its training and awareness session research support

ITS Training and Awareness SessionITS Training and Awareness Session

Research SupportResearch Support

Jeremy Maris & Tom Armour

ITS

[email protected]

Research SupportResearch Support

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

Our RemitOur Remit

Meet with research groups on a regular basis to ensure the university’s core infrastructure provides appropriate

support for researcher’s computing requirements

Our RemitOur Remit


support for researcher’s computing requirements To simplify and minimise the work needed by research

groups to use the University’s core infrastructure;

Our RemitOur Remit



groups to use the University’s core infrastructure; Provide advice and support to researchers about using IT

systems within their research (including HPC)

Our RemitOur Remit



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

Research Group MeetingsResearch Group Meetings

Astronomy Particle Physics Informatics Geography Sussex Research Hive Engineering Thermo-Fluids Life Sciences Economics Sussex Doctoral School

Work So FarWork 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




• 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

High Performance Computing (HPC)High Performance Computing (HPC)

• About HPC …• Cluster configuration• Software available• Users

What is High Performance Computing ?What is High Performance Computing ?

High performance computing– Maximising number of cycles per second



High throughput computing– Maximising number of cycles per year



High throughput computing– Maximising number of cycles per year

Facilitating the storage, access and processing of data– Coping with the massive growth in data

High Performance Computing 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

High throughput computingHigh 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)

Growth in data 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

New ways to process dataNew 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

Interdisciplinary researchInterdisciplinary 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

Computational fluid dynamics 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.

New HPC facilitiesNew 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)

Other HPC systemsOther 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

Software 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

Trial UsersTrial Users

Maths Physics Chemistry Economics Informatics

Plans for the FuturePlans for the Future

• Integration of Legacy HPC Systems


• Integration of Legacy HPC Systems• Involve non-traditional users, especially Humanities and Social

Sciences



Sciences • Evaluate use of GPU technology (Sackler Centre for Consciousness,

Physics)




Physics)• Assisting Physics re GridPP integration




Physics)• Assisting Physics re GridPP integration• Access to external facilities eg the National Grid Service and others.




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)




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.




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




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

Questions?Questions?

its training and awareness session research support

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