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Register a new userPerformance Analysis of CP2K Code for Ab Initio Molecular Dynamics
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Added by
Dewi Yokelson
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Using a realistic molecular catalyst system, we conduct scaling studies of ab initio molecular dynamics simulations using the CP2K code on both Intel Xeon CPU and NVIDIA V100 GPU architectures. We explore using process placement and affinity to gain additional performance improvements. We also use statistical methods to understand performance changes in spite of the variability in runtime for each molecular dynamics timestep. We found ideal conditions for CPU runs included at least four MPI ranks per node, bound evenly across each socket, and fully utilizing processing cores with one OpenMP thread per core, no benefit was shown from reserving cores for the system. The CPU-only simulations scaled at 70% or more of the ideal scaling up to 10 compute nodes, after which the returns began to diminish more quickly. Simulations on a single 40-core node with two NVIDIA V100 GPUs for acceleration achieved over 3.7x speedup compared to the fastest single 36-core node CPU-only version, and showed 13% speedup over the fastest time we achieved across five CPU-only nodes.
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We extend the ab initio molecular dynamics (AIMD) method based on density functional theory to the nonequilibrium situation where an electronic current is present in the electronic system. The dynamics is treated using the semi-classical generalized Langevin equation. We demonstrate how the full anharmonic description of the inter-atomic forces is important in order to understand the current-induced heating and the energy distribution both in frequency and in real space.
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