k-Wave

1. qiangbo
   

   Member
   Joined: Jul '13
   Posts: 15

   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

   Posted 10 years ago #

2. Jiri Jaros
   

   Developer
   Joined: Feb '12
   Posts: 115

   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

   Posted 10 years ago #

3. qiangbo
   

   Member
   Joined: Jul '13
   Posts: 15

   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

   Posted 10 years ago #

4. Jiri Jaros
   

   Developer
   Joined: Feb '12
   Posts: 115

   Hi Bo,

   Yes, you can change the default location of the C++ I/O files.
   Open file kspaceFirstOrder3DC.m and locate

   date_string = getDateString;
   input_filename = [tempdir 'kwave_input_data' date_string '.h5'];
   output_filename = [tempdir 'kwave_output_data' date_string '.h5'];

   Then you can change tempdir variable to point at a different location.

   Jiri

   Posted 10 years ago #

5. qiangbo
   

   Member
   Joined: Jul '13
   Posts: 15

   Jiri,

   Thanks for your response. The problem is solved. There was a strange user right policy on the computer.

   Bo

   Posted 10 years ago #

6. zhili
   

   Member
   Joined: Oct '13
   Posts: 7

   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');

   Posted 10 years ago #

7. zhili
   

   Member
   Joined: Oct '13
   Posts: 7

   Jiri:
   It seems to be ok to run in my PC, I will figure it out and sorry for the confusion.

   thanks

   Posted 10 years ago #

8. mattouB
   

   Member
   Joined: Apr '16
   Posts: 1

   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

   Posted 8 years ago #

9. Jiri Jaros
   

   Developer
   Joined: Feb '12
   Posts: 115

   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

   Posted 8 years ago #

10. ruben
    

    Member
    Joined: Apr '20
    Posts: 1

    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

    Posted 4 years ago #

11. Bradley Treeby
    

    Developer
    Joined: Mar '10
    Posts: 1,640

    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.

    Posted 4 years ago #

12. arunima0111
    

    Member
    Joined: Oct '19
    Posts: 1

    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

    Posted 4 years ago #

13. Jiri Jaros
    

    Developer
    Joined: Feb '12
    Posts: 115

    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

    Posted 4 years ago #

14. anirudh.parag
    

    Member
    Joined: Jun '21
    Posts: 1

    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

    Posted 2 years ago #

15. Bradley Treeby
    

    Developer
    Joined: Mar '10
    Posts: 1,640

    Hi Anirudh,

    See the discussion here. Note, if you're using a later version of MATLAB (>=2021), you don't need the patch from the MATLAB side any longer.

    Brad.

    Posted 2 years ago #

16. maoqq
    

    Member
    Joined: Oct '21
    Posts: 1

    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

    Posted 1 year ago #

17. DaisyZ
    

    Member
    Joined: Jul '24
    Posts: 1

    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

    Posted 1 week ago #

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