The parallel implementation of MUPHY,a concurrent multiscale code for large-scale hemodynamic simulations in anatomically realistic geometries,for multi-GPU platforms is presented.Performance tests show excellent resu...The parallel implementation of MUPHY,a concurrent multiscale code for large-scale hemodynamic simulations in anatomically realistic geometries,for multi-GPU platforms is presented.Performance tests show excellent results,with a nearly linear parallel speed-up on up to 32GPUs and a more than tenfold GPU/CPU acceleration,all across the range of GPUs.The basic MUPHY scheme combines a hydrokinetic(Lattice Boltzmann)representation of the blood plasma,with a Particle Dynamics treatment of suspended biological bodies,such as red blood cells.To the best of our knowledge,this represents the first effort in the direction of laying down general design principles for multiscale/physics parallel Particle Dynamics applications in non-ideal geometries.This configures the present multi-GPU version of MUPHY as one of the first examples of a high-performance parallel code for multiscale/physics biofluidic applications in realistically complex geometries.展开更多
The spatial domain of Molecular Dynamics simulations is usually a regular box that can be easily divided in subdomains for parallel processing.Recent efforts aimed at simulating complex biological systems,like the blo...The spatial domain of Molecular Dynamics simulations is usually a regular box that can be easily divided in subdomains for parallel processing.Recent efforts aimed at simulating complex biological systems,like the blood flow inside arteries,require the execution of Parallel Molecular Dynamics(PMD)in vessels that have,by nature,an irregular shape.In those cases,the geometry of the domain becomes an additional input parameter that directly influences the outcome of the simulation.In this paper we discuss the problems due to the parallelization of MD in complex geometries and show an efficient and general method to perform MD in irregular domains.展开更多
文摘The parallel implementation of MUPHY,a concurrent multiscale code for large-scale hemodynamic simulations in anatomically realistic geometries,for multi-GPU platforms is presented.Performance tests show excellent results,with a nearly linear parallel speed-up on up to 32GPUs and a more than tenfold GPU/CPU acceleration,all across the range of GPUs.The basic MUPHY scheme combines a hydrokinetic(Lattice Boltzmann)representation of the blood plasma,with a Particle Dynamics treatment of suspended biological bodies,such as red blood cells.To the best of our knowledge,this represents the first effort in the direction of laying down general design principles for multiscale/physics parallel Particle Dynamics applications in non-ideal geometries.This configures the present multi-GPU version of MUPHY as one of the first examples of a high-performance parallel code for multiscale/physics biofluidic applications in realistically complex geometries.
文摘The spatial domain of Molecular Dynamics simulations is usually a regular box that can be easily divided in subdomains for parallel processing.Recent efforts aimed at simulating complex biological systems,like the blood flow inside arteries,require the execution of Parallel Molecular Dynamics(PMD)in vessels that have,by nature,an irregular shape.In those cases,the geometry of the domain becomes an additional input parameter that directly influences the outcome of the simulation.In this paper we discuss the problems due to the parallelization of MD in complex geometries and show an efficient and general method to perform MD in irregular domains.
