pnetcdf bug?

[Bill Sacks]

I have put the attachment on a public ftp server:

ftp ftp.cgd.ucar.edu <http://ftp.cgd.ucar.edu/>

user name: anonymous
password: (your email address)

cd pub/sacks
get pnetcdf_bug.tar.gz

Thanks,
Bill

> On Oct 27, 2015, at 11:11 AM, Wei-keng Liao <wkliao at eecs.northwestern.edu> wrote:
> 
> 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
>>> 
>>> 
>>> 
>> 
> 

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