Does the C++ code support u_non_staggered

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Does the C++ code support u_non_staggered

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Started 8 years ago by twistor59
Latest reply from twistor59

twistor59

Member
Joined: Sep '15
Posts: 4

Hi, I've been using k-wave to perform 40Khz airborne ultrasound simulations, and have a need to be able to plot the intensities in the acoustic field. For this purpose, I believe the code would need access to u_non_staggered. I added what I believe is the appropriate parameter set to record:

% define the field parameters to record
sensor.record = {'p', 'p_final', 'u', 'I'};

The presence of 'I' automatically makes a request for u_non_staggered. When running this using the C++ binaries, however, I encounter the error 'ux_non_staggered' doesn't exist - see trace:

Running k-Wave simulation...
start time: 08-Aug-2016 08:49:35
reference sound speed: 343m/s
dt: 500ns, t_end: 1ms, time steps: 2001
input grid size: 236 by 236 by 236 grid points (168.6417 by 168.6417 by 168.6417mm)
maximum supported frequency: 240kHz
expanding computational grid...
computational grid size: 256 by 256 by 256 grid points
precomputation completed in 7.2038s
saving input files to disk...
completed in 3.5143s
--------------------------------
kspaceFirstOrder3D-OMP v1.1
--------------------------------
List of enabled parameters:
Input file /private/tmp/kwave_input_data08-Aug-2016-08-49-35.h5
Output file /private/tmp/kwave_output_data08-Aug-2016-08-49-35.h5

Number of threads 8
Verbose interval[%] 5
Compression level 0

Benchmark flag 0
Benchmark time steps 0

Checkpoint_file
Checkpoint_interval 0

Store p_raw 1
Store p_rms 0
Store p_max 0
Store p_min 0
Store p_max_all 0
Store p_min_all 0
Store p_final 1

Store u_raw 1
Store u_non_staggered_raw 1
Store u_rms 0
Store u_max 0
Store u_min 0
Store u_max_all 0
Store u_min_all 0
Store u_final 0

Copy sensor mask 0

Collection begins at 1
Number of CPU threads: 8
Domain dims: [ 256, 256, 256]
Simulation time steps: 2001
--------------------------------
........ Initialization ........
Memory allocation ..........Done
Data loading................Done
Elapsed time: 0.33s
--------------------------------
.......... Computation .........
FFT plans creation..........Done
Pre-processing phase........Done
Current memory in use: 1900112MB
Elapsed time: 6.51s
-------------------------------------------------------------
....................... Simulation ..........................
Progress...ElapsedTime........TimeToGo......TimeOfTermination

........

-------------------------------------------------------------
Elapsed time: 1967.82s
-------------------------------------------------------------
Post-processing phase.......Done
Elapsed time: 0.32s
--------------------------------
............ Summary ...........
Peak memory in use: 1913592MB
Total execution time: 1975.68s
--------------------------------
End of computation
--------------------------------
Error using h5readc
The HDF5 library encountered an error and produced the following stack trace information:

H5G_loc_find_cb object 'ux_non_staggered' doesn't exist
H5G_traverse_real traversal operator failed
H5G_traverse internal path traversal failed
H5G_loc_find can't find object
H5Dopen2 not found

Error in h5read (line 58)
[data,var_class] = h5readc(Filename,Dataset,start,count,stride);

Error in kspaceFirstOrder3DC (line 462)
sensor_data.ux_non_staggered = h5read(output_filename, '/ux_non_staggered');

Error in uharray (line 301)
sensor_data = kspaceFirstOrder3DC(kgrid, medium, source, sensor, 'PMLInside', false);

As the simulations are quite intensive, I need the C++ code - Matlab alone would be a bit slow for this. The question I have is whether or not this is already supported in the C++ code. If yes, I must be doing something wrong. If not, I'm happy to have a dig around the code to see what I need to modify. I just thought I'd check with people in the know before I go down this route!

Posted 8 years ago #
Jiri Jaros

Developer
Joined: Feb '12
Posts: 115

Hi twistor59
The u_non_staggered flag is supported by the C++ version 1.1. Could you call h5ls on the output file to take a look what happened. Alternatively, could you try to run the code outside matlab (providing the input file, and the list of sampling flags).

I can also see you made some changes in the code, maybe something went wrong.
I'd recommend you downloading the latest official version. If it doesn't help, send me the script and I'll take a look

Jiri

Posted 8 years ago #
twistor59

Member
Joined: Sep '15
Posts: 4

Hi Jiri,

thanks for the response. Sorry I've been a bit slow in getting back, I ran h5ls on the output file:

h5ls kwave_output_data28-Oct-2016-08-41-04.h5
Nt Dataset {1, 1, 1}
Nx Dataset {1, 1, 1}
Ny Dataset {1, 1, 1}
Nz Dataset {1, 1, 1}
absorbing_flag Dataset {1, 1, 1}
alpha_power Dataset {1, 1, 1}
c_ref Dataset {1, 1, 1}
dt Dataset {1, 1, 1}
dx Dataset {1, 1, 1}
dy Dataset {1, 1, 1}
dz Dataset {1, 1, 1}
nonlinear_flag Dataset {1, 1, 1}
nonuniform_grid_flag Dataset {1, 1, 1}
p Dataset {1, 501, 25488}
p0_source_flag Dataset {1, 1, 1}
p_final Dataset {256, 256, 128}
p_source_flag Dataset {1, 1, 1}
p_source_many Dataset {1, 1, 1}
p_source_mode Dataset {1, 1, 1}
pml_x_alpha Dataset {1, 1, 1}
pml_x_size Dataset {1, 1, 1}
pml_y_alpha Dataset {1, 1, 1}
pml_y_size Dataset {1, 1, 1}
pml_z_alpha Dataset {1, 1, 1}
pml_z_size Dataset {1, 1, 1}
t_index Dataset {1, 1, 1}
transducer_source_flag Dataset {1, 1, 1}
ux Dataset {1, 501, 25488}
ux_non_staggered01 Dataset {1, 501, 25488}
ux_source_flag Dataset {1, 1, 1}
uy Dataset {1, 501, 25488}
uy_non_staggered Dataset {1, 501, 25488}
uy_source_flag Dataset {1, 1, 1}
uz Dataset {1, 501, 25488}
uz_non_staggered\ Vh\371\257\177 Dataset {1, 501, 25488}
uz_source_flag Dataset {1, 1, 1}

Clearly the non_staggered filenames seem to have been corrupted. I tried running the C object outside Matlab:

/Users/philjones/FEM/k-wave/k-Wave/binaries/kspaceFirstOrder3D-OMP -i /private/tmp/kwave_input_data28-Oct-2016-09-58-19.h5 -o /private/tmp/kwave_output_data28-Oct-2016-09-58-19.h5 --p_raw --p_final --u_raw --u_non_staggered_raw

I'm still getting the strange non_staggered filenames:

h5ls kwave_output_data28-Oct-2016-09-58-19.h5
Nt Dataset {1, 1, 1}
Nx Dataset {1, 1, 1}
Ny Dataset {1, 1, 1}
Nz Dataset {1, 1, 1}
absorbing_flag Dataset {1, 1, 1}
alpha_power Dataset {1, 1, 1}
c_ref Dataset {1, 1, 1}
dt Dataset {1, 1, 1}
dx Dataset {1, 1, 1}
dy Dataset {1, 1, 1}
dz Dataset {1, 1, 1}
nonlinear_flag Dataset {1, 1, 1}
nonuniform_grid_flag Dataset {1, 1, 1}
p Dataset {1, 501, 25488}
p0_source_flag Dataset {1, 1, 1}
p_final Dataset {256, 256, 128}
p_source_flag Dataset {1, 1, 1}
p_source_many Dataset {1, 1, 1}
p_source_mode Dataset {1, 1, 1}
pml_x_alpha Dataset {1, 1, 1}
pml_x_size Dataset {1, 1, 1}
pml_y_alpha Dataset {1, 1, 1}
pml_y_size Dataset {1, 1, 1}
pml_z_alpha Dataset {1, 1, 1}
pml_z_size Dataset {1, 1, 1}
t_index Dataset {1, 1, 1}
transducer_source_flag Dataset {1, 1, 1}
ux Dataset {1, 501, 25488}
ux_non_staggered01 Dataset {1, 501, 25488}
ux_source_flag Dataset {1, 1, 1}
uy Dataset {1, 501, 25488}
uy_non_staggered Dataset {1, 501, 25488}
uy_source_flag Dataset {1, 1, 1}
uz Dataset {1, 501, 25488}
uz_non_staggered04 Dataset {1, 501, 25488}
uz_source_flag Dataset {1, 1, 1}

I could try doing a clean rebuild of the C code. Incidentally I'm working on OS/X 10.10.4. I originally built with g++-5 and had to set the linking in the Makefile to Dynamic (static linking doesn't work on OS/X) I'm not sure if this could cause problems.

Posted 8 years ago #
twistor59

Member
Joined: Sep '15
Posts: 4

I found the problem: there is a small bug in line 104 of OutputHDF5Stream.h in the c++ code: The string allocation needs an extra byte to include space for the null character, i.e. this->HDF5_RootObjectName = new char[1+strlen(HDF5_RootObjectName)];

Without this the filenames were being corrupted as shown in the h5ls dump

Posted 8 years ago #

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k-Wave

A MATLAB toolbox for the time-domain simulation of acoustic wave fields

Does the C++ code support u_non_staggered

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A MATLAB toolbox for the time-domain
simulation of acoustic wave fields