相关论文: Portability for GPU-accelerated molecular docking …

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…

Next generation High-Energy Physics (HEP) experiments are presented with significant computational challenges, both in terms of data volume and processing power. Using compute accelerators, such as GPUs, is one of the promising ways to…

Portability is critical to ensuring high productivity in developing and maintaining scientific software as the diversity in on-node hardware architectures increases. While several programming models provide portability for diverse GPU…

Recent trends in the HPC field have introduced new CPU architectures with improved vectorization capabilities that require optimization to achieve peak performance and thus pose challenges for performance portability. The deployment of…

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…

GPUs have become the dominant source of computing power for high performance computing and are increasingly being used across the High Energy Physics computing landscape for a wide variety of tasks. Though NVIDIA is currently the main…

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…

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…

In this work we present the porting to Graphics Processing Units (GPUs, using OpenMP target directives) and optimization of a key module within the cosmological {\pinocchio} code, a Lagrangian Perturbation Theory (LPT)-based framework…

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…

The drug discovery process involves several tasks to be performed in vivo, in vitro and in silico. Molecular docking is a task typically performed in silico. It aims at finding the three-dimensional pose of a given molecule when it…

We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables…

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…

CUDA is one of the most popular choices for GPU programming, but it can only be executed on NVIDIA GPUs. Executing CUDA on non-NVIDIA devices not only benefits the hardware community, but also allows data-parallel computation in…

In drug discovery, molecular docking aims at characterizing the binding of a drug-like molecule to a macromolecule. AutoDock-GPU, a state-of-the-art docking software, estimates the geometrical conformation of a docked ligand-protein complex…

With the advent of high-performance computing techniques, the data for analysis has grown significantly. Here, graphic processing unit (GPU) based program kernels are discussed to exploit parallelism in the analysis codes specific to…

GPUs have been widely used to accelerate computations exhibiting simple patterns of parallelism - such as flat or two-level parallelism - and a degree of parallelism that can be statically determined based on the size of the input dataset.…

Improving the throughput of molecular docking, a computationally intensive phase of the virtual screening process, is a highly sought area of research since it has a significant weight in the drug designing process. With such improvements,…

Accelerating molecular docking -- the process of predicting how molecules bind to protein targets -- could boost small-molecule drug discovery and revolutionize medicine. Unfortunately, current molecular docking tools are too slow to screen…

The present panorama of HPC architectures is extremely heterogeneous, ranging from traditional multi-core CPU processors, supporting a wide class of applications but delivering moderate computing performance, to many-core GPUs, exploiting…