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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)
—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)
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)
  • D K Berry
  • 1986
A number of inhalable air pollutants have been found likely to cause human cancer. Section 112 of the Clean Air Act requires EPA to protect public health from exposure to these and other hazardous air pollutants. During the past several years, however, state officials, Congress, environmental advocates, and EPA managers have expressed concern about EPA's(More)
  • D K Berry
  • 1990
Over the past several years, substantial concern has been expressed by some in Congress, environmental groups, and members of the public concerning the lack of progress in regulating toxic air pollutants by the U.S. Environmental Protection Agency (EPA). As a result, a number of amendments to the Federal Clean Air Act have been introduced to require EPA to(More)
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