0002442: Corrupted memory (double free?) when attempting to load an .stl file

ID	Project	Category	View Status	Date Submitted	Last Update

0002442	Slicer4	Core: Base Code	public	2012-08-28 12:43	2014-03-06 06:09

Reporter	slisse	Assigned To	sankhesh
Priority	normal	Severity	crash	Reproducibility	always
Status	closed	Resolution	fixed
Product Version	Slicer 4.1.0 RC
Target Version	Slicer 4.2.0	Fixed in Version	Slicer 4.2.0

Summary	0002442: Corrupted memory (double free?) when attempting to load an .stl file
Description	Slicer developers, I wanted to notify you of a memory error that I'm getting when running Slicer4. Here's the background info: My machine is Ubuntu 12.04 64-bit Linux ("Linux slisse-G75VW 3.2.0-29-generic 0000046-Ubuntu SMP Fri Jul 27 17:03:23 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux). I'm working from the nightly build which I git-pulled and remade this AM (with the usual make -k workaround). I have slightly modified one of the vtkSTLReader.cxx to catch a SIGABRT which was probably related to the below, but otherwise am pretty close to stock code. Here's how I reproduce my crash: 1) Start Slicer4 (in DDD). 2) Choose "Load Data", select the attached STL file (040 sacrum .stl). Click "OK". 3) The following memory error appears when loading (specifically, usually when at 99% of loading, seems like it might be relate to the fclose(p) on line 171 of vtkSTLReader.cxx). Please let me know if any additional information is needed and I can provide it.
Additional Information	DDD Trace: *glibc detected* /home/slisse/working/external_software/Slicer4_binary/Slicer-build/bin/SlicerApp-real: double free or corruption (!prev): 0x0000000001436bb0 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x7e626)[0x7ffff47ea626] /lib/x86_64-linux-gnu/libc.so.6(fclose+0x155)[0x7ffff47da2a5] /home/slisse/working/external_software/Slicer4_binary/VTK-build/bin/libvtkIO.so.5.10(ZN12vtkSTLReader11RequestDataEP14vtkInformationPP20vtkInformationVectorS3+0x712)[0x7fffeb4d4430] /home/slisse/working/external_software/Slicer4_binary/VTK-build/bin/libvtkFiltering.so.5.10(ZN20vtkPolyDataAlgorithm14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3+0x5e)[0x7ffff355456e] /home/slisse/working/external_software/Slicer4_binary/VTK-build/bin/libvtkFiltering.so.5.10(ZN12vtkExecutive13CallAlgorithmEP14vtkInformationiPP20vtkInformationVectorS3+0x87)[0x7ffff33dad75] /home/slisse/working/external_software/Slicer4_binary/VTK-build/bin/libvtkFiltering.so.5.10(ZN23vtkDemandDrivenPipeline11ExecuteDataEP14vtkInformationPP20vtkInformationVectorS3+0x6f)[0x7ffff33c35b3] /home/slisse/working/external_software/Slicer4_binary/VTK-build/bin/libvtkFiltering.so.5.10(ZN23vtkDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3+0x517)[0x7ffff33c2c71] /home/slisse/working/external_software/Slicer4_binary/VTK-build/bin/libvtkFiltering.so.5.10(ZN32vtkStreamingDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3+0x714)[0x7ffff35daf20] /home/slisse/working/external_software/Slicer4_binary/VTK-build/bin/libvtkFiltering.so.5.10(_ZN23vtkDemandDrivenPipeline10UpdateDataEi+0x2d8)[0x7ffff33c337a] /home/slisse/working/external_software/Slicer4_binary/VTK-build/bin/libvtkFiltering.so.5.10(_ZN32vtkStreamingDemandDrivenPipeline6UpdateEi+0xd6)[0x7ffff35db13e] /home/slisse/working/external_software/Slicer4_binary/VTK-build/bin/libvtkFiltering.so.5.10(_ZN12vtkExecutive6UpdateEv+0x43)[0x7ffff33d9019] /home/slisse/working/external_software/Slicer4_binary/VTK-build/bin/libvtkFiltering.so.5.10(_ZN23vtkDemandDrivenPipeline6UpdateEv+0x18)[0x7ffff33c2d0c] /home/slisse/working/external_software/Slicer4_binary/VTK-build/bin/libvtkFiltering.so.5.10(_ZN32vtkStreamingDemandDrivenPipeline6UpdateEv+0x18)[0x7ffff35db066] /home/slisse/working/external_software/Slicer4_binary/VTK-build/bin/libvtkFiltering.so.5.10(_ZN12vtkAlgorithm6UpdateEv+0x2a)[0x7ffff3340f68] /home/slisse/working/external_software/Slicer4_binary/Slicer-build/bin/libMRMLCore.so(_ZN23vtkMRMLModelStorageNode16ReadDataInternalEP11vtkMRMLNode+0xf02)[0x7ffff3bffbc2] /home/slisse/working/external_software/Slicer4_binary/Slicer-build/bin/libMRMLCore.so(_ZN18vtkMRMLStorageNode8ReadDataEP11vtkMRMLNodeb+0x70e)[0x7ffff3d059b2] /home/slisse/working/external_software/Slicer4_binary/Slicer-build/lib/Slicer-4.1/qt-loadable-modules/libvtkSlicerModelsModuleLogic.so(_ZN20vtkSlicerModelsLogic8AddModelEPKc+0xa6c)[0x7fffbb570620] /home/slisse/working/external_software/Slicer4_binary/Slicer-build/lib/Slicer-4.1/qt-loadable-modules/libqSlicerModelsModule.so(_ZN15qSlicerModelsIO4loadERK4QMapI7QString8QVariantE+0x1a6)[0x7fffa8382738] /home/slisse/working/external_software/Slicer4_binary/Slicer-build/bin/libqSlicerBaseQTCore.so(_ZN20qSlicerCoreIOManager9loadNodesERK7QStringRK4QMapIS0_8QVariantEP13vtkCollection+0x733)[0x7ffff64915e1] /home/slisse/working/external_software/Slicer4_binary/Slicer-build/bin/libqSlicerBaseQTGUI.so(_ZN16qSlicerIOManager9loadNodesERK7QStringRK4QMapIS0_8QVariantEP13vtkCollection+0x152)[0x7ffff7262a7a] /home/slisse/working/external_software/Slicer4_binary/Slicer-build/bin/libqSlicerBaseQTGUI.so(_ZN16qSlicerIOManager9loadNodesERK5QListI4QMapI7QString8QVariantEEP13vtkCollection+0x12b)[0x7ffff7262c3d] /home/slisse/working/external_software/Slicer4_binary/Slicer-build/bin/libqSlicerBaseQTGUI.so(_ZN17qSlicerDataDialog4execERK4QMapI7QString8QVariantE+0x316)[0x7ffff7255696] /home/slisse/working/external_software/Slicer4_binary/Slicer-build/bin/libqSlicerBaseQTGUI.so(_ZN16qSlicerIOManager10openDialogE7QStringN17qSlicerFileDialog8IOActionE4QMapIS0_8QVariantE+0x268)[0x7ffff726204e] /home/slisse/working/external_software/Slicer4_binary/Slicer-build/bin/libqSlicerApp.so(_ZN16qSlicerIOManager17openAddDataDialogEv+0x57)[0x7ffff7b66555] /home/slisse/working/external_software/Slicer4_binary/Slicer-build/lib/Slicer-4.1/qt-loadable-modules/libqSlicerWelcomeModule.so(_ZN26qSlicerWelcomeModuleWidget16loadNonDicomDataEv+0x46)[0x7fff61e7fa24] /home/slisse/working/external_software/Slicer4_binary/Slicer-build/lib/Slicer-4.1/qt-loadable-modules/libqSlicerWelcomeModule.so(+0x1278f)[0x7fff61e8478f] /usr/lib/x86_64-linux-gnu/libQtCore.so.4(_ZN11QMetaObject8activateEP7QObjectPKS_iPPv+0x2b1)[0x7ffff51ce281] /usr/lib/x86_64-linux-gnu/libQtGui.so.4(_ZN15QAbstractButton7clickedEb+0x32)[0x7ffff5d6cc72] /usr/lib/x86_64-linux-gnu/libQtGui.so.4(+0x599a4e)[0x7ffff5aaaa4e] /usr/lib/x86_64-linux-gnu/libQtGui.so.4(+0x59ad8b)[0x7ffff5aabd8b] /usr/lib/x86_64-linu
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2012-08-28 12:43	OPII044_Sacrum_Model_Ax.stl (2,259,458 bytes)

2012-08-28 12:45	cxx_diffs.txt (1,210 bytes) cxx_diffs.txt (1,210 bytes)

slisse 2012-08-28 12:46 reporter ~0005840	Just in case, I've uploaded the diffs from my vtkSTLReader.cxx file (it's some simple signal debugging stuff and not worth merging into the tree, IMO).

pieper 2012-08-29 07:32 administrator ~0005852	Hi - Thanks for providing the data and info. I wasn't able to replicate this issue - I tested on a mac in xcode with extra memory debugging turned on but the model loaded okay. Can you try with a slicer nightly and/or release build to see if it also crashes on your machine with this data? -Steve

slisse 2012-08-29 08:23 reporter ~0005854	I'll download a premade build and see whether it reproduces the problem. Thanks, Sean

slisse 2012-08-29 08:39 reporter ~0005855	Confirmed, it also crashes on premade "4.1.0-2012-08-28-linux-amd64", with the above steps.

pieper 2012-08-29 10:13 administrator ~0005857	This is an odd one - I don't get any errors on windows or mac, but do see a consistent crash on linux (tested Ubuntu 11.04). The crash occurs in vtkSTLReader and I can replicate this in pure vtk by instantiating the reader and trying to read the attached file using the vtkpython interpreter in slicer superbuild. @Jcfr - can you try on your machine ? The file seems well formed.

sankhesh 2012-09-12 07:19 developer ~0006042	This issue is fixed in the development version of VTK. http://paraview.org/Bug/view.php?id=13101 Confirmed this by building with the current VTK development HEAD and reading in the attached file.

jcfr 2012-09-13 11:20 administrator ~0006062	As discussed this morning, would be great if you could cherry-pick and integrate commit(s) into Slicer fork. See also here for commit message guideline regarding the corresponding commit into Slicer itself. See http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Style_Guide#Importing_changes_from_external_project.2Frepository Thanks Jc

sankhesh 2012-09-14 04:27 developer ~0006068	Topic pushed to https://github.com/sankhesh/Slicer/tree/2442-vtkSTLReader-corrupted-memory

jcfr 2012-09-14 08:37 administrator ~0006070 Last edited: 2012-09-14 08:38	Looks good to me. Thanks The change in VTK is fairly minimal, I suggest you go ahead and integrate into Slicer. Do you anticipate any side effect ?

sankhesh 2012-09-14 09:46 developer ~0006074	Its in. I don't think this would break anything.

jcfr 2012-09-14 09:57 administrator ~0006075	Thanks Sankhesh. Sean> Make sure to close issue if you confirm that the issue is fixed.

slisse 2012-09-17 09:25 reporter ~0006111	Success! Thank you, developers!

Date Modified	Username	Field	Change
2012-08-28 12:43	slisse	New Issue
2012-08-28 12:43	slisse	Status	new => assigned
2012-08-28 12:43	slisse	Assigned To	=> pieper
2012-08-28 12:43	slisse	File Added: OPII044_Sacrum_Model_Ax.stl
2012-08-28 12:45	slisse	File Added: cxx_diffs.txt
2012-08-28 12:46	slisse	Note Added: 0005840
2012-08-29 07:32	pieper	Note Added: 0005852
2012-08-29 08:23	slisse	Note Added: 0005854
2012-08-29 08:39	slisse	Note Added: 0005855
2012-08-29 10:10	pieper	Assigned To	pieper => jcfr
2012-08-29 10:13	pieper	Note Added: 0005857
2012-08-29 13:36	jcfr	Assigned To	jcfr => sankhesh
2012-08-29 13:36	jcfr	Target Version	=> Slicer 4.3.0
2012-09-12 07:19	sankhesh	Note Added: 0006042
2012-09-13 11:20	jcfr	Note Added: 0006062
2012-09-14 04:27	sankhesh	Note Added: 0006068
2012-09-14 08:37	jcfr	Note Added: 0006070
2012-09-14 08:38	jcfr	Note Edited: 0006070
2012-09-14 09:46	sankhesh	Note Added: 0006074
2012-09-14 09:46	sankhesh	Status	assigned => resolved
2012-09-14 09:46	sankhesh	Resolution	open => fixed
2012-09-14 09:55	jcfr	Target Version	Slicer 4.3.0 => Slicer 4.2.0 - coming release
2012-09-14 09:57	jcfr	Note Added: 0006075
2012-09-17 09:25	slisse	Note Added: 0006111
2012-09-17 09:25	slisse	Status	resolved => closed
2014-03-06 06:09	jcfr	Fixed in Version	=> Slicer 4.2.0

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