相关论文: OpenACC Acceleration of an Agent-Based Biological …
Researchers in biology are faced with the tough challenge of developing high-performance computer simulations of their increasingly complex agent-based models. BioDynaMo is an open-source agent-based simulation platform that aims to…
Multiphase compressible flows are often characterized by a broad range of space and time scales. Thus entailing large grids and small time steps, simulations of these flows on CPU-based clusters can thus take several wall-clock days.…
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…
A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…
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…
The Particle-In-Cell (PIC) method is a computational technique widely used in plasma physics to model plasmas at the kinetic level. In this work, we present our effort to prepare the semi-implicit energy-conserving PIC code ECsim for…
Agent-based modeling is indispensable for studying complex systems across many domains. However, existing simulation platforms exhibit two major issues: performance and modularity. Low performance prevents simulations with a large number of…
GPUs are the heart of the latest generations of supercomputers. We efficiently accelerate a compressible multiphase flow solver via OpenACC on NVIDIA and AMD Instinct GPUs. Optimization is accomplished by specifying the directive clauses…
We present a portable platform, called PIC_ENGINE, for accelerating Particle-In-Cell (PIC) codes on heterogeneous many-core architectures such as Graphic Processing Units (GPUs). The aim of this development is efficient simulations on…
The rapid development in computing technology has paved the way for directive-based programming models towards a principal role in maintaining software portability of performance-critical applications. Efforts on such models involve a least…
This work presents a comprehensive performance analysis and optimization of a multiscale agent-based cellular simulation. The optimizations applied are guided by detailed performance analysis and include memory management, load balance, and…
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…
Motivation: Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulators do not always take full advantage of modern hardware and often have a field-specific software design. Results:…
Open-source simulation tools play a crucial role for neuromorphic application engineers and hardware architects to investigate performance bottlenecks and explore design optimizations before committing to silicon. Reconfigurable…
Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale…
This paper presents the GPU porting through OpenACC directives of the Dutch Atmospheric Large-Eddy Simulation (DALES) application, a high-resolution atmospheric model. The code is written in Fortran~90 and features parallel (distributed)…
Agent-based simulation is an indispensable paradigm for studying complex systems. These systems can comprise billions of agents, requiring the computing resources of multiple servers to simulate. Unfortunately, the state-of-the-art…
This paper deals with the cellular biological network analysis of the tumor-growth model, consisting of multiple spaces and time scales. In this paper, we present a model in graph simulation using ABM for tumor growth. In particular, we…
The use of high-fidelity computational simulations promises to enable high-throughput hypothesis testing and optimisation of cancer therapies. However, increasing realism comes at the cost of increasing computational requirements. This…
We utilize the Open Accelerator (OpenACC) approach for graphics processing unit (GPU) accelerated particle-resolved thermal lattice Boltzmann (LB) simulation. We adopt the momentum-exchange method to calculate fluid-particle interactions to…