How Does Hyperthreading Affect an ALLPATHS-LG Run?

Submitted by John on Thu, 2014-10-23 08:50

In running ALLPATHS-LG, a short read genome assembler, on a Dell PowerEdge R920 with four Xeon E7-4860v2 processors running at 2.60GHz, I did one run with hyperthreading on and one with hyperthreading off. This was mainly to see if the increased cache size on the physical CPU core with hyperthreading off had a positive effect on performance.

I'll take all the anticipation away: Nope. Hyperthreading wins.

No Hyperthreading Hyperthreading
available cpus 24 48
GB of total available memory 1511.6 1511.6
hours of total elapsed time 30.32 28.81
hours of total per-module elapsed 30.33 28.82
hours of total per-module user time 357.57 630.52
effective parallelization factor 11.79 21.88
GB memory usage peak 457.13 457.13
Topic: 
Bioinformatics