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SC ... conference proceedings. SC (Conference : Supercomputing) Pub Date : 2015-11-01 DOI: 10.1145/2807591.2807595

Patricia Kovatch, Anthony Costa, Zachary Giles, Eugene Fluder, Hyung Min Cho, Svetlana Mazurkova

{"title":"Big Omics Data Experience.","authors":"Patricia Kovatch, Anthony Costa, Zachary Giles, Eugene Fluder, Hyung Min Cho, Svetlana Mazurkova","doi":"10.1145/2807591.2807595","DOIUrl":"https://doi.org/10.1145/2807591.2807595","url":null,"abstract":"As personalized medicine becomes more integrated into healthcare, the rate at which human genomes are being sequenced is rising quickly together with a concomitant acceleration in compute and storage requirements. To achieve the most effective solution for genomic workloads without re-architecting the industry-standard software, we performed a rigorous analysis of usage statistics, benchmarks and available technologies to design a system for maximum throughput. We share our experiences designing a system optimized for the \"Genome Analysis ToolKit (GATK) Best Practices\" whole genome DNA and RNA pipeline based on an evaluation of compute, workload and I/O characteristics. The characteristics of genomic-based workloads are vastly different from those of traditional HPC workloads, requiring different configurations of the scheduler and the I/O subsystem to achieve reliability, performance and scalability. By understanding how our researchers and clinicians work, we were able to employ techniques not only to speed up their workflow yielding improved and repeatable performance, but also to make more efficient use of storage and compute resources.","PeriodicalId":90723,"journal":{"name":"SC ... conference proceedings. SC (Conference : Supercomputing)","volume":"2015 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2015-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1145/2807591.2807595","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36578649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation. 不规则环面拓扑映射及其他千万亿级生物分子模拟技术。

SC ... conference proceedings. SC (Conference : Supercomputing) Pub Date : 2014-01-01 DOI: 10.1109/SC.2014.12

James C Phillips, Yanhua Sun, Nikhil Jain, Eric J Bohm, Laxmikant V Kalé

{"title":"Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation.","authors":"James C Phillips, Yanhua Sun, Nikhil Jain, Eric J Bohm, Laxmikant V Kalé","doi":"10.1109/SC.2014.12","DOIUrl":"https://doi.org/10.1109/SC.2014.12","url":null,"abstract":"Currently deployed petascale supercomputers typically use toroidal network topologies in three or more dimensions. While these networks perform well for topology-agnostic codes on a few thousand nodes, leadership machines with 20,000 nodes require topology awareness to avoid network contention for communication-intensive codes. Topology adaptation is complicated by irregular node allocation shapes and holes due to dedicated input/output nodes or hardware failure. In the context of the popular molecular dynamics program NAMD, we present methods for mapping a periodic 3-D grid of fixed-size spatial decomposition domains to 3-D Cray Gemini and 5-D IBM Blue Gene/Q toroidal networks to enable hundred-million atom full machine simulations, and to similarly partition node allocations into compact domains for smaller simulations using multiple-copy algorithms. Additional enabling techniques are discussed and performance is reported for NCSA Blue Waters, ORNL Titan, ANL Mira, TACC Stampede, and NERSC Edison.","PeriodicalId":90723,"journal":{"name":"SC ... conference proceedings. SC (Conference : Supercomputing)","volume":"2014 ","pages":"81-91"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/SC.2014.12","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32980387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 31