Can't create hdf5 file using batch scripts.

I'm trying to create an hdf5 file to store many large arrays. When I run my test script the lines,

file_name = strcat('/home/usr/test_results1');
h5create(file_name,'variable',[10, Inf],'ChunkSize',[10 1]);

work just fine. When I execute the script as a batch job I get a failure: "Unable to create file with specified filename. Filename may have unsupported characters".

Any thoughts?

Answer 1

[per isakson]

The function, strcat, has no effect in the statement

file_name = strcat('/home/usr/test_results1');

which is equivalent to

file_name = '/home/usr/test_results1';

If you want to combine parts to a file specification use fullfile, Build full file name from parts

I guess your problem is caused by the relative path; your current path isn't the same when you run interactively and with the script. The function, cd, shows the current path.

Answer 2

[Mohammad Abu Zafer Siddik]

Hi,

I am getting the same error; Here is my code.

filename='A_B_C_1';
filename_r=fullfile([filename '.h5']);
filename_r(regexp(filename_r,'[_]'))=[]; % remove "_" from filename
fcpl = H5P.create('H5P_FILE_CREATE');
fapl = H5P.create('H5P_FILE_ACCESS');
fileID=H5F.create(filename_r,'H5F_ACC_TRUNC',fcpl,fapl);

Would you guys have any idea how can i solve this issue?

Error:
Error using hdf5lib2
Unable to create file with specified filename. Filename may have unsupported characters.

Error in H5F.create (line 40)
file_id = H5ML.hdf5lib2('H5Fcreate', varargin{:});

Thanks in advance

[per isakson]

Post this as a new question.

[Walter Roberson]

Instead of using regexp to remove the _ it would seem to make more sense to use

filename_r(filename_r == '_') = [];

Is that the exact filename you are using? The code works on my system.

[Mohammad Abu Zafer Siddik]

Thanks Walter, I really appreciate it.

Yes. Sometimes it works sometimes it don't work. Now it works for my system as well.