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Leveraging HPC for Alzheimer’s Research and Beyond
Joseph Lombardo
Executive Director, UNLV’s National Supercomputing Center
September 2015
2
Agenda
• About the NSCEE @ Switch
• Computing Challenges
• Spotlight on Alzheimer’s Research
• Other Research Areas that Benefit from HPC
• Solution with Altair PBS Professional
• Project Highlights
• Next Steps
3
About the NSCEE
• Full-service supercomputing facility
• Mission for excellence in education and research in
supercomputing and its applications
• Provides supercomputing training and services to
academic and research institutions, government and
private industry
• Supports energy, the environment, medical informatics
and health care
• Serves researchers at the University of Nevada Las
Vegas and other statewide, nationwide and global
research
4
NSCEE @ Switch
• In Q4 2014, UNLV moved its NSCEE
facilities to Switch facility in Las Vegas
• Hosted on Cherry Creek system – large
Intel system for scientific and economic
R&D
• 26,000 compute cores
• Intel Xeon E5-2697v2 12C 2.700GHz, Intel
Truscale, Intel Xeon Phi 7120P
• Dedicated Research Network (DMZ) with
200Gb/s potential
Switch SUPERNAP and Intel Partner with UNLV to Boost
Scientific Research and Economic Development
Intel’s “Cherry Creek” supercomputer brings world-class
computing power to UNLV; Switch SUPERNAP to lead high-
tech industry partnerships.
5
NSCEE Computing Challenges
• Numerous and complex workloads
• Hundreds of projects worldwide
• Highly compute-intensive research
• Massive data needs
• Users must access massive data remotely to do their work
• Time-sensitive projects
• Many NSCEE projects have critical governmental and
environmental significance, so timely and reliable performance
is a key requirement
Thus, a powerful and reliable infrastructure is a key requirement!
6
Spotlight: Alzheimer’s Research
• The need for innovation
• Alzheimer's Disease continue to cause tremendous
familial, social, and economic burdens to modern society
• Despite substantial progress, existing treatment
approaches are limited – so new therapeutic approaches
are desperately needed
• The NSCEE project
• NSCEE works with researchers to compare genomes of Alzheimer's patient with normal
patients
• Challenge: Researchers wanted to enhance the statistical power of previous analyses by
including more than 10,000 additional patients (and thus genomic data sets) in the study –
meaning a massive leap in computational requirements
7
Alzheimer’s Project Results
• Reduced overall runtimes for processing workload
• PBS Professional in conjunction with Rocks and an improved system
with shared memory compute node, reduced processing time by
more than 50%
• Alzheimer’s project researchers can process a genome in about 3
hours instead of the 8+ hours it previously took
• Fast, easy implementation
• Powerful, flexible customization capabilities -- can be easily
extended by adding site-specific processing plugins/hooks
• Improved system manageability and extensibility:
• Lightweight solution
• Very easy to manage
• Not dependent on any specific operating system
“PBS Professional has simplified the
administration of our compute clusters
immensely. What used to cause
problems with our old workload
management software is now simple.
In addition, Altair is an outstanding
supplier and partner -- their
responsiveness and support have made
a huge difference and really
differentiate them from our previous
supplier.”
--Ron Young, Research support analyst at NSCEE
8
Other NSCEE Research that Benefits from HPC…
Quantum Dynamics of Chemical Reactions
• HPC dramatically improves ability to understand how atoms and molecules interact and the chemical reactions
that occur in different environments
• Researchers use complex theoretical calculations to explore how molecules behave at absolute zero
temperatures and other conditions
Fracking
• Hydraulic fracturing often takes place >1 mile below groundwater supplies
• Mechanical engineers use sophisticated numerical models to more accurately predict prime locations for
extraction and assess possible contamination associated with the process
Magnetically Dominated Jets in Gamma-Ray Burst
• Gamma-ray bursts are the most luminous, and violent, explosions in the universe -- they signify the deaths,
collisions or swallowing up of stars
• Astrophysicists’ computational research advances our understanding of the physical mechanisms behind GRBs
and other high-energy astrophysical phenomena
9
HPC Scheduling Solution: Altair PBS Professional
• Market-leading workload manager
• Proven for 20+ years at thousands of sites
• Fast, easy implementation
• Powerful, flexible customization capabilities
• Simplified management
• PBS Works suite won “Best HPC Software” in 2014
• Reliable vendor
• 30-year track record of customer satisfaction
• Global presence with 40+ offices in 22 countries
• “Altair is an outstanding supplier and partner -- their
responsiveness and support have made a huge difference.”
10
Acknowledgements
• Alzheimer’s Research:
• Martin R. Schiller, Executive Director, Nevada Institute of Personalized Medicine and
Professor School of Life Science
• martin.schiller@unlv.edu
• Quantum Dynamics of Chemical Reactions:
• Balakrishnan Naduvalath, Professor of Chemistry
• naduvala@unlv.nevada.edu
• Fracking:
• Darrell Pepper, Professor of Mechanical Engineering
• darrell.pepper@unlv.edu
• Magnetically Dominated Jets in Gamma-Ray Burst:
• Bing Zhang Professor of Astrophysics
• zhang@physics.unlv.edu
SIN City:
Success in
Neuroscience
Thank you for your attention!
Joseph Lombardo
Executive Director
UNLV’s National Supercomputing Center
and Dedicated Research Network (DMZ)
lombardo@nscee.edu
Questions?

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Leveraging HPC for Alzheimer’s Research and Beyond

  • 1. Leveraging HPC for Alzheimer’s Research and Beyond Joseph Lombardo Executive Director, UNLV’s National Supercomputing Center September 2015
  • 2. 2 Agenda • About the NSCEE @ Switch • Computing Challenges • Spotlight on Alzheimer’s Research • Other Research Areas that Benefit from HPC • Solution with Altair PBS Professional • Project Highlights • Next Steps
  • 3. 3 About the NSCEE • Full-service supercomputing facility • Mission for excellence in education and research in supercomputing and its applications • Provides supercomputing training and services to academic and research institutions, government and private industry • Supports energy, the environment, medical informatics and health care • Serves researchers at the University of Nevada Las Vegas and other statewide, nationwide and global research
  • 4. 4 NSCEE @ Switch • In Q4 2014, UNLV moved its NSCEE facilities to Switch facility in Las Vegas • Hosted on Cherry Creek system – large Intel system for scientific and economic R&D • 26,000 compute cores • Intel Xeon E5-2697v2 12C 2.700GHz, Intel Truscale, Intel Xeon Phi 7120P • Dedicated Research Network (DMZ) with 200Gb/s potential Switch SUPERNAP and Intel Partner with UNLV to Boost Scientific Research and Economic Development Intel’s “Cherry Creek” supercomputer brings world-class computing power to UNLV; Switch SUPERNAP to lead high- tech industry partnerships.
  • 5. 5 NSCEE Computing Challenges • Numerous and complex workloads • Hundreds of projects worldwide • Highly compute-intensive research • Massive data needs • Users must access massive data remotely to do their work • Time-sensitive projects • Many NSCEE projects have critical governmental and environmental significance, so timely and reliable performance is a key requirement Thus, a powerful and reliable infrastructure is a key requirement!
  • 6. 6 Spotlight: Alzheimer’s Research • The need for innovation • Alzheimer's Disease continue to cause tremendous familial, social, and economic burdens to modern society • Despite substantial progress, existing treatment approaches are limited – so new therapeutic approaches are desperately needed • The NSCEE project • NSCEE works with researchers to compare genomes of Alzheimer's patient with normal patients • Challenge: Researchers wanted to enhance the statistical power of previous analyses by including more than 10,000 additional patients (and thus genomic data sets) in the study – meaning a massive leap in computational requirements
  • 7. 7 Alzheimer’s Project Results • Reduced overall runtimes for processing workload • PBS Professional in conjunction with Rocks and an improved system with shared memory compute node, reduced processing time by more than 50% • Alzheimer’s project researchers can process a genome in about 3 hours instead of the 8+ hours it previously took • Fast, easy implementation • Powerful, flexible customization capabilities -- can be easily extended by adding site-specific processing plugins/hooks • Improved system manageability and extensibility: • Lightweight solution • Very easy to manage • Not dependent on any specific operating system “PBS Professional has simplified the administration of our compute clusters immensely. What used to cause problems with our old workload management software is now simple. In addition, Altair is an outstanding supplier and partner -- their responsiveness and support have made a huge difference and really differentiate them from our previous supplier.” --Ron Young, Research support analyst at NSCEE
  • 8. 8 Other NSCEE Research that Benefits from HPC… Quantum Dynamics of Chemical Reactions • HPC dramatically improves ability to understand how atoms and molecules interact and the chemical reactions that occur in different environments • Researchers use complex theoretical calculations to explore how molecules behave at absolute zero temperatures and other conditions Fracking • Hydraulic fracturing often takes place >1 mile below groundwater supplies • Mechanical engineers use sophisticated numerical models to more accurately predict prime locations for extraction and assess possible contamination associated with the process Magnetically Dominated Jets in Gamma-Ray Burst • Gamma-ray bursts are the most luminous, and violent, explosions in the universe -- they signify the deaths, collisions or swallowing up of stars • Astrophysicists’ computational research advances our understanding of the physical mechanisms behind GRBs and other high-energy astrophysical phenomena
  • 9. 9 HPC Scheduling Solution: Altair PBS Professional • Market-leading workload manager • Proven for 20+ years at thousands of sites • Fast, easy implementation • Powerful, flexible customization capabilities • Simplified management • PBS Works suite won “Best HPC Software” in 2014 • Reliable vendor • 30-year track record of customer satisfaction • Global presence with 40+ offices in 22 countries • “Altair is an outstanding supplier and partner -- their responsiveness and support have made a huge difference.”
  • 10. 10 Acknowledgements • Alzheimer’s Research: • Martin R. Schiller, Executive Director, Nevada Institute of Personalized Medicine and Professor School of Life Science • martin.schiller@unlv.edu • Quantum Dynamics of Chemical Reactions: • Balakrishnan Naduvalath, Professor of Chemistry • naduvala@unlv.nevada.edu • Fracking: • Darrell Pepper, Professor of Mechanical Engineering • darrell.pepper@unlv.edu • Magnetically Dominated Jets in Gamma-Ray Burst: • Bing Zhang Professor of Astrophysics • zhang@physics.unlv.edu
  • 12. Thank you for your attention! Joseph Lombardo Executive Director UNLV’s National Supercomputing Center and Dedicated Research Network (DMZ) lombardo@nscee.edu Questions?