Yes it is still the case that you cannot enable C++ or Fortran (or the High Level APIs) when threadsafe is enabled. —enable-unsupported can override this behavior.
Scot > On Sep 22, 2016, at 12:36 PM, Elvis Stansvik <[email protected]> > wrote: > > 2016-09-22 19:23 GMT+02:00 Elvis Stansvik <[email protected]>: >> 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. > > I spoke a little too soon. I now found this bug filed against the Arch > package: > > https://bugs.archlinux.org/task/33805 > > The reporter asked the package maintainer to add --enable-threadsafe, > but the package maintainer closed the bug saying that > --enable-threadsafe is not compatible with the Fortran build (in Arch, > the C++ and Fortran APIs are bundled into one package > hdf5-cpp-fortran). > > Anyone know if that is still the case? If so I can't open a bug > against the package again asking for --enable-threadsafe to be added. > But I could open a bug asking the package to be split I guess. > > Elvis > >> >> 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. > [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
