k-Wave User Forum » Topic: problem when running kspaceFirstOrder3DC()

k-Wave User Forum » Topic: problem when running kspaceFirstOrder3DC() http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 23:01:17 +0000 http://bbpress.org/?v=1.0.2 <![CDATA[Search]]> q http://www.k-wave.org/forum/search.php Toshini on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-9203 Sun, 30 Mar 2025 09:37:44 +0000 Toshini 9203@http://www.k-wave.org/forum/ Hi, I've gone through all the threads, and it looks like all the changes are implemented in MATLAB (2024b) and k-Wave 1.4, but I'm still encountering this issue. Also, I can't locate the Temp folder. Error using h5readc Unable to open 'C:\Users\toshi\AppData\Local\Temp\kwave_output_data29-Mar-2025-14-31-12.h5'. File or folder not found. Error in h5read (line 95) [data,var_class] = h5readc(Filename,Dataset,start,count,stride); Error in kspaceFirstOrder3DC (line 569) Nx = h5read(output_filename, '/Nx'); Error in kspaceFirstOrder2DG (line 76) sensor_data = kspaceFirstOrder3DC(kgrid, medium, source, sensor, input_args{:}); Error in simSPA (line 36) sensor_data = kspaceFirstOrder2DG(kgrid, medium, source, sensor, input_args{:}); Error in OpticalSimulation (line 299) simSPA(vmcmesh, vmcmedium, vmcboundary, vmcoptions, kgrid, medium, ...) Thank you. mapesir on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-9146 Thu, 03 Oct 2024 15:45:36 +0000 mapesir 9146@http://www.k-wave.org/forum/ Hi, my PC does the something similar to Tina's, it has a problem with creating the output. It's as if MATLAB doesn't find the folder because it puts another folder in the path that doesn't exist. For example, the first time pinted: Unable to open '/home/MATLAB/Add-Ons/...' and then I though it was because all Matlab stuff should be in the same folder, so I created the MATLAB folder and moved all the things there and I tryed again. The result was the same: Unable to open '/home/MATLAB/MATLAB/Add-Ons/...' How could I fix it? And I have some addicional questions; on Linux it's better to uses binaries or source files for C, and if I use sources, how? Thank you in advance, Maria DaisyZ on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-9114 Thu, 18 Jul 2024 09:29:59 +0000 DaisyZ 9114@http://www.k-wave.org/forum/ Hi Jiri, I got the same problem. My system is Windows.,with MATLAB 2023b、k-wave version 1.4 and cuda version 1.3. The MATLAB has created the kwave_input_data_.....h5 file in the TEMP folder, but it did not have the output...h5. The disk space is enough. How can i fix it? Thanks for your reply. Nancy maoqq on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-8618 Wed, 05 Oct 2022 08:59:06 +0000 maoqq 8618@http://www.k-wave.org/forum/ Hi, I got the same problem. And my system is Linux. The MATLAB has created the kwave_input_data_.....h5 file in the /tmp. But it did not have the output...h5. The disk space is enough. How can i fix it? Thanks, Tina Bradley Treeby on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-8362 Thu, 16 Dec 2021 10:20:05 +0000 Bradley Treeby 8362@http://www.k-wave.org/forum/ Hi Anirudh, See the discussion <a href="http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries">here</a>. Note, if you're using a later version of MATLAB (>=2021), you don't need the patch from the MATLAB side any longer. Brad. anirudh.parag on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-8355 Thu, 09 Dec 2021 01:30:51 +0000 anirudh.parag 8355@http://www.k-wave.org/forum/ Hi Bradley, Thank you for making this toolbox openly accessible. Is the problem raised above by Ruben (regarding the fatal error in MATLAB 2020a) resolved, since I am getting the same issue? Please find it below: export: Command not found. OMP_PLACES=cores: Command not found. OMP_PROC_BIND=SPREAD: Command not found. ┌───────────────────────────────────────────────────────────────┐ │ kspaceFirstOrder-OMP v1.3 │ ├───────────────────────────────────────────────────────────────┤ │ Reading simulation configuration: Failed │ └───────────────────────────────────────────────────────────────┘ ┌───────────────────────────────────────────────────────────────┐ │ !!! K-Wave experienced a fatal error !!! │ ├───────────────────────────────────────────────────────────────┤ │ Error: Invalid format of the input file: iostream error │ ├───────────────────────────────────────────────────────────────┤ │ Execution terminated │ └───────────────────────────────────────────────────────────────┘ Error using h5readc The filename specified was either not found on the MATLAB path or it contains unsupported characters. Error in h5read (line 66) [data,var_class] = h5readc(Filename,Dataset,start,count,stride); Error in kspaceFirstOrder3DC (line 569) Nx = h5read(output_filename, '/Nx'); Thanks, Anirudh Jiri Jaros on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-7520 Thu, 21 May 2020 22:01:30 +0000 Jiri Jaros 7520@http://www.k-wave.org/forum/ Hi arunima0111 I don't think this is the same problem. This looks more like Matlab not being able to find a C++ binary, or the file doesn't have +x permission on linux. Jiri arunima0111 on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-7498 Thu, 14 May 2020 12:25:25 +0000 arunima0111 7498@http://www.k-wave.org/forum/ Hi Brad, I am using 2019b and I am also getting a similar error. Error using h5readc The filename specified was either not found on the MATLAB path or it contains unsupported characters. Error in h5read (line 66) [data,var_class] = h5readc(Filename,Dataset,start,count,stride); Error in kspaceFirstOrder3DC (line 569) Nx = h5read(output_filename, '/Nx'); Error in kspaceFirstOrder2DC (line 89) sensor_data = kspaceFirstOrder3DC(varargin{:}); Error in v06 (line 114) sensor_data_2D = kspaceFirstOrder2DC(kgrid, medium, source, sensor, input_args{:}); ...................................................... I tried using the method which has been posted on the forum (making changes to h5writeatt) but even that didn't help here. Can you suggest something else which can be done? Thanks Bradley Treeby on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-7430 Tue, 21 Apr 2020 12:48:49 +0000 Bradley Treeby 7430@http://www.k-wave.org/forum/ Are you using MATLAB 2020a? If so, this is a known issue. I'm working with Mathworks at the moment on a solution. In the meantime, it should work if you using 2019b and earlier. ruben on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-7425 Mon, 20 Apr 2020 15:25:04 +0000 ruben 7425@http://www.k-wave.org/forum/ Good day, I'm trying to run the example "Simulating ultrasound beam patterns" and I get this error. +---------------------------------------------------------------+ | kspaceFirstOrder-OMP v1.3 | +---------------------------------------------------------------+ | Reading simulation configuration: Failed | +---------------------------------------------------------------+ +---------------------------------------------------------------+ | !!! K-Wave experienced a fatal error !!! | +---------------------------------------------------------------+ | Error: Invalid format of the input file: iostream stream | | error | +---------------------------------------------------------------+ | Execution terminated | +---------------------------------------------------------------+ Error using h5readc The filename specified was either not found on the MATLAB path or it contains unsupported characters. Error in h5read (line 66) [data,var_class] = h5readc(Filename,Dataset,start,count,stride); Error in kspaceFirstOrder3DC (line 569) Nx = h5read(output_filename, '/Nx'); How can I solve it? Thanks Jiri Jaros on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-5549 Fri, 24 Jun 2016 11:37:28 +0000 Jiri Jaros 5549@http://www.k-wave.org/forum/ Hi Mark, this has something to do with the window permissions. Could you try a simple trick and let me know. 1. create an input file, say d:\test\input.h5 2. copy the binary into the same folder 3. run commandline and type kspacefirstorder3D-OMP -i input.h5 -o output.h5 and then let me know what happened? Cheers, Jiri mattouB on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-5533 Mon, 13 Jun 2016 13:53:38 +0000 mattouB 5533@http://www.k-wave.org/forum/ Hi, I've encountered the same problem: The HDF5 library encountered an error and produced the following stack trace information: H5FD_sec2_open unable to open file: name = 'D:\test\kwave_output_data13-Jun-2016-14-28-05.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0 H5FD_open open failed H5F_open unable to open file: time = Mon Jun 13 14:28:32 2016 , name = 'D:\test\kwave_output_data13-Jun-2016-14-28-05.h5', tent_flags = 0 H5Fopen unable to open file Error in h5read (line 58) [data,var_class] = h5readc(Filename,Dataset,start,count,stride); Error in kspaceFirstOrder3DC (line 347) Nx = h5read(output_filename, '/Nx'); I can't cope with the reason why the input file is written in the right directory but not the output file. I use the SS3 first download link for kspaceFirstOrder3DC, on matlab 2015b and I've already tried the option 'DataPath': input_args = {'DataPath','D:\test' }; Still it doesn't work. Would you have a solution for me ? Thank you, Mat zhili on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-4018 Thu, 24 Oct 2013 04:32:58 +0000 zhili 4018@http://www.k-wave.org/forum/ Jiri: It seems to be ok to run in my PC, I will figure it out and sorry for the confusion. thanks zhili on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-4017 Thu, 24 Oct 2013 03:24:30 +0000 zhili 4017@http://www.k-wave.org/forum/ Dear Jiri: I encountered similar issue, please help to check, and I've created another dir(c:\test) for it, but still the same: Error using h5readc The HDF5 library encountered an error and produced the following stack trace information: H5FD_windows_open unable to open file, errno = 2, error message = 'No such file or directory' H5FD_open open failed H5F_open unable to open file: time = Thu Oct 24 09:56:08 2013 , name = 'c:\test\kwave_output_data24-Oct-2013-09-56-03.h5', tent_flags = 0 H5Fopen unable to open file Error in h5read (line 59) [data,var_class] = h5readc(Filename,Dataset,start,count,stride); Error in kspaceFirstOrder3DC (line 225) sensor_data = h5read(output_filename, '/p'); qiangbo on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-3848 Wed, 07 Aug 2013 22:31:20 +0000 qiangbo 3848@http://www.k-wave.org/forum/ Jiri, Thanks for your response. The problem is solved. There was a strange user right policy on the computer. Bo Jiri Jaros on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-3845 Tue, 06 Aug 2013 20:12:32 +0000 Jiri Jaros 3845@http://www.k-wave.org/forum/ Hi Bo, Yes, you can change the default location of the C++ I/O files. Open file kspaceFirstOrder3DC.m and locate <pre><code>date_string = getDateString; input_filename = [tempdir 'kwave_input_data' date_string '.h5']; output_filename = [tempdir 'kwave_output_data' date_string '.h5'];</code></pre> Then you can change tempdir variable to point at a different location. Jiri qiangbo on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-3844 Mon, 05 Aug 2013 19:29:18 +0000 qiangbo 3844@http://www.k-wave.org/forum/ Hi Jiri, The h5 file was created and I can find it in the TEMP folder. There is a lot of disk space in the drive. Could the default location be changed, at least to try a different folder to see if the same error pops up. Thanks for your reply. Bo Jiri Jaros on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-3843 Mon, 05 Aug 2013 19:11:57 +0000 Jiri Jaros 3843@http://www.k-wave.org/forum/ Hi Bo. This is an interesting error. Could you check, if MATLAB succeeded with the creation of the kwave_input_data_.....h5 file. If it did, than it means, you can write into your TEMP folder (no user permission issues). Otherwise, there's something wrong with your TEMP folder. If the input file was created and the output one could not be, then I'd bet that you don't have enough disk space on your C disk drive. Could you check this please? Jiri qiangbo on "problem when running kspaceFirstOrder3DC()" http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-3842 Mon, 05 Aug 2013 16:48:21 +0000 qiangbo 3842@http://www.k-wave.org/forum/ Hi, When I change kspaceFirstOrder3D() to kspaceFirstOrder3DC(), Matlab reports the following error: Error: File "C:\Users\m066760\AppData\Local\Temp\kwave_output_data05-Aug-2013-10-40-57.h5" could not be created! Thanks Bo