[ITK] Threading issues

[Laurențiu Nicola]

Hi,
 
This is a bit of a shot in the dark asking this, but we're working on a
project that uses a library based on ITK (OTB). We noticed two issues:
 
1. We've seen processes with a single remaining thread that's stuck in
   pthread_join().
2. We're getting some segfaults in libpthread.so:
 
[Jul13 09:42] otbApplicationL[37610]: segfault at 7ff2f27fc9d0 ip
00007ff3375c2e61 sp 00007ffd9ef0d620 error 4 in libpthread-
2.17.so[7ff3375ba000+16000]
[  +0.002159] otbApplicationL[31064]: segfault at 2d3 ip
00007fd3bf636e61 sp 00007fff2446f210 error 4 in libpthread-
2.17.so[7fd3bf62e000+16000]
[  +0.007911] otbApplicationL[10366]: segfault at 7feb000008cc ip
00007febeaa15e61 sp 00007ffe34bb1e10 error 4 in libpthread-
2.17.so[7febeaa0d000+16000]
[Jul13 09:44] maccs-processin[39138]: segfault at 7f6b713979d0 ip
00007f6b767cae61 sp 00007ffe09fe6410 error 4 in libpthread-
2.17.so[7f6b767c2000+16000]
[  +0.000092] otbApplicationL[22007]: segfault at 2d0 ip
00007f06a6541e61 sp 00007fffb4299660 error 4 in libpthread-
2.17.so[7f06a6539000+16000]
[  +0.000384] otbApplicationL[33830]: segfault at 100001626 ip
00007f37c1f90e61 sp 00007fff8a0f44d0 error 4 in libpthread-
2.17.so[7f37c1f88000+16000]
 
My theory is that 2d0 is an offset into a NULL pthread struct, but I
couldn't find the definition of that structure (pthread_t is an
opaque handle).
 
I suspect that the two issues are related. The weird part is that those
segfaults tend to happen for multiple processes at the same time. The
system was probably loaded, but I don't think it was an OOM situation.
 
Right now we're on ITK 4.9.1. Is there anyone else who encountered this
or knows about recent ITK fixes related to multithreading?
 
Regards,
Laurentiu Nicola
 
(gdb) bt
#  0x00007f0d74650ef7 in pthread_join () from /usr/lib64/libpthread.so.0
#1  0x00007f0d74dd1cca in
#itk::MultiThreader::SpawnWaitForSingleMethodThread
#(this=this at entry=0x2411670, threadHandle=<optimized out>)
    at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-
    BUILD/ITK/src/ITK/Modules/Core/Common/src/itkMultiThreaderPThrea-
    ds.cxx:239
#2  0x00007f0d74dd244b in itk::MultiThreader::WaitForSingleMethodThread
#(this=this at entry=0x2411670, threadHandle=<optimized out>)
    at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-
    BUILD/ITK/src/ITK/Modules/Core/Common/src/itkMultiThreader.cxx:480
#3  0x00007f0d74dd2f7d in itk::MultiThreader::SingleMethodExecute
#(this=0x2411670) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-
#BUILD/ITK/src/ITK/Modules/Core/Common/src/itkMultiThreader.cxx:389
#4  0x00007f0d7cedb87d in itk::ImageSource<otb::VectorImage<float, 2u>
#>::GenerateData (this=0x23fff10) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/install/otb-
#install/usr/include/ITK-4.8/itkImageSource.hxx:254
#5  0x00007f0d74dcdc00 in itk::ProcessObject::UpdateOutputData
#(this=0x23fff10) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-
#BUILD/ITK/src/ITK/Modules/Core/Common/src/itkProcessObject.cxx:1739
#6  0x00007f0d74dcdcc0 in itk::ProcessObject::UpdateOutputData
#(this=0x23e9b00) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-5.0-
#BUILD/ITK/src/ITK/Modules/Core/Common/src/itkProcessObject.cxx:1700
#7  0x00007f0d4af29368 in
#otb::StreamingImageVirtualWriter<otb::VectorImage<float, 2u>
#>::GenerateData (this=0x23e9700)
    at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
    5.0/Modules/Core/Streaming/include/otbStreamingImageVirtualWrit-
    er.txx:248
#8  0x00007f0d4af1c8ce in
#otb::StreamingImageVirtualWriter<otb::VectorImage<float, 2u> >::Update
#(this=0x23e9700)
    at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
    5.0/Modules/Core/Streaming/include/otbStreamingImageVirtualWrit-
    er.txx:156
#9  0x00007f0d4af11aad in otb::PersistentFilterStreamingDecorator<otb::-
#PersistentShrinkImageFilter<otb::VectorImage<float, 2u>,
#otb::VectorImage<float, 2u> > >::GenerateData (this=0x2466c20)
    at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
    5.0/Modules/Core/Streaming/include/otbPersistentFilterStreamingDeco-
    rator.txx:52
#10 0x00007f0d4af1f4be in otb::Wrapper::Quicklook::DoExecute
#(this=0x23a9540) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
#5.0/Modules/Applications/AppImageUtils/app/otbQuicklook.cxx:272
#11 0x00007f0d7d2026c8 in otb::Wrapper::Application::Execute
#(this=this at entry=0x23a9540) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
#5.0/Modules/Wrappers/ApplicationEngine/src/otbWrapperApplicatio-
#n.cxx:223
#12 0x00007f0d7d202789 in
#otb::Wrapper::Application::ExecuteAndWriteOutput
#(this=0x23a9540) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
#5.0/Modules/Wrappers/ApplicationEngine/src/otbWrapperApplicatio-
#n.cxx:230
#13 0x00007f0d7d60b2c9 in
#otb::Wrapper::CommandLineLauncher::ExecuteAndWriteOutput
#(this=0x2366aa0) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
#5.0/Modules/Wrappers/CommandLine/src/otbWrapperCommandLineLaunche-
#r.cxx:158
#14 0x00000000004034a8 in main (argc=<optimized out>, argv=<optimized
#out>) at /home/cudroiu/sen2agri/packaging/Sen2AgriPlatform/build/OTB-
#5.0/Modules/Wrappers/CommandLine/src/otbApplicationLauncherCommandLin-
#e.cxx:299
 
(gdb) info threads
  Id   Target Id         Frame
* 1    Thread 0x7f0d63055880 (LWP 21145) "otbApplicationL"
  0x00007f0d74650ef7 in pthread_join () from /usr/lib64/libpthread.so.0
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