Closed jie0314ouc closed 2 years ago
yantosca
commented
2 years ago Thanks for writing @jie0314ouc. Can you confirm that you have the file:
/home/zhangj/Geos-Chem/data/ExtData/HEMCO/TIMEZONES/v2015-02/timezones_voronoi_1x1.nc
on disk. I think if you are missing this file then it would produce the error that you are seeing.
jie0314ouc
commented
2 years ago I’m sure I have this ncfile in the right location, and it can’t be read by ncdump. And prompting it was unrecognized file type.
------------------ Original ------------------ From: Bob Yantosca @.> Date: Thu,Feb 24,2022 11:07 PM To: geoschem/geos-chem @.> Cc: jie0314ouc @.>, Mention @.> Subject: Re: [geoschem/geos-chem] [BUG/ISSUE] (Issue #1137)
Thanks for writing @jie0314ouc. Can you confirm that you have the file:
/home/zhangj/Geos-Chem/data/ExtData/HEMCO/TIMEZONES/v2015-02/timezones_voronoi_1x1.nc
on disk. I think if you are missing this file then it would produce the error that you are seeing.
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yantosca
commented
2 years ago Thanks @jie0314ouc . If it can't be read by ncdump then the file is corrupted. Can you try downloading it again from: http://geoschemdata.computecanada.ca/ExtData/HEMCO/TIMEZONES/v2015-02/timezones_voronoi_1x1.nc
jie0314ouc
commented
2 years ago I redownload the file, but it still didn’t work.
yantosca
commented
2 years ago @jie0314ouc, if you type
$ ncdump /home/zhangj/Geos-Chem/data/ExtData/HEMCO/TIMEZONES/v2015-02/timezones_voronoi_1x1.ncdo you get output or is the files still corrupted?
jie0314ouc
commented
2 years ago Thanks for your suggestions @yantosca ， After ncdump /home/zhangj/Geos-Chem/data/ExtData/HEMCO/TIMEZONES/v2015-02/timezones_voronoi_1x1.nc error information :
lxh3: ~/Geos-Chem/data/ExtData/HEMCO/TIMEZONES/v2015-02$ ncdump timezones_voronoi_1x1.nc
ncdump: timezones_voronoi_1x1.nc: timezones_voronoi_1x1.nc: NetCDF: Attempt to use feature that was not turned on when netCDF was built.But I can ncdump other downloaing ncfile like WHET_Hg0.geos.1x1.2010_final.nc successfully.
lxh3: ~/Geos-Chem/data/ExtData/HEMCO/MERCURY/v2018-04$ ncdump WHET_Hg2.geos.1x1.2010_final.nc|less
netcdf WHET_Hg2.geos.1x1.2010_final {
dimensions:
lon = 360 ;
lat = 180 ;
variables:
double lon(lon) ;
lon:units = "degrees_east" ;
lon:long_name = "lon" ;
double lat(lat) ;
lat:units = "degrees_north" ;
lat:long_name = "lat" ;
float Hg2(lat, lon) ;Luckily, I updated the version of NetCDF to 4.8.1 and finally I could ncdump the file timezones_voronoi_1x1.nc. But I rerun the the gccglasic , there was still error information:
lxh3: ~/Geos-Chem/rundir/test3/gc_merra2_Hg$ ./gcclassic
INIT_DRYDEP: List of dry deposition species:
# Name Species DEPVEL Henry's React. Molec. Aerosol?
Number Index Law Const Factor Weight (T or F)
----------------------------------------------------------------------
1 Hg0 1 1 1.1E-01 0.000 0.201 F
2 Hg2 2 2 1.0E+14 0.000 0.201 F
3 HgP 3 3 0.0E+00 0.000 0.201 T
INIT_WETSCAV: List of soluble species:
# Name Species Mol Wt Henry K0 Henry CR Henry pKa
ID g/mol M/atm K 1
----------------------------------------------------------------------
1 Hg2 2 200.6 1.40E+06 8.40E+03 -
2 HgP 3 200.6 - - -
Registered variables contained within grid_registry_mod.F90:
===============================================================================
GRID_LONBND | Longitude bounds (CF | bx | degrees_east
GRID_LONE | Longitude edges | x | degrees_east
GRID_LON | Longitude | x | degrees_east
GRID_LATBND | Latitude bounds (CF- | by | degrees_north
GRID_LATE | Latitude edges | y | degrees_north
GRID_LAT | Latitude | y | degrees_north
GRID_ILEV | hybrid level at inte | z | level
GRID_HYBI | hybrid B coefficient | z | 1
GRID_HYAI | hybrid A coefficient | z | hPa
GRID_LEV | hybrid level at midp | z | level
GRID_HYBM | hybrid B coefficient | z | 1
GRID_HYAM | hybrid A coefficient | z | hPa
GRID_TIME | Time | t | minutes since YYYY-MM-DD hh:mm:ss
GRID_P0 | reference pressure | - | hPa
GRID_AREA | Surface area | xy | m2
HISTORY (INIT): Opening ./HISTORY.rc
===============================================================================
DEFINED DIAGNOSTIC COLLECTIONS:
===============================================================================
Collection Restart
-> FileName ./GEOSChem.Restart.%y4%m2%d2_%h2%n2z.nc4
-> Format not found
-> Frequency End
-> Duration End
-> Mode instantaneous
Collection SpeciesConc
-> FileName OutputDir/GEOSChem.SpeciesConc.%y4%m2%d2_%h2%n2z.nc4
-> Format not found
-> Frequency 00000100000000
-> Duration 00000100000000
-> Mode time-averaged
===============================================================================
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% HEMCO: Harmonized Emissions Component %%%%%
%%%%% You are using HEMCO version 3.0.0 %%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Reading settings & switches of HEMCO configuration file: HEMCO_Config.rc
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Switches read from HEMCO_Config.rc:
EMISSIONS : T
LightNOx : F
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Reading fields of HEMCO configuration file: HEMCO_Config.rc
HEMCO: Opening /home/zhangj/Geos-Chem/data/ExtData/HEMCO/MERCURY/v2018-04/WHET_Hg0.geos.1x1.2010_final.nc
HEMCO: Opening /home/zhangj/Geos-Chem/data/ExtData/HEMCO/MERCURY/v2018-04/WHET_Hg2.geos.1x1.2010_final.nc
HEMCO: Opening /home/zhangj/Geos-Chem/data/ExtData/HEMCO/MERCURY/v2018-04/WHET_HgP.geos.1x1.2010_final.nc
HEMCO: Opening /home/zhangj/Geos-Chem/data/ExtData/HEMCO/MERCURY/v2014-09/NATURAL/newnatural.geos.4x5.nc
HEMCO: Opening /home/zhangj/Geos-Chem/data/ExtData/HEMCO/MERCURY/v2014-09/SOIL/soilHg.presentday.v11-01.geosfp.4x5.nc
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
In Ncop_Rd, cannot open: /home/zhangj/Geos-Chem/data/ExtData/HEMCO/TIMEZONES/v2015-02/timezones_voronoi_1x1.nc
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Code stopped from DO_ERR_OUT (in module NcdfUtil/m_do_err_out.F90)
This is an error that was encountered in one of the netCDF I/O modules,
which indicates an error in writing to or reading from a netCDF file!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!I still think that this is caused by a corrupted file on your end.
@YanshunLi-washu, can you verify that the timezones_voronoi_1x1.nc file at the WashU data portal is OK?
YanshunLi-washu
commented
2 years ago Hi @Bob, thanks for letting me know. I just downloaded that file from our washu data portal http://geoschemdata.wustl.edu/ExtData/HEMCO/TIMEZONES/v2015-02/timezones_voronoi_1x1.nc. I opened it using Panoply and didn't see any anomaly. I attached the data views as below:
yantosca
commented
2 years ago Thanks @YanshunLi-washu! @jie0314ouc, could you try downloading this file again from the http://geoschemdata.wustl.edu/ExtData/HEMCO/TIMEZONES/v2015-02/timezones_voronoi_1x1.nc?
jie0314ouc
commented
2 years ago Thanks @yantosca ！I redownloaded the file from http://geoschemdata.wustl.edu/ExtData/HEMCO/TIMEZONES/v2015-02/timezones_voronoi_1x1.nc, but there was still the same error information prompts here. I wondered if there was something wrong with my environment variables?
yantosca
commented
2 years ago I don't know what the issue is. If you've downloaded the file (which was shown to be uncorrupted at WashU) and it still doesn't work then maybe it's an issue with your netCDF or Linux environment setup. Regrettably, we cannot assist you with fixing issues that are local to your computer system.
Maybe try re-installing netCDF and the other required software libraries and see if that helps.
Sorry we cannot do more.
stale[bot]
commented
2 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.
yantosca
commented
2 years ago Closing out this issue.
XR-peking
commented
2 years ago Hi Bob, If our study area is in China, do we need to adjust the time different in the output file like add 8 hours? and if that is true, what 'timezones_voronoi_1x1.nc' do for us. Best
What institution are you from?
I am a graduate student in the school of environment, Ocean University of China.
Description of the problem
After ./gcclassic , there was a error In Ncop_Rd, cannot open: /home/zhangj/Geos-Chem/data/ExtData/HEMCO/TIMEZONES/v2015-02/timezones_voronoi_1x1.nc
Code stopped from DO_ERR_OUT (in module NcdfUtil/m_do_err_out.F90) This is an error that was encountered in one of the netCDF I/O modules, which indicates an error in writing to or reading from a netCDF file!
Description of troubleshooting performed
At first, I suspected that it was a file permission problem, so I gave the highest permission to the file, but there were still the same errors
GEOS-Chem version
Enter your GEOS-Chem version here.
Description of modifications
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Log files
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