pnetcdf bug?

[Bill Sacks]

Hi Wei-keng,

Thanks very much for looking into this. I'm happy to submit a bug to the netCDF group if you think that's the best next step.

Superficially, this sure sounds similar to https://bugtracking.unidata.ucar.edu/browse/NCF-234 <https://bugtracking.unidata.ucar.edu/browse/NCF-234> – but maybe there are details that make it differ.

Thanks,
Bill

> On Oct 27, 2015, at 1:11 PM, Wei-keng Liao <wkliao at eecs.northwestern.edu> wrote:
> 
> Hi, Bill
> 
> I checked the file starting offsets for the two newly added variables.
> It appears that ncks (netCDF underneath) does not respect the offset
> alignment used in the files created by PnetCDF.
> 
> Your file created by netCDF has no alignment in between two adjacent variables.
> The other file created by PnetCDF has an alignment of 512 bytes.
> So, when ncks adds 2 new variables, I found the file offsets of the
> two new variables overlap with the last variable of the existing file.
> This indicates a bug in netCDF library, as ncks does not use PnetCDF library.
> 
> I will dig into netCDF library to see what happens internally.
> 
> Wei-keng
> 
> On Oct 27, 2015, at 1:41 PM, Bill Sacks wrote:
> 
>> Looking back at my notes, it seems that this problem sometimes appears in differences in actual values – i.e., it doesn't appear to just be a difference in where there are fill values.
>> 
>> Thank you,
>> Bill
>> 
>>> On Oct 27, 2015, at 12:30 PM, Wei-keng Liao <wkliao at eecs.northwestern.edu> wrote:
>>> 
>>> Hi, Bill
>>> 
>>> I can reproduce what you are seeing.
>>> 
>>> If the differences happen only to those missing array elements (fill values),
>>> then this is because PnetCDF supports the fill mode only in 1.6.1.
>>> Please note the way fill mode is used differs from netCDF. See the release note
>>> and example codes in
>>> http://trac.mcs.anl.gov/projects/parallel-netcdf/wiki/ReleaseNotes-1.6.1
>>> 
>>> Please let me know if this is the case.
>>> 
>>> Wei-keng
>>> 
>>> On Oct 27, 2015, at 12:41 PM, Bill Sacks wrote:
>>> 
>>>> I have put the attachment on a public ftp server:
>>>> 
>>>> ftp 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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