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Erwin Laure

Erwin Laure. erwinl@pdc.kth.se ScalaLife Project Director. Rationale for ScalaLife. Simulation/computation is now essential in life science Very complex & large problems are being dealt with: genomes, drug design, systems biology

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Erwin Laure

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  1. Erwin Laure erwinl@pdc.kth.se ScalaLife Project Director

  2. Rationale for ScalaLife • Simulation/computation is now essential in life science • Very complex & large problems are being dealt with: • genomes, • drug design, • systems biology • This puts high demands on standardized open source software and requires to exploit parallelism both on the algorithm and problem level • ScalaLife will deliver: • Hierarchical parallelization of key European open source codes • Ensemble & high-throughput techniques for multi-core and streaming architectures to parallelize in the problem domain • Establish open software standards for data storage and exchange • Implement, document, and maintain such techniques in pilot European open-source codes – using licenses that allow code reuse • Create a Competence Centre to strengthen Europe as a software provider and enable the community to exploit European e-Infrastructures to their full extent. “How should my problem be parallelized to use 1M cores, and on what hardware will it run best?” 2/5

  3. A Window of Opportunity • The establishment of sustained European eInfrastructures through EGI and DEISA/PRACE asks for a concerted approach to software • Many Life Science codes have a long history of development and large amounts of previously invested work • Ad-hoc efforts by individual researchers no longer sustainable • Standard one-size-fits-all models don’t work for 2M lines of code • Adaptations to hardware characteristics are essential • It is critical to joint efforts between life science software authors, parallelization experts, and infrastructure providers • ScalaLife will pair eInfrastructure excellence with networks of software excellence to strengthen Europe’s leadership in eScience

  4. The ScalaLife Approach • WP6 will analyze the properties of the pilot applications and develop scalable techniques • WP7 will optimize the interfaces and data formats used for life science applications • WP3 will integrate new concepts into the pilot applications and maintain and release them • WP4 will validate the results by analyzing their impact on end applications running on European e-infrastructures • WP2 will widely disseminate the results and train members of the European life science software communities • WP5 will collect and make widely available the knowledge and best practices developed by the project to the community and provide expert services

  5. The ScalaLife Consortium • The ScalaLife Consortium includes the software authors involved to make sure results get used long-term, and to cover different types of parallelization requirements • KTH (Dalton, Gromacs), IRB (Discrete), LRZ (Bioinformatics) • Parallelization experts find bottlenecks and new ideas, eScience infrastructure centers take responsibility for validation and user training • KTH (PDC), BSC, LRZ, OeRC • Industrial partners that are experts on new hardware (GPUs) • Synective Labs 5/5

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