This issue occurs because the temporary directory for FileDependencies is added to the MATLAB path only, and not to the system path. This is the expected behavior. If you are using Release R2006b or later, use the getFileDependencyDir function in your task function to locate the executable on the workers' path, for example:
ddir = getFileDependencyDir;
cdir = cd(ddir);
[OK, output] = system('myexecutable');
cd(ddir);
The getFileDependencyDir function does not ship with versions of MATLAB Distributed Computing Engine prior to Release R2006b. If you are using an older version, download the attached P-file, getFileDependencyDir.p, and make it available to your workers via the "FileDependencies" property of the job:
set(job, 'FileDependencies', {'myFile.exe', 'getFileDependencyDir.p'})
In your task code, use getFileDependencyDir in the same way as shown above, i.e., have the workers navigate to the directory containing the executable to run it from there.
An alternative to using "FileDependencies" is to put the executable on a shared file system accessible to all workers and update the system paths of all workers to include the path to the executable.
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