相关论文: Exploiting OpenMP & OpenACC to Accelerate a Molecu…
Output-intensive scientific applications are highly sensitive to low storage throughput. While existing scientific application stacks are optimized for traditional High-Performance Computing (HPC) environments with high remote storage and…
The HPC community is actively researching and evaluating tools to support execution of scientific applications in cloud-based environments. Among the various technologies, containers have recently gained importance as they have…
Scientific applications are often complex, irregular, and computationally-intensive. To accommodate the ever-increasing computational demands of scientific applications, high-performance computing (HPC) systems have become larger and more…
Machine learning shows great potential in virtual screening for drug discovery. Current efforts on accelerating docking-based virtual screening do not consider using existing data of other previously developed targets. To make use of the…
The trend towards highly parallel multi-processing is ubiquitous in all modern computer architectures, ranging from handheld devices to large-scale HPC systems; yet many applications are struggling to fully utilise the multiple levels of…
Docking is a crucial component in drug discovery aimed at predicting the binding conformation and affinity between small molecules and target proteins. ML-based docking has recently emerged as a prominent approach, outpacing traditional…
We conducted a systematic survey of emerging quantum-HPC platforms, which integrate quantum computers and High-Performance Computing (HPC) systems through co-location. Currently, it remains unclear whether such platforms provide tangible…
Heterogeneous MPSoCs comprise diverse processing units of varying compute capabilities. To date, the mapping strategies of neural networks (NNs) onto such systems are yet to exploit the full potential of processing parallelism, made…
Parallel programming is central to HPC and AI, but producing code that is correct and fast remains challenging, especially for OpenMP GPU offload, where data movement and tuning dominate. Autonomous coding agents can compile, test, and…
High Energy Physics (HEP) experiments are making increasing use of GPUs and GPU dominated High Performance Computer facilities. Both the software and hardware of these systems are rapidly evolving, creating challenges for experiments to…
Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial…
Heterogeneous embedded systems on chip (HESoCs) co-integrate a standard host processor with programmable manycore accelerators (PMCAs) to combine general-purpose computing with domain-specific, efficient processing capabilities. While…
The increasing demands for computing performance have been a reality regardless of the requirements for smaller and more energy efficient devices. Throughout the years, the strategy adopted by industry was to increase the robustness of a…
Heterogeneous computing is emerging as a mandatory requirement for power-efficient system design. With this aim, modern heterogeneous platforms like Zynq All-Programmable SoC, that integrates ARM-based SMP and programmable logic, have been…
This article presents an automatic approach to quickly derive a good solution for hardware resource partition and task granularity for task-based parallel applications on heterogeneous many-core architectures. Our approach employs a…
CPU-GPU heterogeneous architectures are now commonly used in a wide variety of computing systems from mobile devices to supercomputers. Maximizing the throughput for multi-programmed workloads on such systems is indispensable as one single…
We present a highly scalable Monte Carlo (MC) three-dimensional photon transport simulation platform designed for heterogeneous computing systems. Through the development of a massively parallel MC algorithm using the Open Computing…
Asymmetric multicore processors (AMPs) couple high-performance big cores and low-power small cores with the same instruction-set architecture but different features, such as clock frequency or microarchitecture. Previous work has shown that…
Molecular docking is critical to structure-based virtual screening, yet the throughput of such workflows is limited by the expensive optimization of scoring functions involved in most docking algorithms. We explore how machine learning can…
Computational biology has increasingly turned to agent-based modeling to explore complex biological systems. Biological diffusion (diffusion, decay, secretion, and uptake) is a key driver of biological tissues. GPU computing can vastly…