View Issue Details Jump to Notes ] Print ]
IDProjectCategoryView StatusDate SubmittedLast Update
0013249ParaView(No Category)public2012-06-19 08:382016-08-12 09:59
ReporterPaul Melis 
Assigned ToLeo Liu 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusclosedResolutionmoved 
PlatformOSOS Version
Product Version3.14.1 
Target VersionFixed in Version 
Summary0013249: Segfaults with dataset read from .csv
DescriptionGiven the attached csv file I get different segfaults. This is all with PV 3.14.1, happens in official binaries, as well as in a custom-compiled RelWithDebInfo build. Ubuntu Lucid, x86_64.

1st situation:
- Open csv file, apply default reader settings, data in table looks good
- Add a Table to Points filter, X column=x, etc
- Interestingly, the data at this point consists of a single cell with 25000 points
- Add a calculator filter, name result array 'v', expression 'vx*iHat+vy*jHat+vz*kHat'
- Newly added vector data looks good in table view
- Add a Mask points filter to the calculator output, #points=200, random sampling
- Add Streamtracer with custom source, input=calculator, source=maskpoints, apply
- SEGFAULT

Partial stack trace:
#0 0x00007f0390642976 in _int_malloc (av=0x7f0390945e40, bytes=112) at malloc.c:4635
#1 0x00007f03906437de in *__GI___libc_malloc (bytes=112) at malloc.c:3660
#2 0x00007f0390c2c24d in operator new(unsigned long) () from /usr/lib/libstdc++.so.6
#3 0x00007f0391eba342 in vtkPoints::New (dataType=10) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Common/vtkPoints.cxx:51
#4 0x00007f0392b8e830 in vtkCell (this=0x330cea0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkCell.cxx:24
#5 0x00007f0392d7f94e in vtkVertex (this=0x0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkVertex.cxx:29
#6 0x00007f0392d7fa40 in vtkVertex::New () at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkVertex.cxx:25
#7 0x00007f0392d0c840 in vtkPolyVertex (this=0x3a6f1c0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkPolyVertex.cxx:31
#8 0x00007f0392d0c910 in vtkPolyVertex::New () at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkPolyVertex.cxx:26
0000009 0x00007f0392be49fc in vtkGenericCell::SetCellType (this=0x3a7bde0, cellType=2) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkGenericCell.cxx:364
#10 0x00007f0392cf2a75 in vtkGenericCell::SetCellTypeToPolyVertex (this=0x3a0a260, cellId=<value optimized out>, cell=0x3a7bde0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkGenericCell.h:98
0000011 vtkPolyData::GetCell (this=0x3a0a260, cellId=<value optimized out>, cell=0x3a7bde0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkPolyData.cxx:396
#12 0x00007f0392b64942 in vtkAbstractInterpolatedVelocityField::FunctionValues (this=0x27daaa0, dataset=0x3a0a260, x=0x2526450, f=0x3a14010) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkAbstractInterpolatedVelocityField.cxx:134
#13 0x00007f0392c82715 in vtkInterpolatedVelocityField::FunctionValues (this=0x27daaa0, x=0x2526450, f=0x3a14010) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkInterpolatedVelocityField.cxx:79
#14 0x00007f0391ecb8f2 in vtkRungeKutta45::ComputeAStep (this=0x28b1380, xprev=0x7fff94dd5c60, dxprev=<value optimized out>, xnext=<value optimized out>, t=<value optimized out>, delT=@0x7fff94dd5cb0, error=<value optimized out>)
    at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Common/vtkRungeKutta45.cxx:268
#15 0x00007f0391ecbd3f in vtkRungeKutta45::ComputeNextStep (this=0x28b1380, xprev=0x7fff94dd5c60, dxprev=0x0, xnext=0x7fff94dd5c40, t=<value optimized out>, delT=@0x7fff94dd5cb0, delTActual=<value optimized out>, minStep=24, maxStep=0, maxError=39, estErr=@0x7fff94dd5cc8)
    at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Common/vtkRungeKutta45.cxx:127
#16 0x00007f0391ecc36c in vtkRungeKutta45::ComputeNextStep (this=0x0, xprev=0x4000122c, xnext=<value optimized out>, t=0, delT=<value optimized out>, delTActual=<value optimized out>, minStep=0, maxStep=0, maxError=39, error=<value optimized out>)
    at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Common/vtkRungeKutta45.h:93
#17 0x00007f03944ef742 in vtkStreamTracer::Integrate (this=0x3aef950, input0=<value optimized out>, output=<value optimized out>, seedSource=0x29e8a60, seedIds=<value optimized out>, integrationDirections=<value optimized out>, lastPoint=0x7fff94dd5d80, func=0x27daaa0,
    maxCellSize=25000, vecName=0x1da3680 "v", inPropagation=@0x7fff94dd5da8, inNumSteps=@0x7fff94dd5da0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Graphics/vtkStreamTracer.cxx:827
#18 0x00007f03944f106c in vtkStreamTracer::RequestData (this=0x3aef950, inputVector=<value optimized out>, outputVector=<value optimized out>) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Graphics/vtkStreamTracer.cxx:468
#19 0x00007f03974b62e5 in vtkPStreamTracer::RequestData (this=0x3aef950, request=0x347f9d0, inputVector=0x3b0d920, outputVector=0x3af1040) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Parallel/vtkPStreamTracer.cxx:334
#20 0x00007f0392bd7da4 in vtkExecutive::CallAlgorithm (this=0x3af0700, request=0x347f9d0, direction=<value optimized out>, inInfo=0x3b0d920, outInfo=0x3af1040) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkExecutive.cxx:747
#21 0x00007f0392bcb71c in vtkDemandDrivenPipeline::ExecuteData (this=0x3af0700, request=0x347f9d0, inInfo=0x3b0d920, outInfo=0x3af1040) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkDemandDrivenPipeline.cxx:507
#22 0x00007f0392bac711 in vtkCompositeDataPipeline::ExecuteData (this=0x3af0700, request=0x347f9d0, inInfoVec=0x3b0d920, outInfoVec=0x3af1040) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkCompositeDataPipeline.cxx:391
#23 0x00007f0392bce7cb in vtkDemandDrivenPipeline::ProcessRequest (this=0x3af0700, request=0x347f9d0, inInfoVec=0x3b0d920, outInfoVec=0x3af1040) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkDemandDrivenPipeline.cxx:279
#24 0x00007f0392d580f9 in vtkStreamingDemandDrivenPipeline::ProcessRequest (this=0x3af0700, request=0x347f9d0, inInfoVec=0x3b0d920, outInfoVec=0x3af1040) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkStreamingDemandDrivenPipeline.cxx:276
#25 0x00007f0392ba95d1 in vtkCompositeDataPipeline::ProcessRequest (this=0x3af0700, request=0x347f9d0, inInfoVec=0x3b0d920, outInfoVec=0x3af1040) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkCompositeDataPipeline.cxx:292
#26 0x00007f0392baa886 in vtkCompositeDataPipeline::ForwardUpstream (this=0x2a554c0, request=0x347f9d0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkCompositeDataPipeline.cxx:215
#27 0x00007f0392bce775 in vtkDemandDrivenPipeline::ProcessRequest (this=0x2a554c0, request=0x347f9d0, inInfoVec=0x1d75470, outInfoVec=0x3a8f300) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkDemandDrivenPipeline.cxx:265
#28 0x00007f0392d580f9 in vtkStreamingDemandDrivenPipeline::ProcessRequest (this=0x2a554c0, request=0x347f9d0, inInfoVec=0x1d75470, outInfoVec=0x3a8f300) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkStreamingDemandDrivenPipeline.cxx:276
#29 0x00007f0392ba95d1 in vtkCompositeDataPipeline::ProcessRequest (this=0x2a554c0, request=0x347f9d0, inInfoVec=0x1d75470, outInfoVec=0x3a8f300) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkCompositeDataPipeline.cxx:292
#30 0x00007f0392bce50f in vtkDemandDrivenPipeline::UpdateData (this=0x2a554c0, outputPort=<value optimized out>) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkDemandDrivenPipeline.cxx:449
#31 0x00007f0392d5713b in vtkStreamingDemandDrivenPipeline::Update (this=0x2a554c0, port=0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkStreamingDemandDrivenPipeline.cxx:326
#32 0x00007f03a3364d73 in vtkSISourceProxyCommand (arlu=0x16ac8d0, ob=0x3af78a0, method=<value optimized out>, msg=..., resultStream=...) at /home/paulmlocal/c/paraview-3.14.1-reldebinfo/ParaViewCore/ServerImplementation/vtkSISourceProxyClientServer.cxx:114
#33 0x00007f039936069f in vtkClientServerInterpreter::ProcessCommandInvoke (this=0x16ac8d0, css=..., midx=0) at /home/paulmlocal/c/ParaView-3.14.1-Source/Utilities/VTKClientServer/vtkClientServerInterpreter.cxx:379
#34 0x00007f039935f53e in vtkClientServerInterpreter::ProcessOneMessage (this=0x16ac8d0, css=..., message=0) at /home/paulmlocal/c/ParaView-3.14.1-Source/Utilities/VTKClientServer/vtkClientServerInterpreter.cxx:214
#35 0x00007f039935f68d in vtkClientServerInterpreter::ProcessStream (this=0x16ac8d0, css=...) at /home/paulmlocal/c/ParaView-3.14.1-Source/Utilities/VTKClientServer/vtkClientServerInterpreter.cxx:183

2nd situation (similar, but using Python calculator):
- Open csv file, apply default reader settings, data in table looks good
- Add a Table to Points filter, X column=x, etc
- Add a Python calculator filter, name result array 'v', expression 'hstack([vx,vy,vz])'
- Newly added vector data looks good in table view
- Add a Mask points filter to the calculator output, #points=200, random sampling
- Add Streamtracer with custom source, input=calculator, source=maskpoints, apply
- SEGFAULT

Partial stack trace:
#0 vtkPointLocator::FindClosestPoint (this=0x2aa6b20, x=0x7fffbda168b0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkPointLocator.cxx:205
#1 0x00007fd0e433e9bc in vtkPointSet::FindCell (this=0x32f1350, x=0x7fffbda168b0, cell=0x0, gencell=0x40dde40, cellId=-1, tol2=<value optimized out>, subId=@0x7fffbda1665c, pcoords=0x2e57390, weights=0x2e5f020)
    at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkPointSet.cxx:291
#2 0x00007fd0e41b97f4 in vtkAbstractInterpolatedVelocityField::FunctionValues (this=0x2e57330, dataset=0x32f1350, x=0x7fffbda168b0, f=0x7fffbda168d0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkAbstractInterpolatedVelocityField.cxx:160
#3 0x00007fd0e42d7715 in vtkInterpolatedVelocityField::FunctionValues (this=0x2e57330, x=0x7fffbda168b0, f=0x7fffbda168d0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkInterpolatedVelocityField.cxx:79
#4 0x00007fd0e5b44323 in vtkStreamTracer::Integrate (this=0x2e2d3e0, input0=0x1, output=<value optimized out>, seedSource=0x40dbb80, seedIds=<value optimized out>, integrationDirections=<value optimized out>, lastPoint=0x7fffbda169d0, func=0x2e57330, maxCellSize=25000,
    vecName=0x3eca270 "v", inPropagation=@0x7fffbda169f8, inNumSteps=@0x7fffbda169f0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Graphics/vtkStreamTracer.cxx:696
#5 0x00007fd0e5b4606c in vtkStreamTracer::RequestData (this=0x2e2d3e0, inputVector=<value optimized out>, outputVector=<value optimized out>) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Graphics/vtkStreamTracer.cxx:468
#6 0x00007fd0e8b0b2e5 in vtkPStreamTracer::RequestData (this=0x2e2d3e0, request=0x40daaf0, inputVector=0x2e233b0, outputVector=0x41150f0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Parallel/vtkPStreamTracer.cxx:334
#7 0x00007fd0e422cda4 in vtkExecutive::CallAlgorithm (this=0x2e28a20, request=0x40daaf0, direction=<value optimized out>, inInfo=0x2e233b0, outInfo=0x41150f0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkExecutive.cxx:747
#8 0x00007fd0e422071c in vtkDemandDrivenPipeline::ExecuteData (this=0x2e28a20, request=0x40daaf0, inInfo=0x2e233b0, outInfo=0x41150f0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkDemandDrivenPipeline.cxx:507
0000009 0x00007fd0e4201711 in vtkCompositeDataPipeline::ExecuteData (this=0x2e28a20, request=0x40daaf0, inInfoVec=0x2e233b0, outInfoVec=0x41150f0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkCompositeDataPipeline.cxx:391
#10 0x00007fd0e42237cb in vtkDemandDrivenPipeline::ProcessRequest (this=0x2e28a20, request=0x40daaf0, inInfoVec=0x2e233b0, outInfoVec=0x41150f0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkDemandDrivenPipeline.cxx:279
0000011 0x00007fd0e43ad0f9 in vtkStreamingDemandDrivenPipeline::ProcessRequest (this=0x2e28a20, request=0x40daaf0, inInfoVec=0x2e233b0, outInfoVec=0x41150f0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkStreamingDemandDrivenPipeline.cxx:276
#12 0x00007fd0e41fe5d1 in vtkCompositeDataPipeline::ProcessRequest (this=0x2e28a20, request=0x40daaf0, inInfoVec=0x2e233b0, outInfoVec=0x41150f0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkCompositeDataPipeline.cxx:292
#13 0x00007fd0e41ff886 in vtkCompositeDataPipeline::ForwardUpstream (this=0x2aa7360, request=0x40daaf0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkCompositeDataPipeline.cxx:215
#14 0x00007fd0e4223775 in vtkDemandDrivenPipeline::ProcessRequest (this=0x2aa7360, request=0x40daaf0, inInfoVec=0x411f910, outInfoVec=0x40d6a70) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkDemandDrivenPipeline.cxx:265
#15 0x00007fd0e43ad0f9 in vtkStreamingDemandDrivenPipeline::ProcessRequest (this=0x2aa7360, request=0x40daaf0, inInfoVec=0x411f910, outInfoVec=0x40d6a70) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkStreamingDemandDrivenPipeline.cxx:276
#16 0x00007fd0e41fe5d1 in vtkCompositeDataPipeline::ProcessRequest (this=0x2aa7360, request=0x40daaf0, inInfoVec=0x411f910, outInfoVec=0x40d6a70) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkCompositeDataPipeline.cxx:292
#17 0x00007fd0e422350f in vtkDemandDrivenPipeline::UpdateData (this=0x2aa7360, outputPort=<value optimized out>) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkDemandDrivenPipeline.cxx:449
#18 0x00007fd0e43ac13b in vtkStreamingDemandDrivenPipeline::Update (this=0x2aa7360, port=0) at /home/paulmlocal/c/ParaView-3.14.1-Source/VTK/Filtering/vtkStreamingDemandDrivenPipeline.cxx:326
#19 0x00007fd0f49b9d73 in vtkSISourceProxyCommand (arlu=0x2370780, ob=0x2e2ccf0, method=<value optimized out>, msg=..., resultStream=...) at /home/paulmlocal/c/paraview-3.14.1-reldebinfo/ParaViewCore/ServerImplementation/vtkSISourceProxyClientServer.cxx:114
#20 0x00007fd0ea9b569f in vtkClientServerInterpreter::ProcessCommandInvoke (this=0x2370780, css=..., midx=0) at /home/paulmlocal/c/ParaView-3.14.1-Source/Utilities/VTKClientServer/vtkClientServerInterpreter.cxx:379
#21 0x00007fd0ea9b453e in vtkClientServerInterpreter::ProcessOneMessage (this=0x2370780, css=..., message=0) at /home/paulmlocal/c/ParaView-3.14.1-Source/Utilities/VTKClientServer/vtkClientServerInterpreter.cxx:214
#22 0x00007fd0ea9b468d in vtkClientServerInterpreter::ProcessStream (this=0x2370780, css=...) at /home/paulmlocal/c/ParaView-3.14.1-Source/Utilities/VTKClientServer/vtkClientServerInterpreter.cxx:183
#23 0x00007fd0f43d970c in vtkPVSessionCore::ExecuteStreamInternal (this=0x236aca0, stream=..., ignore_errors=<value optimized out>) at /home/paulmlocal/c/ParaView-3.14.1-Source/ParaViewCore/ServerImplementation/vtkPVSessionCore.cxx:636
#24 0x00007fd0f43d7368 in vtkPVSessionCore::ExecuteStream (this=0x236aca0, location=1, stream=..., ignore_errors=<value optimized out>) at /home/paulmlocal/c/ParaView-3.14.1-Source/ParaViewCore/ServerImplementation/vtkPVSessionCore.cxx:606
#25 0x00007fd0f43d49f2 in vtkPVSessionBase::ExecuteStream (this=0x236e920, location=1, stream=..., ignore_errors=false) at /home/paulmlocal/c/ParaView-3.14.1-Source/ParaViewCore/ServerImplementation/vtkPVSessionBase.cxx:173
#26 0x00007fd0f4cfde65 in vtkSMProxy::ExecuteStream (this=<value optimized out>, stream=..., ignore_errors=false, location=1) at /home/paulmlocal/c/ParaView-3.14.1-Source/ParaViewCore/ServerManager/vtkSMProxy.cxx:2091
#27 0x00007fd0f4ce9110 in vtkSMOutputPort::UpdatePipelineInternal (this=0x303b7b0, time=<value optimized out>, doTime=<value optimized out>) at /home/paulmlocal/c/ParaView-3.14.1-Source/ParaViewCore/ServerManager/vtkSMOutputPort.cxx:211
#28 0x00007fd0f4d49d10 in vtkSMSourceProxy::UpdatePipeline (this=0x303c760, time=<value optimized out>) at /home/paulmlocal/c/ParaView-3.14.1-Source/ParaViewCore/ServerManage

TagsNo tags attached.
ProjectTBD
Topic Name
Typecrash
Attached Filestxt file icon wervel.txt [^] (802,624 bytes) 2012-06-19 08:38
csv file icon wervel.csv [^] (752,552 bytes) 2012-06-19 10:37

 Relationships

  Notes
(0028702)
Paul Melis (reporter)
2012-06-19 10:37

Please ignore the attached wervel.txt, I uploaded the wrong file intially
(0028703)
Paul Melis (reporter)
2012-06-19 10:43

According to http://www.paraview.org/Wiki/Display_points_and_normals_from_a_plain_text_%28x_y_z_nx_ny_nz%29_file [^] at least the part about combining 3 scalars to vectors with Calculators should be legal ;-)
(0029427)
Utkarsh Ayachit (administrator)
2012-10-18 17:13

I think what's "illegal" is trying to trace a streamline in a dataset comprising of just points. There are no cells in the dataset. You need to write a special reader that reads your raw data as an vtkImageData or a vtkStructuredGrid or something of that sort and then the stream tracer would work.
(0029464)
Paul Melis (reporter)
2012-10-22 05:38

I admit that there's only a single cell in the TableToPoints and Calculator outputs. But it's the Mask points filter that creates a set with 0 cells. Enabling "Generate vertices" the mask points filter leads to a set with 1 cells. On this the stream tracer also segfaults.
(0029715)
Sebastien Jourdain (manager)
2012-11-14 15:13

What Utkarsh mean by "dataset comprising of just points", is that is not composed of 3D cell but only 1D cell. And the stream tracer can only work in a volume of 3D cells.
(0038230)
Kitware Robot (administrator)
2016-08-12 09:59

Resolving issue as `moved`.

This issue tracker is no longer used. Further discussion of this issue may take place in the current ParaView Issues page linked in the banner at the top of this page.

 Issue History
Date Modified Username Field Change
2012-06-19 08:38 Paul Melis New Issue
2012-06-19 08:38 Paul Melis File Added: wervel.txt
2012-06-19 10:37 Paul Melis File Added: wervel.csv
2012-06-19 10:37 Paul Melis Note Added: 0028702
2012-06-19 10:43 Paul Melis Note Added: 0028703
2012-10-09 08:26 Sebastien Jourdain Assigned To => Leo Liu
2012-10-18 14:05 Utkarsh Ayachit Target Version => 4.0
2012-10-18 17:13 Utkarsh Ayachit Note Added: 0029427
2012-10-18 17:14 Utkarsh Ayachit Target Version 4.0 =>
2012-10-22 05:38 Paul Melis Note Added: 0029464
2012-11-14 15:13 Sebastien Jourdain Note Added: 0029715
2015-01-02 10:43 Utkarsh Ayachit Fixed in Version => 4.3
2016-08-12 09:59 Kitware Robot Note Added: 0038230
2016-08-12 09:59 Kitware Robot Status backlog => closed
2016-08-12 09:59 Kitware Robot Fixed in Version 4.3 =>
2016-08-12 09:59 Kitware Robot Resolution open => moved


Copyright © 2000 - 2018 MantisBT Team