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Due to decelerating gains in single-core CPU performance, computationally expensive simulations are increasingly executed on highly parallel hardware platforms. Agent-based simulations, where simulated entities act with a certain degree of…
Agent-based modeling plays an essential role in gaining insights into biology, sociology, economics, and other fields. However, many existing agent-based simulation platforms are not suitable for large-scale studies due to the low…
Agent-based cellular models simulate tissue evolution by capturing the behavior of individual cells, their interactions with neighboring cells, and their responses to the surrounding microenvironment. An important challenge in the field is…
We propose a simulation-based approach for performance modeling of parallel applications on high-performance computing platforms. Our approach enables full-system performance modeling: (1) the hardware platform is represented by an abstract…
Maximizing the performance potential of the modern day GPU architecture requires judicious utilization of available parallel resources. Although dramatic reductions can often be obtained through straightforward mappings, further performance…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
Computational biology has increasingly turned to agent-based modeling to explore complex biological systems. Biological diffusion (diffusion, decay, secretion, and uptake) is a key driver of biological tissues. GPU computing can vastly…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
Currently, agent-based simulation frameworks force the user to choose between simulations involving a large number of agents (at the expense of limited agent reasoning capability) or simulations including agents with increased reasoning…
This article presents an automatic approach to quickly derive a good solution for hardware resource partition and task granularity for task-based parallel applications on heterogeneous many-core architectures. Our approach employs a…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the…
Multiscale simulations are essential in the biomedical domain to accurately model human physiology. We present a modular approach for designing, constructing and executing multiscale simulations on a wide range of resources, from desktops…
Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase…
The development and the implementation of a Particle-in-Cell code written in the Unified Parallel C (UPC) language for plasma simulations with application to astrophysics and fusion nuclear energy machines are presented. A simple one…
Many important computational problems require utilization of high performance computing (HPC) systems that consist of multi-level structures combining higher and higher numbers of devices with various characteristics. Utilizing full power…
Comprehending the performance bottlenecks at the core of the intricate hardware-software interactions exhibited by highly parallel programs on HPC clusters is crucial. This paper sheds light on the issue of automatically asynchronous MPI…
Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…
Recently, task-based programming models have emerged as a prominent alternative among shared-memory parallel programming paradigms. Inherently asynchronous, these models provide native support for dynamic load balancing and incorporate data…