[Paraview] segmentation fault with netCDF when loading state file
Aashish Chaudhary
aashish.chaudhary at kitware.com
Wed Oct 21 09:50:22 EDT 2015
Ryan,
would it be possible for you to share a sample dataset? The NetCDF reader
has fails to read data in certain corner cases but without having the data
to reproduce the issue it is kind of little tricky to get to the problem.
- Aashish
On Wed, Oct 21, 2015 at 9:44 AM, Ryan Abernathey <ryan.abernathey at gmail.com>
wrote:
> Does anyone have any feedback on this issue?
>
> I have no idea how to debug or continue. I will have to abandon paraview
> for my project unless I can get some help somehow.
>
> Thanks,
>
> Ryan Abernathey
> Assistant Professor
> Columbia University, Department of Earth & Environmental Sciences
> Lamont-Doherty Earth Observatory, Division of Ocean & Climate Physics
> 205 C Oceanography
> 61 Route 9W - PO Box 1000
> Palisades, NY 10964-8000
> http://rabernat.github.io
> rpa at ldeo.columbia.edu
>
>
> On Mon, Oct 19, 2015 at 4:59 PM, Ryan Abernathey <
> ryan.abernathey at gmail.com> wrote:
>
>> Hello,
>>
>> I am extremely frustrated and stuck on this problem. Any advice would be
>> appreciated.
>>
>> I am working with a dataset of 2400 sequentially numbered netCDF files
>> (generic & CF conventions).
>>
>> In a fresh pipeline, Paraview is able to recognizes these files as a
>> single source and load them correctly. I then create a standard pipeline
>> involving various filters (contour, etc., nothing funny) and save a state
>> file.
>>
>> When I attempt to load the state file, I get the following segmentation
>> fault. Further down you can see a ncdump of the offending file.
>>
>> Would appreciate any advice on how to debug / overcome this issue. Is it
>> a bug? It sure feels like one...
>>
>> Best,
>> Ryan Abernathey
>>
>>
>> ERROR: In
>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/NetCDF/vtkNetCDFReader.cxx,
>> line 822
>> vtkNetCDFCFReader (0x55c0620): netCDF Error: NetCDF: Index exceeds
>> dimension bound
>>
>>
>> ERROR: In
>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
>> line 784
>> vtkPVCompositeDataPipeline (0x5be23d0): Algorithm
>> vtkFileSeriesReader(0x4c0c3e0) returned failure for request: vtkInformation
>> (0x8141700)
>> Debug: Off
>> Modified Time: 999905
>> Reference Count: 1
>> Registered Events: (none)
>> Request: REQUEST_DATA
>> FORWARD_DIRECTION: 0
>> FROM_OUTPUT_PORT: 0
>> ALGORITHM_AFTER_FORWARD: 1
>>
>>
>>
>>
>> ERROR: In
>> /home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
>> line 784
>> vtkCompositeDataPipeline (0x744fde0): Algorithm
>> vtkPVGeometryFilter(0x7436500) returned failure for request: vtkInformation
>> (0x5737250)
>> Debug: Off
>> Modified Time: 999943
>> Reference Count: 1
>> Registered Events: (none)
>> Request: REQUEST_DATA_OBJECT
>> FORWARD_DIRECTION: 0
>> FROM_OUTPUT_PORT: 0
>> ALGORITHM_AFTER_FORWARD: 1
>>
>>
>>
>>
>> Segmentation fault (core dumped)
>>
>>
>>
>>
>>
>> ------------------------
>> $ ncdump -h rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_0000000300.nc
>> netcdf rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_0000000300 {
>> dimensions:
>> x = 512 ;
>> y = 512 ;
>> z = 64 ;
>> time = UNLIMITED ; // (1 currently)
>> variables:
>> float x(x) ;
>> x:units = "m" ;
>> float y(y) ;
>> y:units = "m" ;
>> float z(z) ;
>> z:units = "m" ;
>> z:long_name = "height" ;
>> float time(time) ;
>> time:units = "d" ;
>> time:long_name = "time" ;
>> float p(z) ;
>> p:units = "mb" ;
>> p:long_name = "pressure" ;
>> float zi(z) ;
>> zi:units = "m" ;
>> zi:long_name = "intfc_ht" ;
>> float U(time, z, y, x) ;
>> U:long_name = "X Wind
>> Component " ;
>> U:units = "m/s " ;
>> float V(time, z, y, x) ;
>> V:long_name = "Y Wind
>> Component " ;
>> V:units = "m/s " ;
>> float W(time, z, y, x) ;
>> W:long_name = "Z Wind
>> Component " ;
>> W:units = "m/s " ;
>> float PP(time, z, y, x) ;
>> PP:long_name = "Pressure
>> Perturbation " ;
>> PP:units = "Pa " ;
>> float QRAD(time, z, y, x) ;
>> QRAD:long_name = "Radiative heating
>> rate " ;
>> QRAD:units = "K/day " ;
>> float TABS(time, z, y, x) ;
>> TABS:long_name = "Absolute
>> Temperature " ;
>> TABS:units = "K " ;
>> float QV(time, z, y, x) ;
>> QV:long_name = "Water
>> Vapor "
>> ;
>> QV:units = "g/kg " ;
>> float QN(time, z, y, x) ;
>> QN:long_name = "Non-precipitating Condensate
>> (Water+Ice) " ;
>> QN:units = "g/kg " ;
>> float QP(time, z, y, x) ;
>> QP:long_name = "Precipitating Water
>> (Rain+Snow) " ;
>> QP:units = "g/kg " ;
>> float LQRAD(time, z, y, x) ;
>> LQRAD:long_name = "LW Radiative heating
>> rate " ;
>> LQRAD:units = "K/day " ;
>> float SQRAD(time, z, y, x) ;
>> SQRAD:long_name = "SW Radiative heating
>> rate " ;
>> SQRAD:units = "K/day " ;
>> }
>>
>>
>
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--
*| Aashish Chaudhary | Technical Leader | Kitware Inc. *
*| http://www.kitware.com/company/team/chaudhary.html
<http://www.kitware.com/company/team/chaudhary.html>*
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