Running simulation code using GEANT4 (large Monte Carlo C++ simulation framework, lots of shared libraries). Compiled and linked GEANT and my app with gold linker and with stand
As far as the statistics go, lowest time taken is not a valid measure. If you are really curious you need to compute the average time to completion for each program, then divide the difference in the averages by the standard deviation of the pooled sample.
Suppose both programs had the exact same average time to completion, but one always took the same amount of time, the other had huge variation. Picking the one with the single fastest completion would always choose the latter, even though the more consistent program is the one with better performance.