1. MP-PIPE for Soybean Proteome Brad Barnes 27/11/15 COMP 5704

2. Problem  High protein plant, grown in Canada  Contains over 70,000 different proteins  Unsigned Short: 2^16 = 65534  Unable to use with PIPE

3. The Cluster  18 nodes  32 GB RAM  8 core processors  100 GB SSD Source: www.dehne.net

4. PIPE Pipeline 1. Prepare data 2. Run genTab to build database 3. Run MP-PIPE to predict interactions

5. Software Construction  Version Control  Testing  Memory management  Logging  Debugging  Performance Tuning

6. Memory  Error: Proc killed with Signal 9  Running out of memory Top output:

7. Logging  Errors in regular PIPE:  Process killed with signal 11 (Segmentation Fault)  Need logging to file!

8. Debugging  Debug in single threaded mode  Attach gdb debugger to file  Trace error: to hash table lookup (with very long protein)  Issue: very large protein sizes lead to integer overflow

9. Testing “The principle objective of software testing is to give confidence in the software.” – Anonymous  Small datasets with known results  Large dataset for final test

10. Performance Tuning  # threads vs speed up MP-PIPE Source: (A. Schoenrock et al. 2011)

11. Version Control Checkpoint resultsWork on different things

12. Version Control

13. Conclusion  Modified PIPE to work for Soybeans  genTab limited by memory => doubled runtime  MP-PIPE performance constant  Validated with tests  Added logging to file  Fixed integer overflow issue

14. Questions 1. What was the issue with PIPE? 2. How were changes verified? 3. What’s one useful tool for software development