[Insight-users] Crash not caught by exception upon reading
Robert.Atwood at diamond.ac.uk
Robert.Atwood at diamond.ac.uk
Thu Aug 9 05:05:59 EDT 2012
Hi,
I get a memory corruption upon reading a file , though the same program has worked on a different file as input. The reader->Update() is called from inside a try..catch but this mechanism is not activated.
I am not sure what is the easiest way to find out what the problem is!
I tried building ITK with git pull yesterday
Thanks for any advice!
Robert
Code section :
177 reader->SetFileName (ctrl->infile);
178 reader->ReleaseDataFlagOn();
179 if (ctrl->verbose >= 1 ) std::cout << reader << std::endl;
180 if (ctrl->verbose >=2){
181 timestamp("starting the reader... ");
182 }
183
184 try {
185 reader->Update ();
186 } catch (itk::ExceptionObject & exp) {
187
Output:
ImageFileReader (0x66f54d0)
RTTI typeinfo: itk::ImageFileReader<itk::Image<float, 3u>, itk::DefaultConvertPixelTraits<float> >
Reference Count: 2
Modified Time: 46
Debug: Off
Observers:
none
Inputs:
FileName: (0x66fa120)
No Required Input Names
Outputs:
Primary: (0x66f9920)
NumberOfIndexedInputs: 0
NumberOfRequiredInputs: 0
NumberOfIndexedOutputs: 1
NumberOfRequiredOutputs: 1
Number Of Threads: 16
ReleaseDataFlag: On
ReleaseDataBeforeUpdateFlag: Off
AbortGenerateData: Off
Progress: 0
Multithreader:
RTTI typeinfo: itk::MultiThreader
Reference Count: 1
Modified Time: 30
Debug: Off
Observers:
none
Thread Count: 16
Global Maximum Number Of Threads: 128
Global Default Number Of Threads: 16
ImageIO: (null)
UserSpecifiedImageIO flag: 0
m_UseStreaming: 1
0.002900 1344502793.982344 0.002857 starting the reader...
*** glibc detected *** /home/kny48981/progs/itk_progs/build_master/itk_mreduce_rca: malloc(): memory corruption: 0x00000000066fc480 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3176e71a1e]
/lib64/libc.so.6(__libc_malloc+0x6e)[0x3176e7374e]
/lib64/libc.so.6[0x3176e6017a]
/usr/lib64/libstdc++.so.6(_ZNSt12__basic_fileIcE4openEPKcSt13_Ios_Openmodei+0x54)[0x317bebbc94]
/usr/lib64/libstdc++.so.6(_ZNSt13basic_filebufIcSt11char_traitsIcEE4openEPKcSt13_Ios_Openmode+0x83)[0x317be6a583]
/dls_sw/apps/itk/itk-master/lib/libITKMetaIO-4.3.so.1(_ZN9MetaImage10ReadStreamEiPSt14basic_ifstreamIcSt11char_traitsIcEEbPv+0x818)[0x2b9a973c76a8]
/dls_sw/apps/itk/itk-master/lib/libITKMetaIO-4.3.so.1(_ZN9MetaImage4ReadEPKcbPv+0x16b)[0x2b9a973c2f2b]
/dls_sw/apps/itk/itk-master/lib/libITKIOMeta-4.3.so.1(_ZN3itk11MetaImageIO4ReadEPv+0x1e2)[0x2b9a9b2edff2]
/home/kny48981/progs/itk_progs/build_master/itk_mreduce_rca(_ZN3itk15ImageFileReaderINS_5ImageIfLj3EEENS_25DefaultConvertPixelTraitsIfEEE12GenerateDataEv+0xdce)[0x4a35a8]
/dls_sw/apps/itk/itk-master/lib/libITKCommon-4.3.so.1(_ZN3itk13ProcessObject16UpdateOutputDataEPNS_10DataObjectE+0xd3)[0x2b9a966acd03]
/home/kny48981/progs/itk_progs/build_master/itk_mreduce_rca(_ZN3itk9ImageBaseILj3EE16UpdateOutputDataEv+0x6d)[0x485705]
/home/kny48981/progs/itk_progs/build_master/itk_mreduce_rca(main+0x35a)[0x44c9fc]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x3176e1d994]
/home/kny48981/progs/itk_progs/build_master/itk_mreduce_rca(_ZN3itk34PNGImageIOFactoryRegister__PrivateEv+0x61)[0x44bdb9]
======= Memory map: ========
00400000-004cf000 r-xp 00000000 00:13 53510401 /home/kny48981/progs/itk_progs/build_master/itk_mreduce_rca
006ce000-006d8000 rw-p 000ce000 00:13 53510401 /home/kny48981/progs/itk_progs/build_master/itk_mreduce_rca
062a1000-06852000 rw-p 062a1000 00:00 0 [heap]
3176a00000-3176a1c000 r-xp 00000000 fd:00 3306410 /lib64/ld-2.5.so
3176c1c000-3176c1d000 r--p 0001c000 fd:00 3306410 /lib64/ld-2.5.so
3176c1d000-3176c1e000 rw-p 0001d000 fd:00 3306410 /lib64/ld-2.5.so
3176e00000-3176f4d000 r-xp 00000000 fd:00 3306582 /lib64/libc-2.5.so
3176f4d000-317714d000 ---p 0014d000 fd:00 3306582 /lib64/libc-2.5.so
317714d000-3177151000 r--p 0014d000 fd:00 3306582 /lib64/libc-2.5.so
3177151000-3177152000 rw-p 00151000 fd:00 3306582 /lib64/libc-2.5.so
3177152000-3177157000 rw-p 3177152000 00:00 0
3177200000-3177202000 r-xp 00000000 fd:00 3306601 /lib64/libdl-2.5.so
3177202000-3177402000 ---p 00002000 fd:00 3306601 /lib64/libdl-2.5.so
3177402000-3177403000 r--p 00002000 fd:00 3306601 /lib64/libdl-2.5.so
3177403000-3177404000 rw-p 00003000 fd:00 3306601 /lib64/libdl-2.5.so
3177600000-3177682000 r-xp 00000000 fd:00 3306600 /lib64/libm-2.5.so
3177682000-3177881000 ---p 00082000 fd:00 3306600 /lib64/libm-2.5.so
3177881000-3177882000 r--p 00081000 fd:00 3306600 /lib64/libm-2.5.so
3177882000-3177883000 rw-p 00082000 fd:00 3306600 /lib64/libm-2.5.so
3177e00000-3177e16000 r-xp 00000000 fd:00 3306628 /lib64/libpthread-2.5.so
3177e16000-3178015000 ---p 00016000 fd:00 3306628 /lib64/libpthread-2.5.so
3178015000-3178016000 r--p 00015000 fd:00 3306628 /lib64/libpthread-2.5.so
3178016000-3178017000 rw-p 00016000 fd:00 3306628 /lib64/libpthread-2.5.so
3178017000-317801b000 rw-p 3178017000 00:00 0
317b600000-317b60d000 r-xp 00000000 fd:00 3306608 /lib64/libgcc_s-4.1.2-20080825.so.1
317b60d000-317b80d000 ---p 0000d000 fd:00 3306608 /lib64/libgcc_s-4.1.2-20080825.so.1
317b80d000-317b80e000 rw-p 0000d000 fd:00 3306608 /lib64/libgcc_s-4.1.2-20080825.so.1
317be00000-317bee6000 r-xp 00000000 fd:00 11229786 /usr/lib64/libstdc++.so.6.0.8
317bee6000-317c0e5000 ---p 000e6000 fd:00 11229786 /usr/lib64/libstdc++.so.6.0.8
317c0e5000-317c0eb000 r--p 000e5000 fd:00 11229786 /usr/lib64/libstdc++.so.6.0.8
317c0eb000-317c0ee000 rw-p 000eb000 fd:00 11229786 /usr/lib64/libstdc++.so.6.0.8
317c0ee000-317c100000 rw-p 317c0ee000 00:00 0
2b9a95907000-2b9a95909000 rw-p 2b9a95907000 00:00 0
2b9a95909000-2b9a9594a000 r-xp 00000000 00:1f 101777739 /dls_sw/apps/itk/itk-master/lib/libitksys-4.3.so.1
2b9a9594a000-2b9a95b49000 ---p 00041000 00:1f 101777739 /dls_sw/apps/itk/itk-master/lib/libitksys-4.3.so.1
2b9a95b49000-2b9a95b4b000 rw-p 00040000 00:1f 101777739 /dls_sw/apps/itk/itk-master/lib/libitksys-4.3.so.1
2b9a95b4b000-2b9a95bb8000 r-xp 00000000 00:1f 105712941 /dls_sw/apps/itk/itk-master/lib/libitkvnl_algo-4.3.so.1
2b9a95bb8000-2b9a95db8000 ---p 0006d000 00:1f 105712941 /dls_sw/apps/itk/itk-master/lib/libitkvnl_algo-4.3.so.1
2b9a95db8000-2b9a95dba000 rw-p 0006d000 00:1f 105712941 /dls_sw/apps/itk/itk-master/lib/libitkvnl_algo-4.3.so.1
2b9a95dba000-2b9a95dbb000 rw-p 2b9a95dba000 00:00 0
2b9a95dbb000-2b9a96163000 r-xp 00000000 00:1f 102040246 /dls_sw/apps/itk/itk-master/lib/libitkvnl-4.3.so.1
2b9a96163000-2b9a96362000 ---p 003a8000 00:1f 102040246 /dls_sw/apps/itk/itk-master/lib/libitkvnl-4.3.so.1
2b9a96362000-2b9a9636b000 rw-p 003a7000 00:1f 102040246 /dls_sw/apps/itk/itk-master/lib/libitkvnl-4.3.so.1
2b9a9636b000-2b9a9636c000 rw-p 2b9a9636b000 00:00 0
2b9a9636c000-2b9a96450000 r-xp 00000000 00:1f 102040242 /dls_sw/apps/itk/itk-master/lib/libitkv3p_netlib-4.3.so.1
2b9a96450000-2b9a9664f000 ---p 000e4000 00:1f 102040242 /dls_sw/apps/itk/itk-master/lib/libitkv3p_netlib-4.3.so.1
2b9a9664f000-2b9a96651000 rw-p 000e3000 00:1f 102040242 /dls_sw/apps/itk/itk-master/lib/libitkv3p_netlib-4.3.so.1
2b9a96651000-2b9a96652000 rw-p 2b9a96651000 00:00 0
2b9a96652000-2b9a96704000 r-xp 00000000 00:1f 105712945 /dls_sw/apps/itk/itk-master/lib/libITKCommon-4.3.so.1
2b9a96704000-2b9a96904000 ---p 000b2000 00:1f 105712945 /dls_sw/apps/itk/itk-master/lib/libITKCommon-4.3.so.1
2b9a96904000-2b9a9690c000 rw-p 000b2000 00:1f 105712945 /dls_sw/apps/itk/itk-master/lib/libITKCommon-4.3.so.1
2b9a9690c000-2b9a96920000 rw-p 2b9a9690c000 00:00 0
2b9a96920000-2b9a96925000 r-xp 00000000 00:1f 105712947 /dls_sw/apps/itk/itk-master/lib/libitkNetlibSlatec-4.3.so.1
2b9a96925000-2b9a96b24000 ---p 00005000 00:1f 105712947 /dls_sw/apps/itk/itk-master/lib/libitkNetlibSlatec-4.3.so.1
2b9a96b24000-2b9a96b25000 rw-p 00004000 00:1f 105712947 /dls_sw/apps/itk/itk-master/lib/libitkNetlibSlatec-4.3.so.1
2b9a96b25000-2b9a96b40000 r-xp 00000000 00:1f 105712949 /dls_sw/apps/itk/itk-master/lib/libITKStatistics-4.3.so.1
2b9a96b40000-2b9a96d3f000 ---p 0001b000 00:1f 105712949 /dls_sw/apps/itk/itk-master/lib/libITKStatistics-4.3.so.1
2b9a96d3f000-2b9a96d41000 rw-p 0001a000 00:1f 105712949 /dls_sw/apps/itk/itk-master/lib/libITKStatistics-4.3.so.1
2b9a96d41000-2b9a96d6b000 r-xp 00000000 00:1f 105712951 /dls_sw/apps/itk/itk-master/lib/libITKIOImageBase-4.3.so.1
2b9a96d6b000-2b9a96f6a000 ---p 0002a000 00:1f 105712951 /dls_sw/apps/itk/itk-master/lib/libITKIOImageBase-4.3.so.1
2b9a96f6a000-2b9a96f6c000 rw-p 00029000 00:1f 105712951 /dls_sw/apps/itk/itk-master/lib/libITKIOImageBase-4.3.so.1
2b9a96f6c000-2b9a96f6d000 rw-p 2b9a96f6c000 00:00 0
2b9a96f6d000-2b9a96f71000 r-xp 00000000 00:1f 105712953 /dls_sw/apps/itk/itk-master/lib/libITKMesh-4.3.so.1
2b9a96f71000-2b9a97170000 ---p 00004000 00:1f 105712953 /dls_sw/apps/itk/itk-master/lib/libITKMesh-4.3.so.1
2b9a97170000-2b9a97171000 rw-p 00003000 00:1f 105712953 /dls_sw/apps/itk/itk-master/lib/libITKMesh-4.3.so.1
2b9a97171000-2b9a97185000 r-xp 00000000 00:1f 168624136 /dls_sw/apps/itk/itk-master/lib/libitkzlib-4.3.so.1
2b9a97185000-2b9a97384000 ---p 00014000 00:1f 168624136 /dls_sw/apps/itk/itk-master/lib/libitkzlib-4.3.so.1
2b9a97384000-2b9a97385000 rw-p 00013000 00:1f 168624136 /dls_sw/apps/itk/itk-master/lib/libitkzlib-4.3.so.1
2b9a97385000-2b9a9740e000 r-xp 00000000 00:1f 168624138 /dls_sw/apps/itk/itk-master/lib/libITKMetaIO-4.3.so.1
2b9a9740e000-2b9a9760e000 ---p 00089000 00:1f 168624138 /dls_sw/apps/itk/itk-master/lib/libITKMetaIO-4.3.so.1
2b9a9760e000-2b9a97611000 rw-p 00089000 00:1f 168624138 /dls_sw/apps/itk/itk-master/lib/libITKMetaIO-4.3.so.1
2b9a97611000-2b9a97612000 rw-p 2b9a97611000 00:00 0
2b9a97612000-2b9a9765a000 r-xp 00000000 00:1f 168624140 /dls_sw/apps/itk/itk-master/lib/libITKSpatialObjects-4.3.so.1
2b9a9765a000-2b9a97859000 ---p 00048000 00:1f 168624140 /dls_sw/apps/itk/itk-master/lib/libITKSpatialObjects-4.3.so.1
2b9a97859000-2b9a9785e000 rw-p 00047000 00:1f 168624140 /dls_sw/apps/itk/itk-master/lib/libITKSpatialObjects-4.3.so.1
2b9a9785e000-2b9a9786a000 r-xp 00000000 00:1f 168624142 /dls_sw/apps/itk/itk-master/lib/libITKPath-4.3.so.1
2b9a9786a000-2b9a97a6a000 ---p 0000c000 00:1f 168624142 /dls_sw/apps/itk/itk-master/lib/libITKPath-4.3.so.1
2b9a97a6a000-2b9a97a6c000 rw-p 0000c000 00:1f 168624142 /dls_sw/apps/itk/itk-master/lib/libITKPath-4.3.so.1
2b9a97a6c000-2b9a97a6d000 r-xp 00000000 00:1f 168624144 /dls_sw/apps/itk/itk-master/lib/libITKLabelMap-4.3.so.1
2b9a97a6d000-2b9a97c6d000 ---p 00001000 00:1f 168624144 /dls_sw/apps/itk/itk-master/lib/libITKLabelMap-4.3.so.1
2b9a97c6d000-2b9a97c6e000 rw-p 00001000 00:1f 168624144 /dls_sw/apps/itk/itk-master/lib/libITKLabelMap-4.3.so.1
2b9a97c6e000-2b9a97c6f000 rw-p 2b9a97c6e000 00:00 0
2b9a97c6f000-2b9a97c72000 r-xp 00000000 00:1f 168624146 /dls_sw/apps/itk/itk-master/lib/libITKQuadEdgeMesh-4.3.so.1
2b9a97c72000-2b9a97e71000 ---p 00003000 00:1f 168624146 /dls_sw/apps/itk/itk-master/lib/libITKQuadEdgeMesh-4.3.so.1
2b9a97e71000-2b9a97e72000 rw-p 00002000 00:1f 168624146 /dls_sw/apps/itk/itk-master/lib/libITKQuadEdgeMesh-4.3.so.1
2b9a97e72000-2b9a97ed5000 r-xp 00000000 00:1f 168624148 /dls_sw/apps/itk/itk-master/lib/libITKOptimizers-4.3.so.1
2b9a97ed5000-2b9a980d5000 ---p 00063000 00:1f 168624148 /dls_sw/apps/itk/itk-master/lib/libITKOptimizers-4.3.so.1
2b9a980d5000-2b9a980da000 rw-p 00063000 00:1f 168624148 /dls_sw/apps/itk/itk-master/lib/libITKOptimizers-4.3.so.1
2b9a980da000-2b9a980df000 r-xp 00000000 00:1f 168624150 /dls_sw/apps/itk/itk-master/lib/libITKPolynomials-4.3.so.1
2b9a980df000-2b9a982de000 ---p 00005000 00:1f 168624150 /dls_sw/apps/itk/itk-master/lib/libITKPolynomials-4.3.so.1
2b9a982de000-2b9a982df000 rw-p 00004000 00:1f 168624150 /dls_sw/apps/itk/itk-master/lib/libITKPolynomials-4.3.so.1
2b9a982df000-2b9a982e0000 rw-p 2b9a982df000 00:00 0
2b9a982e0000-2b9a982e3000 r-xp 00000000 00:1f 168624152 /dls_sw/apps/itk/itk-master/lib/libITKBiasCorrection-4.3.so.1
2b9a982e3000-2b9a9Aborted
[kny48981 at i12-ws011 reduced]$
____________________
Dr. Robert C. Atwood
Senior Support Scientist
Beamline I12-JEEP
The Joint Engineering and Environmental Processing Beamline
Diamond Light Source
The Harwell Science and Innovation Campus
Didcot,OXON
OX11 0DE
+44 (0) 1235 778 670
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