Re: [Paraview] Segmentation fault in protobuf
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 "", line 2, in Traceback (most recent call last): Traceback (most recent call last): File "", line 2, in File "", line 2, in Traceback (most recent call last): File "", line 2, in Traceback (most recent call last): File "", line 2, in Traceback (most recent call last): File "", line 2, in Traceback (most recent call last): File "", line 2, in Traceback (most recent call last): File "", line 2, in 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/para
Re: [Paraview] Segmentation fault in protobuf
On Tue, Aug 15, 2017 at 17:59:47 +0300, u.utku.turunco...@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
___
Powered by www.kitware.com
Visit other Kitware open-source projects at
http://www.kitware.com/opensource/opensource.html
Please keep messages on-topic and check the ParaView Wiki at:
http://paraview.org/Wiki/ParaView
Search the list archives at: http://markmail.org/search/?q=ParaView
Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview
Re: [Paraview] Segmentation fault in protobuf
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
wrote:
> On Tue, Aug 15, 2017 at 17:59:47 +0300, u.utku.turunco...@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
>
from paraview.simple import *
from paraview import coprocessing
# the frequency to output everything
outputfrequency = 5
# --- CoProcessor definition ---
def CreateCoProcessor():
def _CreatePipeline(coprocessor, datadescription):
class Pipeline:
for i in range(datadescription.GetNumberOfInputDescriptions()):
inputdescription = datadescription.GetInputDescription(i)
name = datadescription.GetInputDescriptionName(i)
adaptorinput = coprocessor.CreateProducer( datadescription, name )
grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
extension = None
if grid.IsA('vtkImageData') or grid.IsA('vtkUniformGrid'):
writer = servermanager.writers.XMLPImageDataWriter(Input=adaptorinput)
extension = '.pvti'
elif grid.IsA('vtkRectilinearGrid'):
writer = servermanager.writers.XMLPRectilinearGridWriter(Input=adaptorinput)
extension = '.pvtr'
elif grid.IsA('vtkStructuredGrid'):
writer = servermanager.writers.XMLPStructuredGridWriter(Input=adaptorinput)
extension = '.pvts'
elif grid.IsA('vtkPolyData'):
writer = servermanager.writers.XMLPPolyDataWriter(Input=adaptorinput)
extension = '.pvtp'
elif grid.IsA('vtk
Re: [Paraview] Segmentation fault in protobuf
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
> wrote:
>
>> On Tue, Aug 15, 2017 at 17:59:47 +0300, u.utku.turunco...@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 thanâ¦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
>>
>
__
Re: [Paraview] Segmentation fault in protobuf
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, 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
> > wrote:
> >
> >> On Tue, Aug 15, 2017 at 17:59:47 +0300, u.utku.turunco...@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
>
Re: [Paraview] Segmentation fault in protobuf
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, 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 prob
Re: [Paraview] Segmentation fault in protobuf
Hmm, how about making that Python code into a file and running it with both:
mpirun -np 4 pvbatch
mpirun -np 4 pvbatch -sym
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, 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,
> 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
Re: [Paraview] Segmentation fault in protobuf
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 > mpirun -np 4 pvbatch -sym 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 > mpirun -np 4 pvbatch -sym > > 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, 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, >> 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 gri
Re: [Paraview] Segmentation fault in protobuf
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().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, 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
> > mpirun -np 4 pvbatch -sym
>
> 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
> > mpirun -np 4 pvbatch -sym
> >
> > 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,
> 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,Zm
