View Issue Details [ Jump to Notes ] [ Print ]
IDProjectCategoryView StatusDate SubmittedLast Update
0012647VTK(No Category)public2011-10-12 14:572014-10-02 15:51
ReporterPaul Melis 
Assigned ToUtkarsh Ayachit 
PrioritynormalSeverityminorReproducibilityhave not tried
StatusclosedResolutionfixed 
PlatformOSOS Version
Product Version5.8.0 
Target VersionFixed in Version6.2.0 
Summary0012647: Segfault when reading parallel image data
DescriptionRan across this in PV 3.8.1 and 3.10.1, turned out to be a bug in VTK.

I originally converted a set of DICOM slices into a .pvti + 16*.vti dataset, using GDCM's VTK DICOM reader and the regular VTK parallel .vti writer class.

The resulting dataset can't be read back in as it causes a segfault. See the attached two scripts. The gen.py script generates a dataset (similar to the one originally causing the problem). The read.py script reads it back in, but segfaults:

paulm@v41-8:~/projects/acta_scans/CT-dataset/dicom_3/dicom_3/pv$ ./read.py
Segmentation fault (core dumped)
paulm@v41-8:~/projects/acta_scans/CT-dataset/dicom_3/dicom_3/pv$ gdb `which python` core
(gdb) bt
#0 memcpy () at ../sysdeps/x86_64/memcpy.S:162
#1 0x00007f4292a3767b in vtkXMLPStructuredDataReader::CopySubExtent(int*, int*, long long*, int*, int*, long long*, int*, int*, vtkDataArray*, vtkDataArray*) ()
   from /software/vtk/5.8.0/lib/vtk-5.8/libvtkIO.so.5.8
#2 0x00007f4292a37900 in vtkXMLPStructuredDataReader::CopyArrayForPoints(vtkDataArray*, vtkDataArray*) () from /software/vtk/5.8.0/lib/vtk-5.8/libvtkIO.so.5.8
#3 0x00007f4292a311d7 in vtkXMLPDataReader::ReadPieceData() () from /software/vtk/5.8.0/lib/vtk-5.8/libvtkIO.so.5.8
#4 0x00007f4292a3082b in vtkXMLPDataReader::ReadPieceData(int) () from /software/vtk/5.8.0/lib/vtk-5.8/libvtkIO.so.5.8
#5 0x00007f4292a38c4b in vtkXMLPStructuredDataReader::ReadXMLData() () from /software/vtk/5.8.0/lib/vtk-5.8/libvtkIO.so.5.8
#6 0x00007f4292a44a4d in vtkXMLReader::RequestData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /software/vtk/5.8.0/lib/vtk-5.8/libvtkIO.so.5.8
#7 0x00007f4292a4372d in vtkXMLReader::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /software/vtk/5.8.0/lib/vtk-5.8/libvtkIO.so.5.8
#8 0x00007f42934fe224 in vtkExecutive::CallAlgorithm(vtkInformation*, int, vtkInformationVector**, vtkInformationVector*) () from /software/vtk/5.8.0/lib/vtk-5.8/libvtkFiltering.so.5.8
0000009 0x00007f42934f0f6c in vtkDemandDrivenPipeline::ExecuteData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /software/vtk/5.8.0/lib/vtk-5.8/libvtkFiltering.so.5.8
#10 0x00007f42934f401b in vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /software/vtk/5.8.0/lib/vtk-5.8/libvtkFiltering.so.5.8
0000011 0x00007f429367ac79 in vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /software/vtk/5.8.0/lib/vtk-5.8/libvtkFiltering.so.5.8
#12 0x00007f42934f3d5f in vtkDemandDrivenPipeline::UpdateData(int) () from /software/vtk/5.8.0/lib/vtk-5.8/libvtkFiltering.so.5.8
#13 0x00007f4293679e5b in vtkStreamingDemandDrivenPipeline::Update(int) () from /software/vtk/5.8.0/lib/vtk-5.8/libvtkFiltering.so.5.8
#14 0x00007f4293a21509 in PyvtkAlgorithm_Update(_object*, _object*) () from /software/vtk/5.8.0/lib/vtk-5.8/libvtkFilteringPythonD.so.5.8
#15 0x00000000004a7ba5 in PyEval_EvalFrameEx ()
#16 0x00000000004a95c1 in PyEval_EvalCodeEx ()
#17 0x00000000004a9692 in PyEval_EvalCode ()
#18 0x00000000004c98be in PyRun_FileExFlags ()
#19 0x00000000004c9ad4 in PyRun_SimpleFileExFlags ()
#20 0x000000000041a6bd in Py_Main ()
#21 0x00007f4295950c4d in __libc_start_main (main=<value optimized out>, argc=<value optimized out>, ubp_av=<value optimized out>, init=<value optimized out>, fini=<value optimized out>,
    rtld_fini=<value optimized out>, stack_end=0x7fffeb8c8b88) at libc-start.c:228
#22 0x00000000004198d9 in _start ()

Tagshackaton
ProjectTBD
Typecrash
Attached Files? file icon gen.py [^] (539 bytes) 2011-10-12 14:57
? file icon read.py [^] (108 bytes) 2011-10-12 14:57
? file icon gen6.py [^] (540 bytes) 2013-07-29 04:57

 Relationships
related to 0011607closedUtkarsh Ayachit Segfault with vtkXMLPImageDataReader 

  Notes
(0027569)
Paul Melis (reporter)
2011-10-12 15:04

 Bloody hell, guys. It turns out I reported the exact same issue almost a year ago in 0011607, which has since expired :-/
(0031155)
Dave DeMarle (administrator)
2013-07-22 12:45

 Please feel free to reopen if you find this is not working in 6.0.0
(0031351)
Paul Melis (reporter)
2013-07-29 04:40

 Still segfaults with 6.0.0

dr.Update()paulm@v40-5:/scratch$ py
Python 2.7.3 (default, Jan 2 2013, 13:56:14)
[GCC 4.7.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import vtk
v>>> v=vtk.vtkVersion()
>>> v.GetVTKVersion()
'6.0.0'
>>> dr = vtk.vtkXMLPImageDataReader()
>>> dr.SetFileName('dummy.pvti')
>>> dr.Update()
Segmentation fault

(gdb) bt
#0 0x00007f7308d7ec54 in ?? () from /lib/x86_64-linux-gnu/libc.so.6
#1 0x00007f72ed30d133 in vtkXMLPStructuredDataReader::CopySubExtent(int*, int*, long long*, int*, int*, long long*, int*, int*, vtkDataArray*, vtkDataArray*) () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkIOXML-6.0.so.1
#2 0x00007f72ed30d394 in vtkXMLPStructuredDataReader::CopyArrayForPoints(vtkDataArray*, vtkDataArray*) () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkIOXML-6.0.so.1
#3 0x00007f72ed2ff8f7 in vtkXMLPDataReader::ReadPieceData() () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkIOXML-6.0.so.1
#4 0x00007f72ed2ffd1b in vtkXMLPDataReader::ReadPieceData(int) () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkIOXML-6.0.so.1
#5 0x00007f72ed30df02 in vtkXMLPStructuredDataReader::ReadXMLData() () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkIOXML-6.0.so.1
#6 0x00007f72ed310e45 in vtkXMLReader::RequestData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkIOXML-6.0.so.1
#7 0x00007f72ed3117d5 in vtkXMLReader::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkIOXML-6.0.so.1
#8 0x00007f7303eda2a4 in vtkExecutive::CallAlgorithm(vtkInformation*, int, vtkInformationVector**, vtkInformationVector*) () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkCommonExecutionModel-6.0.so.1
0000009 0x00007f7303ed16fc in vtkDemandDrivenPipeline::ExecuteData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkCommonExecutionModel-6.0.so.1
#10 0x00007f7303ecddf1 in vtkCompositeDataPipeline::ExecuteData(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkCommonExecutionModel-6.0.so.1
0000011 0x00007f7303ed4449 in vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkCommonExecutionModel-6.0.so.1
#12 0x00007f7303eef5f1 in vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, vtkInformationVector**, vtkInformationVector*) () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkCommonExecutionModel-6.0.so.1
#13 0x00007f7303ed2dc9 in vtkDemandDrivenPipeline::UpdateData(int) () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkCommonExecutionModel-6.0.so.1
#14 0x00007f7303ef0381 in vtkStreamingDemandDrivenPipeline::Update(int) () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkCommonExecutionModel-6.0.so.1
#15 0x00007f730413e851 in PyvtkAlgorithm_Update(_object*, _object*) () from /home/paulm/c/vtk-6.0.0-release/lib/libvtkCommonExecutionModelPython27D-6.0.so.1
#16 0x00000000004ac5ce in call_function (oparg=<optimized out>, pp_stack=0x7fff90072000) at ../Python/ceval.c:4021
#17 PyEval_EvalFrameEx (f=f@entry=Frame 0x104be20, for file /home/paulm/t/read.py, line 6, in <module> (), throwflag=throwflag@entry=0) at ../Python/ceval.c:2666
#18 0x00000000004b3fd8 in PyEval_EvalCodeEx (co=co@entry=0x7f7309bdfc30, globals=globals@entry=
    {'__builtins__': <module at remote 0x7f7309c5fad0>, '__file__': '/home/paulm/t/read.py', '__doc__': None, '__name__': '__main__', '__package__': None, 'dr': <vtkobject at remote 0x7f7309b739b0>, 'vtk': <module at remote 0x7f7309b97788>},
    locals=locals@entry=
    {'__builtins__': <module at remote 0x7f7309c5fad0>, '__file__': '/home/paulm/t/read.py', '__doc__': None, '__name__': '__main__', '__package__': None, 'dr': <vtkobject at remote 0x7f7309b739b0>, 'vtk': <module at remote 0x7f7309b97788>},
    args=args@entry=0x0, argcount=argcount@entry=0, kws=kws@entry=0x0, kwcount=kwcount@entry=0, defs=defs@entry=0x0, defcount=defcount@entry=0, closure=closure@entry=0x0) at ../Python/ceval.c:3253
#19 0x0000000000536723 in PyEval_EvalCode (locals=
    {'__builtins__': <module at remote 0x7f7309c5fad0>, '__file__': '/home/paulm/t/read.py', '__doc__': None, '__name__': '__main__', '__package__': None, 'dr': <vtkobject at remote 0x7f7309b739b0>, 'vtk': <module at remote 0x7f7309b97788>}, globals=
    {'__builtins__': <module at remote 0x7f7309c5fad0>, '__file__': '/home/paulm/t/read.py', '__doc__': None, '__name__': '__main__', '__package__': None, 'dr': <vtkobject at remote 0x7f7309b739b0>, 'vtk': <module at remote 0x7f7309b97788>}, co=
    0x7f7309bdfc30) at ../Python/ceval.c:667
#20 run_mod (mod=<optimized out>, filename=<optimized out>, globals=
    {'__builtins__': <module at remote 0x7f7309c5fad0>, '__file__': '/home/paulm/t/read.py', '__doc__': None, '__name__': '__main__', '__package__': None, 'dr': <vtkobject at remote 0x7f7309b739b0>, 'vtk': <module at remote 0x7f7309b97788>}, locals=
    {'__builtins__': <module at remote 0x7f7309c5fad0>, '__file__': '/home/paulm/t/read.py', '__doc__': None, '__name__': '__main__', '__package__': None, 'dr': <vtkobject at remote 0x7f7309b739b0>, 'vtk': <module at remote 0x7f7309b97788>},
    flags=<optimized out>, arena=<optimized out>) at ../Python/pythonrun.c:1365
#21 0x0000000000446bf2 in PyRun_FileExFlags (fp=fp@entry=0x104b140, filename=filename@entry=0x7fff90073f79 "/home/paulm/t/read.py", start=start@entry=257, globals=globals@entry=
    {'__builtins__': <module at remote 0x7f7309c5fad0>, '__file__': '/home/paulm/t/read.py', '__doc__': None, '__name__': '__main__', '__package__': None, 'dr': <vtkobject at remote 0x7f7309b739b0>, 'vtk': <module at remote 0x7f7309b97788>},
    locals=locals@entry=
    {'__builtins__': <module at remote 0x7f7309c5fad0>, '__file__': '/home/paulm/t/read.py', '__doc__': None, '__name__': '__main__', '__package__': None, 'dr': <vtkobject at remote 0x7f7309b739b0>, 'vtk': <module at remote 0x7f7309b97788>},
    closeit=closeit@entry=1, flags=flags@entry=0x7fff90072260) at ../Python/pythonrun.c:1351
#22 0x00000000004470ec in PyRun_SimpleFileExFlags (fp=fp@entry=0x104b140, filename=<optimized out>, filename@entry=0x7fff90073f79 "/home/paulm/t/read.py", closeit=closeit@entry=1, flags=flags@entry=0x7fff90072260) at ../Python/pythonrun.c:943
#23 0x00000000004471ac in PyRun_AnyFileExFlags (fp=fp@entry=0x104b140, filename=filename@entry=0x7fff90073f79 "/home/paulm/t/read.py", closeit=closeit@entry=1, flags=flags@entry=0x7fff90072260) at ../Python/pythonrun.c:747
#24 0x0000000000447cdc in Py_Main (argc=<optimized out>, argv=0x7fff90072418) at ../Modules/main.c:639
#25 0x00007f7308c75ead in __libc_start_main () from /lib/x86_64-linux-gnu/libc.so.6
#26 0x00000000004c7f39 in _start ()
(0031352)
Paul Melis (reporter)
2013-07-29 04:56

 Does this reopen?
(0031353)
Paul Melis (reporter)
2013-07-29 04:57

 Attached updated gen.py script for 6.0.0
(0033522)
Utkarsh Ayachit (administrator)
2014-10-02 15:10

 Topic for review:

http://review.source.kitware.com/#/t/4768 [^]
(0033536)
Utkarsh Ayachit (administrator)
2014-10-02 15:51

 merged in git/master

 Issue History
Date Modified Username Field Change
2011-10-12 14:57 Paul Melis New Issue
2011-10-12 14:57 Paul Melis File Added: gen.py
2011-10-12 14:57 Paul Melis File Added: read.py
2011-10-12 15:04 Paul Melis Note Added: 0027569
2013-07-22 12:45 Dave DeMarle Note Added: 0031155
2013-07-22 12:45 Dave DeMarle Status backlog => expired
2013-07-22 12:45 Dave DeMarle Resolution open => fixed
2013-07-22 12:45 Dave DeMarle Assigned To => Dave DeMarle
2013-07-29 04:40 Paul Melis Note Added: 0031351
2013-07-29 04:56 Paul Melis Note Added: 0031352
2013-07-29 04:56 Paul Melis Status expired => backlog
2013-07-29 04:56 Paul Melis Resolution fixed => reopened
2013-07-29 04:57 Paul Melis File Added: gen6.py
2013-07-29 04:57 Paul Melis Note Added: 0031353
2014-09-30 10:50 Dave DeMarle Assigned To Dave DeMarle =>
2014-10-02 11:21 Berk Geveci Assigned To => Berk Geveci
2014-10-02 11:22 Berk Geveci Tag Attached: hackaton
2014-10-02 15:07 Utkarsh Ayachit Relationship added related to 0011607
2014-10-02 15:10 Utkarsh Ayachit Note Added: 0033522
2014-10-02 15:10 Utkarsh Ayachit Assigned To Berk Geveci => Utkarsh Ayachit
2014-10-02 15:10 Utkarsh Ayachit Status backlog => gerrit review
2014-10-02 15:51 Utkarsh Ayachit Note Added: 0033536
2014-10-02 15:51 Utkarsh Ayachit Status gerrit review => closed
2014-10-02 15:51 Utkarsh Ayachit Resolution reopened => fixed
2014-10-02 15:51 Utkarsh Ayachit Fixed in Version => 6.2.0

Copyright © 2000 - 2018 MantisBT Team