[Paraview] Segmentation fault in protobuf
Andy Bauer
andy.bauer at kitware.com
Tue Aug 15 15:41:55 EDT 2017
Hmm, can you check that you've set the vtkCPInputDataDescription grid
through the SetGrid() method? You can add in something like "print("input
is ", datadescription.GetInputDescriptionByName(<name>).GetGrid())" a
couple of places in your Python script to see if there is actually a grid
added there for that input.
Best,
Andy
On Tue, Aug 15, 2017 at 3:30 PM, <u.utku.turuncoglu at be.itu.edu.tr> wrote:
> Without support of you and also Ben, i could not even reach to this point.
> Thanks again. At least, code runs now. I think that this is big
> improvement.
>
> Anyway, both command is working as expected,
>
> > mpirun -np 4 pvbatch <file>
> > mpirun -np 4 pvbatch -sym <file>
>
> I also tested allinputsgridwriter_new.py with CFullExample (and also
> Fortran90FullExample) and it works without any problem. As I mentioned
> before, CFullExample was also working before upgrading protobuf (still, i
> don't know why). So, it is not a good way to find the source of the
> problem.
>
> --ufuk
>
>
> > 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
> >> >> >>
> >> >> >
> >> >>
> >> >>
> >> >
> >>
> >>
> >>
> >
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/paraview/attachments/20170815/93a9864b/attachment.html>
More information about the ParaView
mailing list