Choosing the appropriate thread level

The blast portion of the analysis is the most time-consuming though the run time can be greatly reduced by spreading the job over many CPU cores. The goal is use as many CPUs as are available on your machine. The sample configuration on the Quick Start page would be appropriate if your machine has at least 24 CPUs. That is, you must multiply the thread number by the CPU number in the configuration to determine how many CPUs will be utilized, which is , in that example. The sequence_num in the configuration file determines how many sequences go to each CPU. The optimal solution is satisfy the equation:

where n is the total number of sequences, i is the subset size, t is the thread number, and c is the CPU number.

If,

then you will not be using c CPUs; you will be using CPUs instead.