Parallel Molecular Dynamics with Irregular Domain Decomposition

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 domain

A factored sparse approximate inverse preconditioned conjugate gradient solver on graphics processing units

Graphics Processing Units (GPUs) exhibit significantly higher peak performance than conventional CPUs. However, in general only highly parallel algorithms can exploit their potential. In this scenario, the iterative solution to sparse linear systems of equations could be carried out quite efficiently on a GPU as it requires only matrix-by-vector products, dot products, and vector updates. However, to be really effective, any iterative solver needs to be properly preconditioned and this represents a major bottleneck for a successful GPU implementation. Due to its inherent parallelism, the factored sparse approximate inverse (FSAI) preconditioner represents an optimal candidate for the conjugate gradient-like solution of sparse linear systems. However, its GPU implementation requires a nontrivial recasting of multiple computational steps. We present our GPU version of the FSAI preconditioner along with a set of results that show how a noticeable speedup with respect to a highly tuned CPU counterpart is obtained

Multiscale Hemodynamics Using GPU Clusters

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 geometrie

Parallel Molecular Dynamics with Irregular Domain Decomposition

The spatial domain of Molecular Dynamics simulations is usually a regular box that 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

GPU peer-to-peer techniques applied to a cluster interconnect

Modern GPUs support special protocols to exchange data directly across the PCI Express bus. While these protocols could be used to reduce GPU data transmission times, basically by avoiding staging to host memory, they require specific hardware features which are not available on current generation network adapters. In this paper we describe the architectural modifications required to implement peer-to-peer access to NVIDIA Fermi- and Kepler-class GPUs on an FPGA-based cluster interconnect. Besides, the current software implementation, which integrates this feature by minimally extending the RDMA programming model, is discussed, as well as some issues raised while employing it in a higher level API like MPI. Finally, the current limits of the technique are studied by analyzing the performance improvements on low-level benchmarks and on two GPU-accelerated applications, showing when and how they seem to benefit from the GPU peer-to-peer method.Comment: paper accepted to CASS 201

GPU-optimized approaches to molecular docking-based virtual screening in drug discovery: A comparative analysis

Finding a novel drug is a very long and complex procedure. Using computer simulations, it is possible to accelerate the preliminary phases by performing a virtual screening that filters a large set of drug candidates to a manageable number. This paper presents the implementations and comparative analysis of two GPU-optimized implementations of a virtual screening algorithm targeting novel GPU architectures. This work focuses on the analysis of parallel computation patterns and their mapping onto the target architecture. The first method adopts a traditional approach that spreads the computation for a single molecule across the entire GPU. The second uses a novel batched approach that exploits the parallel architecture of the GPU to evaluate more molecules in parallel. Experimental results showed a different behavior depending on the size of the database to be screened, either reaching a performance plateau sooner or having a more extended initial transient period to achieve a higher throughput (up to 5x), which is more suitable for extreme-scale virtual screening campaigns

Multiscale Hemodynamics Using GPU Clusters

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

The effects of vent location, event scale and time forecasts on pyroclastic density current hazard maps at Campi Flegrei caldera (Italy)

This study presents a new method for producing long-term hazard maps for pyroclastic density currents (PDC) originating at Campi Flegrei caldera. Such method is based on a doubly stochastic approach and is able to combine the uncertainty assessments on the spatial location of the volcanic vent, the size of the flow and the expected time of such an event. The results are obtained by using a Monte Carlo approach and adopting a simplified invasion model based on the box model integral approximation. Temporal assessments are modeled through a Cox-type process including self-excitement effects, based on the eruptive record of the last 15 kyr.Mean and percentilemaps of PDC invasion probability are produced, exploring their sensitivity to some sources of uncertainty and to the effects of the dependence between PDC scales and the caldera sector where they originated. Conditional maps representative of PDC originating inside limited zones of the caldera, or of PDC with a limited range of scales are also produced. Finally, the effect of assuming different time windows for the hazard estimates is explored, also including the potential occurrence of a sequence of multiple events. Assuming that the last eruption of Monte Nuovo (A.D. 1538) marked the beginning of a new epoch of activity similar to the previous ones, results of the statistical analysis indicate a mean probability of PDC invasion above 5% in the next 50 years on almost the entire caldera (with a probability peak of 25% in the central part of the caldera). In contrast, probability values reduce by a factor of about 3 if the entire eruptive record is considered over the last 15 kyr, i.e., including both eruptive epochs and quiescent periods