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DTSTAMP:20260522T150117Z
LOCATION:C140/142
DTSTART;TZID=America/Chicago:20181113T133000
DTEND;TZID=America/Chicago:20181113T150000
UID:submissions.supercomputing.org_SC18_sess206@linklings.com
SUMMARY:Biology Applications
DESCRIPTION:Redesigning LAMMPS for Petascale and Hundred-Billion-Atom Simu
 lation on Sunway TaihuLight\n\nLarge-scale molecular dynamics (MD) simulat
 ions on supercomputers play an increasingly important role in many researc
 h areas. In this paper, we present our efforts on redesigning the widely u
 sed LAMMPS MD simulator for Sunway TaihuLight supercomputer and its ShenWe
 i many-core architecture (SW26010)....\n\n\nXiaohui Duan, Ping Gao, Tingji
 an Zhang, Meng Zhang, and Weiguo Liu (Shandong University); Wusheng Zhang,
  Wei Xue, Haohuan Fu, Lin Gan, and Dexun Chen (Tsinghua University); Xiang
 xu Meng (Shandong University); and Guangwen Yang (Tsinghua University)\n--
 -------------------\nExtreme Scale De Novo Metagenome Assembly\n\nMetageno
 me assembly is the process of transforming a set of short, overlapping, an
 d potentially erroneous DNA segments from environmental samples into the a
 ccurate representation of the underlying microbiomes's genomes. State-of-t
 he-art tools require large shared memory machines and cannot handle co...\
 n\n\nEvangelos Georganas (Intel Corporation) and Rob Egan, Steven Hofmeyr,
  Eugene Goltsman, Bill Arndt, Andrew Tritt, Aydin Buluc, Leonid Oliker, an
 d Katherine Yelick (Lawrence Berkeley National Laboratory)\n--------------
 -------\nOptimizing High Performance Distributed Memory Parallel Hash Tabl
 es for DNA k-mer Counting\n\nHigh-throughput DNA sequencing is the mainsta
 y of modern genomics research. A common operation used in bioinformatic an
 alysis for many applications of high-throughput sequencing is the counting
  and indexing of fixed length substrings of DNA sequences called k-mers. C
 ounting k-mers is often accomplis...\n\n\nTony C. Pan (Georgia Institute o
 f Technology, School of Computational Science and Engineering); Sanchit Mi
 sra (Intel Corporation, Parallel Computing Lab); and Srinivas Aluru (Georg
 ia Institute of Technology, School of Computational Science and Engineerin
 g)\n\nTag: Algorithms, Applications, Computational Biology, Scientific Com
 puting\n\nRegistration Category: Tech Program Reg Pass\n\nFinalist: BP Fin
 alist\n\nSession Chair: Allison H. Baker (National Center for Atmospheric 
 Research (NCAR))
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