Workshop Program

[8:15am - 8:30am] Opening Remarks

Yong Chen, Pavan Balaji, Abhinav Vishnu

[8:30am - 9:30am] Session 1: Keynote Talk

Genomes Galore: Parallel Methods and Software for Tackling NGS Big Data Challenges

Prof. Srinivas Aluru, Georgia Institute of Technology


High-throughput DNA sequencing (a.k.a. next generation sequencing) instruments have revolutionized genomics by bringing orders of magnitude improvements in both the scale and cost of sequencing. Their usage has become ubiquitous, enabling single investigators with modest budgets to carry out what could only be accomplished by a network of major sequencing centers just over a decade ago. As a result, routine biological investigations must now deal with big data sets. The rate and scale of data generation is pushing the limits of bioinformatics software. Rapid development of parallel methods, and community-driven specifications and implementations of parallel open source software libraries, can assist the bioinformatics community in developing HPC solutions to meet this need. This talk will present our current research and community building efforts in this direction.


Srinivas Aluru is a professor in the School of Computational Science and Engineering at Georgia Institute of Technology. He co-directs the Georgia Tech Interdisciplinary Research Institute in Data Engineering and Science (IDEaS), and co-leads the NSF South Big Data Regional Innovation Hub which serves 16 Southern States in the U.S. and Washington D.C. Aluru conducts research in high performance computing, bioinformatics and systems biology, combinatorial scientific computing, and applied algorithms. He is currently serving as the Chair of the ACM Special Interest Group on Bioinformatics, Computational Biology and Biomedical Informatics (SIGBIO). He is a Fellow of the American Association for the Advancement of Science (AAAS) and the Institute of Electrical and Electronics Engineers (IEEE).

[9:30am - 10:00am] Tea/Coffee Break

[10:00am - 12:00pm] Session 2: Programming Models and Runtime Systems

Session Chair: Dong Dai, Texas Tech University

  • "Towards An Event-Driven Programming Model for OpenMP", Xing Fan, Oliver Sinnen, and Nasser Giacaman.
  • "Extending a Work-Stealing Framework with Probabilistic Guards", Hiroshi Yoritaka, Ken Matsui, Masahiro Yasugi, Tasuku Hiraishi, and Seiji Umatani.
  • "Cyclone: Unified Stream and Batch Processing", Matúš Harvan, Thomas Locher, and Ana Claudia Sima.
  • "Evaluation of an MPI-Based Implementation of the Tascell Task-Parallel Language on Massively Parallel Systems", Daisuke Muraoka, Masahiro Yasugi, Tasuku Hiraishi, and Seiji Umatani.

[12:00pm - 1:00pm] Lunch Break

[1:00pm - 3:00pm] Session 3: Applications

Session Chair: Eun Sung Jung, Argonne National Laboratory

  • "Computing the Expected Makespan of Task Graphs in the Presence of Silent Errors", Henri Casanova, Julien Herrmann, and Yves Robert.
  • "A Robust Fault Tolerance Scheme for Lifeline-Based Taskpools", Claudia Fohry and Marco Bungart.
  • "Block2Vec: A Deep Learning Strategy on Mining Block Correlations in Storage Systems", Dong Dai, Forrest Sheng Bao, Jiang Zhou, and Yong Chen.
  • "Using HPX and OP2 for Improving Parallel Scaling Performance of Unstructured Grid Applications", Zahra Khatami, Hartmut Kaiser, and Jagannathan Ramanujam.

[3:00pm - 3:30pm] Tea/Coffee Break

[3:30pm - 5:00pm] Session 4: I/O and Heterogeneous Systems

Session Chair: Federico Silla, Technical University of Valencia, Spain

  • "Log-assisted Straggler-aware I/O Scheduler for High-End Computing", Neda Tavakoli, Dong Dai, and Yong Chen.
  • "Combinatorial Optimization of Work Distribution on Heterogeneous Systems", Suejb Memeti and Sabri Pllana.
  • "Manila: Using a Densely Populated PMC-Space for Power Modeling within Large-Scale Systems", Jason Mair, Zhiyi Huang, and David Eyers.

[5:00pm - 5:10pm] Closing Remarks