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Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environment

Paul Marshall, Matthew Woitaszek, Henry M. Tufo, Rob Knight, Daniel McDonald, Julia Goodrich
2009 Proceedings of the 2nd Workshop on Many-Task Computing on Grids and Supercomputers - MTAGS '09  
modules  Create one generator for each ensemble  Examine output directories for recovery  SHll slow  PossibiliHes:  Ensemble dispatcherBlue Gene/L  Looking closer:  ...  end nodes  Ensemble dispatcher imports generators  Launcher (wri7en in C) executes on compute nodes  CommunicaHon between dispatcher and launchers over TCP with a custom protocol  Iterate  ... 
doi:10.1145/1646468.1646481 dblp:conf/sc/MarshallWTKMG09 fatcat:flf6cms745bnnamzx4qlwzr7pa

Many-task computing for grids and supercomputers

Ioan Raicu, Ian T. Foster, Yong Zhao
2008 2008 Workshop on Many-Task Computing on Grids and Supercomputers  
We also thank the Argonne Leadership Computing Facility for allowing us to test MTC in practice on the IBM Blue Gene/P.  ...  We also thank our many colleagues for their contributions to the implementations and applications of making many task computing a reality; in no particular order, we would like to thank Michael Wilde,  ...  IBM Blue Gene/L [1] and Blue Gene/P [2]) because the lack of efficient support in those systems for the "scripting" programming model [3] .  ... 
doi:10.1109/mtags.2008.4777912 dblp:conf/sc/RaicuFZ08 fatcat:u3fyhpolcrav7ggrmrgron4qja

Software challenges in extreme scale systems

Vivek Sarkar, William Harrod, Allan E Snavely
2009 Journal of Physics, Conference Series  
Prior parallel machines included the IBM 3838 Array Processor which for a time was the fastest single precision floating point processor marketed by IBM, and the Space Shuttle Input/Output Processor which  ...  Carlson is a member of the research staff at the IDA Center for Computing Sciences where, since 1990, his focus has been on applications and system tools for large-scale parallel and distributed computers  ...  In the case of Blue Gene/L [105] , the specialized OS operates at the level of a processing set (pset) which consists of one I/O node and a collection of compute nodes.  ... 
doi:10.1088/1742-6596/180/1/012045 fatcat:iukutry2dvbitfdh6ng7kgz564

Towards Data Intensive Many-Task Computing [chapter]

Ioan Raicu, Ian Foster, Yong Zhao, Alex Szalay, Philip Little, Christopher M. Moretti, Amitabh Chaudhary, Douglas Thain
Advances in Systems Analysis, Software Engineering, and High Performance Computing  
The second largest open science supercomputer, the IBM Blue Gene/P from Argonne National Laboratory, has 160K processors, and a parallel file system (i.e. also GPFS) rated at 8GB/s, yielding a mere 0.05MB  ...  In the bioinformatics domain, the rate of growth of DNA databases such as GenBank [19] and European Molecular Biology Laboratory (EMBL) [20] has been following an exponential trend, with a doubling time  ...  We thank the Computation Institute at University of Chicago for hosting part of the experiments.  ... 
doi:10.4018/978-1-61520-971-2.ch002 fatcat:wp5tkphsgrfi7evpubfqhz5hbu