GROMACS 5.1 vs 2016 performance in GPU-accelerated ceramide pull simulations

2016-06-09T15:35:38Z (GMT) by Szilárd Páll Magnus Lundborg

Computational modeling of the skin barrier, the lipid matrix of the stratum corneum, using molecular dynamics simulations. These studies give further insight about the largest organ in the human body and will further clinical experiments. Thanks to the highly optimized heterogeneous parallelization in GROMACS, complex computational studies can be carried out quickly and efficiently. The right panel shows the modeled molecular system with ceramide molecules in green, cholesterols in white, and fatty acids in red.

Recent work focused on improving SIMD, GPU, and thread parallelization and resulted in speeding up the aforementioned calculations by up to 50%. The left panel illustrates the execution time breakdown of the CPU and GPU tasks in GROMACS versions 5.1 and 2016; improved performance of multiple tasks leads to an increase in simulation throughput from 61 ns/day to 95 ns/day.

The simulations were performed on a workstation equipped with a Core i7-5960X CPU and a GeForce TITAN X GPU.

Benchmarks and performance illustration (left panel) by S.P., the ceramide system model and rendering by M.L.