ENCORE: Software for Quantitative Ensemble Comparison
Fig 5
Computational scaling of ENCORE calculations.
We determined how the runtime of ENCORE scales with (A) the number of computer cores when executing ENCORE in a parallel fashion and (B) when varying the number of frames for a fixed number of computer cores. In (A) the black line illustrates how the pairwise RMSD calculation can be sped up by distributing the calculations over multiple cores. As the clustering and dimensionality reduction methods that have so far been implemented have not been parallelized they appear as horizontal lines that will eventually (above 8–16 cores) limit the overall calculations. In (B) we show how the overall runtime increases for both the RMSD calculations, clustering and dimensionality reduction as the number of frames are also increased. We used 16 processor cores for the calculations.