Molecular dynamics performance evaluation with modern computer architecture. (English) Zbl 07250764
Sergeyev, Yaroslav D. (ed.) et al., Numerical computations: theory and algorithms. Third international conference, NUMTA 2019, Crotone, Italy, June 15–21, 2019. Revised selected papers. Part II. Cham: Springer. Lect. Notes Comput. Sci. 11974, 322-329 (2020).
Summary: An important task of chemical biology is to discover the mechanism of recognition and binding between proteins. Despite the simplicity of the ligand-based model, fundamental mechanisms that regulate these interactions are poorly understood. An adequate equipment is mandatory to unravel this scientific challenge, not only through cost savings but also with high-quality results. With this in mind, we performed molecular dynamics simulations using the Gromacs package on two promising platforms: Cavium ThunderX2 ARM based cluster setup and shared-memory Intel based single-node machine. Aforementioned tests were also performed on common Intel based servers as a reference. Acquired results shown that shared-memory machine features the higest performance, although ARM and Intel clutsers are only slightly slower when more than four sockets are employed. During measurements, idle and job-execution consumptions were sampled in order to evaluate the energy required by a single simulation step. Results show that ARM and Intel servers are much less power-hungry with respect to shared-memory machine. The latter, on the other hand, features a decrement in power consumption when more resources are employed. Said unexpected behaviour is later discussed.
For the entire collection see [Zbl 1435.65017].
For the entire collection see [Zbl 1435.65017].
MSC:
| 65-XX | Numerical analysis |
References:
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