GROMACS: Atomic Simulations on Massively Parallel Machines

The most highly­ used MD program in recent years is the GROMACS molecular simulation toolkit. GROMACS is cited by ~2,500 scientific articles per year, a rate that has been rapidly increasing recently. GROMACS is known for its high performance and its efficient, effective use of system resources, but new, massively parallel HPC (high-performance computing) architectures present a continuing challenge. At CMB, we are helping to meet this challenge. Specifically, we are working to upgrade GROMACS’ threading framework to keep all CPU cores busy by overlapping computing and communication. This requires careful rescheduling of threads to different tasks during data transfers, which was previously time that threads spent idle. This must be done while avoiding thread-management overhead, which can erode performance gains. Finally, all this has to be done within the narrow two millisecond window when GROMACS computes atom positions, forces, etc. for the next simulation step. To meet this goal, we are developing a new threading framework, called STS (static thread scheduler) (https://github.com/eblen/sts) and integrating it into GROMACS.

Funding provided through the INTEL(R) IPCC Program

This research uses the Cori KNL machine of the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility operated under Contract No. DE-AC02-05CH11231.