Vahid Jafari
ABSTRACT
Molecular dynamics (MD) simulations exhibit big computational efforts, which makes them very time-consuming. This particularly holds for molecular-continuum simulations in fluid dynamics, which rely on the simulation of MD ensembles that are coupled to computational fluid dynamics (CFD) solvers. Massively parallel implementations for MD simulations and the respective ensembles are therefore of utmost importance.
However, the more processors are used for the molecular-continuum simulation, the higher the probability of software- and hardware-induced failures or malfunctions of one processor becomes, which may lead to the issue that the entire simulation crashes. To avoid long re-calculation times for the simulation, a fault tolerance mechanism is required, especially considering respective simulations carried out at the exascale.
In this paper, we introduce a fault tolerance method for molecular-continuum simulations implemented in the macro-micro-coupling tool (MaMiCo), an open-source coupling tool for such multiscale simulations which allows the re-use of one’s favorite MD and CFD solvers. The method makes use of a dynamic ensemble handling approach that has been used previously to estimate statistical errors due to thermal fluctuations in the MD ensemble. The dynamic ensemble is always homogeneously distributed and, thus, balanced on the computational resources to minimize the overall induced overhead overhead. The method further relies on an MPI implementation with fault tolerance support. We report scalability results with and without modeled system failures on three TOP500 supercomputers—Fugaku/RIKEN with ARM technology, Hawk/HLRS with AMD EPYC technology and HSUper/Helmut Schmidt University with Intel Icelake processors—to demonstrate the feasibility of our approach.
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Index Terms
- Fault Tolerance for Ensemble-based Molecular-Continuum Flow Simulations
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