[Paraview] Segmentation fault in protobuf
Andy Bauer
andy.bauer at kitware.com
Tue Aug 15 15:05:54 EDT 2017
Hmm, how about making that Python code into a file and running it with both:
mpirun -np 4 pvbatch <file>
mpirun -np 4 pvbatch -sym <file>
Just to verify, the allinputsgridwriter.py didn't work with any of the
Catalyst examples (e.g. CFullExample), correct?
I think this is going to be some issue where we continually bisect the
problem space so I appreciate your patience on this.
Best,
Andy
On Tue, Aug 15, 2017 at 2:49 PM, <u.utku.turuncoglu at be.itu.edu.tr> wrote:
> 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 than…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
> >> >>
> >> >
> >>
> >>
> >
>
>
>
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