2 research outputs found
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations
The molecular dynamics simulation package GROMACS runs efficiently on a wide
variety of hardware from commodity workstations to high performance computing
clusters. Hardware features are well exploited with a combination of SIMD,
multi-threading, and MPI-based SPMD/MPMD parallelism, while GPUs can be used as
accelerators to compute interactions offloaded from the CPU. Here we evaluate
which hardware produces trajectories with GROMACS 4.6 or 5.0 in the most
economical way. We have assembled and benchmarked compute nodes with various
CPU/GPU combinations to identify optimal compositions in terms of raw
trajectory production rate, performance-to-price ratio, energy efficiency, and
several other criteria. Though hardware prices are naturally subject to trends
and fluctuations, general tendencies are clearly visible. Adding any type of
GPU significantly boosts a node's simulation performance. For inexpensive
consumer-class GPUs this improvement equally reflects in the
performance-to-price ratio. Although memory issues in consumer-class GPUs could
pass unnoticed since these cards do not support ECC memory, unreliable GPUs can
be sorted out with memory checking tools. Apart from the obvious determinants
for cost-efficiency like hardware expenses and raw performance, the energy
consumption of a node is a major cost factor. Over the typical hardware
lifetime until replacement of a few years, the costs for electrical power and
cooling can become larger than the costs of the hardware itself. Taking that
into account, nodes with a well-balanced ratio of CPU and consumer-class GPU
resources produce the maximum amount of GROMACS trajectory over their lifetime