[Paraview] segmentation fault with netCDF when loading state file
Ryan Abernathey
ryan.abernathey at gmail.com
Wed Oct 28 21:47:57 EDT 2015
Yes, I can confirm that this state loads without crashing in 4.4.
The fields are not actually accessible at the current timestep (appear with
a "?"), but can be rewound to the beginning and restarted without crashing.
On Tue, Oct 27, 2015 at 1:16 PM, Ryan Abernathey <ryan.abernathey at gmail.com>
wrote:
> 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
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>>> Please keep messages on-topic and check the ParaView Wiki at:
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>>> Search the list archives at: http://markmail.org/search/?q=ParaView
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>>
>
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