2016-09-22 20:25 GMT+02:00 Werner Benger <wer...@cct.lsu.edu>:
> 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 <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/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
>>>>
>>>> _______________________________________________
>>>> 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.org
>> 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.
> 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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