2016-09-22 19:17 GMT+02:00 Dana Robinson <[email protected]>: > Hi Elvis, > > Did you build your HDF5 library with thread-safety enabled > (--enable-threadsafe w/ configure)?
Hi Dana, and thanks for the quick reply. I think we just e-mailed past each other (see my previous mail). I wrongly called it --thread-safe in that mail, but it was --enable-threadsafe I was referring to. But yes, I'm pretty sure this is the problem. I'm rebuilding the Arch package now with --enable-threadsafe. Elvis > > Dana Robinson > Software Engineer > The HDF Group > > Get Outlook for Android > > From: Elvis Stansvik > Sent: Thursday, September 22, 12:43 > Subject: [Hdf-forum] Simply using the library from separate threads (C++ > API) > To: HDF Users Discussion List > > Hi all, I'm using the C++ API to read HDF5 files from separate threads (no > writing). None of my threads read the same file, but they do execute > simultaneously. The reason I'm using threading is not to speed things up or > get better throughput, but simply to not block the UI (it's Qt application) > while reading. So this is not about "Parallel HDF5" or anything, just simply > using the serial library "from scratch" from multiple threads. This has been > working fine when testing on Ubuntu 16.04 (our target OS), which has HDF5 > 1.8.16. I recently tested on my personal Arch Linux machine though, which > has HDF5 1.10.0, and got this segmentation fault: (gdb) bt #0 > 0x00007ffff67c57d9 in H5SL_search () from /usr/lib/libhdf5.so.100 #1 > 0x00007ffff678dd19 in H5P_copy_plist () from /usr/lib/libhdf5.so.100 #2 > 0x00007ffff66a7fc0 in H5F_new () from /usr/lib/libhdf5.so.100 #3 > 0x00007ffff66a8f55 in H5F_open () from /usr/lib/libhdf5.so.100 #4 > 0x00007ffff66a155d in H5Fopen () from /usr/lib/libhdf5.so.100 #5 > 0x00007ffff6b79546 in H5::H5File::p_get_file(char const*, unsigned int, > H5::FileCreatPropList const&, H5::FileAccPropList const&) () from > /usr/lib/libhdf5_cpp.so.100 #6 0x00007ffff6b79750 in H5::H5File::H5File(char > const*, unsigned int, H5::FileCreatPropList const&, H5::FileAccPropList > const&) () from /usr/lib/libhdf5_cpp.so.100 #7 0x000000000041f00e in > HDF5ImageReader::RequestInformation (this=0x7fffbc002de0, > request=0x7fffbc010da0, inputVector=0x0, outputVector=0x7fffbc0039d0) at > /home/estan/Projekt/orexplore/dev/src/insight/src/model/HDF5ImageReader.cpp:91 > #8 0x00007fffee8200d0 in vtkExecutive::CallAlgorithm(vtkInformation*, int, > vtkInformationVector**, vtkInformationVector*) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #9 0x00007fffee837fa9 in > vtkStreamingDemandDrivenPipeline::ExecuteInformation(vtkInformation*, > vtkInformationVector**, vtkInformationVector*) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #10 0x00007fffee81ce05 in > vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, > vtkInformationVector**, vtkInformationVector*) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #11 0x00007fffee835c55 in > vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, > vtkInformationVector**, vtkInformationVector*) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #12 0x00007fffee816e1a in > vtkCompositeDataPipeline::ForwardUpstream(vtkInformation*) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #13 0x00007fffee81ccb5 in > vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, > vtkInformationVector**, vtkInformationVector*) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #14 0x00007fffee835c55 in > vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, > vtkInformationVector**, vtkInformationVector*) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #15 0x00007fffee816e1a in > vtkCompositeDataPipeline::ForwardUpstream(vtkInformation*) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #16 0x00007fffee81ccb5 in > vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, > vtkInformationVector**, vtkInformationVector*) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #17 0x00007fffee835c55 in > vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, > vtkInformationVector**, vtkInformationVector*) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #18 0x00007fffee816e1a in > vtkCompositeDataPipeline::ForwardUpstream(vtkInformation*) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #19 0x00007fffee81ccb5 in > vtkDemandDrivenPipeline::ProcessRequest(vtkInformation*, > vtkInformationVector**, vtkInformationVector*) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #20 0x00007fffee835c55 in > vtkStreamingDemandDrivenPipeline::ProcessRequest(vtkInformation*, > vtkInformationVector**, vtkInformationVector*) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #21 0x00007fffee836482 in > vtkStreamingDemandDrivenPipeline::Update(int) () from > /usr/lib/libvtkCommonExecutionModel.so.1 #22 0x00007ffff1289a76 in > vtkAbstractVolumeMapper::GetBounds() () from > /usr/lib/libvtkRenderingCore.so.1 #23 0x00007ffff13459f9 in > vtkVolume::GetBounds() () from /usr/lib/libvtkRenderingCore.so.1 #24 > 0x000000000043f235 in createVolume (image=..., from=0, > to=2.7803999378532183, opacityFunction=..., colorFunction=...) at > /home/estan/Projekt/orexplore/dev/src/insight/src/view/Pipeline.cpp:123 #25 > 0x00000000004295c4 in CreateVolume::operator() (this=0x829248, image=...) at > /home/estan/Projekt/orexplore/dev/src/insight/src/view/Pipeline.h:45 #26 > 0x000000000042bc7a in QtConcurrent::MappedEachKernel::const_iterator, > CreateVolume>::runIteration (this=0x829210, it=..., result=0x7fffbc002da8) > at /usr/include/qt/QtConcurrent/qtconcurrentmapkernel.h:176 #27 > 0x000000000042bd5d in QtConcurrent::MappedEachKernel::const_iterator, > CreateVolume>::runIterations (this=0x829210, sequenceBeginIterator=..., > begin=1, end=2, results=0x7fffbc002da8) at > /usr/include/qt/QtConcurrent/qtconcurrentmapkernel.h:186 #28 > 0x000000000042c4e1 in QtConcurrent::IterateKernel::const_iterator, > vtkSmartPointer >::forThreadFunction (this=0x829210) at > /usr/include/qt/QtConcurrent/qtconcurrentiteratekernel.h:256 #29 > 0x000000000042bedc in QtConcurrent::IterateKernel::const_iterator, > vtkSmartPointer >::threadFunction (this=0x829210) at > /usr/include/qt/QtConcurrent/qtconcurrentiteratekernel.h:218 #30 > 0x00007ffff7bd5cfd in QtConcurrent::ThreadEngineBase::run() () from > /usr/lib/libQt5Concurrent.so.5 #31 0x00007ffff489a01f in ?? () from > /usr/lib/libQt5Core.so.5 #32 0x00007ffff489dd78 in ?? () from > /usr/lib/libQt5Core.so.5 #33 0x00007fffeb3f5454 in start_thread () from > /usr/lib/libpthread.so.0 #34 0x00007fffec5f07df in clone () from > /usr/lib/libc.so.6 (gdb) Before I start digging into what is happening here > I'd just like to ask: Do I have to do something special when using the HDF5 > library from two different threads? I'm not reading the same files or > anything, it's simply two completely separate usages of the library in > threads that run in parallel. Does the library have any global structures or > something that must be initialized before spawning any threads that use it? > The reason I'm a little worried is that perhaps I've just been lucky when > running under Ubuntu / HDF5 1.8.16. My usage in each thread basically looks > like: 1) Create a H5::H5File 2) Open a dataset using file.openDataset 3) Get > the dataspace for the dataset and select a hyperslab 4) Create a memory > dataspace 5) Perform a single read(..) operation from the dataset dataspace > to the memory dataspace And it's always different files that the threads > work with. Is there some step 0 I'm missing? Thanks in advance for any > advice. Elvis _______________________________________________ Hdf-forum is > for HDF software users discussion. [email protected] > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > Twitter: https://twitter.com/hdf5 > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > Twitter: https://twitter.com/hdf5 _______________________________________________ Hdf-forum is for HDF software users discussion. 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