Related papers: OpenACC Acceleration of an Agent-Based Biological …
Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial…
To accelerate the solution of large eigenvalue problems arising from many-body calculations in nuclear physics on distributed-memory parallel systems equipped with general-purpose Graphic Processing Units (GPUs), we modified a previously…
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…
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 study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…
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…
Recent increases in supercomputing power, driven by the multi-core revolution and accelerators such as the IBM Cell processor, graphics processing units (GPUs) and Intel's Many Integrated Core (MIC) technology have enabled kinetic…
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.…
We present new results on the strong parallel scaling for the OpenACC-accelerated implementation of the high-order spectral element fluid dynamics solver Nek5000. The test case considered consists of a direct numerical simulation of…
Complex workflows play a critical role in accelerating scientific discovery. In many scientific domains, efficient workflow management can lead to faster scientific output and broader user groups. Workflows that can leverage resources…
High-fidelity simulations of unsteady fluid flow are now possible with advancements in high-performance computing hardware and software frameworks. Since computational fluid dynamics (CFD) computations are dominated by linear algebraic…
As fusion energy devices advance, plasma simulations are crucial for reactor design. Our work extends BIT1 hybrid parallelization by integrating MPI with OpenMP and OpenACC, focusing on asynchronous multi-GPU programming. Results show…
This paper is focused on improving multi-GPU performance of a research CFD code on structured grids. MPI and OpenACC directives are used to scale the code up to 16 GPUs. This paper shows that using 16 P100 GPUs and 16 V100 GPUs can be…
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…
In this paper, we develop a low-order three-dimensional finite-element solver for fast multiple-case crust deformation analysis on GPU-based systems. Based on a high-performance solver designed for massively parallel CPU based systems, we…
Computational fluid dynamics and fluid-structure interaction simulations involving moving and deforming bodies is extremely hard. In this work, we present a graphical processing unit (GPU) optimized implementation of the sharp-interface…
In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated. Biological organs are assumed to follow linear elastostatic material behavior, and constant boundary element is…
In drug discovery, molecular docking is the task in charge of estimating the position of a molecule when interacting with the docking site. This task is usually used to perform screening of a large library of molecules, in the early phase…
GPU architectures have become popular for executing general-purpose programs. Their many-core architecture supports a large number of threads that run concurrently to hide the latency among dependent instructions. In modern GPU…
Novel methods are presented in this initial study for the fusion of GPU kernels in the artificial compressibility method (ACM), using tensor product elements with constant Jacobians and flux reconstruction. This is made possible through the…