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@INPROCEEDINGS{Kitayama:279895,
      author       = {Kitayama, Itaru and Wylie, Brian J. N. and Maeda,
                      Toshiyuki},
      title        = {{E}xecution {P}erformance {A}nalysis of the {AB}y{SS}
                      {G}enome {S}equence {A}ssembler using {S}calasca on the {K}
                      computer},
      reportid     = {FZJ-2015-07771},
      year         = {2015},
      note         = {pdf darf NICHT open access sein},
      abstract     = {Performance analysis of the ABySS genome sequence assembler
                      (ABYSS-P) executing on the K computer with up to 8192
                      compute nodes is described which identified issues that
                      limited scalability to less than 1024 compute nodes and
                      required prohibitive message buffer memory with 16384 or
                      more compute nodes. The open-source Scalasca toolset was
                      employed to analyse executions, revealing the impact of
                      massive amounts of MPI point-to-point communication used
                      particularly for master/worker process coordination, and
                      inefficient parallel file operations that manifest as
                      waiting time at later MPI collective synchronisations and
                      communications. Initial remediation via use of collective
                      communication operations and alternate strategies for
                      parallel file handling show large performance and
                      scalability improvements, with partial executions validated
                      on the full 82,944 compute nodes of the K computer.},
      month         = {Sep},
      date          = {2015-09-01},
      organization  = {International Conference on Parallel
                       Computing, Edinburgh (Scotland), 1 Sep
                       2015 - 4 Sep 2015},
      subtyp        = {After Call},
      cin          = {JSC},
      cid          = {I:(DE-Juel1)JSC-20090406},
      pnm          = {511 - Computational Science and Mathematical Methods
                      (POF3-511) / ATMLPP - ATML Parallel Performance (ATMLPP)},
      pid          = {G:(DE-HGF)POF3-511 / G:(DE-Juel-1)ATMLPP},
      typ          = {PUB:(DE-HGF)6},
      url          = {https://juser.fz-juelich.de/record/279895},
}