pnetcdf bug?

[Bill Sacks]

Hi,

I have run into what appears to be a bug in pnetcdf: I have a file written by pnetcdf (via CESM). When I try to append a variable onto it using ncks -A, the new variable gets written properly, but a different variable on the file gets garbage values put into it. If the original file is written with standard netcdf rather than pnetcdf, the problem does not occur.

I am attaching a tar file that contains files needed to see the problem. It contains two restart files written by CESM (file names beginning check_ncks...): one written with pnetcdf and one with standard netcdf (the latter has "netcdf" in its name). It also contains a third file from which I was trying to copy variables onto this file.

To reproduce:

cp check_ncks_problem_noInterp_1027.clm2.r.0001-01-01-01800.nc test.nc
ncks -A -v COL_Z_p,LEVGRND_CLASS_p finidat_interp_dest.nc test.nc 
ncdump -v plant_nalloc check_ncks_problem_noInterp_1027.clm2.r.0001-01-01-01800.nc > dump1
ncdump -v plant_nalloc test.nc > dump2
diff dump1 dump2 | less

Notice that many points that were FillValue have been replaced by garbage. 

If you do the same thing, but using check_ncks_problem_noInterp_netcdf_1027.clm2.r.0001-01-01-01800.nc, then the dumps are identical.

I originally filed a bug report with NCO <https://sourceforge.net/p/nco/bugs/84/ <https://sourceforge.net/p/nco/bugs/84/>>, but Charlie Zender and Jim Edwards both feel that this is most likely a problem in the writing of the original file, which points to a possible pnetcdf problem.

CESM was built with

        module load netcdf-mpi/4.3.3.1
        module load pnetcdf/1.6.0

(on NCAR's yellowstone machine).

Thank you,
Bill

--
Bill Sacks
CESM Software Engineering Group
National Center for Atmospheric Research
(303) 497-1762



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