[Paraview] Segmentation fault in protobuf

Tue Aug 15 14:49:56 EDT 2017

Hi,

Yes. It works and produces same output.

--ufuk

> Hi Ufuk,
>
> It looks like the script line that is not working properly is:
>         grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
>
> grid is set to None here for your build. Trying something simpler, in
> pvpython can you try the following and let us know if it works:
> =============
> from paraview.simple import *
> a = Wavelet()
> a.UpdatePipeline()
> b = a.GetClientSideObject()
> c = b.GetOutputDataObject(0)
> print c
> =============
>
>
>
> It should give output like the following if it works:
> vtkImageData (0x4586a00)
>   Debug: Off
>   Modified Time: 204809
>   Reference Count: 2
>   Registered Events: (none)
>   Information: 0x4586450
>   Data Released: False
>   Global Release Data: Off
>   UpdateTime: 204810
>   Field Data:
>     Debug: Off
>     Modified Time: 204775
>     Reference Count: 1
>     Registered Events: (none)
>     Number Of Arrays: 0
>     Number Of Components: 0
>     Number Of Tuples: 0
>   Number Of Points: 9261
>   Number Of Cells: 8000
>   Cell Data:
>     Debug: Off
>     Modified Time: 204783
>     Reference Count: 1
>     Registered Events:
>       Registered Observers:
>         vtkObserver (0x4586550)
>           Event: 33
>           EventName: ModifiedEvent
>           Command: 0x45864a0
>           Priority: 0
>           Tag: 1
>     Number Of Arrays: 0
>     Number Of Components: 0
>     Number Of Tuples: 0
>     Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 )
>     Interpolate Flags: ( 1 1 1 1 1 0 0 1 )
>     Pass Through Flags: ( 1 1 1 1 1 1 1 1 )
>     Scalars: (none)
>     Vectors: (none)
>     Normals: (none)
>     TCoords: (none)
>     Tensors: (none)
>     GlobalIds: (none)
>     PedigreeIds: (none)
>     EdgeFlag: (none)
>   Point Data:
>     Debug: Off
>     Modified Time: 204809
>     Reference Count: 1
>     Registered Events:
>       Registered Observers:
>         vtkObserver (0x45864f0)
>           Event: 33
>           EventName: ModifiedEvent
>           Command: 0x45864a0
>           Priority: 0
>           Tag: 1
>     Number Of Arrays: 1
>     Array 0 name = RTData
>     Number Of Components: 1
>     Number Of Tuples: 9261
>     Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 )
>     Interpolate Flags: ( 1 1 1 1 1 0 0 1 )
>     Pass Through Flags: ( 1 1 1 1 1 1 1 1 )
>     Scalars:
>       Debug: Off
>       Modified Time: 204809
>       Reference Count: 2
>       Registered Events: (none)
>       Name: RTData
>       Data type: float
>       Size: 9261
>       MaxId: 9260
>       NumberOfComponents: 1
>       Information: 0
>       Name: RTData
>       Number Of Components: 1
>       Number Of Tuples: 9261
>       Size: 9261
>       MaxId: 9260
>       LookupTable: (none)
>     Vectors: (none)
>     Normals: (none)
>     TCoords: (none)
>     Tensors: (none)
>     GlobalIds: (none)
>     PedigreeIds: (none)
>     EdgeFlag: (none)
>   Bounds:
>     Xmin,Xmax: (-10, 10)
>     Ymin,Ymax: (-10, 10)
>     Zmin,Zmax: (-10, 10)
>   Compute Time: 204875
>   Spacing: (1, 1, 1)
>   Origin: (0, 0, 0)
>   Dimensions: (21, 21, 21)
>   Increments: (0, 0, 0)
>   Extent: (-10, 10, -10, 10, -10, 10)
>
>
>
> On Tue, Aug 15, 2017 at 2:27 PM, <u.utku.turuncoglu at be.itu.edu.tr> wrote:
>
>> Hi Andy,
>>
>> Thanks for your help and the script. Actually, I was adding input names
>> to
>> the script by hand. Anyway, I tested your script and it gives similar
>> error as follows,
>>
>>   File
>> "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/
>> egl/lib/site-packages/paraview/coprocessing.py",
>> line 305, in CreateProducer
>>     if grid.IsA("vtkImageData") == True or \
>> AttributeError: 'NoneType' object has no attribute 'IsA'
>>     grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
>>   File
>> "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/
>> egl/lib/site-packages/paraview/coprocessing.py",
>> line 305, in CreateProducer
>>     if grid.IsA("vtkImageData") == True or \
>> AttributeError: 'NoneType' object has no attribute 'IsA'
>>     grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
>>   File
>> "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/
>> egl/lib/site-packages/paraview/coprocessing.py",
>> line 305, in CreateProducer
>>     if grid.IsA("vtkImageData") == True or \
>> AttributeError: 'NoneType' object has no attribute 'IsA'
>>
>> I'll tested whole environment once again with Intel compiler to see it
>> helps or not. Let me know if you have any other idea.
>>
>> Regards,
>>
>> --ufuk
>>
>>
>> > Hi Ufuk,
>> >
>> > For the allinputsgridwriter.py you currently need to manually add in
>> the
>> > inputs yourself (i.e. replace the "namedinputs = ['input']" line with
>> the
>> > name of your inputs. That has caught me in the past as well so I
>> decided
>> > to
>> > fix that. Attached is my new version of that script where it doesn't
>> > require you to specify the input names in case you want to try this
>> new
>> > one
>> > instead. If you do, please let us know if that solves your problem or
>> not.
>> >
>> > Best,
>> > Andy
>> >
>> >
>> > On Tue, Aug 15, 2017 at 12:40 PM, Ben Boeckel
>> <ben.boeckel at kitware.com>
>> > wrote:
>> >
>> >> On Tue, Aug 15, 2017 at 17:59:47 +0300,
>> u.utku.turuncoglu at be.itu.edu.tr
>> >> wrote:
>> >> > I solved the problem and i am able to run the simulation code with
>> >> > Catalyst support by installing PV (5.4.0 rc4 and 5.3.0) with newer
>> >> version
>> >> > of protobuf library (3.3.0) and compiling the model code with this
>> >> version
>> >> > of PV (using gcc).
>> >> >
>> >> > Now, the problem is that the code gives following warnings and do
>> >> nothing
>> >> > with standard allinputsgridwriter.py script. Do you think that it
>> is
>> >> > related with protobuf library. The same setup is working without
>> any
>> >> > problem in an other system using Intel compiler.
>> >>
>> >> It'd be better to try with one MPI process rather thanÃ¢â‚¬Â¦I count
>> 10 to
>> >> get
>> >> the error? Not sure what's up though, Andy?
>> >>
>> >> > "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl
>> >> /lib/site-packages/paraview/coprocessing.py",
>> >> > line 305, in CreateProducer
>> >> >     grid =
>> adaptorinput.GetClientSideObject().GetOutputDataObject(0)
>> >> >     grid =
>> adaptorinput.GetClientSideObject().GetOutputDataObject(0)
>> >> >     if grid.IsA("vtkImageData") == True or \
>> >> >   File
>> >> > "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl
>> >> /lib/site-packages/paraview/coprocessing.py",
>> >> > line 305, in CreateProducer
>> >> > AttributeError: 'NoneType' object has no attribute 'IsA'
>> >> >   File
>> >> > "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl
>> >> /lib/site-packages/paraview/coprocessing.py",
>> >> > line 305, in CreateProducer
>> >> >     if grid.IsA("vtkImageData") == True or \
>> >> >     if grid.IsA("vtkImageData") == True or \
>> >> > AttributeError: 'NoneType' object has no attribute 'IsA'
>> >> >     grid =
>> adaptorinput.GetClientSideObject().GetOutputDataObject(0)
>> >> >   File
>> >> > "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl
>> >> /lib/site-packages/paraview/coprocessing.py",
>> >> > line 305, in CreateProducer
>> >> >     grid =
>> adaptorinput.GetClientSideObject().GetOutputDataObject(0)
>> >> >     if grid.IsA("vtkImageData") == True or \
>> >> >     if grid.IsA("vtkImageData") == True or \
>> >> > AttributeError: 'NoneType' object has no attribute 'IsA'
>> >> > AttributeError: 'NoneType' object has no attribute 'IsA'
>> >> >     if grid.IsA("vtkImageData") == True or \
>> >> > AttributeError: 'NoneType' object has no attribute 'IsA'
>> >> >   File
>> >> > "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl
>> >> /lib/site-packages/paraview/coprocessing.py",
>> >> > line 305, in CreateProducer
>> >> >     if grid.IsA("vtkImageData") == True or \
>> >> > AttributeError: 'NoneType' object has no attribute 'IsA'
>> >> > [PERFLOG] :: COPROC          2     0.01404021SEC.
>> >> >  Running COP Component: 2005-08-27T00:12:00 --> 2005-08-27T00:18:00
>> >> Time
>> >> > Step:     2 [         720.00]
>> >> > ATM-TO-COP: redist mask [CROSS] to mask [CROSS]
>> >> > ATM-TO-COP: redist topo [CROSS] to topo [CROSS]
>> >> > AttributeError: 'NoneType' object has no attribute 'IsA'
>> >> >     grid =
>> adaptorinput.GetClientSideObject().GetOutputDataObject(0)
>> >> >   File
>> >> > "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl
>> >> /lib/site-packages/paraview/coprocessing.py",
>> >> > line 305, in CreateProducer
>> >> >     if grid.IsA("vtkImageData") == True or \
>> >>
>> >> --Ben
>> >>
>> >
>>
>>
>