http://www.k-wave.org/forum/forum/c-binaries Support for the k-Wave MATLAB toolbox en-US Fri, 06 Mar 2026 01:49:06 +0000 http://bbpress.org/?v=1.0.2 q http://www.k-wave.org/forum/search.php http://www.k-wave.org/forum/topic/issue-with-xxx_outputh5-files#post-9219 Mon, 07 Jul 2025 14:35:39 +0000 mcdannold 9219@http://www.k-wave.org/forum/ <p>Hello,</p> <p>The computing cluster I run kWave code on was recently migrated to RedHat from centOS. The compiled kspaceFirstOrder3DC code seems to be running fine, but there seems to be an issue with the output temporary files. The XXX_output.h5 files are only 1 kB, and there are additional files starting with '.nfs' that are generated (such as '.nfs7eed9ff995d7a06200000304'). These files don't seem to be deleted.</p> <p>I am using matlab2024b. I used to use an older version, but that version was not installed after the OS migration.</p> <p>Any idea what is going on?</p> <p>Thanks,<br /> Nathan </p> http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-9203 Sun, 30 Mar 2025 08:37:44 +0000 Toshini 9203@http://www.k-wave.org/forum/ <p>Hi, </p> <p>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.</p> <p>Error using h5readc<br /> Unable to open 'C:\Users\toshi\AppData\Local\Temp\kwave_output_data29-Mar-2025-14-31-12.h5'. File or folder not found.</p> <p>Error in h5read (line 95)<br /> [data,var_class] = h5readc(Filename,Dataset,start,count,stride);</p> <p>Error in kspaceFirstOrder3DC (line 569)<br /> Nx = h5read(output_filename, '/Nx');</p> <p>Error in kspaceFirstOrder2DG (line 76)<br /> sensor_data = kspaceFirstOrder3DC(kgrid, medium, source, sensor, input_args{:});</p> <p>Error in simSPA (line 36)<br /> sensor_data = kspaceFirstOrder2DG(kgrid, medium, source, sensor, input_args{:});</p> <p>Error in OpticalSimulation (line 299)<br /> simSPA(vmcmesh, vmcmedium, vmcboundary, vmcoptions, kgrid, medium, ...)</p> <p>Thank you. </p> http://www.k-wave.org/forum/topic/running-the-c-code-on-multiple-nodes#post-9193 Thu, 06 Mar 2025 10:37:53 +0000 Jiayi Sun 9193@http://www.k-wave.org/forum/ <p>Would you please also send a email to me? I have the same question. Thank you </p> http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-9146 Thu, 03 Oct 2024 14:45:36 +0000 mapesir 9146@http://www.k-wave.org/forum/ <p>Hi,<br /> 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.</p> <p>For example, the first time pinted:</p> <p>Unable to open '/home/MATLAB/Add-Ons/...'</p> <p>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:</p> <p>Unable to open '/home/MATLAB/MATLAB/Add-Ons/...'</p> <p>How could I fix it?</p> <p>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?</p> <p>Thank you in advance,<br /> Maria </p> http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-9114 Thu, 18 Jul 2024 08:29:59 +0000 DaisyZ 9114@http://www.k-wave.org/forum/ <p>Hi Jiri,</p> <p>I got the same problem. My system is Windows.,with MATLAB 2023b、k-wave version 1.4 and cuda version 1.3.<br /> 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?</p> <p>Thanks for your reply.</p> <p>Nancy </p> http://www.k-wave.org/forum/topic/kspacefirstorder3dc#post-9065 Wed, 20 Mar 2024 19:51:49 +0000 Bradley Treeby 9065@http://www.k-wave.org/forum/ <p>What version of k-Wave are you using? The binaries are now called kspaceFirstOrder-OMP (the same code is used for 2D and 3D). </p> http://www.k-wave.org/forum/topic/kspacefirstorder3dc#post-9034 Thu, 08 Feb 2024 08:54:39 +0000 Corentin Alix 9034@http://www.k-wave.org/forum/ <p>Hello,<br /> I need to run kspaceFirstOrder3DC and I downloaded the CPU binary files for Linux64 ("k-wave-toolbox-version-1.3-cpp-linux-binaries.zip"), but when I unzip there is no kspaceFirstOrder3D-OMP file and therefore the kspaceFirstOrder3DC returns an error.<br /> Could you please tell me where to find this file ?</p> <p>Thank you very much </p> http://www.k-wave.org/forum/topic/kspacefirstorder3dc#post-8831 Tue, 13 Jun 2023 18:46:37 +0000 Bradley Treeby 8831@http://www.k-wave.org/forum/ <p>Try saving the input file somewhere else (on your desktop for example) using the ‘DataPath’ optional input. </p> http://www.k-wave.org/forum/topic/kspacefirstorder3dc#post-8828 Tue, 13 Jun 2023 07:56:53 +0000 QZW 8828@http://www.k-wave.org/forum/ <p>I unzipped the package and put it in the corresponding folder and ran kspaceFirstOrder3DC and the following error occurred</p> <p>h5readc was used incorrectly</p> <p>Unable to open 'C:\Users\ hey \AppData\Local\Temp\kwave_output_data13-Jun-2023-15-52-51.h5'. File or folder not found.</p> <p>I'd like to know how to solve this problem, please </p> http://www.k-wave.org/forum/topic/running-the-c-code-on-multiple-nodes#post-8801 Wed, 07 Jun 2023 12:42:46 +0000 Jiri Jaros 8801@http://www.k-wave.org/forum/ <p>Sent by email :) </p> http://www.k-wave.org/forum/topic/fatal-error-could-not-write-into-dataset-iostream-stream-error#post-8792 Tue, 06 Jun 2023 11:51:25 +0000 Jiri Jaros 8792@http://www.k-wave.org/forum/ <p>It is the problem of HDF5 incompatibility in new Matlab versions, we released a fix in version v1.4 that saves HDF5Atributes using system encoding. </p> http://www.k-wave.org/forum/topic/fatal-error-could-not-write-into-dataset-iostream-stream-error#post-8715 Wed, 08 Mar 2023 06:28:57 +0000 subhadip627@ 8715@http://www.k-wave.org/forum/ <p>Hi<br /> I am facing a compilation problem with the following code, i can't understand the solution as i am a new user for cpp code.</p> <p>clear all<br /> run([getkWavePath 'private/getH5Literals']);<br /> filename = 'input12.h5';</p> <p>% create the computational grid<br /> Nx = 64; % number of grid points in the x direction<br /> Ny = 64; % number of grid points in the y direction<br /> Nz = 64; % number of grid points in the z direction<br /> dx = 0.1e-3; % grid point spacing in the x direction [m]<br /> dy = 0.1e-3; % grid point spacing in the y direction [m]<br /> dz = 0.1e-3; % grid point spacing in the z direction [m]<br /> kgrid = kWaveGrid(Nx, dx, Ny, dy, Nz, dz);</p> <p>% define the properties of the propagation medium<br /> medium.sound_speed = 1500 * ones(Nx, Ny, Nz); % [m/s]<br /> % medium.sound_speed(1:Nx/2, :, :) = 1800; % [m/s]<br /> medium.density = 1000 * ones(Nx, Ny, Nz); % [kg/m^3]<br /> % medium.density(:, Ny/4:end, :) = 1200; % [kg/m^3]<br /> c0=medium.sound_speed;<br /> % make sure the input is in the correct data format<br /> eval(['c0 = ' MATRIX_DATA_TYPE_MATLAB '(c0);']);</p> <p>% save the sound speed matrix<br /> writeMatrix([filename], c0, 'c0');<br /> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br /> % % % % create initial pressure distribution using makeBall<br /> ball_magnitude = 10; % [Pa]<br /> ball_x_pos = 38; % [grid points]<br /> ball_y_pos = 32; % [grid points]<br /> ball_z_pos = 32; % [grid points]<br /> ball_radius = 5; % [grid points]<br /> p_mask = makeBall(Nx, Ny, Nz, ball_x_pos, ball_y_pos, ball_z_pos, ball_radius);<br /> ball_1 = ball_magnitude *p_mask ;</p> <p>source.p0 = ball_1;<br /> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br /> % define a square source mask facing in the x-direction using the<br /> % find linear source indices<br /> p_source_index = find(p_mask == 1);<br /> p_source_index = reshape(p_source_index, [], 1);</p> <p>% make sure the input is in the correct data format<br /> eval(['p_source_index = ' INTEGER_DATA_TYPE_MATLAB '(p_source_index);']);<br /> % save the source index matrix<br /> writeMatrix([filename], p_source_index, 'p_source_index');</p> <p>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br /> % cast matrix to single precision<br /> eval(['ball_1 = ' MATRIX_DATA_TYPE_MATLAB '(ball_1);']);<br /> % save the input signal<br /> writeMatrix([filename], ball_1, 'ball_1');<br /> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br /> % define a sensor mask through the central plane<br /> sensor_mask = false(Nx, Ny, Nz);<br /> sensor_mask(:, :, Nz/2) = 1;</p> <p>% extract the indices of the active sensor mask elements<br /> sensor_mask_index = find(sensor_mask);<br /> sensor_mask_index = reshape(sensor_mask_index, [], 1);</p> <p>% make sure the input is in the correct data format<br /> eval(['sensor_mask_index = ' INTEGER_DATA_TYPE_MATLAB '(sensor_mask_index);']);<br /> sensor.mask=sensor_mask;<br /> % save the sensor mask<br /> writeMatrix([filename], sensor_mask_index, 'sensor_mask_index');<br /> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br /> % write grid parameters<br /> writeGrid([filename], [Nx, Ny, Nz], [dx, dy, dz], ...<br /> [10, 10, 10], [10, 10,10], ...<br /> Nt, dt, 1500);</p> <p>% write flags<br /> writeFlags([filename]);</p> <p>% set additional file attributes<br /> writeAttributes([filename]);</p> <p>kspaceFirstOrder3D(kgrid, medium, source, sensor, 'SaveToDisk', filename);<br /> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</p> <p>here i am able to make .h5 file but while compiling the .h5 file with kspaceFirstOrder-OMP</p> <p>i got ----</p> <p>+---------------------------------------------------------------+<br /> | kspaceFirstOrder-OMP v1.3 |<br /> +---------------------------------------------------------------+<br /> | Reading simulation configuration: Failed |<br /> +---------------------------------------------------------------+<br /> +---------------------------------------------------------------+<br /> | !!! K-Wave experienced a fatal error !!! |<br /> +---------------------------------------------------------------+<br /> | Error: Invalid format of the input file: iostream stream |<br /> | error |<br /> +---------------------------------------------------------------+<br /> | Execution terminated |<br /> +---------------------------------------------------------------+ </p> http://www.k-wave.org/forum/topic/problem-when-running-kspacefirstorder3dc#post-8618 Wed, 05 Oct 2022 07:59:06 +0000 maoqq 8618@http://www.k-wave.org/forum/ <p>Hi,</p> <p>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?</p> <p>Thanks,<br /> Tina </p> http://www.k-wave.org/forum/topic/linux-c-binary-sees-less-nodes-than-job-submission-system-assigns#post-8533 Fri, 13 May 2022 14:12:23 +0000 ahmedsallam 8533@http://www.k-wave.org/forum/ <p>Hello Jiri,</p> <p>Can you also please send me the OpenMPI code? I have sent you an email. </p> <p>Thanks, </p> http://www.k-wave.org/forum/topic/tips-to-keep-memory-requirements-low#post-8498 Thu, 14 Apr 2022 14:05:28 +0000 ahmedsallam 8498@http://www.k-wave.org/forum/ <p>Hello,</p> <p>I'm doing high memory demanding 3D nonlinear simulations and I was wondering if there are some tips or any compromises that can be made which would make the simulation less demanding overall. Are there optimal ways to define the source/sensor masks to save memory, also are there any assumptions that can be made about the propagation medium that would also save memory (linear, lossless, or homogenous)? I also wanted to know if there is a way to reduce the size of the output file not by compression but by not saving certain variables data and so on?</p> <p>Lastly, I really want to thank you for a fantastic and extremely useful tool. </p> http://www.k-wave.org/forum/topic/running-the-c-code-on-multiple-nodes#post-8497 Mon, 11 Apr 2022 19:48:22 +0000 ahmedsallam 8497@http://www.k-wave.org/forum/ <p>Hello,</p> <p>I'm using the c++ code to run large 3D simulations. I was wondering if the code supports the parallelization across multiple nodes in a cluster? I'm trying to provide the simulation with more memory and core resources.</p> <p>Thank you, </p> http://www.k-wave.org/forum/topic/running-simulating-b-mode-ultrasound-images-examples-in-linux-terminal#post-8467 Wed, 02 Mar 2022 07:41:58 +0000 chiragjin 8467@http://www.k-wave.org/forum/ <p>I have successfully resolved the issues myself. This issue can be closed. </p> http://www.k-wave.org/forum/topic/running-simulating-b-mode-ultrasound-images-examples-in-linux-terminal#post-8464 Fri, 25 Feb 2022 15:14:04 +0000 chiragjin 8464@http://www.k-wave.org/forum/ <p>Hi everyone,<br /> I am trying to run a simulation to generate ultrasound b-mode images using the example "Simulating B-mode Ultrasound Images" as a template. I want to run the simulation using kspaceFirstOrder-OMP binary in Linux. </p> <p>The problem is that the medium for each scan line is different in this case so for each scan line there needs to be a different input and output file. Is there any way to run this simulation iteratively so that kspaceFirstOrder-OMP is executed with different input and output files in each iteration?</p> <p>Thanks!!</p> <p>Regards!</p> <p>Chirag </p> http://www.k-wave.org/forum/topic/c-simulations-memory-requirements#post-8441 Tue, 01 Feb 2022 09:09:52 +0000 Bradley Treeby 8441@http://www.k-wave.org/forum/ <p>The C++ code will be more memory efficient, yes, especially if you run it outside of MATLAB. There is a formula given in the user manual that will let you calculate the approximate memory usage. </p> http://www.k-wave.org/forum/topic/c-simulations-memory-requirements#post-8440 Sun, 30 Jan 2022 02:33:03 +0000 ahmedsallam 8440@http://www.k-wave.org/forum/ <p>Hello Dr. Brad,</p> <p>I'm working on memory consuming nonlinear simulations and I wanted to look into the C++ codes. I know the simulations should be faster, however, I was wondering about the memory requirements. Should I expect the C++ simulations to be more memory efficient compared to running the same simulation using MATLAB?</p> <p>Thanks, </p>