[Paraview] Segmentation fault in protobuf
u.utku.turuncoglu at be.itu.edu.tr
u.utku.turuncoglu at be.itu.edu.tr
Wed Aug 16 11:09:08 EDT 2017
Hi,
I add print statement to python script and it shows that three input port
is ok but one of them is empty. The new allinputsgridwriter.py that has
automatic detection of input port fail in this case but if I use old one
with manual configuration of the ports (there is no definition of empty
port in this case) work fine. Anyway, the issue seems solved with external
installation of protobuf library and I tested both gcc and intel
compilers. It could be the version issue of the internal protobuf library
in PV. So, you may consider to update it. Thanks to both of you for your
help.
Regards,
--ufuk
> 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
>> >> >> >>
>> >> >> >
>> >> >>
>> >> >>
>> >> >
>> >>
>> >>
>> >>
>> >
>>
>>
>
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