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Fig. 3 | Genome Biology

Fig. 3

From: MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions

Fig. 3

Benchmarking MoDLE and OpenMM. A Median memory usage (in MBs) of MoDLE with multithreading (blue) compared to OpenMM with GPU (orange) for chromosome regions ranging in size from 1 to 250 Mbp. Inset shows comparison between MoDLE (blue) OpenMM with CPU (gray) for chromosome regions ranging in size from 1 to 5 Mbp. B Median elapsed execution time (hours) of MoDLE with multithreading (blue), OpenMM with CPU (gray), OpenMM with GPU (orange), and the ratio of OpenMM (GPU) to MoDLE. Dotted lines are extrapolated. C Comparison of the median elapsed execution time (seconds) of MoDLE with (blue) and without (pink) multithreading for chromosome regions ranging in size from 1 to 500 Mbp. D Comparison of median elapsed execution time (hours) of MoDLE utilizing from 1 to 52 CPU cores. Blue line shows elapsed wall clock time (hours), whereas the orange line shows the CPU time (hours). The dotted line illustrates the corresponding theoretical perfect scaling of the executing time. Green line shows median peak memory usage (right axis; MB)

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