1. High Performance Computing on an IBM Cell Processor --- Bioinformatics
May08-24
Advisor: Dr. Zhao Zhang
Kyle Byerly
Shannon McCormick
Matt Rohlf
Bryan Venteicher
shannon

2. Introduction Problem Statement Proposed Solution
Researchers need to tackle more complex and computational demanding problems, but are trying to maximize performance within their budget
Proposed Solution
Use the PlayStation 3 (PS3) and Cell Broadband Engine (Cell/B.E.) to achieve improved performance of bioinformatics applications at a low cost
shannon
Senior Design May08-24
4/30/08

3. Requirements Functional Requirements Non-functional requirements
Application ported shall run on the Cell/B.E.
Ported application shall return the same results as the original application
Ported application shall return its running time for comparison to original application
Non-functional requirements
The ported application shall run faster on the PS3
The user interface will not be altered
shannon
Senior Design May08-24
4/30/08

4. Cell Processor Sony, Toshiba, and IBM
Work began in 2000
February 2005 – First technical disclosures
May 2005 – First public demonstration
“Super-computer on a chip”
Multi-core processor
Home entertainment to distributed computing
Heterogeneous Processor
Power Processor Element (PPE)
Synergistic Processing Element (SPE)
Element Interconnect Bus (EIB)
shannon
L1T1H1-02 Cell Overview
Senior Design May08-24
4/30/08

5. Ported Program Selection
Criteria:
Manageable size given our timeframe
Suitable documentation of the algorithm exists
Application suitable to be parallelized
Not previously ported to the Cell/B.E.
ClustalW and DNAPenny both met the first three criteria
ClustalW had already been ported
DNAPenny was selected as the main focus
matt
Senior Design May08-24
4/30/08

6. ClustalW Prototype Created un-optimized port of ClustalW
Started with an already parallelized version: clustalw_smp
Concentrated on making working, correct port
Not interested in performance
Working version completed
Useful in gauging work involved in porting DNAPenny
matt
Senior Design May08-24
4/30/08

7. DNAPenny Takes set of DNA sequences as input
Returns set of parsimonious trees
Represent the shortest evolutionary path between individual DNA sequences
Team had identified hotspots in code
matt
Senior Design May08-24
4/30/08

8. General Parallel DNAPenny
Profiling DNAPenny showed a single function was responsible for 90% of runtime
Analyzed function to determine suitability for parallelizing
Data is divided among threads
bryan
Senior Design May08-24
4/30/08

9. Cell/B.E. Port of DNAPenny
Done in several iterations
Load and execute code on a single SPE
Load code once on SPE, execute for duration of program
Load code once on multiple SPEs
Use compiler optimizations
Hand vectorized SPE code
bryan
Senior Design May08-24
4/30/08

10. Test Hardware PlayStation 3 Powerful server Cell/B.E., 256MB RAM
Quad-core Intel Xeon 3.0GHz, 6GB RAM
kyle
Senior Design May08-24
4/30/08

11. Testing Methodology Input files Two phases Six were selected
Execute, verify, and benchmark
Aggregation and graphing of data
kyle
Senior Design May08-24
4/30/08

12. Benchmark Results infile.orig Code revision
4-Way 3.0GHz Machine (seconds)
X Speedup
PlayStation 3 (seconds)
dnapenny_orig 1
dnapenny_slimmer
parallel_dnapenny_1.0
supplement_spe_parallel_1SPE
N/A
supplement_spe_parallel_3SPE
supplement_spe_parallel_6SPE
supplement_parallel_vector_1SPE
supplement_parallel_vector_3SPE
supplement_parallel_vector_6SPE
130.59
kyle
Senior Design May08-24
4/30/08

13. Benchmarking Results (cont)
kyle
Senior Design May08-24
4/30/08

14. Earned Value Analysis Task Estimated Hours Actual Hours % Complete
Budgeted Costs of Work Scheduled
Problem Definition
100
100.5
100%
$1,000.00
Technology and Implementation Considerations 36 37
$360.00
End-Product Design 20
17.5
$200.00
End-Product Prototype Implementation
320
272
$3,200.00
End-Product Testing 60
78.5
$600.00
End-Product Documentation 40 42
$400.00
End-Product Demonstration 48 35
$480.00
Project Reporting
140 99
$1,400.00
Total
764
681.5
$7,640.00
matt
Senior Design May08-24
4/30/08

15. Earned Value Analysis (cont.)
Task
Budgeted Costs of Work Performed
Actual Costs of Work Performed
Cost Variance
Cost Performance Index
Problem Definition
$1,000.00
$1,005.00
-$5.00
99.5%
Technology and Implementation Considerations
$360.00
$370.00
-$10.00
97.3%
End-Product Design
$200.00
$175.00
$25.00
114.3%
End-Product Prototype Implementation
$3,200.00
$2,720.00
$480.00
117.6%
End-Product Testing
$600.00
$785.00
-$185.00
76.4%
End-Product Documentation
$400.00
$420.00
-$20.00
95.2%
End-Product Demonstration
$350.00
$130.00
137.1%
Project Reporting
$1,400.00
$990.00
$410.00
141.4%
Total
$7,640.00
$6,815.00
$825.00
112.1%
matt
Senior Design May08-24
4/30/08

16. Lessons Learned Cell/B.E. is a unique programming challenge
Many tools available to help understand poorly documented code
bryan
Senior Design May08-24
4/30/08

17. Conclusion Significant speedup achieved
Surprised at the impact of hand vectorization
Cell/B.E. is well suited for this type of application
shannon
Senior Design May08-24
4/30/08

18. Questions
Everyone!111
Senior Design May08-24
4/30/08