The reason that the higher-level library/language wrappers (Java, Fortran, C++, 
high-level) are not officially supported under thread-safety is that the 
thread-safety lock is only maintained at the C library level. We'd like to 
officially support thread-safe access to those wrappers but that hasn't ever 
made it to the head of the priority queue.

Dana

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-boun...@lists.hdfgroup.org] On Behalf Of 
Elvis Stansvik
Sent: Thursday, September 22, 2016 2:16 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] Simply using the library from separate threads (C++ 
API)

2016-09-22 19:58 GMT+02:00 Scot Breitenfeld <brtn...@hdfgroup.org>:
> 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 <elvis.stans...@orexplore.com> 
>> wrote:
>>
>> 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/HDF5ImageRe
>>>> ader.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:4
>>>> 5 #26 0x000000000042bc7a in 
>>>> QtConcurrent::MappedEachKernel::const_iterator,
>>>> CreateVolume>::runIteration (this=0x829210, it=..., 
>>>> CreateVolume>result=0x7fffbc002da8)
>>>> at /usr/include/qt/QtConcurrent/qtconcurrentmapkernel.h:176 #27 
>>>> 0x000000000042bd5d in 
>>>> QtConcurrent::MappedEachKernel::const_iterator,
>>>> CreateVolume>::runIterations (this=0x829210, 
>>>> CreateVolume>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
>>
>> _______________________________________________
>> Hdf-forum is for HDF software users discussion.
>> Hdf-forum@lists.hdfgroup.org
>> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.o
>> rg
>> 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.or
> g
> Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
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Twitter: https://twitter.com/hdf5
_______________________________________________
Hdf-forum is for HDF software users discussion.
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