http://www.k-wave.org/forum/topic/problems-with-hdf5 Support for the k-Wave MATLAB toolbox en-US Wed, 13 May 2026 05:18:42 +0000 http://bbpress.org/?v=1.0.2 q http://www.k-wave.org/forum/search.php http://www.k-wave.org/forum/topic/problems-with-hdf5#post-4546 Fri, 23 May 2014 14:52:13 +0000 pjrusello 4546@http://www.k-wave.org/forum/ <p>Brad,<br /> No problem. Here's a link to the r2012b HDF5 file just in case it's helpful: <a href="https://www.dropbox.com/s/hccmbzllbgal10k/photoacousticWaveform3D_r2012b.h5" rel="nofollow">https://www.dropbox.com/s/hccmbzllbgal10k/photoacousticWaveform3D_r2012b.h5</a></p> <p>P.J. </p> http://www.k-wave.org/forum/topic/problems-with-hdf5#post-4534 Thu, 22 May 2014 14:39:27 +0000 Bradley Treeby 4534@http://www.k-wave.org/forum/ <p>Hi PJ,</p> <p>Thanks for the feedback - that's helpful. We will try and get to the bottom of the what's happening in R2013a.</p> <p>Brad </p> http://www.k-wave.org/forum/topic/problems-with-hdf5#post-4533 Thu, 22 May 2014 13:50:13 +0000 pjrusello 4533@http://www.k-wave.org/forum/ <p>Turns out it was Matlab related. It appears there are problems with HDF5 file writing for r2013a (at least on a Mac). I generated a new HDF5 input file with r2012b (also on a Mac) and it worked one with the Linux binary on Ubuntu 12.04.</p> <p>P.J. </p> http://www.k-wave.org/forum/topic/problems-with-hdf5#post-4531 Wed, 21 May 2014 21:13:15 +0000 pjrusello 4531@http://www.k-wave.org/forum/ <p>I'm trying to run some simulations using kspaceFirstOrder3D-OMP, but am having some problems with the HDF5 libraries.</p> <p>Here's the text of the error using a binary I compiled under Mac OS X 10.9.3 using icc and MKL:</p> <pre><code>-------------------------------- kspaceFirstOrder3D-OMP v1.0 -------------------------------- HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0: #000: H5A.c line 557 in H5Aopen(): unable to load attribute info from object header for attribute: &#39;file_type&#39; major: Attribute minor: Unable to initialize object #001: H5Oattribute.c line 537 in H5O_attr_open_by_name(): can&#39;t locate attribute: &#39;file_type&#39; major: Attribute minor: Object not found libc++abi.dylib: terminating with uncaught exception of type std::__1::ios_base::failure: Error: Could not read from &quot;file_type&quot; attribute of &quot;/&quot; dataset! : unspecified iostream_category error Abort trap: 6</code></pre> <p>And here's the text of the error using the pre-compiled binary from k-wave.org on Ubuntu 12.04</p> <pre><code>-------------------------------- kspaceFirstOrder3D-OMP v1.0 -------------------------------- HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0: #000: H5A.c line 550 in H5Aopen(): unable to load attribute info from object header major: Attribute minor: Unable to initialize object #001: H5Oattribute.c line 530 in H5O_attr_open_by_name(): can&#39;t locate attribute major: Attribute minor: Object not found terminate called after throwing an instance of &#39;std::ios_base::failure&#39; what(): Error: Could not read from &quot;file_type&quot; attribute of &quot;/&quot; dataset! Aborted (core dumped)</code></pre> <p>I think the problem is with the HDF5 input file being created with kspaceFirstOrder3d in Matlab (R2013a 8.1.0.604). I'm just using the IVP photo acoustic waveform example to test if the C++ code is working and compare against the Matlab output. The HDF5 input file I'm using is available here: <a href="https://www.dropbox.com/s/ksgtgkkgt3qfuws/photoacousticWaveform3D.h5" rel="nofollow">https://www.dropbox.com/s/ksgtgkkgt3qfuws/photoacousticWaveform3D.h5</a></p> <p>Any ideas on what could be causing this or a possible solution? I'm contemplating writing my own function to generate the input file since I need to run fairly large domains (~10 cm largest dimension for a 10 MHz transducer) for the applications I'm working on.</p> <p>thanks for any ideas,</p> <p>P.J. </p>