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Extreme GPU Computing
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4.5 Accelerating Molecular Dynamics with GROMACS
Figure 14: GROMACS performance and acceleration compared to CPU-only
In this section, we evaluate the performance of the third molecular dynamics application. GROMACS is
short for “Groningen Machine for Chemical Simulations.” The primary usage for GROMACS is simulations
for biochemical molecules (bonded interactions). Because of its efficiency in calculating non-bonded
interactions (atoms not linked by covalent bonds), the user base is expanding to non-biological
systems. GROMACS performance quantified as “ns/day” (inverse of the number of days required to
simulate 1 nanosecond of real-time), the higher score is better. The benchmark ran in GROMACS is the
“Water 0768.”
Figure 14 shows the performance of GROMACS on the five C4130 configurations, and the CPU only
configuration. Among the quad CPU configurations A, B and C, B performs the best. In addition to the
four GPUs attached to CPU1, GROMACS also uses the second CPU2, making B the best performing
configuration. It seems GROMACS benefits from the second CPU as well as the switch. It is likely that
application has substantial GPU to GPU communication. Configuration C outperforms A. This is due to
the balanced nature of C, and additional latency introduced due to the PCIe switch in configuration A.
In the dual GPU configurations D and E, D, which is the balanced of the two, slightly outperforms E.
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