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 _______________________________________________
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_______________________________________________
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
