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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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Corrupt files in GEOS_0.5x0.625_NA/MERRA2/ #1910

Closed Row-Bean closed 10 months ago

Row-Bean commented 12 months ago

Name and Institution (Required)

Name: Robin Stevens Institution: Université de Montréal

Description of your issue or question

Hi, I'm running GEOS-Chem 13.3.3, and I ran into the following error:

HEMCO: Opening /home/rstevens/projects/rrg-hayesp/rstevens/GC/ExtData//GEOS_0.5x0.625_NA/MERRA2/1983/09/MERRA2.19830927.A3dyn.05x0625.NA.nc4

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

In Ncrd_4d_R4 #2:  NetCDF: HDF error
    327680         7

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

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 used ncview to take a look at MERRA2.19830927.A3dyn.05x0625.NA.nc4, and when I try to view the RH, ncview crashes with the following error:

calculating min and maxes for RH...netcdf_fi_get_data: error on nc_get_vara_float call
cdfid=65536   variable=RH
start, count:
[0]: 3  1
[1]: 0  72
[2]: 0  121
[3]: 0  161
NetCDF: HDF error

I re-downloaded the file from the WashU collection using Globus, but the file still seems to be corrupt in the same way.

msulprizio commented 12 months ago

@SaptSinha Could you please reprocess this file when you have a chance?

SaptSinha commented 11 months ago

@Row-Bean I uploaded the reprocessed "MERRA2.19830927.A3dyn.05x0625.NA.nc4" file. You can access it from WashU's 1983/09 MERRA2 collection.

Row-Bean commented 11 months ago

Excellent, thank you! I downloaded the new file, it appears not to have any problems.

yantosca commented 11 months ago

Thanks @SaptSinha and @Row-Bean! I will close out this issue now.

Row-Bean commented 11 months ago

I found another one: GEOS_0.5x0.625_NA/MERRA2/1983/11/MERRA2.19831102.A3mstC.05x0625.NA.nc4

The GEOS-Chem error is similar: In Ncop_Rd, cannot open: /home/rstevens/projects/rrg-hayesp/rstevens/GC/ExtData//GEOS_0.5x0.625_NA/MERRA2/1983/11/MERRA2.19831102.A3mstC.05x0625.NA.nc4

And I cannot open this file with ncview at all: ncview: can't recognize format of input file MERRA2.19831102.A3mstC.05x0625.NA.nc4

Again, I tried re-downloading via Globus from the WashU collection, but I still cannot open the file with ncview.

SaptSinha commented 11 months ago

Thank you for letting us know about this earlier. I have reprocessed and uploaded the MERRA2.19831102.A3mstC.05x0625.NA.nc4 file. You can find it from our 1983/11 MERRA2 collection.

Row-Bean commented 11 months ago

Thank you very much! I have downloaded the new file, ncview can read it without any problems.

SaptSinha commented 11 months ago

Excellent! I am closing this issue for now but please do not hesitate to open a new one in case you encounter any further data corruptions.

I also wanted to let you know that I will post an update regarding your other issue #1544 sometime this month as we have finally resolved some of the problems that we were previously encountering with inconsistent global dust strength values.

Row-Bean commented 11 months ago

I have found another one:

In Ncop_Rd, cannot open: /home/rstevens/projects/rrg-hayesp/rstevens/GC/ExtData//GEOS_0.5x0.625_NA/MERRA2/1983/11/MERRA2.19831105.I3.05x0625.NA.nc4

ncview: can't recognize format of input file ~/GC/ExtData//GEOS_0.5x0.625_NA/MERRA2/1983/11/MERRA2.19831105.I3.05x0625.NA.nc4

Would you prefer for me to open a new issue when I find more corrupt files, or would it be best for me to continue to post them here?

msulprizio commented 11 months ago

@Row-Bean I reopened this issue and renamed it to reflect that there are multiple problematic files within GEOS_0.5x0.625_NA/MERRA2. Feel free to continue reporting them here and tag @SaptSinha, as he is the one that will reprocess them for you.

Row-Bean commented 11 months ago

Thank you! I have one more file for @SaptSinha :

I looked ahead and found one more file that doesn't appear to open with ncview: GEOS_0.5x0.625_NA/MERRA2/1983/11/MERRA2.19831106.A3mstE.05x0625.NA.nc4

I did a quick check of the rest of 1983 and 1984, but I didn't find any more corrupt files yet.

SaptSinha commented 11 months ago

Thanks for reporting about these corrupted files, @Row-Bean. I have reprocessed and uploaded the files "MERRA2.19831105.I3.05x0625.NA.nc4" and "MERRA2.19831106.A3mstE.05x0625.NA.nc4". You can find them at our 1983/11 MERRA2 collection.

Row-Bean commented 11 months ago

Thank you again! I downloaded the new files, and ncview can read them without problems.

SaptSinha commented 11 months ago

Great! We can keep this issue open in case you encounter any more corrupted files.

Row-Bean commented 11 months ago

Hi @SaptSinha, I found another one: GEOS_0.5x0.625_NA/MERRA2/1983/11/MERRA2.19831105.A3mstE.05x0625.NA.nc4

SaptSinha commented 11 months ago

No worries, I finished reprocessing and just uploaded the MERRA2.19831105.A3mstE.05x0625.NA.nc4 file in the same location.

Row-Bean commented 11 months ago

Excellent, thanks! I checked the new file, it appears to be corruption-free.

yantosca commented 11 months ago

Thanks @SaptSinha and @Row-Bean. We can close out this issue now.

Row-Bean commented 11 months ago

Hi @SaptSinha, I found another one: GEOS_0.5x0.625_NA/MERRA2/1983/11/MERRA2.19831106.A3dyn.05x0625.NA.nc4

I'm juggling this with a couple of other priorities at the moment, but when I get some free time I'll find a way to look through the files more efficiently to find the corrupt ones. It shouldn't take long to put together a Python script to find them.

msulprizio commented 11 months ago

@laestrada Wrote a script to find corrupted met files. You can give this a try to see if it identifies any files ahead of time for you. See https://github.com/geoschem/integrated_methane_inversion/blob/main/src/utilities/find_corrupt_files.sh. You can remove the lines about AWS. Essentially, you just want the loop over the files.

@SaptSinha It may be worth bringing this script into the met-processing workflow to identify corrupted files at WashU before users download them.

Row-Bean commented 10 months ago

Thanks to @msulprizio for sending that script! I applied it to the rest of the time period I plan to run (up to 1985), and the only corrupt files the script found were GEOS_0.5x0.625_NA/MERRA2/1983/11/MERRA2.19831106.A3dyn.05x0625.NA.nc4 (as listed above) and GEOS_0.5x0.625_NA/MERRA2/1983/11/MERRA2.19831107.A3cld.05x0625.NA.nc4

So once @SaptSinha uploads those two files, that should be all that I need.

SaptSinha commented 10 months ago

Hello @Row-Bean, the files below have now been reprocessed and uploaded to http://geoschemdata.wustl.edu/ExtData/GEOS_0.5x0.625_NA/MERRA2/1983/11/. Please feel free to reach out if you need any further assistance.

GEOS_0.5x0.625_NA/MERRA2/1983/11/MERRA2.19831106.A3dyn.05x0625.NA.nc4 GEOS_0.5x0.625_NA/MERRA2/1983/11/MERRA2.19831107.A3cld.05x0625.NA.nc4

Row-Bean commented 10 months ago

Excellent, thank you very much! I have downloaded and checked the new files. Fingers crossed, this issue should be closed for the last time this time. I appreciate your assistance with this.