MantisBT - ParaView
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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 
ProjectTBD
Topic Name
Typecrash
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

Steps To Reproduce
Additional Information
TagsNo tags attached.
Relationships
Attached Filestxt wervel.txt (802,624) 2012-06-19 08:38
https://www.vtk.org/Bug/file/9213/wervel.txt
csv wervel.csv (752,552) 2012-06-19 10:37
https://www.vtk.org/Bug/file/9214/wervel.csv
Issue History
Date ModifiedUsernameFieldChange
2012-06-19 08:38Paul MelisNew Issue
2012-06-19 08:38Paul MelisFile Added: wervel.txt
2012-06-19 10:37Paul MelisFile Added: wervel.csv
2012-06-19 10:37Paul MelisNote Added: 0028702
2012-06-19 10:43Paul MelisNote Added: 0028703
2012-10-09 08:26Sebastien JourdainAssigned To => Leo Liu
2012-10-18 14:05Utkarsh AyachitTarget Version => 4.0
2012-10-18 17:13Utkarsh AyachitNote Added: 0029427
2012-10-18 17:14Utkarsh AyachitTarget Version4.0 =>
2012-10-22 05:38Paul MelisNote Added: 0029464
2012-11-14 15:13Sebastien JourdainNote Added: 0029715
2015-01-02 10:43Utkarsh AyachitFixed in Version => 4.3
2016-08-12 09:59Kitware RobotNote Added: 0038230
2016-08-12 09:59Kitware RobotStatusbacklog => closed
2016-08-12 09:59Kitware RobotFixed in Version4.3 =>
2016-08-12 09:59Kitware RobotResolutionopen => moved

Notes
(0028702)
Paul Melis   
2012-06-19 10:37   
Please ignore the attached wervel.txt, I uploaded the wrong file intially
(0028703)
Paul Melis   
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   
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   
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   
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   
2016-08-12 09:59   
Resolving issue as `moved`.

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