Search · four archives
Search · four archives
13 papers · ranked by Valyu relevance
Alessandro Petrini, Marco Mesiti, Max Schubach, Marco Frasca + 7 more
The idea on which multi-core parSMURF builds is that all operations performed on the different parts of the partition can be assigned to multiple core/threads and processed in parallel. Namely, given q threads, the data parts N1, …, Nn are equally distributed among threads so that thread i receives a subset (chunk) Ci…
Johann M Kraus, Hans A Kestler
Background In recent years, the demand for computational power in computational biology has increased due to rapidly growing data sets from microarray and other high-throughput technologies. This demand is likely to increase. Standard algorithms for analyzing data, such as cluster algorithms, need to be parallelized…
Yann Garniron, Thomas Applencourt, Kevin Gasperich, Anouar Benali + 15 more
Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven…
Viacheslav Bolnykh, Jógvan Magnus Haugaard Olsen, Simone Meloni, Martin P. Bircher + 3 more
We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting…
David Díaz, Francisco J. Esteban, Pilar Hernández, Juan Antonio Caballero + 4 more
'Juan Antonio Caballero' 'Antonio Guevara' 'Gabriel Dorado' 'Sergio Gálvez' 'Charles Y. Chiu'] We have developed the MC64-ClustalWP2 as a new implementation of the Clustal W algorithm, integrating a novel parallelization strategy and significantly increasing the performance when aligning long sequences in architectures…
Fen Ge, Chenchen Cui, Fang Zhou, Ning Wu + 1 more
More and more attention is being paid to the use of massive parallel computing performed on many-core Networks-on-Chip (NoC) in order to accelerate performance. Simultaneously deploying multiple applications on NoC is one feasible way to achieve this. In this paper, we propose a multi-phase-based multi-application…
Sirilak Ketchaya, Apisit Rattanatranurak
Quicksort is an important algorithm that uses the divide and conquer concept, and it can be run to solve any problem. The performance of the algorithm can be improved by implementing this algorithm in parallel. In this paper, the parallel sorting algorithm named the Multi-Deque Partition Dual-Deque Merge Sorting…
Sungju Lee, Heegon Kim, Yongwha Chung, Daihee Park
In transmitting image/video data over Video Sensor Networks (VSNs), energy consumption must be minimized while maintaining high image/video quality. Although image/video compression is well known for its efficiency and usefulness in VSNs, the excessive costs associated with encoding computation and complexity still…
Authors not listed
Computing electrostatic interactions remains the bottleneck of molecular dynamics (MD) simulations despite more than a century of effort in developing methods to accelerate the calculation. Previously we have developed the Spherical Grid and Treecode (SGT) and Gauss-Legendre-Spherical-t (GLST) algorithms for…
Hao Li, Yi-Cheng Tu, Bo Zeng, Rashid Mehmood
The unrivaled computing capabilities of modern GPUs meet the demand of processing massive amounts of data seen in many application domains. While traditional HPC systems support applications as standalone entities that occupy entire GPUs, there are GPU-based DBMSs where multiple tasks are meant to be run at the same…
J. Harry Moore, Matthias R. Bauer, Jeff Guo, Atanas Patronov + 2 more
We present Icolos, a workflow manager written in Python as a tool for automating complex structure-based workflows. Icolos can be used as a standalone tool, for example in virtual screening campaigns, or can be used in conjunction with deep learning-based molecular generation facilitated for example by REINVENT, a…
Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Goetz, Kenneth M. Merz + 1 more
We have ported and optimized the GPU accelerated QUICK and AMBER based ab initio QM/MM implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra…
Authors not listed
The era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. While the transition from petaflops to exascale computing has been marked by a steady increase in computational power, the shift towards heterogeneous architectures, particularly the dominant…