[Paraview] Segmentation fault in protobuf
u.utku.turuncoglu at be.itu.edu.tr
u.utku.turuncoglu at be.itu.edu.tr
Tue Aug 15 15:30:28 EDT 2017
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
>> >> >>
>> >> >
>> >>
>> >>
>> >
>>
>>
>>
>
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