remapcon leading to "segmentation fault (core dumped)" error
Added by Andreas Prein about 9 years ago
Hi,
I want to remap netcdf files with cdo (v1.6.3) remapcon and get a "segmentation fault (core dumped)" error. Strangely, if I try the same command several times it succeeds every ~3rd time and sometimes crashes with different error messages (Bus error (core dumped); Error (cdf_close) : NetCDF: HDF error). For larger files (longer time periods) it never succeeds.
Here is the cdo comand that I am using for the remapping:
cdo remapcon,tar_grid.nc -selvar,Data -setgrid,src_grid.nc SourceData.nc TargetData.nc
The according netcdf files are attached.
Thank you for your help,
Andreas
| src_grid.nc (5.04 MB) src_grid.nc | |||
| SourceData.nc (7.2 MB) SourceData.nc | |||
| tar_grid.nc (1.26 MB) tar_grid.nc |
Replies (2)
RE: remapcon leading to "segmentation fault (core dumped)" error - Added by Uwe Schulzweida about 9 years ago
If you are using more than one CDO operator then all these operators are running in parallel and on different threads. Therefor the netCDF/HDF5 library must be compiled thread-safe. It seems that your netCDF/HDF installation is not thread-safe.
In this case you always need to use the CDO option -L to serialize the netCDF/HDF I/O access:
cdo -L remapcon,tar_grid.nc -selvar,Data -setgrid,src_grid.nc SourceData.nc TargetData.nc
RE: remapcon leading to "segmentation fault (core dumped)" error - Added by Andreas Prein about 9 years ago
That solved the problem.
Thank you very much for your help!
Best,
Andreas