ALLPATHS-LG much faster with Transparent Huge Pages

Starting with version 2.6.38, the Linux kernel allows for Transparent Huge Pages (THP), a mechanism whereby memory pages of size 2MB are used in ‘situations where they would be useful’, rather than the standard 4KB pages. We have found that for large assemblies ALLPATHS-LG is ~33% faster! THP is enabled by default in CENTOS 6 and can be turned on in other kernels (≥ 2.6.38). More information is here. You should also use ALLPATHS-LG revision ≥ 37727 which has been appropriately modified for use with THP.