21 citations · 191 across the 67 of their papers we have counts for
9 papers · 1 filter
Optimizing AIREBO: Navigating the Journey from Complex Legacy Code to High Performance
Markus Höhnerbach, Paolo Bientinesi
Despite initiatives to improve the quality of scientific codes, there still is a large presence of legacy code. Such code often needs to implement a lot of functionality under time…
The Tersoff many-body potential: Sustainable performance through vectorization
Markus Höhnerbach, Ahmed E. Ismail, Paolo Bientinesi
Molecular dynamics models materials by simulating each individual particle's trajectory. Many-body potentials lead to a more accurate trajectory simulation, and are used in materia…
LAMMPS' PPPM Long-Range Solver for the Second Generation Xeon Phi
William McDoniel, Markus Höhnerbach, Rodrigo Canales +2
Molecular Dynamics is an important tool for computational biologists, chemists, and materials scientists, consuming a sizable amount of supercomputing resources. Many of the invest…
Accelerating scientific codes by performance and accuracy modeling
Diego Fabregat-Traver, Ahmed E. Ismail, Paolo Bientinesi
Scientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly comple…
The Vectorization of the Tersoff Multi-Body Potential: An Exercise in Performance Portability
Markus Höhnerbach, Ahmed E. Ismail, Paolo Bientinesi
Molecular dynamics simulations, an indispensable research tool in computational chemistry and materials science, consume a significant portion of the supercomputing cycles around t…
High-performance generation of the Hamiltonian and Overlap matrices in FLAPW methods
Edoardo Di Napoli, Elmar Peise, Markus Hrywniak +1
One of the greatest efforts of computational scientists is to translate the mathematical model describing a class of physical phenomena into large and complex codes. Many of these…
Large-scale linear regression: Development of high-performance routines
Alvaro Frank, Diego Fabregat-Traver, Paolo Bientinesi
In statistics, series of ordinary least squares problems (OLS) are used to study the linear correlation among sets of variables of interest; in many studies, the number of such var…
Algorithms for Large-scale Whole Genome Association Analysis
Elmar Peise, Diego Fabregat, Yurii Aulchenko +1
In order to associate complex traits with genetic polymorphisms, genome-wide association studies process huge datasets involving tens of thousands of individuals genotyped for mill…
High-throughput Genome-wide Association Analysis for Single and Multiple Phenotypes
Diego Fabregat-Traver, Yurii S. Aulchenko, Paolo Bientinesi
The variance component tests used in genomewide association studies of thousands of individuals become computationally exhaustive when multiple traits are analysed in the context o…