The FAQ has been updated. Thanks! https://support.hdfgroup.org/hdf5-quest.html#tsafe
Dana -----Original Message----- From: Hdf-forum [mailto:[email protected]] On Behalf Of Elvis Stansvik Sent: Thursday, September 22, 2016 2:35 PM To: HDF Users Discussion List <[email protected]> Subject: Re: [Hdf-forum] Simply using the library from separate threads (C++ API) 2016-09-22 20:25 GMT+02:00 Werner Benger <[email protected]>: > There was some recent discussion that only the C API of HDF5 is > threadsafe, but not the C++ layer on top of it. To be safe you should > probably keep at the C API. Aha. Thanks for the heads up Werner. The FAQ has this to say: "By default, you cannot build either Parallel HDF5 with C++ or Parallel HDF5 with the thread-safe feature. You will receive a configure error if you try either of these combinations." But it does not say that C++ with the thread-safe is unsupported (when using serial HDF5). Maybe the FAQ should be updated? This is quite unfortunate since our app is C++ and the C++ API is so much more convenient, but I guess I'll port our code to the C API (it's not that much code). So far we haven't had any problems under Ubuntu (where the package is built with --enable-threadsafe --enable-unsupported), but I guess we've just been lucky. Elvis > > Cheers, > > Werner > > > > On 22.09.2016 20:15, Elvis Stansvik wrote: >> >> 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/HDF5Image >>>>>> Reader.cpp:91 >>>>>> #8 0x00007fffee8200d0 in >>>>>> vtkExecutive::CallAlgorithm(vtkInformation*, >>>>>> int, >>>>>> vtkInformationVector**, vtkInformationVector*) () from >>>>>> /usr/lib/libvtkCommonExecutionModel.so.1 #9 0x00007fffee837fa9 in >>>>>> vtkStreamingDemandDrivenPipeline::ExecuteInformation(vtkInformati >>>>>> on*, 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.c >>>>>> pp: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.hdfgro >>>>>> up.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.hdfgro >>>>>> up.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.o >> rg >> Twitter: https://twitter.com/hdf5 > > > -- > ___________________________________________________________________________ > Dr. Werner Benger Visualization Research > Center for Computation & Technology at Louisiana State University > (CCT/LSU) > 2019 Digital Media Center, Baton Rouge, Louisiana 70803 > Tel.: +1 225 578 4809 Fax.: +1 225 578-5362 > > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.or > g > 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
