http://www.k-wave.org/forum/topic/cudaomp-c-file-io-problems Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 23:38:51 +0000 http://bbpress.org/?v=1.0.2 q http://www.k-wave.org/forum/search.php http://www.k-wave.org/forum/topic/cudaomp-c-file-io-problems#post-8476 Mon, 14 Mar 2022 08:36:37 +0000 frli8848 8476@http://www.k-wave.org/forum/ <p>Thanks Bradley, this solved it (I'm on 2020b Update 3 on Gentoo Linux)!</p> <p>/Fredrik </p> http://www.k-wave.org/forum/topic/cudaomp-c-file-io-problems#post-8475 Fri, 11 Mar 2022 19:15:07 +0000 Bradley Treeby 8475@http://www.k-wave.org/forum/ <p>Hi Fredrick,</p> <p>Have you tried the solution <a href="http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries">here</a>? </p> http://www.k-wave.org/forum/topic/cudaomp-c-file-io-problems#post-8473 Fri, 11 Mar 2022 16:23:34 +0000 frli8848 8473@http://www.k-wave.org/forum/ <p>I made a small test program:<br /> <pre><code>#include &lt;assert.h&gt; #include &lt;stdlib.h&gt; #include &quot;hdf5.h&quot; #include &quot;hdf5_hl.h&quot; int main() { herr_t status; hid_t file_id = H5Fopen(&quot;/tmp/example_input.h5&quot;, H5F_ACC_RDONLY, H5P_DEFAULT); assert(file_id &gt;= 0); char string[256] = &quot;&quot;; fprintf(stderr, &quot;string : %s\n&quot;, string); fprintf(stderr, &quot;---- reading attribute ----\n&quot;); status = H5LTget_attribute_string(file_id, &quot;/&quot;, &quot;file_type&quot;, string); assert(status &gt;= 0); fprintf(stderr, &quot;string : %s\n&quot;, string); status = H5Fclose(file_id); assert(status &gt;= 0); }</code></pre> <pre><code>$ gcc test_attribute.c -lhdf5 -lhdf5_hl -o test_h5_attr $ ./test_h5_attr string : ---- reading attribute ---- string : @u�U</code></pre> <p>Not sure why this fails since the Attribute looks OK in hdfview? </p> http://www.k-wave.org/forum/topic/cudaomp-c-file-io-problems#post-8472 Fri, 11 Mar 2022 15:15:52 +0000 frli8848 8472@http://www.k-wave.org/forum/ <p>After some more debuggin i realized that <code>file_type</code> is an h5 Attribute and not a Dataset:<br /> <pre><code>$ h5dump -a file_type /tmp/example_input.h5 HDF5 &quot;/tmp/example_input.h5&quot; { ATTRIBUTE &quot;file_type&quot; { DATATYPE H5T_STRING { STRSIZE H5T_VARIABLE; STRPAD H5T_STR_NULLTERM; CSET H5T_CSET_UTF8; CTYPE H5T_C_S1; } DATASPACE SCALAR DATA { (0): &quot;input&quot; } } }</code></pre> <p>but reading that Attribute seems to fail. </p> http://www.k-wave.org/forum/topic/cudaomp-c-file-io-problems#post-8471 Fri, 11 Mar 2022 13:55:33 +0000 frli8848 8471@http://www.k-wave.org/forum/ <p>Looking closer at the <code>/tmp/example_input.h5</code> file there seems to be no <code>file_type</code> entry (Dataset):<br /> <pre><code>$ h5ls /tmp/example_input.h5 | grep file_type</code></pre> <p>returns nothing. </p> http://www.k-wave.org/forum/topic/cudaomp-c-file-io-problems#post-8470 Fri, 11 Mar 2022 13:38:38 +0000 frli8848 8470@http://www.k-wave.org/forum/ <p>Hi all,</p> <p>I'm new to k-Wave and trying out the demos but I run into problems with the CUDA and C++ (OMP) code. I tried the <code>example_cpp_running_simulations.m</code> demo and I just get:<br /> <pre><code>$ ./kspaceFirstOrder-OMP -i /tmp/example_input.h5 -o /tmp/example_output.h5 --p_final --p_max -snip- Error: Invalid format of the input file: iostream error -snip-</code></pre> <p>I have traced that down to the file:<br /> <pre><code>kspaceFirstOrder-OMP/Hdf5/Hdf5FileHeader.cpp</code></pre> <p>where <code>getFileType()</code> returns 3 and <code>FileType::kInput</code> is 0 in the function:<br /> <pre><code>void Hdf5FileHeader::readHeaderFromInputFile(Hdf5File&amp; inputFile)</code></pre> <p>Is this an installation issue or a bug? (the pre-compiled binaries have the same problem).</p> <p>/Fredrik </p>