2016-09-22 19:58 GMT+02:00 Scot Breitenfeld <[email protected]>: > 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.
Aha, so that's why I had to enable that option :) I see now that this is what the Ubuntu package does. I'll ask the Arch package maintainer if he's willing to do the same. I've confirmed now that I don't have any problems with my program if I re-built the Arch package with --enable-threadsafe --enable-unsupported. Thanks for the info! Elvis > > 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 _______________________________________________ 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
