What I was doing was wrong way to do things as describe in this post . I also got reply from MATLAB Support Team.
FROM MATLAB SUPPORT
JARs generated using Builder JA are generally platform independent, only if they do not use MEX files internally (as those are platform dependent). So it may be possible for you to use a Java package (jar file) in Linux platform that was originally created in the Windows platform if it does not use mex files and other toolbox functions that are OS-dependent.
Also, it is necessary for you to download the correct version of MATLAB Compiler Runtime for your Linux platform. Please refer the following link for more information.
For your question related to verifying whether MCR is installed, we just need to check the directory structure and verify if the path to MCR libraries is prepended to the "LD_LIBRARY_PATH" environment variable. The path described in MATLAB R2016a documentation is correct. Here, "matlabroot" stands for the root folder where the matlab files are installed and corresponds to a location depending on where you installed MCR on your system.
I suggest you to try compiling a simple program like magic square on the Windows platform and test this on the Linux platform using a driver program that calls the jar file. This will also help you verify if MCR is functioning correctly.