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DTSTART;TZID=America/Chicago:20181112T140000
DTEND;TZID=America/Chicago:20181112T142500
UID:submissions.supercomputing.org_SC18_sess140_ws_isav112@linklings.com
SUMMARY:In-Transit Molecular Dynamics Analysis with Apache Flink
DESCRIPTION:Henrique Colao and Bruno Raffin (Univ. Grenoble Alpes, Inria, 
 CNRS, Grenoble INP, LIG) and Omar A. Mures and Emilio J. Padrón (Universid
 ade da Coruña)\n\nIn this paper, an on-line parallel analytics framework i
 s proposed to process and store in transit all the data being generated by
  a Molecular Dynamics (MD) simulation run using staging nodes in the same 
 cluster executing the simulation. The implementation and deployment of suc
 h a parallel workflow with standard HPC tools, managing problems such as d
 ata partitioning and load balancing can be a hard task for scientists. In 
 this paper we propose to leverage Apache Flink, a scalable stream processi
 ng engine from the Big Data domain, in this HPC context. Flink enables to 
 program analyses within a simple window based map/reduce model, while the 
 runtime takes care of the deployment, load balancing  and fault tolerance.
  We build a complete in transit analytics workflow, connecting an MD simul
 ation to Apache Flink and to a distributed database, Apache HBase, to pers
 ist all the desired data. To demonstrate the expressivity of this programm
 ing model and its suitability for HPC scientific environments, two common 
 analytics in the MD field have been implemented. We assessed the performan
 ce of this framework, concluding that it can handle simulations of sizes u
 sed in the literature while providing an effective and versatile tool for 
 scientists to easily incorporate on-line parallel analytics in their curre
 nt workflows.\n\nTag: Data Analytics, Data Management, Visualization\n\nRe
 gistration Category: Workshop Reg Pass\n\nSession Chairs: Earl P.N. Duque 
 (Intelligent Light); Nicola Ferrier (Argonne National Laboratory (ANL), Un
 iversity of Chicago); Kenneth Moreland (Oak Ridge National Laboratory (ORN
 L)); and Matthew Wolf (Oak Ridge National Laboratory (ORNL))\n\n
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