Engineering topics

Baxter, Douglas J

Publications and source records attributed to Baxter, Douglas J.

4 records

DOE OSTI2013

ScalaBLAST 2.0: Rapid and robust BLAST calculations on multiprocessor systems

BLAST remains one of the most widely used tools in computational biology. The rate at which new sequence data is available continues to grow exponentially, driving the emergence of new fields of biological research. At the same time multicore systems and conventional clusters are more accessible. ScalaBLAST has been designed to run on conventional multiprocessor systems with an eye to extreme parallelism, enabling parallel BLAST calculations using over 16,000 processing cores with a portable, robust, fault-resilient design. ScalaBLAST 2.0 source code can be freely downloaded from http://omics.pnl.gov/software/ScalaBLAST.php.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2012

Analyzing Data for Systems Biology: Working at the Intersection of Thermodynamics and Data Analytics

Many challenges in systems biology have to do with analyzing data within the framework of molecular phenomena and cellular pathways. How does this relate to thermodynamics that we know govern the behavior of molecules? Making progress in relating data analysis to thermodynamics is essential in systems biology if we are to build predictive models that enable the field of synthetic biology. This report discusses work at the crossroads of thermodynamics and data analysis, and demonstrates that statistical mechanical free energy is a multinomial log likelihood. Applications to systems biology are presented.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2010

Hard scaling challenges for ab initio molecular dynamics capabilities in NWChem: Using 100,000 CPUs per second

An overview of the parallel algorithms for ab initio molecular dynamics (AIMD) used in the NWChem program package is presented, including recent developments for computing exact exchange. These algorithms make use of a two-dimensional processor geometry proposed by Gygi et al for use in AIMD algorithms. Using this strategy, a highly scalable algorithm for exact exchange has been developed and incorporated it into AIMD. This new algorithm for exact exchange employs an incomplete butterfly to overcome the bottleneck associated with exact exchange term, and it makes judicious use of data replication. Initial testing has shown that this algorithm can scale to over 20,000 CPUs even for modest size simulation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2010

Applications in Data-Intensive Computing

This book chapter, to be published in Advances in Computers, Volume 78, in 2010 describes applications of data intensive computing (DIC). This is an invited chapter resulting from a previous publication on DIC. This work summarizes efforts coming out of the PNNL's Data Intensive Computing Initiative. Advances in technology have empowered individuals with the ability to generate digital content with mouse clicks and voice commands. Digital pictures, emails, text messages, home videos, audio, and webpages are common examples of digital content that are generated on a regular basis. Data intensive computing facilitates human understanding of complex problems. Data-intensive applications provide timely and meaningful analytical results in response to exponentially growing data complexity and associated analysis requirements through the development of new classes of software, algorithms, and hardware.

99 GENERAL AND MISCELLANEOUS↗