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Problem with cdo functions, message: Segmentation fault (core dumped)

Added by Alonso Arriagada over 2 years ago

Hello community! I have problems reviewing an NC file which I attach, when I apply CDO functions like sinfon, infon, yearsum, etc. I get this message: Segmentation fault (core dumped)
I guess it's because of the format of the NC file.
Can someone help me to solve it?
Thank you very much!
Regards!


Replies (6)

RE: Problem with cdo functions, message: Segmentation fault (core dumped) - Added by Karin Meier-Fleischer over 2 years ago

Hi Alonso,

in the first two lines returned by the sinfo call, CDO tells you that the files have time varying x- and y-bounds.

Warning (cdf_read_coordinates): Time varying grid x-bounds unsupported, skipped!
Warning (cdf_read_coordinates): Time varying grid y-bounds unsupported, skipped!

This can't be handled by CDO.

RE: Problem with cdo functions, message: Segmentation fault (core dumped) - Added by Alonso Arriagada over 2 years ago

Thanks a lot Karin!
Is there a way to fix the NC files to be alble to use CDO with them?

THANKS!

RE: Problem with cdo functions, message: Segmentation fault (core dumped) - Added by Estanislao Gavilan over 2 years ago

Hi Alonso,

I think the real question is why your lon and lat corners are time dependent. It seems to me that those files come from the cmip6 output models which have a fix coordiantes over time. I took a look to your pr file. I observed that your lon and lat bounds have dimensions x,y,t. However, if you compute the max and min of those bounds, you can see that they are constant over time. Did you make those files by yourself? If that is the case you should remove the time axis from your bounds. I hope it helps

Kind regards,

Estanislao

RE: Problem with cdo functions, message: Segmentation fault (core dumped) - Added by Alonso Arriagada over 2 years ago

Hi Estanislao, thank you so much for your response!
I have downloaded the files from Copernicus web site (https://cds.climate.copernicus.eu/cdsapp#!/dataset/projections-cmip6?tab=form).
My guess is that the files can be modified or simplified to transform them to CF-Convention or something that is applicable to CDO. Perhaps use NCO or NCL, to create a new file where to keep the information of these Copernicus NC and be able to operate with CDO. My problem is that I don't have that much experience with tools other than CDO.
Anyway thank you very much!

Cheers!

Alonso.

RE: Problem with cdo functions, message: Segmentation fault (core dumped) - Added by Ahsan Khan over 2 years ago

Hi, I am also facing the exact same issue in some of the files of CMIP6 , downloaded from cds.climate.copernicus.eu ... Have you Solved it?.

RE: Problem with cdo functions, message: Segmentation fault (core dumped) - Added by Alonso Arriagada over 2 years ago

Hi Ahsan, I used a NCO function to eliminate bounds, I leave you an example:

ncks -C -O -x -v lat_bnds,lon_bnds,time_bnds file_with_bnds.nc outfile.nc

Good luck!

Best!
Alonso

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