pnetcdf bug?

[Bill Sacks]

I wonder if this could be related to this (fixed) bug:

https://bugtracking.unidata.ucar.edu/browse/NCF-234 <https://bugtracking.unidata.ucar.edu/browse/NCF-234>

As with that one, it's possible that the problem is actually in netCDF and not in pnetcdf. Does anyone have an idea for how to determine if this is a pnetcdf problem or a netcdf problem? Or should I go ahead and post this to the netcdf bug list as well?

Charlie: I'm feeling more and more that NCO is probably off the hook here: sorry for dragging you into this initially :-)

Bill


> On Oct 27, 2015, at 9:21 AM, Bill Sacks <wsacks at gmail.com> wrote:
> 
> 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 Notice that many points that were FillValue have been replaced by garbage.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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