Related papers: Enhanced molecular dynamics performance with a pro…
We consider deployment of the particle filter on modern massively parallel hardware architectures, such as Graphics Processing Units (GPUs), with a focus on the resampling stage. While standard multinomial and stratified resamplers require…
The vast amount of processing power and memory bandwidth provided by modern Graphics Processing Units (GPUs) make them a platform for data-intensive applications. The database community identified GPUs as effective co-processors for data…
The ability to perform ab initio molecular dynamics simulations using potential energies calculated on quantum computers would allow virtually exact dynamics for chemical and biochemical systems, with substantial impacts on the fields of…
Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…
Chemical algorithms are statistical algorithms described and represented as chemical reaction networks. They are particularly attractive for traffic shaping and general control of network dynamics; they are analytically tractable, they…
Recent advances in reprogrammable hardware (e.g., FPGAs) and memory technology (e.g., DDR4, HBM) promise to solve performance problems inherent to graph processing like irregular memory access patterns on traditional hardware (e.g., CPU).…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Optimizing the performance of computational fluid dynamics (CFD) applications accelerated by graphics processing units (GPUs) is crucial for efficient simulations. In this study, we employed a machine learning-based autotuning technique to…
We present a customizable soft architecture which allows for the execution of GPGPU code on an FPGA without the need to recompile the design. Issues related to scaling the overlay architecture to multiple GPGPU multiprocessors are…
As graph analytics often involves compute-intensive operations, GPUs have been extensively used to accelerate the processing. However, in many applications such as social networks, cyber security, and fraud detection, their representative…
We present a new adaptive parallel algorithm for the challenging problem of multi-dimensional numerical integration on massively parallel architectures. Adaptive algorithms have demonstrated the best performance, but efficient many-core…
Graph processing on GPUs is gaining momentum due to the high throughputs observed compared to traditional CPUs, attributed to the vast number of processing cores on GPUs that can exploit parallelism in graph analytics. This paper discusses…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…
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…
Searching for sources of electromagnetic emission in spectral-line radio astronomy interferometric data is a computationally intensive process. Parallel programming techniques and High Performance Computing hardware may be used to improve…
Due to the emergence of embedded applications in image and video processing, communication and cryptography, improvement of pictorial information for better human perception like deblurring, denoising in several fields such as satellite…
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…
Over the last ten years, graphics processors have become the de facto accelerator for data-parallel tasks in various branches of high-performance computing, including machine learning and computational sciences. However, with the recent…
The new Cell processor represents a turning point for computing intensive applications. Here, I show that for molecular dynamics it is possible to reach an impressive sustained performance in excess of 30 Gflops with a peak of 45 Gflops for…