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Simulating large-scale microswimmer dynamics in viscous fluid poses significant challenges due to the coupled high spatial and temporal complexity. Conventional high-performance computing (HPC) methods often address these two dimensions in…
Many architects believe that major improvements in cost-energy-performance must now come from domain-specific hardware. This paper evaluates a custom ASIC---called a Tensor Processing Unit (TPU)---deployed in datacenters since 2015 that…
Fast Multipole Methods (FMM) are a fundamental operation for the simulation of many physical problems. The high performance design of such methods usually requires to carefully tune the algorithm for both the targeted physics and the…
This dissertation presents the design, implementation and evaluation of GPU-accelerated simulation frameworks for Evolutionary Spatial Cyclic Games (ESCGs), a class of agent-based models used to study ecological and evolutionary dynamics.…
Phaseless Auxiliary-Field Quantum Monte Carlo (ph-AFQMC) has recently emerged as a promising method for the production of benchmark-level simulations of medium to large-sized molecules, due to its accuracy and favorable polynomial scaling…
The rapid growth of large-scale machine learning (ML) models has led numerous commercial companies to utilize ML models for generating predictive results to help business decision-making. As two primary components in traditional predictive…
Many-body perturbation theory is a powerful method to simulate electronic excitations in molecules and materials starting from the output of density functional theory calculations. By implementing the theory efficiently so as to run at…
Model selection in Gaussian processes scales prohibitively with the size of the training dataset, both in time and memory. While many approximations exist, all incur inevitable approximation error. Recent work accounts for this error in the…
Massively multicore processors, such as Graphics Processing Units (GPUs), provide, at a comparable price, a one order of magnitude higher peak performance than traditional CPUs. This drop in the cost of computation, as any…
The paper presents the aspect of use of modern graphics accelerators supporting CUDA technology for high-performance computing in the field of linear algebra. Fully programmable graphic cards have been available for several years for both…
Recent progress in artificial intelligence (AI) and high-performance computing (HPC) have brought potentially game-changing opportunities in accelerating reactive flow simulations. In this study, we introduce an open-source computational…
The complex regulatory dynamics of a biological network can be succinctly captured using discrete logic models. Given even sparse time-course data from the system of interest, previous work has shown that global optimization schemes are…
The Poisson-Fermi model is an extension of the classical Poisson-Boltzmann model to include the steric and correlation effects of ions and water treated as nonuniform spheres in aqueous solutions. Poisson-Boltzmann electrostatic…
Efficient utilization of GPU resources and power has become critical with the growing demand for GPUs in high-performance computing (HPC). In this paper, we analyze GPU utilization and GPU memory utilization, as well as the power…
Molecular dynamics (MD) is an important research tool extensively applied in materials science. Running MD on a graphics processing unit (GPU) is an attractive new approach for accelerating MD simulations. Currently, GPU implementations of…
We discuss the efficiency of parallelization on graphical processing units (GPUs) for the simulation of the one dimensional Potts model with long range interactions via parallel tempering. We investigate the behaviour of some thermodynamic…
Structural parameters are normally extracted from observed galaxies by fitting analytic light profiles to the observations. Obtaining accurate fits to high-resolution images is a computationally expensive task, requiring many model…
The latest Graphics Processing Units (GPUs) are reported to reach up to 200 billion floating point operations per second (200 Gflops) and to have price performance of 0.1 cents per M flop. These facts raise great interest in the…
This paper presents, to the author's knowledge, the first graphics processing unit (GPU) accelerated program that solves the evolution of interacting scalar fields in an expanding universe. We present the implementation in NVIDIA's Compute…
As an important application of spatial databases in pathology imaging analysis, cross-comparing the spatial boundaries of a huge amount of segmented micro-anatomic objects demands extremely data- and compute-intensive operations, requiring…