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