[QUESTION] GEOSChem 13.0.1 only open the MERRA2 file at the beginning and repeat the meteorology during the run?

[wddpwzz5]

Dear GEOSChem expert,
I download the recent GEOSChem of version 13.0.1. And I followed the createRunDir.sh and creat the run directory and successfully compiled the code. But when I run it, it just read the MERRA2 data at the beginning and repeat the meteorology over and over again without opening the new MERRA2 file.
I did not find a clue and hope someone can help me with this.

Thanks!

Below is the log file.

Reading fields of HEMCO configuration file: HEMCO_Config.rc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/BIO/Net_terrestrial_exch_5.29Pg.generic.1x1.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/TIMEZONES/v2015-02/timezones_voronoi_1x1.nc
HEMCO: Opening /home/liuzq/Data/ExtData/GEOS_4x5/MERRA2/2015/01/MERRA2.20150101.CN.4x5.nc4
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/OLSON_MAP/v2019-02/Olson_2001_Land_Type_Masks.025x025.generic.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/FOSSIL/TIMES_weekly_scale_factors.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/FOSSIL/Aviation_SurfCorr_SclFac.1x1.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2019-12/FOSSIL/ODIAC_CO2.monthly.generic.1x1.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/OCEAN/Scaled_Ocean_CO2_monthly.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CEDS/v2018-08/1980/CO2-em-anthro_CMIP_CEDS_1980.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/AEIC/v2015-01/AEIC.47L.gen.1x1.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2019-12/FOSSIL/ODIAC_CO2.monthly.generic.1x1.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/CHEM/CH4_source.geos.2x25.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/CHEM/Isoprene-2004.geos.2x25.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/CHEM/Monoterpene-2004.geos.2x25.nc
HEMCO: Opening /home/liuzq/Data/ExtData/GEOS_4x5/MERRA2/2010/07/MERRA2.20100701.A1.4x5.nc4
HEMCO: Opening /home/liuzq/Data/ExtData/GEOS_4x5/MERRA2/2010/07/MERRA2.20100701.A3cld.4x5.nc4
HEMCO: Opening /home/liuzq/Data/ExtData/GEOS_4x5/MERRA2/2010/07/MERRA2.20100701.A3dyn.4x5.nc4
HEMCO: Opening /home/liuzq/Data/ExtData/GEOS_4x5/MERRA2/2010/07/MERRA2.20100701.A3mstC.4x5.nc4
HEMCO: Opening /home/liuzq/Data/ExtData/GEOS_4x5/MERRA2/2010/07/MERRA2.20100701.A3mstE.4x5.nc4
HEMCO: Opening /home/liuzq/Data/ExtData/GEOS_4x5/MERRA2/2010/07/MERRA2.20100701.I3.4x5.nc4
HEMCO: Opening /home/liuzq/Data/ExtData/GEOS_4x5/MERRA2/2010/07/MERRA2.20100702.I3.4x5.nc4
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/Yuan_XLAI/v2019-03/Yuan_proc_MODIS_XLAI.025x025.2005.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/BIO/SiB3_3hr_NEP.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/FOSSIL/TIMES_diurnal_scale_factors.nc
- Found all CN met fields for 2011/01/01 00:00
- Found all A1 met fields for 2010/07/01 00:30
- Found all A3cld met fields for 2010/07/01 01:30
- Found all A3dyn met fields for 2010/07/01 01:30
- Found all A3mstC met fields for 2010/07/01 01:30
- LightNOX extension is off. Skipping FLASH_DENS and CONV_DEPTH fields in FlexGrid_Read_A3mstE.
- Found all A3mstE met fields for 2010/07/01 01:30
- Found all I3 met fields for 2010/07/01 00:00
TMPU1 not found in restart, keep as value at t=0
SPHU1 not found in restart, keep as value at t=0
PS1_WET not found in restart, keep as value at t=0
PS1_DRY not found in restart, keep as value at t=0
DELP_DRY not found in restart, set to zero
- Found all I3 met fields for 2010/07/01 03:00

R E S T A R T F I L E I N P U T

Min and Max of each species in restart file [mol/mol]:
Species 1, CO2: Use background = 3.549999965E-04

Init_Vdiff: pbl height will be limited to bottom 25 model levels.
Top is 423.23396395474481 hpa

---

• B e g i n T i m e S t e p p i n g !! *

---

---> DATE: 2010/07/01 UTC: 00:00 X-HRS: 0.000000
HEMCO already called for this timestep. Returning.

TPCORE_FVDAS (based on GMI) Tracer Transport Module successfully initialized

---> DATE: 2010/07/01 UTC: 00:10 X-HRS: 0.166667
---> DATE: 2010/07/01 UTC: 00:20 X-HRS: 0.333333
---> DATE: 2010/07/01 UTC: 00:30 X-HRS: 0.500000
---> DATE: 2010/07/01 UTC: 00:40 X-HRS: 0.666667
---> DATE: 2010/07/01 UTC: 00:50 X-HRS: 0.833333
---> DATE: 2010/07/01 UTC: 01:00 X-HRS: 1.000000
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/BIO/SiB3_3hr_NEP.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/FOSSIL/TIMES_diurnal_scale_factors.nc
- Found all A1 met fields for 2010/07/01 01:30
---> DATE: 2010/07/01 UTC: 01:10 X-HRS: 1.166667
---> DATE: 2010/07/01 UTC: 01:20 X-HRS: 1.333333
---> DATE: 2010/07/01 UTC: 01:30 X-HRS: 1.500000
---> DATE: 2010/07/01 UTC: 01:40 X-HRS: 1.666667
---> DATE: 2010/07/01 UTC: 01:50 X-HRS: 1.833333
---> DATE: 2010/07/01 UTC: 02:00 X-HRS: 2.000000
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/BIO/SiB3_3hr_NEP.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/FOSSIL/TIMES_diurnal_scale_factors.nc
- Found all A1 met fields for 2010/07/01 02:30
---> DATE: 2010/07/01 UTC: 02:10 X-HRS: 2.166667
---> DATE: 2010/07/01 UTC: 02:20 X-HRS: 2.333333
---> DATE: 2010/07/01 UTC: 02:30 X-HRS: 2.500000
---> DATE: 2010/07/01 UTC: 02:40 X-HRS: 2.666667
---> DATE: 2010/07/01 UTC: 02:50 X-HRS: 2.833333
---> DATE: 2010/07/01 UTC: 03:00 X-HRS: 3.000000
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/BIO/SiB3_3hr_NEP.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/FOSSIL/TIMES_diurnal_scale_factors.nc
- Found all A1 met fields for 2010/07/01 03:30
- Found all A3cld met fields for 2010/07/01 04:30
- Found all A3dyn met fields for 2010/07/01 04:30
- Found all A3mstC met fields for 2010/07/01 04:30
- LightNOX extension is off. Skipping FLASH_DENS and CONV_DEPTH fields in FlexGrid_Read_A3mstE.
- Found all A3mstE met fields for 2010/07/01 04:30
- Found all I3 met fields for 2010/07/01 06:00
---> DATE: 2010/07/01 UTC: 03:10 X-HRS: 3.166667
---> DATE: 2010/07/01 UTC: 03:20 X-HRS: 3.333333
---> DATE: 2010/07/01 UTC: 03:30 X-HRS: 3.500000
---> DATE: 2010/07/01 UTC: 03:40 X-HRS: 3.666667
---> DATE: 2010/07/01 UTC: 03:50 X-HRS: 3.833333
---> DATE: 2010/07/01 UTC: 04:00 X-HRS: 4.000000
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/BIO/SiB3_3hr_NEP.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/FOSSIL/TIMES_diurnal_scale_factors.nc
- Found all A1 met fields for 2010/07/01 04:30
---> DATE: 2010/07/01 UTC: 04:10 X-HRS: 4.166667
---> DATE: 2010/07/01 UTC: 04:20 X-HRS: 4.333333
---> DATE: 2010/07/01 UTC: 04:30 X-HRS: 4.500000
---> DATE: 2010/07/01 UTC: 04:40 X-HRS: 4.666667
---> DATE: 2010/07/01 UTC: 04:50 X-HRS: 4.833333
---> DATE: 2010/07/01 UTC: 05:00 X-HRS: 5.000000
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/BIO/SiB3_3hr_NEP.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/FOSSIL/TIMES_diurnal_scale_factors.nc
- Found all A1 met fields for 2010/07/01 05:30
---> DATE: 2010/07/01 UTC: 05:10 X-HRS: 5.166667
---> DATE: 2010/07/01 UTC: 05:20 X-HRS: 5.333333
---> DATE: 2010/07/01 UTC: 05:30 X-HRS: 5.500000
---> DATE: 2010/07/01 UTC: 05:40 X-HRS: 5.666667
---> DATE: 2010/07/01 UTC: 05:50 X-HRS: 5.833333
---> DATE: 2010/07/01 UTC: 06:00 X-HRS: 6.000000
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/BIO/SiB3_3hr_NEP.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/FOSSIL/TIMES_diurnal_scale_factors.nc
- Found all A1 met fields for 2010/07/01 06:30
- Found all A3cld met fields for 2010/07/01 07:30
- Found all A3dyn met fields for 2010/07/01 07:30
- Found all A3mstC met fields for 2010/07/01 07:30
- LightNOX extension is off. Skipping FLASH_DENS and CONV_DEPTH fields in FlexGrid_Read_A3mstE.
- Found all A3mstE met fields for 2010/07/01 07:30
- Found all I3 met fields for 2010/07/01 09:00
---> DATE: 2010/07/01 UTC: 06:10 X-HRS: 6.166667
---> DATE: 2010/07/01 UTC: 06:20 X-HRS: 6.333333
---> DATE: 2010/07/01 UTC: 06:30 X-HRS: 6.500000
---> DATE: 2010/07/01 UTC: 06:40 X-HRS: 6.666667
---> DATE: 2010/07/01 UTC: 06:50 X-HRS: 6.833333
---> DATE: 2010/07/01 UTC: 07:00 X-HRS: 7.000000
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/BIO/SiB3_3hr_NEP.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/FOSSIL/TIMES_diurnal_scale_factors.nc
- Found all A1 met fields for 2010/07/01 07:30
---> DATE: 2010/07/01 UTC: 07:10 X-HRS: 7.166667
---> DATE: 2010/07/01 UTC: 07:20 X-HRS: 7.333333
---> DATE: 2010/07/01 UTC: 07:30 X-HRS: 7.500000
---> DATE: 2010/07/01 UTC: 07:40 X-HRS: 7.666667
---> DATE: 2010/07/01 UTC: 07:50 X-HRS: 7.833333
---> DATE: 2010/07/01 UTC: 08:00 X-HRS: 8.000000
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/BIO/SiB3_3hr_NEP.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/FOSSIL/TIMES_diurnal_scale_factors.nc
- Found all A1 met fields for 2010/07/01 08:30
---> DATE: 2010/07/01 UTC: 08:10 X-HRS: 8.166667
---> DATE: 2010/07/01 UTC: 08:20 X-HRS: 8.333333
---> DATE: 2010/07/01 UTC: 08:30 X-HRS: 8.500000
---> DATE: 2010/07/01 UTC: 08:40 X-HRS: 8.666667
---> DATE: 2010/07/01 UTC: 08:50 X-HRS: 8.833333
---> DATE: 2010/07/01 UTC: 09:00 X-HRS: 9.000000
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/BIO/SiB3_3hr_NEP.nc
HEMCO: Opening /home/liuzq/Data/ExtData/HEMCO/CO2/v2015-04/FOSSIL/TIMES_diurnal_scale_factors.nc
- Found all A1 met fields for 2010/07/01 09:30
- Found all A3cld met fields for 2010/07/01 10:30
- Found all A3dyn met fields for 2010/07/01 10:30
- Found all A3mstC met fields for 2010/07/01 10:30
- LightNOX extension is off. Skipping FLASH_DENS and CONV_DEPTH fields in FlexGrid_Read_A3mstE.
- Found all A3mstE met fields for 2010/07/01 10:30
- Found all I3 met fields for 2010/07/01 12:00

[wddpwzz5]

I noticed #686 . I turn off the restart file and use background concentration. I followd Bob and update the new brunch bugfix/bmy/TimeCycleEFYO . But it looks like only the HEMCO_Config.rc file are changed? I rerun and the same issue cames out.

[wddpwzz5]

I redownload the GEOSChem and followed #686 . It works now. Seems like I have made some mistake.