If you’ve still using chemfp-1.0 then have I got a treat for you! The new release includes many performance optimizations. When chemfp starts, it looks at your CPU to figure out the fastest popcount method. The built-in POPCNT instruction is about 4x faster than the byte table lookup. It can use OpenMP to take advantage of multiple cores. There’s even special functions for symmetric searches. On some benchmarks, the new code is 30x faster than the old one.
There are other ...Continue Reading →