Notes from Supercomputing Conference (SC12)

Notes from Supercomputing Conference (SC12)

Supercomputing is a yearly conference, where universities, companies and research centers from all over the world meet to discuss latest developments in high performance computing, networking, storage and analysis.

Few highlights -

a) BGI Does not Like Pacbio Yet

We stopped at the BGI booth to ask what they thought of PacBio technology. They were not too excited. ‘Not very reliable’ was the comment of senior researcher sitting at the booth.

Take home messages:

(i) PacBio needs to talk more about how they can make the data appear reliable and less about read length.

(ii) BGI’s rejection of the technology may be an opportunity for other sequencing centers to effectively use PacBio and catch up with BGI’s lead on Illumina.

Based on our experience, we remain positive about PacBio technology. The noises in their sequences are random, and therefore can be easily cleaned up using intelligent algorithms. So, the best way to see the technology is as one with long reads, but read length reduced somewhat (15%) due to loss of information content. We also understand that no amount of scientific argument can float a ship sinking due to bad reputation.

b) Little Bioinformatics Discussed at Superconducting Conference

When we stopped by at the Purdue booth, we were very happy to find the face of Rick Westerman (one of our readers) being displayed on screen. The Purdue representative told us that Rick is a heavy user of their supercomputing facility. Apart from that, we saw little mention of bioinformatics in the booths of various universities. There were exceptions of course. For example, Virginia Bioinformatics Institute had its own booth and so did BGI. Overall, HPC centers did not seem to be aware or appreciative of challenges faced by bioinformaticians except for their involvement in few peripheral projects.

c) HPC Centers are Excited about GPUs

If we are asked to identify the hottest topic in SC12, we would say ‘GPUs’. Those working on numerical simulations seem to be moving toward a GPU world. FPGAs are also increasingly being accepted as high-performance computing tools. Space and power requirement are the most important selling points for hybrid-core technologies. Difficulty of programming are the key negatives, but GPU world managed to get across that barrier due to NVidia’s CUDA programming framework.

d) No Bioinformatics in Japan?

We walked through the booths of various Japanese universities and saw even less mention of bioinformatics than the US universities. That was puzzling.

e) Lousy Internet Connection

For some reason, the wireless internet connection at the conference was lousier than we have seen anywhere else. It is true that we were at a conference, where everyone was carrying two or three internet-connected devices. On the other hand, if a meeting with world’s top computing and networking experts cannot fix their own internet network, how can they address bigger computing issues?


We will add more information to this post, as time permits.

Written by M. //