I understand that your MATLAB program is taking a large amount of time to run in Linux as compared to Windows. As you mentioned that you code is large, to understand which part of the code is consuming the most time, I would recommend you to do code profiling. You can refer to the following MathWorks documentation to understand more about code profiling.
After doing the profiling, you can now pinpoint the bottlenecks that are causing the slowdown. If after profiling you find out that, the slowdown is related to reading a video, you can refer to the following MATLAB answer which deals with a similar issue. Please note this is just an example issue, your case could be different from the one described in the below MATLAB answer. Once you pinpoint which part of your code is creating the slowdown, you can then take action to resolve the same.
Apart from this, I would recommend you to update your MATLAB version since newer versions come with performance enhancements and bug fixes. You can refer to the following MathWorks documentation for any help required for updating the software.
I hope this helps.
