[Paraview] Segmentation fault in protobuf

Tue Aug 15 10:59:47 EDT 2017

Hi,

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.

Traceback (most recent call last):
  File "<string>", line 2, in <module>
Traceback (most recent call last):
Traceback (most recent call last):
  File "<string>", line 2, in <module>
  File "<string>", line 2, in <module>
Traceback (most recent call last):
  File "<string>", line 2, in <module>
Traceback (most recent call last):
  File "<string>", line 2, in <module>
Traceback (most recent call last):
  File "<string>", line 2, in <module>
Traceback (most recent call last):
  File "<string>", line 2, in <module>
Traceback (most recent call last):
  File "<string>", line 2, in <module>
  File "allinputsgridwriter.py", line 97, in DoCoProcessing
  File "allinputsgridwriter.py", line 97, in DoCoProcessing
  File "allinputsgridwriter.py", line 97, in DoCoProcessing
  File "allinputsgridwriter.py", line 97, in DoCoProcessing
  File "allinputsgridwriter.py", line 97, in DoCoProcessing
  File "allinputsgridwriter.py", line 97, in DoCoProcessing
  File "allinputsgridwriter.py", line 97, in DoCoProcessing
  File "allinputsgridwriter.py", line 97, in DoCoProcessing
  File "allinputsgridwriter.py", line 97, in DoCoProcessing
  File "allinputsgridwriter.py", line 97, in DoCoProcessing

  File
"/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl/lib/site-packages/paraview/coprocessing.py",
line 160, in UpdateProducers

    self.CreatePipeline(datadescription)
  File
"/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl/lib/site-packages/paraview/coprocessing.py",
line 160, in UpdateProducers
  File "allinputsgridwriter.py", line 50, in CreatePipeline

    self.CreatePipeline(datadescription)
  File
"/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl/lib/site-packages/paraview/coprocessing.py",
line 160, in UpdateProducers
  File "allinputsgridwriter.py", line 50, in CreatePipeline

  File
"/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl/lib/site-packages/paraview/coprocessing.py",
line 160, in UpdateProducers

  File
"/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl/lib/site-packages/paraview/coprocessing.py",
line 160, in UpdateProducers

    self.CreatePipeline(datadescription)
  File
"/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl/lib/site-packages/paraview/coprocessing.py",
line 160, in UpdateProducers
    self.CreatePipeline(datadescription)

  File "allinputsgridwriter.py", line 23, in _CreatePipeline
  File "allinputsgridwriter.py", line 50, in CreatePipeline
  File "allinputsgridwriter.py", line 50, in CreatePipeline

    self.CreatePipeline(datadescription)
    self.CreatePipeline(datadescription)
  File "allinputsgridwriter.py", line 50, in CreatePipeline
  File
"/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl/lib/site-packages/paraview/coprocessing.py",
line 160, in UpdateProducers
  File "allinputsgridwriter.py", line 50, in CreatePipeline

  File
"/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl/lib/site-packages/paraview/coprocessing.py",
line 160, in UpdateProducers

    self.CreatePipeline(datadescription)
  File
"/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl/lib/site-packages/paraview/coprocessing.py",
line 160, in UpdateProducers
    self.CreatePipeline(datadescription)
  File "allinputsgridwriter.py", line 50, in CreatePipeline
    self.CreatePipeline(datadescription)
  File "allinputsgridwriter.py", line 50, in CreatePipeline

  File "allinputsgridwriter.py", line 50, in CreatePipeline
  File "allinputsgridwriter.py", line 23, in _CreatePipeline
  File
"/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl/lib/site-packages/paraview/coprocessing.py",
line 160, in UpdateProducers
  File "allinputsgridwriter.py", line 23, in _CreatePipeline
    for name in namedinputs:

  File "allinputsgridwriter.py", line 26, in Pipeline
    self.CreatePipeline(datadescription)
  File "allinputsgridwriter.py", line 23, in _CreatePipeline
  File "allinputsgridwriter.py", line 50, in CreatePipeline

  File "allinputsgridwriter.py", line 23, in _CreatePipeline
  File "allinputsgridwriter.py", line 23, in _CreatePipeline
  File "allinputsgridwriter.py", line 23, in _CreatePipeline

  File "allinputsgridwriter.py", line 23, in _CreatePipeline

  File "allinputsgridwriter.py", line 23, in _CreatePipeline
  File "allinputsgridwriter.py", line 23, in _CreatePipeline
    for name in namedinputs:
    for name in namedinputs:
    grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
  File "allinputsgridwriter.py", line 26, in Pipeline
  File "allinputsgridwriter.py", line 26, in Pipeline
  File
"/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl/lib/site-packages/paraview/coprocessing.py",
line 305, in CreateProducer
    for name in namedinputs:
    for name in namedinputs:
  File "allinputsgridwriter.py", line 26, in Pipeline
  File "allinputsgridwriter.py", line 26, in Pipeline
    if grid.IsA("vtkImageData") == True or \
    for name in namedinputs:
AttributeError: 'NoneType' object has no attribute 'IsA'
  File "allinputsgridwriter.py", line 26, in Pipeline
    for name in namedinputs:
    for name in namedinputs:
    for name in namedinputs:
  File "allinputsgridwriter.py", line 26, in Pipeline
  File "allinputsgridwriter.py", line 26, in Pipeline
  File "allinputsgridwriter.py", line 26, in Pipeline
    grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
    for name in namedinputs:
  File
"/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl/lib/site-packages/paraview/coprocessing.py",
line 305, in CreateProducer
  File "allinputsgridwriter.py", line 26, in Pipeline
    grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
    if grid.IsA("vtkImageData") == True or \
    grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
    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
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
  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)
    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 \

> On Mon, Aug 14, 2017 at 20:45:41 +0300, u.utku.turuncoglu at be.itu.edu.tr
> wrote:
>> Again thanks for your help. I tried to use protobuf 3.3.0 with PV
>> 5.4.0rc4
>> but i am getting following error
>>
>>  CMake Warning at
>>  /usr/local/software/spack/develop-290617/spack/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/cmake-3.8.1-hvzxbkmal
>>  ie677klawvpwyipv7giycyh/share/cmake-3.8/Modules/FindProtobuf.cmake:387
>> (message):
>>    Protobuf compiler version doesn't match library version 3.3.0
>>  Call Stack (most recent call first):
>>    VTK/CMake/vtkModuleMacros.cmake:888 (find_package)
>>    ThirdParty/protobuf/CMakeLists.txt:40 (vtk_module_third_party)
>>
>> I have also version 2.5 in the system but I am getting lots of error
>> (see
>> attached log.txt) related with undefined references.
>
> It looks like it's finding the compiler for 2.5 with the 3.3 library.
> Set them both so that they match first.
>
> --Ben
>