT : 3000000000000000000000000000000
Schedule output for NOV : 300000000000000000000000000000
Schedule output for DEC : 3000000000000000000000000000000
------------------------+------------------------------------------------------
%%% GAMAP MENU %%%      :
diaginfo.dat path       : diaginfo.dat
tracerinfo.dat path     : tracerinfo.dat
------------------------+------------------------------------------------------
%%% DIAGNOSTIC MENU %%% :
Binary punch file name  : ./OutputDir/GEOSChem.YYYYMMDD.bpch
Diagnostic Entries ---> :  L   Tracers to print out for each diagnostic
ND03: Hg emissions, P/L :  0   all
ND06: Dust aer source   :  1   all
ND44: Drydep flx/vel    :  1   all
ND53: POPs Emissions    :  0   all
ND59: TOMAS aerosol emis:  0   all
ND60: TOMAS rate        :  0   all
ND61: TOMAS 3D rate     :  0   all
ND72: Radiative output  :  0   all
------------------------+------------------------------------------------------
%%% PLANEFLIGHT MENU %%%:
Turn on plane flt diag? : F
Flight track info file  : Planeflight.dat.YYYYMMDD
Output file name        : plane.log.YYYYMMDD
-------------------------------------------------------------------------------
%%% ND51 MENU %%%       :
Turn on ND51 diagnostic : F
LT avg timeseries file  : ts_satellite.YYYYMMDD.bpch
Output as HDF5?         : F
Tracers to include      : 1
GMT Hour for disk write :   0
Avg Period [LT hours]   :   9  11
IMIN, IMAX of region    :   1  72
JMIN, JMAX of region    :   1  46
LMIN, LMAX of region    :   1  40
-------------------------------------------------------------------------------
%%% ND51b MENU %%%      :
Turn on ND51b diagnstic : F
LT avg timeseries file  : ts_13_15.NA.YYYYMMDD.bpch
Output as HDF5?         : F
Tracers to include      : 1
GMT Hour for disk write :  1
Avg Period [LT hours]   :  13  15
IMIN, IMAX of region    :   1  72
JMIN, JMAX of region    :   1  46
LMIN, LMAX of region    :   1   1
-------------------------------------------------------------------------------
%%% PROD & LOSS MENU %%%: ### ONLY NEEDED FOR TOMAS ###
Turn on P/L (ND65) diag?: T
# of levels for ND65    : 72
------------------------+------------------------------------------------------
END OF FILE             :
------------------------+------------------------------------------------------

HEMCO_Config.rc

#------------------------------------------------------------------------------
#                  Harmonized Emissions Component (HEMCO)                     !
#------------------------------------------------------------------------------
#BOP
#
# !MODULE: HEMCO_Config.rc
#
# !DESCRIPTION: Contains configuration information for HEMCO. Define the
#  emissions inventories and corresponding file paths here. Entire
#  configuration files can be inserted into this configuration file with
#  an '>>>include' statement, e.g. '>>>include HEMCO\_Config\_test.rc'
#  The settings of include-files will be ignored.
#\\
#\\
# !REMARKS:
#  This file has been customized for the Hg simulation.
#  See The HEMCO User's Guide for file details:
#    http://wiki.geos-chem.org/The_HEMCO_User%27s_Guide
#
# !REVISION HISTORY:
#  See https://github.com/geoschem/geos-chem for complete history
#EOP
#------------------------------------------------------------------------------
#BOC
###############################################################################
### BEGIN SECTION SETTINGS
###############################################################################

ROOT:                        /media/data_03/gcgrid/data/ExtData/HEMCO
METDIR:                      /media/data_03/gcgrid/data/ExtData/GEOS_2x2.5/GEOS_FP
Logfile:                     HEMCO.log
DiagnPrefix:                 ./OutputDir/HEMCO_diagnostics
DiagnFreq:                   Monthly
Wildcard:                    *
Separator:                   /
Unit tolerance:              1
Negative values:             0
Only unitless scale factors: false
Verbose:                     0
Warnings:                    1

### END SECTION SETTINGS ###

###############################################################################
### BEGIN SECTION EXTENSION SWITCHES
###############################################################################
# ExtNr ExtName                on/off  Species  Years avail.
0       Base                   : on    *
# ----- MAIN SWITCHES -----------------------------------------
    --> EMISSIONS              :       true
    --> METEOROLOGY            :       true     # 1980-2021
    --> CHEMISTRY_INPUT        :       true
# ----- RESTART FIELDS ----------------------------------------
    --> GC_RESTART             :       true
# ----- NESTED GRID FIELDS ------------------------------------
    --> GC_BCs                 :       false    # 1980-2021
# ----- REGIONAL INVENTORIES ----------------------------------
    --> ZHAOZHANG              :       false    # 2010
    --> CHAKRABORTY            :       false    # 2010
    --> EMISS_CONTROLS         :       false    # 2010
# ----- GLOBAL INVENTORIES ------------------------------------
    --> AMAP_COMB              :       false    # 2010
    --> AMAP_INDS              :       false    # 2010
    --> AMAP_INTW              :       false    # 2010
    --> WHET                   :       true     # 2010
    --> STREETS                :       false    # 2015
    --> ARTISANAL              :       false    # 1985
    --> NATURAL                :       true     # 1985
    --> SOILDIST               :       true     # 1985
    --> QFED2                  :       false    # 2000-2020
    --> EDGAR_TOT              :       false    # 1970-2012
    --> EDGAR_CEM              :       false    # 1970-2012
    --> EDGAR_CHLOR            :       false    # 1970-2012
    --> EDGAR_COMB_A           :       false    # 1970-2012
    --> EDGAR_COMB_B           :       false    # 1970-2012
    --> EDGAR_GLASS            :       false    # 1970-2012
    --> EDGAR_GOLDA            :       false    # 1970-2012
    --> EDGAR_GOLDB            :       false    # 1970-2012
    --> EDGAR_IRO              :       false    # 1970-2012
    --> EDGAR_NFEOTH           :       false    # 1970-2012
    --> EDGAR_SHIP             :       false    # 1970-2012
    --> EDGAR_TRO              :       false    # 1970-2012
    --> EDGAR_WASTE            :       false    # 1970-2012
# ----- NON-EMISSIONS DATA ------------------------------------
    --> OXIDANT_FIELDS         :       true     # 2010-2019
    --> BrOx_GC                :       true     # 2010-2019
    --> JBrO                   :       true     # 2010-2019
    --> LRED_JNO2              :       true     # 2005
    --> AERO_HG2_PARTITION     :       true     # 2010-2019
    --> OCEAN_Hg               :       true     # 1985,2003,2009
    --> TOMS_SBUV_O3           :       true     # 1971-2010
    --> LHALOGENCHEM           :       true
    --> LHGAQCHEM              :       true
    --> LOHO3CHEM              :       false
    --> LRED_INPLUME           :       false
    --> OLSON_LANDMAP          :       true     # 1985
    --> YUAN_MODIS_LAI         :       true     # 2005-2016
# ----------------------------------------------------------------------------
# NOTE: Changing these options will require a change in reduction rate in order
#       to maintain agreement with observations. Please see wiki for details
#       http://wiki.seas.harvard.edu/geos-chem/index.php/Mercury
# ----------------------------------------------------------------------------
111     GFED              : on    Hg0
    --> GFED4             :       true
    --> GFED_daily        :       false
    --> GFED_3hourly      :       false
    --> Scaling_CO        :       1.05
    --> Scaling_NAP       :       2.75e-4
    --> hydrophilic BC    :       0.2
    --> hydrophilic OC    :       0.5
    --> fraction POG1     :       0.49
114     FINN              : on    Hg0
    --> FINN_daily        :       false
    --> Scaling_CO        :       1.0
    --> hydrophilic BC    :       0.2
    --> hydrophilic OC    :       0.5
    --> Scaling_Hg0       :       7.16e-7

### END SECTION EXTENSION SWITCHES ###

######################################################
yantosca commented 3 years ago

Thanks for writing @HarrietGRN. In GEOS-Chem 13.0.2, we changed the behavior of the restart file input so that it will throw an error if the start date and time in input.geos does not match the timestamp of the restart file. This was fixed in pull request #691.

Long story short, your simulation starts on 2015/01/01 but the default Hg restart file probably starts on 2016/01/01. If you go to your run directory and then type this command:

$ ncdump -ct GEOSChem.Restart.20150101_0000z.nc4

You will probably see output such as:

        double time(time) ;
                time:long_name = "Time" ;
                time:units = "minutes since 2016-01-01 00:00:00 UTC" ;
                time:calendar = "gregorian" ;
                time:axis = "T" ;

where the time:units tells you that the restart file start date is for 2016/01/01.

There are a couple of things that you can do:

  1. Start your run from 2016/01/01
  2. Change your restart file date to an earlier date with the NetCDF Operators (NCO) ncatted command such as: 
    $ mv GEOSChem.Restart.20150101_0000z.nc4 GEOSChem.Restart.20140101_0000z.nc4
$ ncatted -a units,time,o,c,"minutes since 2014-01-01 00:00:00" "minutes since 2016-01-01 00:00:00"

    NOTE: The restart files that are provided when you generate a run directory are "sample" restart files that you can use to bootstrap a simulation. You should always run a spin-up simulation (probably for a year or more) to remove the signature of the initial conditions. That is why I suggest changing the restart file date to e.g. 2014-01-01, then spin-up for a year, then start your simulation at 2015-01-01.

CharikleiaGRN commented 3 years ago

Thank you very much for your time. I still haven't manage to complete the run.

the restart file looks ok I think:

netcdf GEOSChem.Restart.20150101_0000z {
dimensions:
    time = UNLIMITED ; // (1 currently)
    lev = 72 ;
    ilev = 73 ;
    lat = 46 ;
    lon = 72 ;
variables:
    double time(time) ;
        time:long_name = "Time" ;
        time:units = "minutes since 2015-01-01 00:00:00" ;
        time:calendar = "gregorian" ;
        time:axis = "T" ;
    double lev(lev)

Basically, in geos-chem 13 run directories, I cannot see any restart file be generated. I copy them by myself from the 10 year benchmark to the run directory. Is it the right way?

Thank you!

OUTPUT

.
.
.
HEMCO: Opening /media/data_03/gcgrid/data/ExtData/GEOS_2x2.5/GEOS_FP/2015/01/GEOSFP.20150102.I3.2x25.nc
HEMCO: Opening /media/data_03/gcgrid/data/ExtData/HEMCO/Yuan_XLAI/v2019-03/Yuan_proc_MODIS_XLAI.025x025.2015.nc
HEMCO: Opening ./GEOSChem.Restart.20150101_0000z.nc4
 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!
===============================================================================

===============================================================================
GEOS-Chem ERROR: Error encountered in "HCOI_GC_Run"!
 -> at Emissions_Run (in module GeosCore/emissions_mod.F90)
===============================================================================

===============================================================================
GEOS-CHEM ERROR: Error encountered in "Emissions_Run", Phase 0

This error can indicate a missing file. Please check the HEMCO log file for 
additional error messages!

STOP at  -> at GEOS-Chem (in GeosCore/main.F90)
===============================================================================
     - CLEANUP: deallocating arrays now...

HEMCO LOG
HEMCO WARNING: Data is treated as unitless, but file attribute suggests it is not: kg kg-1. File: /media/data_03/gcgrid/data/ExtData/GEOS_2x2.5/GEOS_FP/2015/01/GEOSFP.20150101.I3.2x25.nc
--> LOCATION: HCOIO_READ_STD (hcoio_read_std_mod.F90)
HEMCO WARNING: Data is treated as unitless, but file attribute suggests it is not: kg kg-1. File: /media/data_03/gcgrid/data/ExtData/GEOS_2x2.5/GEOS_FP/2015/01/GEOSFP.20150102.I3.2x25.nc
--> LOCATION: HCOIO_READ_STD (hcoio_read_std_mod.F90)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
HEMCO ERROR: Cannot find field SPC_Hg0. Please check variable name in the config. file
ERROR LOCATION: HCOIO_READ_STD (hcoio_read_std_mod.F90)
ERROR LOCATION: HCOIO_DataRead (hcoio_dataread_mod.F90)
ERROR LOCATION: ReadList_Fill (hco_readlist_mod.F90)
ERROR LOCATION: ReadList_Read (hco_readlist_mod.F90)
ERROR LOCATION: HCO_RUN (hco_driver_mod.F90)

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
HEMCO ERROR: Error encountered in routine HCOIO_Read_Std!
ERROR LOCATION: HCOIO_READ_STD (hcoio_read_std_mod.F90)
ERROR LOCATION: HCOIO_DataRead (hcoio_dataread_mod.F90)
ERROR LOCATION: ReadList_Fill (hco_readlist_mod.F90)
ERROR LOCATION: ReadList_Read (hco_readlist_mod.F90)
ERROR LOCATION: HCO_RUN (hco_driver_mod.F90)

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
HEMCO ERROR: Error in HCOIO_DATAREAD called from HEMCO ReadList_Fill: SPC_Hg0
ERROR LOCATION: ReadList_Fill (HCO_ReadList_Mod.F90)

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
HEMCO ERROR: Error in called ReadList_Fill (7) from HEMCO ReadList_Read
ERROR LOCATION: ReadList_Read (HCO_ReadList_Mod.F90)

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

-------------------------------------------------------------------------------
HEMCO 3.0.0 FINISHED.
Warnings (level 1 or lower):     56
-------------------------------------------------------------------------------
yantosca commented 3 years ago

Have you tried running a dry-run simulation:

$ ./gcclassic --dryrun > log.dryrun
$ ./download_data.py log.dryrun -cc

this should get the restart file for you.

yantosca commented 3 years ago

The above commands should work in 13.0.2. In earlier versions you would have needed to copy the GEOSCHEM_RESTARTS folder manually from ComputeCanada.

CharikleiaGRN commented 3 years ago

Thank you very much for the answer and your time! So, I did the run with the 13.0.2 but it is producing the output restart files with this name variable: float SpeciesRst_HgP(time, lev, lat, lon) ; SpeciesRst_HgP:long_name = "Dry mixing ratio of species HgP" ; SpeciesRst_HgP:units = "mol mol-1 dry" ; SpeciesRst_HgP:averaging_method = "time-averaged" ; float SpeciesRst_Hg2(time, lev, lat, lon) ; SpeciesRst_Hg2:long_name = "Dry mixing ratio of species Hg2" ; SpeciesRst_Hg2:units = "mol mol-1 dry" ; SpeciesRst_Hg2:averaging_method = "time-averaged" ; float SpeciesRst_Hg0(time, lev, lat, lon) ; SpeciesRst_Hg0:long_name = "Dry mixing ratio of species Hg0" ; SpeciesRst_Hg0:units = "mol mol-1 dry" ; SpeciesRst_Hg0:averaging_method = "time-averaged" ;

and then when I make a new run using the produced restart file that I want we got an error again:

HEMCO ERROR: Cannot find field with valid time stamp in ./GEOSChem.Restart.20141001_0000z.nc4 - Cannot get field SPC_Hg0. Please check file name and time (incl. time range flag) in the config. file..

Maybe that was the problem also

CharikleiaGRN commented 3 years ago

Also, using the template restart file I run many different (start dates) simulations with EDGAR emissions and the 9th day mercury species got negative values and the simulation stopped

CharikleiaGRN commented 3 years ago 
 - Found all A1     met fields for 2012/04/09 22:30

---> DATE: 2012/04/09 UTC: 22:10 X-HRS: 214.166672 ---> DATE: 2012/04/09 UTC: 22:20 X-HRS: 214.333328 WARNING: Negative concentration for species Hg2 at (I,J,L) = 82 8 2 WARNING: Negative concentration for species Hg2 at (I,J,L) = 82 8 3 WARNING: Negative concentration for species Hg2 at (I,J,L) = 83 8 2 WARNING: Negative concentration for species Hg2 at (I,J,L) = 83 8 3 WARNING: Negative concentration for species Hg2 at (I,J,L) = 83 8 4 WARNING: Negative concentration for species Hg2 at (I,J,L) = 83 8 5 WARNING: Negative concentration for species Hg2 at (I,J,L) = 83 8 6 WARNING: Negative concentration for species Hg2 at (I,J,L) = 84 8 2 WARNING: Negative concentration for species Hg2 at (I,J,L) = 84 8 3 WARNING: Negative concentration for species Hg2 at (I,J,L) = 84 8 4 WARNING: Negative concentration for species Hg2 at (I,J,L) = 84 8 5 WARNING: Negative concentration for species Hg2 at (I,J,L) = 84 8 6 WARNING: Negative concentration for species Hg2 at (I,J,L) = 84 8 7 WARNING: Negative concentration for species Hg2 at (I,J,L) = 85 8 2 WARNING: Negative concentration for species Hg2 at (I,J,L) = 85 8 3 WARNING: Negative concentration for species Hg2 at (I,J,L) = 85 8 4 WARNING: Negative concentration for species Hg2 at (I,J,L) = 85 8 5 WARNING: Negative concentration for species Hg2 at (I,J,L) = 85 8 6 WARNING: Negative concentration for species Hg2 at (I,J,L) = 85 8 7 WARNING: Negative concentration for species Hg2 at (I,J,L) = 86 8 2 WARNING: Negative concentration for species Hg2 at (I,J,L) = 86 8 3 WARNING: Negative concentration for species Hg2 at (I,J,L) = 86 8 4 WARNING: Negative concentration for species Hg2 at (I,J,L) = 86 8 5 WARNING: Negative concentration for species Hg2 at (I,J,L) = 86 8 6 WARNING: Negative concentration for species Hg2 at (I,J,L) = 86 8 7 WARNING: Negative concentration for species Hg2 at (I,J,L) = 87 8 2 WARNING: Negative concentration for species Hg2 at (I,J,L) = 87 8 3 WARNING: Negative concentration for species Hg2 at (I,J,L) = 87 8 4 WARNING: Negative concentration for species Hg2 at (I,J,L) = 87 8 5 WARNING: Negative concentration for species Hg2 at (I,J,L) = 87 8 6 WARNING: Negative concentration for species Hg2 at (I,J,L) = 88 8 2 WARNING: Negative concentration for species Hg2 at (I,J,L) = 88 8 3 WARNING: Negative concentration for species Hg2 at (I,J,L) = 88 8 4 WARNING: Negative concentration for species Hg2 at (I,J,L) = 88 8 5 WARNING: Negative concentration for species Hg2 at (I,J,L) = 88 8 6 WARNING: Negative concentration for species Hg2 at (I,J,L) = 89 8 2 WARNING: Negative concentration for species Hg2 at (I,J,L) = 89 8 3 WARNING: Negative concentration for species Hg2 at (I,J,L) = 89 8 4 WARNING: Negative concentration for species Hg0 at (I,J,L) = 82 8 2 WARNING: Negative concentration for species Hg0 at (I,J,L) = 82 8 3 WARNING: Negative concentration for species Hg0 at (I,J,L) = 83 8 2 WARNING: Negative concentration for species Hg0 at (I,J,L) = 83 8 3 WARNING: Negative concentration for species Hg0 at (I,J,L) = 83 8 4 WARNING: Negative concentration for species Hg0 at (I,J,L) = 83 8 5 WARNING: Negative concentration for species Hg0 at (I,J,L) = 83 8 6 WARNING: Negative concentration for species Hg2 at (I,J,L) = 89 8 5 WARNING: Negative concentration for species Hg2 at (I,J,L) = 89 8 6 WARNING: Negative concentration for species Hg2 at (I,J,L) = 90 8 2 WARNING: Negative concentration for species Hg2 at (I,J,L) = 90 8 3 WARNING: Negative concentration for species Hg0 at (I,J,L) = 84 8 2 WARNING: Negative concentration for species Hg0 at (I,J,L) = 84 8 3 WARNING: Negative concentration for species Hg0 at (I,J,L) = 84 8 4 WARNING: Negative concentration for species Hg0 at (I,J,L) = 84 8 5 WARNING: Negative concentration for species Hg0 at (I,J,L) = 84 8 6 WARNING: Negative concentration for species Hg0 at (I,J,L) = 84 8 7 WARNING: Negative concentration for species Hg0 at (I,J,L) = 85 8 2 WARNING: Negative concentration for species Hg0 at (I,J,L) = 85 8 3 WARNING: Negative concentration for species Hg0 at (I,J,L) = 85 8 4 WARNING: Negative concentration for species Hg0 at (I,J,L) = 85 8 5 WARNING: Negative concentration for species Hg0 at (I,J,L) = 85 8 6 WARNING: Negative concentration for species Hg0 at (I,J,L) = 85 8 7 WARNING: Negative concentration for species Hg2 at (I,J,L) = 90 8 4 WARNING: Negative concentration for species Hg2 at (I,J,L) = 90 8 5 WARNING: Negative concentration for species Hg2 at (I,J,L) = 90 8 6 WARNING: Negative concentration for species Hg2 at (I,J,L) = 91 8 2 WARNING: Negative concentration for species Hg0 at (I,J,L) = 86 8 2 WARNING: Negative concentration for species Hg0 at (I,J,L) = 86 8 3 WARNING: Negative concentration for species Hg0 at (I,J,L) = 86 8 4 WARNING: Negative concentration for species Hg0 at (I,J,L) = 86 8 5 WARNING: Negative concentration for species Hg0 at (I,J,L) = 86 8 6 WARNING: Negative concentration for species Hg0 at (I,J,L) = 86 8 7 WARNING: Negative concentration for species Hg2 at (I,J,L) = 110 8 2 WARNING: Negative concentration for species Hg2 at (I,J,L) = 110 8 3 WARNING: Negative concentration for species Hg2 at (I,J,L) = 111 8 2 WARNING: Negative concentration for species Hg2 at (I,J,L) = 111 8 3 WARNING: Negative concentration for species Hg0 at (I,J,L) = 87 8 2 WARNING: Negative concentration for species Hg0 at (I,J,L) = 87 8 3 WARNING: Negative concentration for species Hg0 at (I,J,L) = 87 8 4 WARNING: Negative concentration for species Hg0 at (I,J,L) = 87 8 5 WARNING: Negative concentration for species Hg0 at (I,J,L) = 87 8 6 WARNING: Negative concentration for species Hg0 at (I,J,L) = 88 8 2 WARNING: Negative concentration for species Hg0 at (I,J,L) = 88 8 3 WARNING: Negative concentration for species Hg0 at (I,J,L) = 88 8 4 WARNING: Negative concentration for species Hg0 at (I,J,L) = 88 8 5 WARNING: Negative concentration for species Hg0 at (I,J,L) = 88 8 6 WARNING: Negative concentration for species Hg0 at (I,J,L) = 89 8 2 WARNING: Negative concentration for species Hg0 at (I,J,L) = 89 8 3 WARNING: Negative concentration for species Hg0 at (I,J,L) = 89 8 4 WARNING: Negative concentration for species Hg0 at (I,J,L) = 89 8 5 WARNING: Negative concentration for species Hg0 at (I,J,L) = 89 8 6 WARNING: Negative concentration for species Hg0 at (I,J,L) = 90 8 2 WARNING: Negative concentration for species Hg0 at (I,J,L) = 90 8 3 WARNING: Negative concentration for species Hg0 at (I,J,L) = 90 8 4 WARNING: Negative concentration for species Hg0 at (I,J,L) = 90 8 5 WARNING: Negative concentration for species Hg0 at (I,J,L) = 90 8 6 WARNING: Negative concentration for species Hg0 at (I,J,L) = 91 8 2 WARNING: Negative concentration for species Hg0 at (I,J,L) = 110 8 2 WARNING: Negative concentration for species Hg0 at (I,J,L) = 110 8 3 WARNING: Negative concentration for species Hg0 at (I,J,L) = 111 8 2 WARNING: Negative concentration for species Hg0 at (I,J,L) = 111 8 3

GEOS-Chem ERROR: ��sU��B�T�U���T�U��sU� ��T�U|�sU���sU���sU���@ 

             ��sU��B�T�U���T�U��sU� ��T�U��sU�

-> at DO_TEND (in module GeosCore/mixing_mod.F90)

=============================================================================== GEOS-Chem ERROR: Error encountred in "DO_TEND"! -> at DO_MIXING (in module GeosCore/mixing_mod.F90)

=============================================================================== GEOS-CHEM ERROR: Error encountered in "Do_Mixing"! STOP at -> at GEOS-Chem (in GeosCore/main.F90)

yantosca commented 3 years ago

@HarrietGRN, have you tried to compile and run with the debugging flags on? You can do this from your run directory

$ rm -rf build/*    # clean out all makefiles
$ cmake ../CodeDir -DCMAKE_BUILD_TYPE=Debug -DRUNDIR=..
$ make -j install
$ cd ..

then run GEOS-Chem and see if it gives you an error. You can also look in GeosCore/mixing_mod.F90, as this is the location of the error.

Also note: the Hg simulation may be a little bit behind the rest of GEOS-Chem development, as we rely on the community of users to maintain it.

stale[bot] commented 3 years ago

This issue has been automatically marked as stale because it has not had recent activity. If there are no updates within 7 days it will be closed. You can add the "never stale" tag to prevent the Stale bot from closing this issue.

stale[bot] commented 3 years ago

Closing due to inactivity

sumengqian commented 3 years ago

@HarrietGRN ,hi~ Did you resolve the promblem that you commented on 2 May about the HEMCO ERROR? I have the same error now when running an aerosol simulation:

HEMCO ERROR: Cannot find field with valid time stamp in ./GEOSChem.Restart.20190701_0000z.nc4 - Cannot get field SPC_BCPI. Please check file name and time (incl. time range flag) in the config. file

If there is a solution, could you please let me know? Thank you!

angothelene commented 11 months ago

Sharing my input here in case others encounter a similar problem. I faced a comparable issue when conducting an Hg simulation using version 14.2.2. The error message I received was "HEMCO ERROR: Cannot find field SPC_Hg0." The provided restart file at http://geoschemdata.wustl.edu/ExtData/GEOSCHEM_RESTARTS/v2021-12/ has a filename of 'GEOSChem.Restart.Hg.20190101_0000z.nc4', but the model is searching for a file named GEOSChem.Restart.20190101_0000z.nc4. Renaming it worked.

CodeCatLZW commented 9 months ago

In fact, this error also occurred when I simulated TaggedCO for nested grids until 2021.11.22, before which the simulation was quite normal. image image My version of geoschem is 14.1.1