Papers & Talks
Papers
During the summers of 2011 and 2012, I worked with professor Jens Mache and a small team of other students to develop materials for teaching parallel programming and computer security to undergraduate students.
Summer, 2012
- Title
- Using the N-Body Problem to Engage Undergraduates in Parallel Programming
- Authors
- Ben White, Miriam Robinson, Christopher T. Mitchell, Jens Mache
- Conference
- The 2012 International Conference on Parallel and Distributed Processing Techniques and Applications
- Supplemental Code
- Code for a 2D n-body simulation (written in C, X11), and a small library for collecting high-resolution timing data are hosted on Bitbucket.
Summer, 2011
- Title
- Parallelizing Tompa’s Exact Algorithm for Finding Short Motifs in DNA
- Authors
- Christopher T. Mitchell, Jonathan Grochowski, Julian H. Dale, Nicolas B. Wilson, Jens Mache
- Abstract
- Motif finding, the search for regulatory sequences in DNA, is a computationally expensive challenge in bioinformatics. This paper presents a pleasantly parallel version of Tompa’s exact method for finding short motifs. We use a distributed-memory computer cluster and MPI to run our parallel algorithm and collect data. We vary motif length and allowed substitutions. Results indicate good speedup and scalability.
- Conference
- The 2011 International Conference on Parallel and Distributed Processing Techniques and Applications (2011-07)
- Code
- Our serial implementation and parallel branch of the “Motif Finder” project are hosted on Launchpad.
- Title
- Learning CUDA: Lab Exercises and Experiences, Part 2
- Authors
- Christopher T. Mitchell, Jens Mache, Karen L. Karavanic
- Abstract
- The rise of multi-core computer hardware has introduced new urgency to learning parallel programming. In this paper, we again focus on CUDA exercises suitable for undergraduate students. Trying to appeal to wide audience of todays learners, we have developed a Game of Life exercise and an introductory CUDA summary. We discuss our classroom-test of the exercise, our experiences, and our lessons learned.
- Resources
- The CUDA webpage and labs we developed
- Published in
- SPLASH '11 Companion (2011-07)
Talks
- Title
- Making database access more object-oriented with the active record design pattern
- Event
- The 70th meeting of the Oregon Academy of Science
- When
- 2011-01-26