Donald K. Berry

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This paper describes the parallel implementation of fastDNAml, a program for the maximum likelihood inference of phylogenetic trees from DNA sequence data. Mathematical means of inferring phylogenetic trees have been made possible by the wealth of DNA data now available. Maximum likelihood analysis of phylogenetic trees is extremely computationally(More)
As part of the SCinet Research Sandbox at the Supercomputing 2011 conference, Indiana University (IU) demonstrated use of the Lustre high performance parallel file system over a dedicated 100 Gbps wide area network (WAN) spanning more than 3,500 km (2,175 mi). This demonstration functioned as a proof of concept and provided an opportunity to study Lustre's(More)
Maximum likelihood analysis is a powerful technique for inferring evolutionary histories from genetic sequence data. During the fall of 2003, an international team of computer scientists, biologists, and computer centers created a global grid to analyze the evolution of hexapods (arthropods with six legs). We created a global grid of computers using systems(More)
D. K. Berry,1,* M. E. Caplan,1,† C. J. Horowitz,1,‡ Greg Huber,2,§ and A. S. Schneider3,‖ 1Center for Exploration of Energy and Matter and Department of Physics, Indiana University, Bloomington, Indiana 47405, USA 2Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, California 93106-4030, USA 3TAPIR, Walter Burke(More)
GPU computing has rapidly gained popularity as a way to achieve higher performance of many scientific applications. In this paper we report on the experience of porting a hybrid MPI+OpenMP molecular dynamics code to a GPU enabled CrayXK7 to make a hybrid MPI+GPU code. The target machine, Indiana University’s Big Red II, consists of a mix of nodes equipped(More)
C. J. Horowitz, ∗ D. K. Berry, † M. E. Caplan, ‡ Greg Huber, § and A. S. Schneider ¶ Center for Exploration of Energy and Matter and Department of Physics, Indiana University, Bloomington, IN 47405, USA Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, California 93106-4030, USA TAPIR, California Institute of(More)
A molecular dynamics code simulating the diffusion in dense nuclear matter in white dwarf stars is analyzed in this collaboration between PTI (Indiana University) and ZIH (Technische Universität Dresden). The code is highly configurable allowing MPI, OpenMP, or hybrid runs and additional fine-tuning with a range of parameters. The first step in the(More)
Background: The “pasta” phase of nuclear matter may play an important role in the structure and evolution of neutron stars. Recent works suggest nuclear pasta has a high resistivity which could be explained by the presence of long-lived topological defects. The defects act as impurities that decrease thermal and electrical conductivity of the pasta.(More)
Creating web-based visualizations around legacy fusion plotting codes written in Fortran has been an effective approach for enhancing the graphics and making an interactive system for collaborating scientists. A multi-tier architecture was developed to optimize computing and display resources while making minimal changes to the original Fortran code. The(More)