Journal Article10.1016/J.JPDC.2009.02.006
Nested parallelism for multi-core HPC systems using Java
96
TL;DR: This paper presents a new Java messaging system called MPJ Express, and introduces nested parallelism in the Java version of the simulation code and is the first time this kind of hybrid parallelism is demonstrated in a high performance Java application.
read more
About: This article is published in Journal of Parallel and Distributed Computing. The article was published on 01 Jun 2009. The article focuses on the topics: Real time Java & Java concurrency.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
ProtTest 3
TL;DR: A high-performance computing (HPC) version of ProtTest that can be executed in parallel in multicore desktops and clusters, called ProtTest 3, includes new features and extended capabilities.
ProtTest 3: fast selection of best-t models of protein evolution
Diego Darriba,Guillermo L. Taboada,David Posada +2 more
- 01 Jan 2011
TL;DR: ProtTest 3 as mentioned in this paper is a HPC version of ProtTest that can be run in parallel in multi-core desktops and clusters, and includes new features and extended capabilities.
1.8K
ProtTest-HPC: fast selection of best-fit models of protein evolution
Diego Darriba,Guillermo L. Taboada,Ramón Doallo,David Posada +3 more
- 31 Aug 2010
TL;DR: A High Performance Computing (HPC) version of ProtTest, a probabilistic models of amino acid replacement, that can be executed in parallel in HPC environments as: a GUI-based desktop version that uses multi-core processors and a cluster-based version that distributes the computational load among nodes.
A Survey of Parallel Programming Models and Tools in the Multi and Many-Core Era
TL;DR: A survey of the different parallel programming models and tools available today with special consideration to their suitability for high-performance computing finds that hybrid parallel programming is the current way of harnessing the capabilities of computer clusters with multi-core nodes.
268
Java for high performance computing: assessment of current research and practice
Guillermo L. Taboada,Juan Touriño,Ramón Doallo +2 more
- 27 Aug 2009
TL;DR: This paper analyzes the current state of Java for HPC, both for shared and distributed memory programming, presents related research projects, and evaluates the performance of current Java HPC solutions and research developments on a multi-core cluster with a high-speed network, InfiniBand, and a 24-core shared memory machine.
References
The Cosmological simulation code GADGET-2
TL;DR: GADGET-2 as mentioned in this paper is a massively parallel tree-SPH code, capable of following a collisionless fluid with the N-body method, and an ideal gas by means of smoothed particle hydrodynamics.
Simulations of the formation, evolution and clustering of galaxies and quasars
Volker Springel,Simon D. M. White,Adrian Jenkins,Carlos S. Frenk,Naoki Yoshida,Liang Gao,Julio F. Navarro,Robert J. Thacker,Darren J. Croton,John C. Helly,John A. Peacock,Shaun Cole,Peter A. Thomas,Hugh M. P. Couchman,August E. Evrard,Jörg M. Colberg,Frazers Pearce +16 more
TL;DR: It is shown that baryon-induced features in the initial conditions of the Universe are reflected in distorted form in the low-redshift galaxy distribution, an effect that can be used to constrain the nature of dark energy with future generations of observational surveys of galaxies.
A hierarchical O(N log N) force-calculation algorithm
Josh Barnes,Piet Hut +1 more
TL;DR: A novel method of directly calculating the force on N bodies that grows only as N log N is described, using a tree-structured hierarchical subdivision of space into cubic cells, each is recursively divided into eight subcells whenever more than one particle is found to occupy the same cell.
4.2K
The art of computer programming, volume 1 (3rd ed.): fundamental algorithms
TL;DR: A container closure assembly for maintaining a sterile sealed container is provided having a ferrule having a central opening in the top annular portion, upwardly projecting locking portions about the periphery of the opening and a weakening line radially outwardly of and concentric with the locking portions.
2.8K
Open MPI: Goals, Concept, and Design of a Next Generation MPI Implementation
Edgar Gabriel,Graham E. Fagg,George Bosilca,Thara Angskun,Jack Dongarra,Jeffrey M. Squyres,Vishal Sahay,Prabhanjan Kambadur,Brian Barrett,Andrew Lumsdaine,Ralph H. Castain,David Daniel,Richard L. Graham,Timothy S. Woodall +13 more
TL;DR: Open MPI provides a unique combination of novel features previously unavailable in an open-source, production-quality implementation of MPI, which provides both a stable platform for third-party research as well as enabling the run-time composition of independent software add-ons.