White Papers

18
HOOMD-blue benchmark suite
HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs.
Performance results in Figure 9 are reported in hours to complete ten million Monte Carlo sweeps, where one sweep is N trial moves
on 1,048,576 particles for 10e6 steps. HOOMD-blue shows almost linear scaling behavior on both CPUs and GPUs. Unlike the results
from Amber, HOOMD-blue does not take an advantage of Lustre for this hexagon benchmark. All other benchmarks such as liquid,
microsphere, quasicrystal and triblock copolymer benchmarks show identical scaling behavior.
NAMD benchmark on Apoa1, F1atpase and STMV
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. The benchmark
APOA1 (92224 atoms) is a high density lipoprotein found in plasma, which helps extraction of cholesterol from tissues to liver. F1-
ATPase (327506 atoms) is responsible for the synthesis of the molecule adenosine triphosphate. STMV is a small, icosahedral virus,
which worsens the symptoms of infections by tobacco mosaic virus. STMV is a large benchmark case with 1,066,628 atoms.
NAMD scales well over number of cores, number of GPUs and the size of data, as shown in Figure 10, Figure 11 and Figure 12. Like
HOOMD-blue, this simulation tool does take advantage of Lustre storage. The performance from 28 CPU cores with 4 GPUs for all
three simulations becomes worse when Lustre is used. This can be explained by NAMD’s strong dependency on CPUs.
Figure 9: Hexagon benchmark results
Figure 10: APOA1 benchmark results