[R] How to speed up R program

[Ragia .]

Dear group
I have two R sessions  running on Ubuntu 14.0x server , and I found that my program will take too long time to be finished( months...!), I used top command and found that   cpu usage is 21.3%. 

the server is Enterprise SP-64 - 64G E5-1630v3 SoftRaid 2x2 TB Server . 6 core

how can I speed the program, kindly I need tutorial or book chapter that helps..
thanks in advance
Ragia