Related papers: Performance Analysis of CP2K Code for Ab Initio Mo…
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.…
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…
It is demonstrated how the non-proprietary OpenACC standard of compiler directives may be used to compactly and efficiently accelerate the rate-determining steps of two of the most routinely applied many-body methods of electronic structure…
Accelerated computing is widely used in high-performance computing. Therefore, it is crucial to experiment and discover how to better utilize GPUGPUs latest generations on relevant applications. In this paper, we present results and share…
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…
High fidelity Computational Fluid Dynamics simulations are generally associated with large computing requirements, which are progressively acute with each new generation of supercomputers. However, significant research efforts are required…
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…
The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well exploited with a combination of SIMD,…
The two main thrusts of computational science are more accurate predictions and faster calculations; to this end, the zeitgeist in molecular dynamics (MD) simulations is pursuing machine learned and data driven interatomic models, e.g.…
Three dimensional particle-in-cell laser-plasma simulation is an important area of computational physics. Solving state-of-the-art problems requires large-scale simulation on a supercomputer using specialized codes. A growing demand in…
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…
Parallel algorithms on CPU and GPU are implemented for the Unified Gas-Kinetic Scheme and their performances are investigated and compared by a two dimensional channel flow case. The parallel CPU algorithm has a one dimensional block…
Over the past decade there has been a growing interest in the development of parallel hardware systems for simulating large-scale networks of spiking neurons. Compared to other highly-parallel systems, GPU-accelerated solutions have the…
When MPI-parallel simulations run on shared Kubernetes clusters, conventional CPU scheduling leaves the vast majority of provisioned cycles idle at synchronization barriers. This paper presents a multiplexing framework that reclaims this…
High-throughput structure-based screening of drug-like molecules has become a common tool in biomedical research. Recently, acceleration with graphics processing units (GPUs) has provided a large performance boost for molecular docking…
Analysis of processing time and similarity of images generated between CPU and GPU architectures and sequential and parallel programming. For image processing a computer with AMD FX-8350 processor and an Nvidia GTX 960 Maxwell GPU was used,…
Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of scalable streaming-multiprocessor hardware…
The high-performance computing (HPC) community has recently seen a substantial diversification of hardware platforms and their associated programming models. From traditional multicore processors to highly specialized accelerators, vendors…
Second-generation Car--Parrinello \textit{ab initio} molecular dynamics (CP2G AIMD) combines a Born--Oppenheimer-like nuclear equation of motion with a predictor-corrector propagation of the one-particle density matrix and a modified…
Automatic compiler phase selection/ordering has traditionally been focused on CPUs and, to a lesser extent, FPGAs. We present experiments regarding compiler phase ordering specialization of OpenCL kernels targeting a GPU. We use iterative…