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HIGH PERFORMANCE
BIOINFORMATICS
Group May 09-06
Bryan McCoy
Kinit Patel
Tyson Williams
What is Bioinformatics?
Genetic sequencing. Massive amounts of data. Simple operations but many of them. Perfect for distributed computing.
Cell Broadband Engine Has 1 central
PowerPC based PPE.
Has 8 surrounding SPEs.
The 8 SPEs are connected via the element interconnect bus.
Cell Broadband Engine
Functional requirements
Ported applications shall run on the Cell B.E.
The results returned shall be the same as the original program.
The applications shall return their runtime.
The applications shall execute in parallel on multiple Cell B.E.s.
Non-Functional Requirements The Cells shall all run on the Linux OS. The resulting runtimes of the ported
applications shall be faster than on the original applications.
The ported application shall be coded in the C language.
Work Breakdown Structure
Port Apps to Cluster PS3s
Problem Definition
Research Cell/B.E
Research Bioperf Suite
Research Distributed Parallel Algorithms
Research Previously Done Work
End Product Design
Design Requirements
Design Process
Design Documents
Considerations and Selections
Decide Which Linux to Install
Decide which applications to port
End Product Implementation
Hardware Implementation
Prototyping Implementation
Software Implementation
End Product Testing
Ensure Correctness of Output Results
Benchmarking
Final Documentation and Demonstration
Create Final Report
Create Project Poster
Prepare for Presentation
Problem Definition Learn more about how
the cell works and the difficulties in programming.
Learn the algorithms behind the BioPerf Suite.
Learn more about how to distribute algorithms across processors and machines.
Get up to speed with work the previous group has done.
Problem Definition
Research Cell/B.E
Research Bioperf Suite
Research Distributed Parallel Algorithms
Research Previously Completed Work
End Product Design Come up with the
design requirements Implement the
engineering design process in our work
Create the design document
End Product Design
Design Requirements
Design Process
Design Documents
Considerations and Selections
Decide on which version of linux to flash to the rom.Yellow Dog
Decide on specific applications in the BioPerf suite to port.
Considerations and Selections
Decide Which Linux to Install
Decide which applications to port
End Product Implementation
Get the hardware together and running
Prototype different software approaches
Code actual software.
End Product Implementation
Hardware Implementation
Prototyping Implementation
Software Implementation
End Product Testing Test to be sure that
the output is correct. Test to be sure the
ported application is faster than the original.
End Product Testing
Ensure Correctness of Output Results
Benchmarking
Final Documentation and Demonstration
Write a report of our findings.
Create a poster to explain the project in a visual way.
Create and prepare a final presentation to explain the project verbally.
Final Documentation and Demonstration
Create Final Report
Create Project Poster
Prepare for Presentation
Work Schedule Gant chart
Questions?
