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Hybrid computational architectures based on the joint power of Central Processing Units and Graphic Processing Units (GPUs) are becoming popular and powerful hardware tools for a wide range of simulations in biology, chemistry, engineering,…
Spatial computing architectures promise a major stride in performance and energy efficiency over the traditional load/store devices currently employed in large scale computing systems. The adoption of high-level synthesis (HLS) from…
Since its inception in 1995, LAMMPS has grown to be a world-class molecular dynamics code, with thousands of users, over one million lines of code, and multi-scale simulation capabilities. We discuss how LAMMPS has adapted to the modern…
There are a number of different phenomena in the early universe that have to be studied numerically with lattice simulations. This paper presents a graphics processing unit (GPU) accelerated Python program called PyCOOL that solves the…
We present SPDL (Scalable and Performant Data Loading), an open-source, framework-agnostic library designed for efficiently loading array data to GPU. Data loading is often a bottleneck in AI applications, and is challenging to optimize…
High-performance computing (HPC) is reshaping computational drug discovery by enabling large-scale, time-efficient molecular simulations. In this work, we explore HPC-driven pipelines for Alzheimer's disease drug discovery, focusing on…
The complex structure of interplanetary magnetic fields and their variability, due to solar activity, make it necessary to compute the Cosmic Ray (CR) modulation with numerical simulations. COde for a Speedy Monte Carlo (MC) Involving Cuda…
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.…
In this paper we would like to share our experience for transforming a parallel code for a Computational Fluid Dynamics (CFD) problem into a parallel version for the RedisDG workflow engine. This system is able to capture heterogeneous and…
iPIC3D is a widely used massively parallel Particle-in-Cell code for the simulation of space plasmas. However, its current implementation does not support execution on multiple GPUs. In this paper, we describe the porting of iPIC3D particle…
Molecular dynamics (MD) simulations have transformed our understanding of the nanoscale, driving breakthroughs in materials science, computational chemistry, and several other fields, including biophysics and drug design. Even on exascale…
Different parallel frameworks for implementing data analysis applications have been proposed by the HPC and Big Data communities. In this paper, we investigate three task-parallel frameworks: Spark, Dask and RADICAL-Pilot with respect to…
Graphics processing units (GPU) had evolved from a specialized hardware capable to render high quality graphics in games to a commodity hardware for effective processing blocks of data in a parallel schema. This evolution is particularly…
Visual Molecular Dynamics (VMD) is one of the most widely used molecular graphics software in the community of theoretical simulations. So far, however, it still lacks a graphical user interface (GUI) for molecular manipulations when doing…
As heterogeneous supercomputing architectures leveraging GPUs become increasingly central to high-performance computing (HPC), it is crucial for computational fluid dynamics (CFD) simulations, a de-facto HPC workload, to efficiently utilize…
A previous study of MD algorithms designed for GPU use is extended to cover more recent developments in GPU architecture. Algorithm modifications are described, together with extensions to more complex systems. New measurements include the…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
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…
Current computational systems are heterogeneous by nature, featuring a combination of CPUs and GPUs. As the latter are becoming an established platform for high-performance computing, the focus is shifting towards the seamless programming…
Heliospheric plasmas require multi-scale and multi-physics considerations. On one hand, MHD codes are widely used for global simulations of the solar-terrestrial environments, but do not provide the most elaborate physical description of…