pnetcdf bug?

[Wei-keng Liao]

Hi, Bill

Bug NCF-234 should not be the cause, as you are using netCDF 4.3.3.1.
The fix has been applied to 4.3.0. I will take a look and get back to you.

Somehow your attachment did not come through my mail system.
I check PnetCDF mail archive and it does not appear there either.
http://lists.mcs.anl.gov/pipermail/parallel-netcdf/2015-October/001746.html

Maybe the file is too big? If that is the case, please send it to me directly.
Thanks

Wei-keng

On Oct 27, 2015, at 10:36 AM, Bill Sacks wrote:

> I wonder if this could be related to this (fixed) bug:
> 
> 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 Notice that many points that were FillValue have been replaced by garbage.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/>, 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
>> 
>> 
>> 
>