Patrick Flick (third from left) was honored with his advisor and co-author, Srinivas Aluru, for "Best Student Paper" at the SC'15 Awards Ceremony.
PhD Candidate Patrick Flick (CSE) won "Best Student Paper" at the Supercomputing '15 conference -- held this week in Austin, Texas -- where a contingent of more than 50 students, faculty and researchers from Georgia Tech advanced the field of high-performance computing (HPC).
Flick, working with Professor Srinivas Aluru (CSE), created parallel algorithms for distributed-memory construction that are 110x times faster than the best method running on a sequential, single computer. Using the human genome as a racetrack to test his speed, Flick was able to index the entire human genome in just 7.3 seconds running on 1024 Intel Xeon cores.
"It is very gratifying to see Patrick win this highly competitive and prestigious award," Aluru said. "He injected a new way of solving an important problem that many have recently worked on, engineered his solution perfectly, and came up with performance that will be hard to beat."
It is believed to be the first algorithm and implementation that uses this approach for distributed-memory parallel systems, and an important one for analyzing complex biological data.
“Bioinformatics is an example of a scientific field that is extremely data intensive; speed matters and speed helps,” Flick said. “We are not aware of any other parallel suffix array or suffix tree construction algorithms which achieve speedups this high.”
Next, Flick is working on a journal paper that includes more improvements, additional techniques, and further showcases the algorithms on real applications. Flick also authored another paper at SC'15 with fellow graduate students Chirag Jain (CSE) and Tony Pan (CSE) about how to partition large graphs that arise in metagenomics -- another data-intensive application area.
PhD Candidates Dipanjan Sengupta (CS) and Kapil Agarwal (CS) also were nominated for best paper at SC'15 after developing a scalable framework (dubbed “GraphReduce”) to process large graphs that exceed a device’s GPU memory.
Other activity by Georgia Tech at SC'15 included:
- Chair David Bader, Assoc. Chair Rich Vuduc and Senior Research Scientist Jason Riedy launched a new effort funded by the National Science Foundation called EMBRACE to address scientific and technical issues related to benchmarking. Vuduc says forward-looking benchmarks are needed because HPC is attracting new people to the field, applications are diverse, and platforms are quickly evolving. The project asks the community to decide how benchmarks are defined, interpreted and used to produce meaningful results for scientists and manufacturers alike.
- Professor Tom Conte (CS), president of IEEE, opened the Computer Society fall meeting among other activities as IEEE continues to champion a movement called "Rebooting Computing" to address the end of Moore's Law.
- Bader was one of six selected panelists at the session, “Supercomputing and Big Data: From Collision to Convergence.”
- Aluru held a session about the new South Big Data Regional Hub (awarded to Georgia Tech and RENCI earlier this month by the National Science Foundation). The workshop was intended to introduce attendees to future research collaboration.
- Professor Edmond Chow led the the Georgia Tech delegation, in addition to meeting with industry partners and attending workshops.
- Flick and Sengupta participated in a panel to guide undergraduate students who are interested in HPC.
- Joint professor Jeffrey Vetter of Oak Ridge National Labs participated in the SC'15 opening media briefing.
- Bader and other university partners released the 11th Graph500 list -- a performance ranking of the world's top supercomputers.
- Numerous other individuals presented papers, led sessions, and met with potential partners to secure research funding and network.
- Vuduc served on the SC'15 conference organizing committee as co-chair of Tutorials planning and noted a dramatic rise in the number of workshops, exhibitors and attendees. More than 350 papers were submitted to the conference this year, but only 80 were accepted. Vuduc said that trend is one to expect at SC'16 in Salt Lake City, Utah, which he has been asked again to help organize.
For more about what happened at this year's conference, visit http://sc15.supercomputing.org/
See photos of Georgia Tech at SC'15 from throughout the week.