"Is this because of compression when the .mat file is saved?"
No, it is beacuse the .mat file includes the date and time when it was created/modified:
You can also see this very simply by opening a (non-compressed) .mat file in a text editor.
"Is there any way to get around this?"
No.
You could in theory remove the preamble part of the .mat file and hash the rest, but
- that is not a trival task,
- you would have to take into account different .mat file versions,
- it does not work with the recent compressed .mat file versions.
The MATLAB documentation shows this interactive approach, which does not help you much:
The simplest code-based approach with the least effort is probably this:
A = load(matfile1);
B = load(matfile2);
isequal(A,B)
