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Extreme-scaleDemonstators TheCaseforBiomolecular ModellingandSimulations Rossen Apostolov KTHRoyalInstituteofTechnology [email protected] Biomolecular Simulations NobelPrizeinChemistry2013 Epidermis Membraneproteins DNA DrugDesign Cellulose Cellfusion Electronicstructure Structural biology Biomarkerdesign Physiology Biomolecular Modelingand Simulations Neuroinformatics Personalizedmedicine Biomaterialsscienceandnanotechnology GROMACS- thesimulationengine • Projectstarted1995;L-GPL;3000-5000users • Highlytunedcodeformoleculardynamics etc.; post-processingtools(>100) • Strongfocusonoptimizedalgorithmsandcode efficiency • Vectorsupportforallmajorarchitecturesincl. GPUs(CUDAandOpenCL),XeonPhi,ARM, PowerN • Extensivelyusedforlarge-scalebenchmarking (e.g.PRACE),inprocurementprocedures,stress testsetc. • ManylargeallocationsontopHPCsystem BioExcelCenterofExcellence Hardwarerequirements Inbrief:low-latency! • Fastcommunication – Fastiterconnects andquietnetworks – FastCPU<->Acceleratortransferrates • NospecialrequirementformemorysizebutlargeL1 Cache • Fatnodes • I/O notabigissue(fornow) • Vectorunitswithlargewidth • Singleprecisionperformance • SIMDunitsthatcanbeusedforintegerandlogicalops
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