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Date Submitted

Last Update

0010775

ParaView

Bug

public

2010-05-28 14:39

2010-10-15 20:21

Reporter

jhgoebbert

Assigned To

David Partyka

Priority

normal

Severity

crash

Reproducibility

always

Status

closed

Resolution

fixed

Platform

OS Version

Product Version

3.8

Target Version

Fixed in Version

3.8.1

Summary

0010775: XDMF-Reader and hdf5-hyperslabs = segfault

Description

Hi,

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>

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]

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Attached Files

XDMF-hyperslab-bug-example.zip [^] (938 bytes) 2010-05-28 14:39

XdmfDataItem-patch.diff [^] (628 bytes) 2010-06-07 12:14 [Show Content] [Hide Content]

--- XdmfDataItem.cxx	2010-06-07 18:11:50.954700131 +0200
+++ XdmfDataItem-patched.cxx	2010-06-07 18:11:22.709716046 +0200
@@ -145,18 +145,18 @@
 }
 
 XdmfInt32 XdmfDataItem::UpdateInformationFunction(){
-    XdmfConstString Value;
     switch(this->ItemType){
         case XDMF_ITEM_FUNCTION :
+           XdmfConstString Value;
            Value = this->Get("Function");
            this->SetFunction(Value);
+           delete Value;
            break;
         case XDMF_ITEM_HYPERSLAB :
             break;
         case XDMF_ITEM_COORDINATES :
             break;
     }
-    delete Value;
     return(XDMF_SUCCESS);
 }

hyperslab_bugfix.patch [^] (440 bytes) 2010-06-14 09:09 [Show Content] [Hide Content]

diff --git a/libsrc/XdmfDataItem.cxx b/libsrc/XdmfDataItem.cxx
index de09a3a..22b59fe 100644
--- a/libsrc/XdmfDataItem.cxx
+++ b/libsrc/XdmfDataItem.cxx
@@ -145,7 +145,7 @@ XdmfDataItem::Copy(XdmfElement *Source){
 }
 
 XdmfInt32 XdmfDataItem::UpdateInformationFunction(){
-    XdmfConstString Value;
+    XdmfConstString Value = 0;
     switch(this->ItemType){
         case XDMF_ITEM_FUNCTION :
            Value = this->Get("Function");

Relationships

Notes
(0020932) Miguel Fosas (reporter) 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 (reporter) 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 (reporter) 2010-09-30 04:41	This bug is fixed in 3.8.1 Please set "status" to "closed".

(0022393) David Partyka (developer) 2010-09-30 10:47	User reports this is no longer an issue in 3.8.1

(0022500) Alan Scott (manager) 2010-10-15 20:21	Closed as per reporter.

Issue History
Date Modified	Username	Field	Change
2010-05-28 14:39	jhgoebbert	New Issue
2010-05-28 14:39	jhgoebbert	File Added: XDMF-hyperslab-bug-example.zip
2010-06-07 12:14	Miguel Fosas	Note Added: 0020932
2010-06-07 12:14	Miguel Fosas	File Added: XdmfDataItem-patch.diff
2010-06-14 09:09	jhgoebbert	File Added: hyperslab_bugfix.patch
2010-06-14 09:11	jhgoebbert	Note Added: 0021000
2010-06-14 10:05	David Partyka	Status	backlog => tabled
2010-06-14 10:05	David Partyka	Assigned To	=> David Partyka
2010-09-30 04:41	jhgoebbert	Note Added: 0022389
2010-09-30 10:47	David Partyka	Note Added: 0022393
2010-09-30 10:47	David Partyka	Status	tabled => @80@
2010-09-30 10:47	David Partyka	Fixed in Version	=> 3.8.1
2010-09-30 10:47	David Partyka	Resolution	open => fixed
2010-10-15 20:21	Alan Scott	Note Added: 0022500
2010-10-15 20:21	Alan Scott	Status	@80@ => closed