2016-09-22 19:23 GMT+02:00 Elvis Stansvik <elvis.stans...@orexplore.com>:
> 2016-09-22 19:17 GMT+02:00 Dana Robinson <derob...@hdfgroup.org>:
>> 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. Hdf-forum@lists.hdfgroup.org
>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
>> Twitter: https://twitter.com/hdf5
>>
>>
>> _______________________________________________
>> Hdf-forum is for HDF software users discussion.
>> Hdf-forum@lists.hdfgroup.org
>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
>> Twitter: https://twitter.com/hdf5

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