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Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient large-scale ensemble sampling
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab). KTH Royal Institute of Technology, Sweden.
Number of Authors: 4
2017 (English)In: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 71, 18-31 p.Article in journal (Refereed) Published
Abstract [en]

Compute-intensive applications have gradually changed focus from massively parallel supercomputers to capacity as a resource obtained on-demand. This is particularly true for the large-scale adoption of cloud computing and MapReduce in industry, while it has been difficult for traditional high-performance computing (HPC) usage in scientific and engineering computing to exploit this type of resources. However, with the strong trend of increasing parallelism rather than faster processors, a growing number of applications target parallelism already on the algorithm level with loosely coupled approaches based on sampling and ensembles. While these cannot trivially be formulated as MapReduce, they are highly amenable to throughput computing. There are many general and powerful frameworks, but in particular for sampling-based algorithms in scientific computing there are some clear advantages from having a platform and scheduler that are highly aware of the underlying physical problem. Here, we present how these challenges are addressed with combinations of dataflow programming, peer-to-peer techniques and peer-to-peer networks in the Copernicus platform. This allows automation of sampling-focused workflows, task generation, dependency tracking, and not least distributing these to a diverse set of compute resources ranging from supercomputers to clouds and distributed computing (across firewalls and fragile networks). Workflows are defined from modules using existing programs, which makes them reusable without programming requirements. The system achieves resiliency by handling node failures transparently with minimal loss of computing time due to checkpointing, and a single server can manage hundreds of thousands of cores e.g. for computational chemistry applications.

Place, publisher, year, edition, pages
2017. Vol. 71, 18-31 p.
Keyword [en]
Peer-too-peer, Distributed computing, Dataflow programming, Scientific computing, Job resiliency
National Category
Computer and Information Science
Identifiers
URN: urn:nbn:se:su:diva-142357DOI: 10.1016/j.future.2016.11.004ISI: 000396950100002OAI: oai:DiVA.org:su-142357DiVA: diva2:1093404
Available from: 2017-05-05 Created: 2017-05-05 Last updated: 2017-05-05Bibliographically approved

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