http://www.k-wave.org/forum/topic/problem-running-kspacefirstorder3d-omp-via-matlab Support for the k-Wave MATLAB toolbox en-US Wed, 03 Jun 2026 01:17:07 +0000 http://bbpress.org/?v=1.0.2 q http://www.k-wave.org/forum/search.php http://www.k-wave.org/forum/topic/problem-running-kspacefirstorder3d-omp-via-matlab#post-5777 Mon, 05 Dec 2016 20:26:41 +0000 xzhan110 5777@http://www.k-wave.org/forum/ <p>Hi Yufeng, </p> <p>Thank you for the solution. It seems like your permission modification commands are for Unix system. Do you happen to know the equivalent for win 7? </p> <p>Thank you in advanced! </p> http://www.k-wave.org/forum/topic/problem-running-kspacefirstorder3d-omp-via-matlab#post-5717 Mon, 24 Oct 2016 09:45:53 +0000 Bradley Treeby 5717@http://www.k-wave.org/forum/ <p>Hi Frankie,</p> <p>Unfortunately at this stage we do not support Mac OS. If you are comfortable with compiling C++ codes, you could download the C++ source codes. It will require some edits (compiler directives etc), but people have told me they have got it to work in the past.</p> <p>Hope that helps,</p> <p>Brad. </p> http://www.k-wave.org/forum/topic/problem-running-kspacefirstorder3d-omp-via-matlab#post-5710 Fri, 14 Oct 2016 01:54:06 +0000 Yufeng Wang 5710@http://www.k-wave.org/forum/ <p>hello Frankie,</p> <p>I have solved this problem by adding +x permission</p> <p>chmod +x ./kspaceFirstOrder3D-OMP<br /> chmod +x ./kspaceFirstOrder3D-CUDA</p> <p>Hope this will be useful for you. </p> http://www.k-wave.org/forum/topic/problem-running-kspacefirstorder3d-omp-via-matlab#post-5703 Wed, 12 Oct 2016 07:35:59 +0000 Yufeng Wang 5703@http://www.k-wave.org/forum/ <p>hello Frankie,</p> <p>I encounted the same error as yours, which reported by Matlab when I was running the kspaceFirstOrder3DC() in the toolbox example,'example_us_beam_patterns.m'. I am using the toolbox in Ubuntu 14.04 and Matlab2014b. So I think it might be a common erros. Error is reported as follow:</p> <p>/bin/bash: ./kspaceFirstOrder3D-OMP: Permission denied<br /> Error using h5readc<br /> The HDF5 library encountered an error and produced the following stack trace information:</p> <p> H5FD_sec2_open unable to open file: name = '/tmp/kwave_output_data12-Oct-2016-14-26-59.h5',<br /> errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0<br /> H5FD_open open failed<br /> H5F_open unable to open file: time = Wed Oct 12 14:27:00 2016<br /> , name = '/tmp/kwave_output_data12-Oct-2016-14-26-59.h5', tent_flags = 0<br /> H5Fopen unable to open file</p> <p>Error in h5read (line 58)<br /> [data,var_class] = h5readc(Filename,Dataset,start,count,stride);</p> <p>Error in kspaceFirstOrder3DC (line 347)<br /> Nx = h5read(output_filename, '/Nx');</p> <p>Error in example_us_beam_patterns (line 178)<br /> sensor_data = kspaceFirstOrder3DC(kgrid, medium, transducer, sensor, input_args{:});</p> <p>I hope someone would solve this problem.</p> <p>thanks in advanced.</p> <p>Yufeng Wang </p> http://www.k-wave.org/forum/topic/problem-running-kspacefirstorder3d-omp-via-matlab#post-5702 Sat, 08 Oct 2016 22:22:11 +0000 frankiepoon1991 5702@http://www.k-wave.org/forum/ <p>Hi all,</p> <p>I encounted an error reported by Matlab when I was running the kspaceFirstOrder3DC() in the toolbox example,'example_cpp_running_simulations.m' with setting example_number = 3 (i.e. testing case 3), and I also got a similar error while testing case 2. I am using the toolbox in Mac and Matlab2016a. I tried to run the the program would stop in the middle with the error:</p> <p>case 3 error:<br /> /bin/bash: ./kspaceFirstOrder3D-OMP: Permission denied<br /> Error using h5readc<br /> Unable to open file. Filename may be<br /> corrupt or have unsupported characters.</p> <p>Error in h5read (line 58)<br /> [data,var_class] =<br /> h5readc(Filename,Dataset,start,count,stride);</p> <p>Error in kspaceFirstOrder3DC (line 348)<br /> Nx = h5read(output_filename, '/Nx');</p> <p>Error in example_cpp_running_simulations<br /> (line 131)<br /> sensor_data =<br /> kspaceFirstOrder3DC(kgrid,<br /> medium, source, sensor,<br /> input_args{:});</p> <p>case 2 error:<br /> Error using h5readc<br /> Unable to open file. Filename may be<br /> corrupt or have unsupported characters.</p> <p>Error in h5read (line 58)<br /> [data,var_class] =<br /> h5readc(Filename,Dataset,start,count,stride);</p> <p>Error in example_cpp_running_simulations<br /> (line 122)<br /> sensor_data.p_final =<br /> h5read([pathname<br /> output_filename], '/p_final');</p> <p>Is the error because of the Mac system? Or does anyone have a solution to this error?</p> <p>Many thanks in advanced.</p> <p>Frankie </p>