Related papers: RUMD: A general purpose molecular dynamics package…
Persistent Memory (PM) makes possible recoverable applications that can preserve application progress across system reboots and power failures. Actual recoverability requires careful ordering of cacheline flushes, currently done in two…
We developed a portable code for dissipative particle dynamics (DPD) simulations. This Fortran program named CAMUS has a couple of notable features. One is the omission of constructing the so-called neighboring particles list, providing a…
This paper assesses and reports the experience of ten teams working to port,validate, and benchmark several High Performance Computing applications on a novel GPU-accelerated Arm testbed system. The testbed consists of eight NVIDIA Arm HPC…
Processing-using-DRAM has been proposed for a limited set of basic operations (i.e., logic operations, addition). However, in order to enable full adoption of processing-using-DRAM, it is necessary to provide support for more complex…
We present MIST, the Molecular Integration Simulation Toolkit, a lightweight and efficient software library written in C++ which provides an abstract in- terface to common molecular dynamics codes, enabling rapid and portable development of…
With high computation power and memory bandwidth, graphics processing units (GPUs) lend themselves to accelerate data-intensive analytics, especially when such applications fit the single instruction multiple data (SIMD) model. However,…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
Solvent-mediated hydrodynamic interactions between colloidal particles can significantly alter their dynamics. We discuss the implementation of Stokesian dynamics in leading approximation for streaming processors as provided by the compute…
To achieve peak performance on modern GPUs, one must balance two frames of mind: issuing instructions to individual threads to control their behavior, while simultaneously tracking the convergence of many threads acting in concert to…
Commercial graphics processors (GPUs) have high compute capacity at very low cost, which makes them attractive for general purpose scientific computing. In this paper we show how graphics processors can be used for N-body simulations to…
In recent years, it has become increasingly common for high performance computers (HPC) to possess some level of heterogeneous architecture - typically in the form of GPU accelerators. In some machines these are isolated within a dedicated…
The Spinsim python package simulates spin-half and spin-one quantum mechanical systems following a time dependent Shroedinger equation. It makes use of numba.cuda, which is an LLVM (Low Level Virtual Machine) compiler for Nvidia Cuda…
Discrete GPUs are a cornerstone of HPC and data center systems, requiring management of separate CPU and GPU memory spaces. Unified Virtual Memory (UVM) has been proposed to ease the burden of memory management; however, at a high cost in…
Processing-using-DRAM (PUD) architectures impose a restrictive data layout and alignment for their operands, where source and destination operands (i) must reside in the same DRAM subarray (i.e., a group of DRAM rows sharing the same row…
RunMC is an object-oriented framework aimed to generate and to analyse high-energy collisions of elementary particles using Monte Carlo simulations. This package, being based on C++ adopted by CERN as the main programming language for the…
Processing-using-DRAM has been proposed for a limited set of basic operations (i.e., logic operations, addition). However, in order to enable the full adoption of processing-using-DRAM, it is necessary to provide support for more complex…
This paper presents the implementation of a HLLC finite volume solver using GPU technology for the solution of shallow water problems in two dimensions. It compares both CPU and GPU approaches for implementing all the solver's steps. The…
In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of…
GPUs have significantly accelerated first-order methods for large-scale optimization, especially in continuous optimization. However, this success has not transferred cleanly to problems with discrete variables, combinatorial structure, and…
This paper presents a heuristic for finding the optimum number of CUDA streams by using tools common to the modern AI-oriented approaches and applied to the parallel partition algorithm. A time complexity model for the GPU realization of…