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Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
The design of message passing (MP) algorithms on factor graphs is an effective manner to implement channel estimation (CE) in wireless communication systems, which performance can be further improved by exploiting prior probability models…
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…
A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the…
We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that…
Heterogeneous memory technologies are increasingly important instruments in addressing the memory wall in HPC systems. While most are deployed in single node setups, CXL.mem is a technology that implements memories that can be attached to…
Large-scale HPC simulations of plasma dynamics in fusion devices require efficient parallel I/O to avoid slowing down the simulation and to enable the post-processing of critical information. Such complex simulations lacking parallel I/O…
The main computing tasks of a finite element code(FE) for solving partial differential equations (PDE's) are the algebraic system assembly and the iterative solver. This work focuses on the first task, in the context of a hybrid MPI+X…
MDMP is a new parallel programming approach that aims to provide users with an easy way to add parallelism to programs, optimise the message passing costs of traditional scientific simulation algorithms, and enable existing MPI-based…
Furthering our understanding of many of today's interesting problems in plasma physics---including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects---requires large-scale kinetic…
Anisotropic mesh adaptation is a powerful way to directly minimise the computational cost of mesh based simulation. It is particularly important for multi-scale problems where the required number of floating-point operations can be reduced…
Deploying deep neural networks (DNNs) on resource-constrained mobile devices presents significant challenges, particularly in achieving real-time performance while simultaneously coping with limited computational resources and battery life.…
Multicore has emerged as a typical architecture model since its advent and stands now as a standard. The trend is to increase the number of cores and improve the performance of the memory system. Providing an efficient multicore…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…
The hybrid MPI+X programming paradigm, where X refers to threads or GPUs, has gained prominence in the high-performance computing arena. This corresponds to a trend of system architectures growing more heterogeneous. The current MPI…
Mass spectrometry (MS) based omics data analysis require significant time and resources. To date, few parallel algorithms have been proposed for deducing peptides from mass spectrometry-based data. However, these parallel algorithms were…
The hybrid method combining particle-in-cell and magnetohydrodynamics can be used to study the interaction between energetic particles and global plasma modes. In this paper we introduce the M3D-C1-K code, which is developed based on the…
Parallel jobs are different from sequential jobs and require a different type of process management. We present here a process management system for parallel programs such as those written using MPI. A primary goal of the system, which we…
This paper presents some of our findings on the scalability of parallel 3D mesh generation on distributed memory machines. The primary objective of this study was to evaluate a distributed memory approach for implementing a 3D parallel…
High-speed signal processing is essential for maximizing data throughput in emerging communication applications, like multiple-input multiple-output (MIMO) systems and radio-frequency (RF) interference cancellation. However, as these…