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ITS Training and Awareness Session Research Support

ITS Training and Awareness Session Research Support. Jeremy Maris & Tom Armour ITS researchsupport@its.sussex.ac.uk. Research Support. Our Remit Research Group Meetings Work So Far High Performance Computing Plans for the Future Questions?. Our Remit.

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ITS Training and Awareness Session Research Support

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  1. ITS Training and Awareness SessionResearch Support Jeremy Maris & Tom Armour ITS researchsupport@its.sussex.ac.uk

  2. Research Support • Our Remit • Research Group Meetings • Work So Far • High Performance Computing • Plans for the Future • Questions?

  3. Our Remit • Meet with research groups on a regular basis to ensure   the university’s core infrastructure provides appropriate  support for researcher’s computing requirements

  4. Our Remit • Meet with research groups on a regular basis to ensure   the university’s core infrastructure provides appropriate  support for researcher’s computing requirements • To simplify and minimise the  work needed by research  groups to use the University’s core  infrastructure; 

  5. Our Remit • Meet with research groups on a regular basis to ensure   the university’s core infrastructure provides appropriate  support for researcher’s computing requirements • To simplify and minimise the  work needed by research  groups to use the University’s core  infrastructure;  • Provide advice and support to researchers about using IT systems within their research (including HPC)

  6. Our Remit • Meet with research groups on a regular basis to ensure   the university’s core infrastructure provides appropriate  support for researcher’s computing requirements • To simplify and minimise the  work needed by research  groups to use the University’s core  infrastructure;  • Provide advice and support to researchers about using IT systems within their research (including HPC) • The HPC support team would arrange appropriate training events and seminars to help research teams make  appropriate and optimal use of HPC systems

  7. Research Group Meetings • Astronomy • Particle Physics • Informatics • Geography • Sussex Research Hive • Engineering Thermo-Fluids • Life Sciences • Economics • Sussex Doctoral School

  8. Work So Far • Have already made good contacts with the research community.

  9. Work So Far • Have already made good contacts with the research community. • Specification, installation and commissioning of HPC clusters for IT Services and Physics (ATLAS analysis)

  10. Work So Far • Have already made good contacts with the research community. • Specification, installation and commissioning of HPC clusters for IT Services and Physics (ATLAS analysis) • Moved new HPC facility from Chichester Machine Room to the new Shawcross Data Centre

  11. Work So Far • Have already made good contacts with the research community. • Specification, installation and commissioning of HPC clusters for IT Services and Physics (ATLAS analysis) • Moved new HPC facility from Chichester Machine Room to the new Shawcross Data Centre • Continuing support for existing HPC Facilities in Maths & Physics – Engineering and Life Sciences

  12. High Performance Computing (HPC) • About HPC … • Cluster configuration • Software available • Users

  13. What is High Performance Computing ? • High performance computing • Maximising number of cycles per second

  14. What is High Performance Computing ? • High performance computing • Maximising number of cycles per second • High throughput computing • Maximising number of cycles per year

  15. What is High Performance Computing ? • High performance computing • Maximising number of cycles per second • High throughput computing • Maximising number of cycles per year • Facilitating the storage, access and processing of data • Coping with the massive growth in data

  16. High Performance Computing • High performance computing • tasks must run quickly • single problem split across many processors • Task parallel, MPI or SMP • Simulations • Markov models (finding patterns over time in complex systems) • Theoretical Chemistry • Computational Fluid Dynamics • Imaging processing (3D image reconstruction, 4D visualisation) • Sequence assembly • Whole genome analysis

  17. High throughput computing • A lot of work done over a long time frame • One program run many times, e.g. searching a large data set • Loosely coupled • Data parallel (embarrassingly parallel) • ATLAS experiment analysis • Computational Linguistics • Parameter exploration (simulations) • Algebraic geometry • Genomics (sequence alignment, BLAST etc) • Virtual Screening (e.g. in drug discovery) • Statistical analysis (e.g. bootstrap analysis)

  18. Growth in data • Explosion of data – store and locate and process • expanding 3 times faster than Moore’s law • 1TB per instrument day from sequencers • 15PB year from CERN LHC • Imaging data eg MRI, CT, Microscopy together with metadata • Gene expression data from high density genomic microarrays • Research data now added to and accessed from repositories • challenges re data warehousing

  19. New ways to process data • New ways to process, explore and model. • Genome wide association studies (GWAS) • Analysis of the genome of multiple individuals • genetic contribution to cancer • Tumour expression data – comparing tumours • Image processing techniques re faster research or diagnosis/treatment (Microscopy, MRI, CT) • Simulations at all scales • Climate (Geography) • Systems Biology – modelling simple organisms • Sackler Centre for Consciousness Science • Computational power required 4 – 10 times that of increase in data

  20. Interdisciplinary research • New techniques – collaborations with other sciences to give new understanding • Sussex Research Themes • Mind and Brain • Digital and Social Media • Culture and Heritage • Citizenship and Democratisation • Global Transformations and Environment and Health

  21. Computational fluid dynamics Modelling flows of cancer cells in blood system to characterise the dynamic forces and biochemistry at work during in vitro cell adhesion. Hoskins, Kunz, Dong Penn State.

  22. New HPC facilities • Feynman • 8 x 12 core nodes (2.67GHz, 4GB/core) • 108 cores, 439GB RAM • 20TB NFS home file system • Apollo • 10 x 12 core nodes • 2 x 48 core nodes (2.2 GHz, 256GB) • 228cores, 1TB RAM • 4 x12 core nodes donated by Dell • 20TB NFS home file system • 81 TB high-performance Lustre parallel file system • QDR infiniband (40GHz)

  23. Other HPC systems • Zeus • 16 x 8 core nodes (2.4GHz, 1.5GB/Core) – 96 cores Infiniband • Archimedes • 20 x 4 core nodes (3GHz, 2GB/Core) - 80 cores Qsnet • Informatics • 7 x 8 core nodes (2.3GHz, >=2GB/Core) 56 cores GigE • Thermofluids • 11 x 8 core nodes ~100 cores GigE • Legacy • Dirac (56 nodes 2 core, 1GB/core) 112 cores GigE • Boston (8 nodes 2 core 1GB/core) 16 cores GigE • Informatics (80 cores @ 1.8GHz, 2GB/core ) replaced with R815 • CCNR (80 cores @ 1.8GHz, 512k/core) 80 cores, GigE

  24. Software • Intel Parallel Studio • Compilers (Fortran, C) • Profiling • Debugging • High Performance Libraries • MKL etc • NAG • Matlab • STATA • AIMPRO, ADF, Gaussian, Amber (Chemistry) • GAP (Maths) • ATHENA (LHC ATLAS software) • Researchers own software • Software built and installed as requested

  25. Trial Users • Maths • Physics • Chemistry • Economics • Informatics

  26. Plans for the Future • Integration of Legacy HPC Systems

  27. Plans for the Future • Integration of Legacy HPC Systems • Involve non-traditional users, especially Humanities and Social Sciences

  28. Plans for the Future • Integration of Legacy HPC Systems • Involve non-traditional users, especially Humanities and Social Sciences • Evaluate use of GPU technology (Sackler Centre for Consciousness, Physics)

  29. Plans for the Future • Integration of Legacy HPC Systems • Involve non-traditional users, especially Humanities and Social Sciences • Evaluate use of GPU technology (Sackler Centre for Consciousness, Physics) • Assisting Physics re GridPP integration

  30. Plans for the Future • Integration of Legacy HPC Systems • Involve non-traditional users, especially Humanities and Social Sciences • Evaluate use of GPU technology (Sackler Centre for Consciousness, Physics) • Assisting Physics re GridPP integration • Access to external facilities eg the National Grid Service and others.

  31. Plans for the Future • Integration of Legacy HPC Systems • Involve non-traditional users, especially Humanities and Social Sciences • Evaluate use of GPU technology (Sackler Centre for Consciousness, Physics) • Assisting Physics re GridPP integration • Access to external facilities eg the National Grid Service and others. • Continuing support for CISC (DICOM archive + fMRI analysis)

  32. Plans for the Future • Integration of Legacy HPC Systems • Involve non-traditional users, especially Humanities and Social Sciences • Evaluate use of GPU technology (Sackler Centre for Consciousness, Physics) • Assisting Physics re GridPP integration • Access to external facilities eg the National Grid Service and others. • Continuing support for CISC (DICOM archive + fMRI analysis) • Access to external facilities eg the National Grid Service and others.

  33. Plans for the Future • Integration of Legacy HPC Systems • Involve non-traditional users, especially Humanities and Social Sciences • Evaluate use of GPU technology (Sackler Centre for Consciousness, Physics) • Assisting Physics re GridPP integration • Access to external facilities e.g. the National Grid Service and others. • Continuing support for CISC (DICOM archive + fMRI analysis) • Access to external facilities e.g. the National Grid Service and others. • Condor pool for Windows programs, e.g. Matlab

  34. Plans for the Future • Integration of Legacy HPC Systems • Involve non-traditional users, especially Humanities and Social Sciences • Evaluate use of GPU technology (Sackler Centre for Consciousness, Physics) • Assisting Physics re GridPP integration • Access to external facilities e.g. the National Grid Service and others. • Continuing support for CISC (DICOM archive + fMRI analysis) • Access to external facilities e.g. the National Grid Service and others. • Condor pool for Windows programs, e.g. Matlab • Integrating with Linux Support

  35. Questions?

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