problem when running kspaceFirstOrder3DC()

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problem when running kspaceFirstOrder3DC()

(18 posts) (11 voices)

Started 11 years ago by qiangbo
Latest reply from mapesir

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 11 years ago #
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 11 years ago #
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 11 years ago #
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 11 years ago #
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 11 years ago #
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 11 years ago #
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 11 years ago #
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 #
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 #
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 #
Bradley Treeby

Developer
Joined: Mar '10
Posts: 1,643

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 #
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 #
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 #
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 3 years ago #
Bradley Treeby

Developer
Joined: Mar '10
Posts: 1,643

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 3 years ago #
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 2 years ago #
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 5 months ago #
mapesir

Member
Joined: Sep '24
Posts: 1

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

Posted 2 months ago #

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problem when running kspaceFirstOrder3DC()

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