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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…
General Purpose Graphics Processing Unit (GPGPU) computing plays a transformative role in deep learning and machine learning by leveraging the computational advantages of parallel processing. Through the power of Compute Unified Device…
Recently, hybrid architectures using accelerators like GPGPUs or the Cell processor have gained much interest in the HPC community. The RapidMind Multi-Core Development Platform is a programming environment that allows generating code which…
Our goal in this dissertation is to provide tools, programming models, and system support for PIM architectures (with a focus on DRAM-based solutions), to ease the adoption of PIM in current and future systems. To this end, we make at least…
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…
Graphics Processing Units (GPUs) are having a transformational effect on numerical lattice quantum chromodynamics (LQCD) calculations of importance in nuclear and particle physics. The QUDA library provides a package of mixed precision…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
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…
Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…
NVIDIA GPUs have recently started to be used in computational biology, yet R users lack integrated GPU monitoring tools, forcing reliance on external utilities like nvidia-smi. We introduce CudaMon, an R package providing real-time…
For many years, systems running Nvidia-based GPU architectures have dominated the heterogeneous supercomputer landscape. However, recently GPU chipsets manufactured by Intel and AMD have cut into this market and can now be found in some of…
This paper introduces open-source computational fluid dynamics software named open computational fluid dynamic code for scientific computation with graphics processing unit (GPU) system (OpenCFD-SCU), developed by the authors for direct…
Computer vision applications, especially those using augmented reality technology, are becoming quite popular in mobile devices. However, this type of application is known as presenting significant demands regarding resources. In order to…
Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived with machine learning…
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…
This paper discusses the potential of graphics processing units (GPUs) in high-dimensional optimization problems. A single GPU card with hundreds of arithmetic cores can be inserted in a personal computer and dramatically accelerates many…
Numerical solution of reaction-diffusion equations in three dimensions is one of the most challenging applied mathematical problems. Since these simulations are very time consuming, any ideas and strategies aiming at the reduction of CPU…
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, 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…
CUDA (formerly an abbreviation of Compute Unified Device Architecture) is a parallel computing platform and API model created by Nvidia allowing software developers to use a CUDA-enabled graphics processing unit (GPU) for general purpose…