How to efficiently use all physical cores?

[jaamarks]

Is there a way to tell whether or not all of the physical cores are being used appropriately? I have been running the MiXeR commands on an interactive compute node with 8 physical cores (1 cpu per core). However, when I execute the linux top command I see that ~87% of the CPUs are idle. This leads me to believe that only 1 physical core is actually being used during the analysis. What do I need to do in order to efficiently use all the cores I have available?