Related papers: Tackling Exascale Software Challenges in Molecular…
Dynamic simulators are computational models governed by differential equations that evolve over time. They are essential for scientific and engineering applications but remain challenging to emulate because of the unpredictable behavior of…
The human neuromuscular system consisting of skeletal muscles and neural circuits is a complex system that is not yet fully understood. Surface electromyography (EMG) can be used to study muscle behavior from the outside. Computer…
Recent advances in both theory and computational power have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble simulations are now widely used to compute a number of…
Witnessing the advancing scale and complexity of chip design and benefiting from high-performance computation technologies, the simulation of Very Large Scale Integration (VLSI) Circuits imposes an increasing requirement for acceleration…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
Large-scale genomic workflows used in precision medicine can process datasets spanning tens to hundreds of gigabytes per sample, leading to high memory spikes, intensive disk I/O, and task failures due to out-of-memory errors. Simple static…
Mesoscopic simulations of hydrocarbon flow in source shales are challenging, in part due to the heterogeneous shale pores with sizes ranging from a few nanometers to a few micrometers. Additionally, the sub-continuum fluid-fluid and…
Molecular dynamics (MD) simulation is one of the past decade's most important tools for enabling biology scientists and researchers to explore human health and diseases. However, due to the computation complexity of the MD algorithm, it…
Molecular dynamics simulations are one of the methods in scientific computing that benefit from GPU acceleration. For those devices, SYCL is a promising API for writing portable codes. In this paper, we present the case study of "HAL's MD…
All-atom, force field-based molecular dynamics simulations are essential tools in computational chemistry, enabling the prediction and analysis of biomolecular systems with atomic-level resolution. However, as system sizes and simulation…
The objective of our research is to demonstrate the practical usage and orders of magnitude speedup of real-world applications by using alternative technologies to support high performance computing. Currently, the main barrier to the…
Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase…
We explore how the big-three computing paradigms -- symmetric multi-processor (SMC), graphical processing units (GPUs), and cluster computing -- can together be brought to bare on large-data Gaussian processes (GP) regression problems via a…
In this work, we present an extension of Gaussian process (GP) models with sophisticated parallelization and GPU acceleration. The parallelization scheme arises naturally from the modular computational structure w.r.t. datapoints in the…
Performance tools for emerging heterogeneous exascale platforms must address two principal challenges when analyzing execution measurements. First, measurement of large-scale executions may record mountains of performance data. Second,…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Many astrophysical simulations involve extreme dynamic range of timescales around 'special points' in the domain (e.g. black holes, stars, planets, disks, galaxies, shocks, mixing interfaces), where processes on small scales couple strongly…
Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…
A new method for the simulation of evolving multi-domains problems has been introduced in a previous work (RealIMotion), Florez et al. (2020). In this article further developments of the model will be presented. The main focus here is a…
We present a data-parallel software package for fitting Gaussian Approximation Potentials (GAPs) on multiple nodes using the ScaLAPACK library with MPI and OpenMP. Until now the maximum training set size for GAP models has been limited by…