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UPPMAX and UPPNEX: Enabling high performance bioinformatics

UPPMAX and UPPNEX: Enabling high performance bioinformatics. Ola Spjuth, UPPMAX. o la.spjuth@farmbio.uu.se. High-performance bioinformatics. Trivial/embarrassingly parallelizable Mass of individual tasks (or divide up problems), run in parallel E.g. analyze several sequences

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UPPMAX and UPPNEX: Enabling high performance bioinformatics

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  1. UPPMAX and UPPNEX:Enabling high performance bioinformatics Ola Spjuth, UPPMAX ola.spjuth@farmbio.uu.se

  2. High-performance bioinformatics • Trivial/embarrassingly parallelizable • Mass of individual tasks (or divide up problems), run in parallel • E.g. analyze several sequences • Non-trivial parallelism • Single task on many processors (data partitioning) • Example: Molecular dynamics

  3. Resources for high-performance computing (HPC) • Supercomputers • “a computer at the frontline of current processing capacity, particularly speed of calculation” • Clusters • Processors in close proximity • GRID computing • Distributed systems, (joined clusters)

  4. UPPMAX • Uppsala university’s resource for high performance computing (HPC) and related know-how • Computational clusters • 6000 cores • Storage • 1.4 PB parallel storage

  5. A project at UPPMAX • 13,152 MSEK from KAW/SNIC (2008-12-30) • ~1 M cpuh/month on a shared cluster (kalkyl) • ~1 PB cluster-attached parallel storage (bubo) • Long term storage on SweStore (>1 PB) • SMP machine, 64 core, 2TB RAM (halvan)

  6. The cluster kalkyl • 348 nodes with 8 cores each • 324 nodes with 24 GB • 16 nodes with 48 GB • 16 nodes with 72 GB • Total: 2784 cores • SLURM queuing system

  7. UPPNEX data flow

  8. Knowledge Base / Community website www.uppnex.uu.se

  9. UPPNEX Application Experts • Assist with NGS Analysis • Available viamailing-list or by direct contact

  10. Project growth

  11. UPPNEX storage usage

  12. Used CPU core h / month 1 week maintenance stop for move to new computer hall

  13. A typical day at UPPMAX

  14. UPPNEX software used

  15. Conclusions: Community needs (storage) • Access to high-availability storage • Access to long term storage • Sustainable file infrastructure

  16. Conclusions:UPPNEX main challenges • Support new types of HPC users and usage • Keep up with the bioinformatics software flood • Managing data growth (previously only computations)

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