Tuning Parallel Applications to
Accelerate Scientific Discoveries

              Robert Henschel
           rhensche@india...
Contents
•   PTI / High Performance Applications
•   Performance of Scientific Codes
•   IU and TeraGrid Compute Resources...
What this talk will be about
• Making you aware of compute resources that you
  can use for your work, to make you more
  ...
PTI and High Performance Applications
• Pervasive Technology Institute
   – Develop and deliver innovative information tec...
Performance of Scientific Codes
• Supercomputing, or High Performance Computing (HPC),
  is not just for computer geeks!

...
IU and TeraGrid Compute Resources
• Two HPC systems at IU
   – BigRed    30 TFLOPS            (3000 cores)
   – Quarry    ...
IU and TeraGrid Compute Resources cont'd




                                     Robert Henschel
IU and TeraGrid Compute Resources cont'd
• TeraGrid
   – NSF funded HPC systems and support infrastructure
   – 11 resourc...
Optimizing for IU's HPC Systems
• Help researchers access the central systems and
  determine what system to use
• Install...
Using TeraGrid HPC Systems
• Low barrier of entry

• Identify if a problem and workflow will work on the
  TeraGrid
• Get ...
Contents – HPA is Here to Help
• HPA is Here to Help
  – What We Do

• Recent Examples
  – Integrating HPC Systems into an...
What We Do
• Consulting about HPC system usage
  – From start to finish
  – Optimize source code for architectures

• Help...
HPC Systems and an Electron Microscope
General Case
  – Users have an instrument that produces a lot of data
    on a dail...
Gas Giant Planets on the TeraGrid
General Case
  – Users have a set workflow for analyzing data
  – Locally available comp...
Predicting Drug-Drug Interactions
General Case
  – Researchers implement proof of concept research
    algorithms
  – Scal...
What this talk was about
• Made you aware of compute resources that you can
  use for your work, to make you more producti...
Acknowledgments
This material is based upon work supported by the National Science
Foundation under Grant Numbers 0116050 ...
Upcoming SlideShare
Loading in …5
×

Statewide It Robert Henschel

767 views
679 views

Published on

Published in: Technology, Education
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total views
767
On SlideShare
0
From Embeds
0
Number of Embeds
10
Actions
Shares
0
Downloads
4
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Statewide It Robert Henschel

  1. 1. Tuning Parallel Applications to Accelerate Scientific Discoveries Robert Henschel rhensche@indiana.edu October 2009
  2. 2. Contents • PTI / High Performance Applications • Performance of Scientific Codes • IU and TeraGrid Compute Resources • Optimizing for IU's HPC Systems • Using TeraGrid HPC Systems • HPA is Here to Help Robert Henschel
  3. 3. What this talk will be about • Making you aware of compute resources that you can use for your work, to make you more productive. • Introducing the High Performance Applications group and how we can help get research done faster. • Give you examples of what we have done for researchers to make them more competitive in their field. Robert Henschel
  4. 4. PTI and High Performance Applications • Pervasive Technology Institute – Develop and deliver innovative information technology to advance research, education, industry and society. – School of Informatics – School of Law – University Information Technology Services • High Performance Applications – Part of the Digital Science Center of PTI – Part of the Research Technologies of UITS – Seven people that help IU researchers make efficient use of IU and TeraGrid compute resources Robert Henschel
  5. 5. Performance of Scientific Codes • Supercomputing, or High Performance Computing (HPC), is not just for computer geeks! • Performance for computer scientists – Amdahls law and scalability – Efficient usage of functional units of processors – Optimally using memory bandwidth – Trying to avoid I/O as much as possible • Performance for researchers – When do I get the answer to my problem? – When does my job run and when is it done? Robert Henschel
  6. 6. IU and TeraGrid Compute Resources • Two HPC systems at IU – BigRed 30 TFLOPS (3000 cores) – Quarry 7 TFLOPS (1000 cores) • Several special purpose systems – Small Cell B.E. Cluster – MDGRAPE-2 machine • Several storage resources – IU Data Capacitor – GPFS, RFS, HPSS • Policy of open access to compute resources Robert Henschel
  7. 7. IU and TeraGrid Compute Resources cont'd Robert Henschel
  8. 8. IU and TeraGrid Compute Resources cont'd • TeraGrid – NSF funded HPC systems and support infrastructure – 11 resource providers – More than 1,500 TFLOPS (150,000 cores) • Central allocation and support structure Robert Henschel
  9. 9. Optimizing for IU's HPC Systems • Help researchers access the central systems and determine what system to use • Install and optimize applications • Provide guidance on compiler and library optimization • Help with job submission, especially running many thousands of jobs Robert Henschel
  10. 10. Using TeraGrid HPC Systems • Low barrier of entry • Identify if a problem and workflow will work on the TeraGrid • Get a startup allocation • Use it and identify if it is worth pursuing this further • Submit a full allocation request Robert Henschel
  11. 11. Contents – HPA is Here to Help • HPA is Here to Help – What We Do • Recent Examples – Integrating HPC Systems into an Electron Microscope Workflow – Migrating Research in Gas Giant Planets from IU to TeraGrid HPC Systems – Developing Computational Models to Predict Drug-Drug Interactions Robert Henschel
  12. 12. What We Do • Consulting about HPC system usage – From start to finish – Optimize source code for architectures • Help with TeraGrid allocation proposals • Adapting and creating workflows for new environments • Consulting for grant proposals Robert Henschel
  13. 13. HPC Systems and an Electron Microscope General Case – Users have an instrument that produces a lot of data on a daily basis – This data needs to be stored and analyzed Electron Microscope in Simon Hall (IU Bloomington) – Microscope stores data on a Windows workstation – Researcher does quality checks on local workstation – IU Data Capacitor links workstations, IU HPC systems and the IU long term archive together Robert Henschel
  14. 14. Gas Giant Planets on the TeraGrid General Case – Users have a set workflow for analyzing data – Locally available compute resources are not big enough to keep up with demand Understanding Gas Giant Planets – IDL is used to visualize simulation data • Commercial software, IU Astronomy has a license – Simulation application needs to run on a large shared memory system – TeraGrid and IU Data Capacitor tie this workflow together Robert Henschel
  15. 15. Predicting Drug-Drug Interactions General Case – Researchers implement proof of concept research algorithms – Scaling from proof of concept to production science is difficult – The ability to add HPC expertise to grant proposals will make the proposal more competitive Computational Models to Predict Drug-Drug Interactions – Drug exposure model developed in R – Scaling to real world data sets not possible without using HPC systems – Porting to C and running on UITS hardware Robert Henschel
  16. 16. What this talk was about • Made you aware of compute resources that you can use for your work, to make you more productive. • Introduced the High Performance Applications group and how we can help get research done faster. • Gave you examples of what we have done for researchers to make them more competitive in their field. Robert Henschel
  17. 17. Acknowledgments This material is based upon work supported by the National Science Foundation under Grant Numbers 0116050 and 0521433. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the National Science Foundation (NSF). This work was support in part by the Indiana Metabolomics and Cytomics Initiative (METACyt). METACyt is supported in part by Lilly Endowment, Inc. This work was support in part by the Indiana Genomics Initiative. The Indiana Genomics Initiative of Indiana University is supported in part by Lilly Endowment, Inc. This work was supported in part by Shared University Research grants from IBM, Inc. to Indiana University. Robert Henschel

×