k-Wave User Forum » Topic: Help needed for error = "Invalid format of the input file = iostream error"

k-Wave User Forum » Topic: Help needed for error = "Invalid format of the input file = iostream error" http://www.k-wave.org/forum/topic/help-needed-for-error-invalid-format-of-the-input-file-iostream-error Support for the k-Wave MATLAB toolbox en-US Wed, 13 May 2026 06:52:23 +0000 http://bbpress.org/?v=1.0.2 <![CDATA[Search]]> q http://www.k-wave.org/forum/search.php Bradley Treeby on "Help needed for error = "Invalid format of the input file = iostream error"" http://www.k-wave.org/forum/topic/help-needed-for-error-invalid-format-of-the-input-file-iostream-error#post-7747 Wed, 19 Aug 2020 15:03:54 +0000 Bradley Treeby 7747@http://www.k-wave.org/forum/ Hi Dogu, Before we dive deeper into your script, can I check if you're using MATLAB 2020a? If so, see <a href="http://www.k-wave.org/forum/topic/error-reading-h5-files-when-using-binaries">this post</a> and the work around that is required. Brad. dzaifoglu on "Help needed for error = "Invalid format of the input file = iostream error"" http://www.k-wave.org/forum/topic/help-needed-for-error-invalid-format-of-the-input-file-iostream-error#post-7738 Tue, 18 Aug 2020 20:46:00 +0000 dzaifoglu 7738@http://www.k-wave.org/forum/ Hello, My name is Dogu and I am a PhD student from the mechanical engineering department of the University of Bath. I have been using k-Wave for a while now to simulate ultrasonic wave propagation into human soft tissue, and I am very thankful for this product that you have put forward. I'm at a stage where the simulation I'm running is too large for my machine to handle (6000 by 6000 2D simulation), hence I am getting the task computed on the University's supercomputer system. I have been attempting to run a C++ version of my simulation on the supercomputer, and to do this, I would produce a .h5 file by using the 'SaveToDisk' input of the function kspaceFirstOrder2D, upload it to my allocated space on the uni supercomputer memory and call it in as an input (-i) of the function kspaceFirstOrder-OMP. I am able to successfully generate the .h5 file on my machine with no problems and upload it to the uni server, yet when the uni supercomputer starts running the task, I get the following error message within seconds: "K-Wave experienced a fatal error. Error = invalid format of the input file = iostream error" I have tried a number of things yet I do not understand where this is going wrong. My best guess if that maybe I have a Matlab code line that is not C++ optimised. Below I have attached the the binbash script I use to remotely submit jobs, and the Matlab script that I use to generate the .h5 files. Any help or advice would be much, much appreciated, as time is ticking on my PhD. Many thanks in advance! Best, Dogu =========================================================== Job submission script: [11/08 11:40] James Grant Hi Dogu apologies for the delay here especially as it's quite a trivial issue that I should have spotted previously. Linux file systems are case sensitive so Position2.h5 is different from position2.d5. The copy command cp ../input.h5 . is only needed if the input file is in the directory above, you have it already in the same directory so your jobscript could be: #!/bin/bash #SBATCH --nodes=1 #SBATCH --ntasks-per-node=24 #SBATCH --mem=60000 #SBATCH --time=6:00:00 #SBATCH --job-name=position2 #SBATCH --account=free #SBATCH --partition=batch-sky #SBATCH --mail-user=dz322@bath.ac.uk #SBATCH --output=StdOut.o.%j #SBATCH --error=StdErr.e.%j module purge module load slurm module load matlab module load hdf5/intel module load intel/compiler/64/18.5.274 module load intel/mkl/64/18.5.274 module load fftw3/intel/avx/3.3.4 module load gcc/9.2.0 export OMP_NUM_THREADS=24 export OMP_PLACES=cores export OMP_PROC_BIND=true ../k-Wave/kspaceFirstOrder-OMP/skylake/kspaceFirstOrder-OMP -i position1.h5 -o pos2_out.h5 --checkpoint_file check_pos2 --checkpoint_interval 20000 =========================================================== Matlab script: %4/6/2020 %This is the script file to use to run scans at 5MHz into the human limb %model. %Script originates from the kWave example titled: %Monopole Point Source In A Homogeneous Propagation Medium Example %% % ========================================================================= % GETTING READY % ========================================================================= clearvars; close all; %Number of measurements to take. m = 1; %Create the computational grid %Number of grid points in x and y directions. Nx = 6000; Ny = 6000; %Grid point spacings and side lengths in x and y directions [m]. dx = 2.3438e-05/4; dy = dx; X_SideLength = dx*Nx; Y_SideLength = dy*Ny; %Kwave function to create the medium. kgrid = kWaveGrid(Nx, dx, Ny, dy); % Space between consecutive measurements. Gap = round(0.0005/dx); %Set medium dimensions. medium.sound_speed = zeros(Ny,Nx); medium.density = zeros(Ny,Nx); %Set how long the simulation will go for. EndTime = 100e-6; %% %Define position number. a = 1; %Calculate amount of gap too move by, in gridpoints. Shift = (a-1)*Gap; %Run Medium Generator Function and shift muscle layer accordingly. Then, %assign sound speed and density values. Medium5MHz = MediumGeneratorFctn(Shift); medium.sound_speed = Medium5MHz.SS; medium.density = Medium5MHz.Den; DM_OG = Medium5MHz.DM; %Create the time array (kgrid.makeTime function). kgrid.makeTime(medium.sound_speed); %Set number of timesteps to measure. kgrid.Nt = round(EndTime/kgrid.dt); % ========================================================================= % SOURCE & SENSOR % Define points needed for source size. For 13 mm, half_of_probe = round((0.013/2)/dx); source_freq = 5e6; % [Hz] source_mag = 2/(1500*1000)/65; % [Pa] [display_mask,sensor,source] = SourcenSensor60mm5MHz(a,Nx,Ny,dx,Gap,half_of_probe,source_mag,source_freq,kgrid,DM_OG,medium); % ========================================================================= % EXECUTION OF 2D SIMULATION %Define the acoustic parameters to record sensor.record = {'p', 'p_final'}; %Display Mask as input argument (PML Input can be adjusted here) input_args = {'DisplayMask',display_mask}; % run the simulation filename = 'position1'; sensor_data = kspaceFirstOrder2D(kgrid, medium, source, sensor, input_args{:},'SaveToDisk',filename); %,input_args{:} %Summing SensorData sensor_data_sum = sum(sensor_data.p); ScanData(a,:,:) = sensor_data.p;