MantisBT - ParaView
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IDProjectCategoryView StatusDate SubmittedLast Update
0010775ParaViewBugpublic2010-05-28 14:392010-10-15 20:21
Reporterjhgoebbert 
Assigned ToDavid Partyka 
PrioritynormalSeveritycrashReproducibilityalways
StatusclosedResolutionfixed 
PlatformOSOS Version
Product Version3.8 
Target VersionFixed in Version3.8.1 
Project
Topic Name
Type
Summary0010775: XDMF-Reader and hdf5-hyperslabs = segfault
DescriptionHi,

since 3.8.0 (tested with Linux-x86 binary version) it is not possible to use hyperslabs in XDMF-files.
The following attributes result in a segfault in libXDMF of paraview.

An example is attached

<Attribute
   Active="1"
   Type="Scalar"
   Center="Node"
   Name="u_with_hyperslab">
   <DataItem ItemType="HyperSlab" Dimensions="8 8 8">
             <DataItem Dimensions="3 3" Format="XML">
                       0 0 0
                       1 1 1
                       8 8 8
             </DataItem>
             <DataItem ItemType="Uniform"
                       Format="HDF"
                       NumberType="Float"
                       Precision="8"
                       Dimensions="8 8 8">
                            test.h5:/u
             </DataItem>
   </DataItem>
</Attribute>
Steps To Reproduce
Additional Information backtrace:
*** glibc detected *** /opt/nfsimport/paraview/paraview-3.8.0/lib/paraview-3.8/paraview-real: free(): invalid pointer: 0x00007fff3219cf00 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3dd82722ef]
/lib64/libc.so.6(cfree+0x4b)[0x3dd827273b]
/opt/nfsimport/paraview/paraview-3.8.0/lib/paraview-3.8/libXdmf.so(_ZN12XdmfDataItem25UpdateInformationFunctionEv+0x31)[0x2ae170ee6871]
/opt/nfsimport/paraview/paraview-3.8.0/lib/paraview-3.8/libvtkXdmf.so(_ZN16vtkXdmfHeavyData13ReadAttributeEP13XdmfAttributeiPi+0xa1)[0x2ae16e7880a1]
/opt/nfsimport/paraview/paraview-3.8.0/lib/paraview-3.8/libvtkXdmf.so(_ZN16vtkXdmfHeavyData14ReadAttributesEP10vtkDataSetP8XdmfGridPi+0xc2)[0x2ae16e78a892]
/opt/nfsimport/paraview/paraview-3.8.0/lib/paraview-3.8/libvtkXdmf.so(_ZN16vtkXdmfHeavyData16RequestImageDataEP8XdmfGridb+0x2ad)[0x2ae16e78b17d]
/opt/nfsimport/paraview/paraview-3.8.0/lib/paraview-3.8/libvtkXdmf.so(_ZN16vtkXdmfHeavyData15ReadUniformDataEP8XdmfGrid+0x1b4)[0x2ae16e78c044]
/opt/nfsimport/paraview/paraview-3.8.0/lib/paraview-3.8/libvtkXdmf.so(_ZN16vtkXdmfHeavyData8ReadDataEv+0x27c)[0x2ae16e78cb5c]
/opt/nfsimport/paraview/paraview-3.8.0/lib/paraview-3.8/libvtkXdmf.so(_ZN13vtkXdmfReader11RequestDataEP14vtkInformationPP20vtkInformationVectorS3_+0x220)[0x2ae16e78e670]
TagsNo tags attached.
Relationships
Attached Fileszip XDMF-hyperslab-bug-example.zip (938) 2010-05-28 14:39
https://www.vtk.org/Bug/file/8152/XDMF-hyperslab-bug-example.zip
diff XdmfDataItem-patch.diff (628) 2010-06-07 12:14
https://www.vtk.org/Bug/file/8169/XdmfDataItem-patch.diff
patch hyperslab_bugfix.patch (440) 2010-06-14 09:09
https://www.vtk.org/Bug/file/8182/hyperslab_bugfix.patch
Issue History
Date ModifiedUsernameFieldChange
2010-05-28 14:39jhgoebbertNew Issue
2010-05-28 14:39jhgoebbertFile Added: XDMF-hyperslab-bug-example.zip
2010-06-07 12:14Miguel FosasNote Added: 0020932
2010-06-07 12:14Miguel FosasFile Added: XdmfDataItem-patch.diff
2010-06-14 09:09jhgoebbertFile Added: hyperslab_bugfix.patch
2010-06-14 09:11jhgoebbertNote Added: 0021000
2010-06-14 10:05David PartykaStatusbacklog => tabled
2010-06-14 10:05David PartykaAssigned To => David Partyka
2010-09-30 04:41jhgoebbertNote Added: 0022389
2010-09-30 10:47David PartykaNote Added: 0022393
2010-09-30 10:47David PartykaStatustabled => @80@
2010-09-30 10:47David PartykaFixed in Version => 3.8.1
2010-09-30 10:47David PartykaResolutionopen => fixed
2010-10-15 20:21Alan ScottNote Added: 0022500
2010-10-15 20:21Alan ScottStatus@80@ => closed

Notes
(0020932)
Miguel Fosas   
2010-06-07 12:14   
The patch attached should fix the problem. Although I don't know the details of the Xdmf library, these changes solved the problem for me.
(0021000)
jhgoebbert   
2010-06-14 09:11   
Kenji Takizawas patch fixes the problem, too. The patch is added as "hyperslab_bugfix.patch".
This patch should already be applied to trunk (as far as I know).
(0022389)
jhgoebbert   
2010-09-30 04:41   
This bug is fixed in 3.8.1
Please set "status" to "closed".
(0022393)
David Partyka   
2010-09-30 10:47   
User reports this is no longer an issue in 3.8.1
(0022500)
Alan Scott   
2010-10-15 20:21   
Closed as per reporter.