CDO

hi Neil!

can you upload the file?

cheers
ralf

Hello Ralf,

The file exceeds the uploading limit. I realise I can normally extract a few time steps from it to make it smaller using CDO, but I cannot get CDO to work with it.

The files I am interested in (all of them) are found at this link:
http://data.ceda.ac.uk/badc/cmip6/data/CMIP6/ScenarioMIP/FIO-QLNM/FIO-ESM-2-0/ssp245/r1i1p1f1/Omon/thetao/gn/files/d20200109
None of these files work with CDO.

I will try to install NCO and compress one of these files for uploading tomorrow morning. You'll hear from me then. Thank you very much for your help.

Best regards,

Neil

I can download them, no problem.

There is also a OpenDAP interface. Could your try this

cdo sinfov http://dap.ceda.ac.uk/thredds/dodsC/badc/cmip6/data/CMIP6/ScenarioMIP/FIO-QLNM/FIO-ESM-2-0/ssp245/r1i1p1f1/Omon/thetao/gn/files/d20200109/thetao_Omon_FIO-ESM-2-0_ssp245_r1i1p1f1_gn_209501-210012.nc

I could reproduce this 'Unknown Error' in windows10 (using cygwin). the same file works without problem with cdo-1.9.8 on a linux box. The OpenDAP call from above also works in cygwin, so this might be a workaround for now. to download the file you could use

 cdo copy http://......

As an alternative you can switch from cygwin to Linux subsystem shipped with Windows10. In there you can install cdo-1.9.3 and this binary can work with thetao_Omon_FIO-ESM-2-0_ssp245_r1i1p1f1_gn_209501-210012.nc without problems.

what I can say about the source of this error is, that it comes from the underlying HDF5 library

I tested more under cygwin and I could rebuild cdo-1.9.8 with clang-8, but not the with current gcc-9.3.0 package (compiler bug with optimization switched on, compile error without optimization). Unfortunately the clang package does not support openmp, so many operators loose possible performance benefit from this.

I have to rethink about how to build the binary for cygwin - the current situation with cygwin is not optimal, but it's not possible to test for stability because every user has his/her own version - there is no release cycle AFAIK. people update as often as they want. IMO for now you better use the Linux subsystem - it behaves very similar to cygwin.

hth
ralf

Hello Ralf,

Thank you very much for the very helpful responses. I've installed the Linux subsystem and have managed to get CDO running nicely.

Again, my sincere thanks for the time and patience needed to help out a beginner!

Best regards,

Neil

your are welcome, Neil!

happy hacking ;-)
ralf

Hello Neil,
I am facing same problem on windows 10 how can I fix that. Can you please guide

I have the same issue, and my Cygwin canot open hdf5 files. If I convert the .nc file to .nc4 with nco, I can process the resulting .nc4 file just fine with cdo
Now how to upgrade the hdf5 libraries in Cygwin... this is definitely funner.

Dear all,
Greetings!

I have installed Cygwin with CDO and am trying to remap climate data but I have got this error open file failed no such file or directory found
could you please help me how to correct it

thank you

hi!

Inside a cygwin-terminal you cannot use the Windows-style path descriptors for harddrives (C:/ or F:/). Instead you have to use `/cygdrive/c` and `/cygdrive/f` as far as I know.

And the error message is clear btw: No such file or directory

some docu: https://cygwin.com/cygwin-ug-net/using.html#cygdrive

cheers
ralf

Hello. I have the same problem but on ubuntu. Is it from the hdf5 library? it is installed

Hello everyone,

I have the same error but it is a bit more complicated. I am running cdo on windows10 con Cygwin.
The netcdf file is downloaded from CORDEX and is a rotated coordinate netcdf EUR-11.

cdo version 2.0.5 (last cdo.exe version)
cygwin version 3.3.6

$ cdo sinfon T1.nc
          cdo    sinfon: Open failed on >T1.nc<
                         Unknown Error

I thought that the problem could have been in missing packages. I have Cygwin on another pc (same versions, but the pc is not very powefull) so I installed the exact same packages I have there (including the mandatory ones like gcc-core, gcc-fortran, ssl, ssh, libssl-devel, openssl, curl, zlib, netcdf-devel, udunits, proj, hdf5, netcdf13, libproj13, fftw3 ecc.......... )
BUT I STILL HAVE THE PROBLEM OF "UKNOWN ERROR"
How it is possible that Cygwin with the same exact packages is not working on a machine and yes in another? WHICH COULD BE MY PROBLEM?

I attach the list of my installed packages... could there be any conflict between some of them for example? or is something important missing?

PLEASE HELP

hi everyone!

Please note that in case of emergency you should consider using the Windows Linux Subsystem (WSL) as an alternative. the command line interface works very similar to the cygwin terminal and the cdo build in there stable.

For cross checking your file you need to uplaod it here are provide a valid download link. This would allow me to exclude a corrupted as a possible source or error.

cheers
ralf