Abstract
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.
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Breuza, E., Colombo, G., Gregori, D., Marchetti, F. (2020). Molecular Dynamics Performance Evaluation with Modern Computer Architecture. In: Sergeyev, Y., Kvasov, D. (eds) Numerical Computations: Theory and Algorithms. NUMTA 2019. Lecture Notes in Computer Science(), vol 11974. Springer, Cham. https://doi.org/10.1007/978-3-030-40616-5_26
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DOI: https://doi.org/10.1007/978-3-030-40616-5_26
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