[Paraview] segmentation fault with netCDF when loading state file
Ryan Abernathey
ryan.abernathey at gmail.com
Tue Oct 27 13:16:02 EDT 2015
David,
Thanks for your investigation. I will be able to try this tomorrow. The
original issue was with Paraview 4.3.1. We recently built the latest
master, so I will be able to confirm whether it was fixed in between.
Best,
Ryan
On Tue, Oct 27, 2015 at 10:23 AM, David Lonie <david.lonie at kitware.com>
wrote:
> Hi Ryan,
>
> I'm looking into this issue.
>
> I download the sample data you provided, and the state file loads and
> renders fine for me with the current (as of this morning) master branch of
> ParaView. What version of ParaView are you using? Can you test the latest
> master branch? It appears that whatever the bug was, it has been fixed.
>
> Dave
>
> On Wed, Oct 21, 2015 at 9:50 AM, Aashish Chaudhary <
> aashish.chaudhary at kitware.com> wrote:
>
>> 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>*
>>
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>> http://paraview.org/Wiki/ParaView
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
>> Follow this link to subscribe/unsubscribe:
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>
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