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1. pjrusello
   

   Member
   Joined: Jul '13
   Posts: 3

   I'm trying to run some simulations using kspaceFirstOrder3D-OMP, but am having some problems with the HDF5 libraries.

   Here's the text of the error using a binary I compiled under Mac OS X 10.9.3 using icc and MKL:

   --------------------------------
     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: 'file_type'
       major: Attribute
       minor: Unable to initialize object
     #001: H5Oattribute.c line 537 in H5O_attr_open_by_name(): can't locate attribute: 'file_type'
       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 "file_type" attribute of "/" dataset!
   : unspecified iostream_category error
   Abort trap: 6

   And here's the text of the error using the pre-compiled binary from k-wave.org on Ubuntu 12.04

   --------------------------------
     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't locate attribute
       major: Attribute
       minor: Object not found
   terminate called after throwing an instance of 'std::ios_base::failure'
     what():  Error: Could not read from "file_type" attribute of "/" dataset!
   
   Aborted (core dumped)

   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: https://www.dropbox.com/s/ksgtgkkgt3qfuws/photoacousticWaveform3D.h5

   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.

   thanks for any ideas,

   P.J.

   Posted 10 years ago #

2. pjrusello
   

   Member
   Joined: Jul '13
   Posts: 3

   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.J.

   Posted 10 years ago #

3. Bradley Treeby
   

   Developer
   Joined: Mar '10
   Posts: 1,643

   Hi PJ,

   Thanks for the feedback - that's helpful. We will try and get to the bottom of the what's happening in R2013a.

   Brad

   Posted 10 years ago #

4. pjrusello
   

   Member
   Joined: Jul '13
   Posts: 3

   Brad,
   No problem. Here's a link to the r2012b HDF5 file just in case it's helpful: https://www.dropbox.com/s/hccmbzllbgal10k/photoacousticWaveform3D_r2012b.h5

   P.J.

   Posted 10 years ago #

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