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Los Alamos lends open source hand to life sciences

Having a BLAST

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Researchers at Los Alamos National Labs have struck computing gold once again with an open source project that could benefit genetic research.

Three scientists have tried their hand at improving the popular BLAST (Basic Local Alignment Search Tool) search algorithms. The group decided to chop up a BLAST database and spread it across a number of servers instead of throwing lots of horsepower at a single data set. In so doing, the need to run I/O requests to disk was eliminated and the researchers saw huge, super-linear performance gains.

The experiment to put little bits of a database in memory instead of on disk proved a success and has since drawn considerable attention to mpiBLAST from pharmaceutical companies, researchers and even Microsoft.

My computer is smaller than yours

Wu-chun Feng, a Los Alamos researcher, originated the idea for mpiBLAST after solving the Gelsinger Coefficient with the introduction of Green Destiny - a Transmeta processor-powered supercomputer. The 240 processor Linux cluster helped show that some scientific computing tasks will run with adequate performance and incredible reliability on a system that can fit in an average closest.

Having a new type of mini-supercomputer is of interest to life sciences researchers. A number of companies are looking for a way to pack tons of computer power in a small space and hope to do so without buying special cooling equipment or adding a new wing to their labs.

With this in mind, Feng and lead researchers Aaron Darling and Lucas Carey set to work tuning BLAST for the Green Destiny Linux cluster.

BLAST helps scientists search databases of protein and DNA sequences. There are many types of BLAST used for different areas of research, making the tool one of the most popular in the life sciences world.

Start chopping

Many bioinformatics databases have grown past the point where they can fit in the core memory of most servers, which means searches have to query a disk. To get around this, the Los Alamos researchers chopped the database up into small parts that could each reside in memory. This has led to astonishing performance gains, according to the researchers.

"The adverse effects of disk I/O are so significant that BLAST searches using database segmentation can exhibit super-linear speedup versus searches on a single node," they wrote in the paper.

Super-linear, you say? Aye, it's the truth.

The researchers used mpi (Message Passing Interface) to handle communications between the servers. They found that speed ups in performance held up even with all of the intercommunication from server to server.

In one instance, the group compared a job run on a single database and one broken up across 128 systems. The "single worker" took 22.4 hours to complete a search, while the cluster crunched through the data in 8 minutes. From zero up to 120 processors, the cluster showed super-linear speed-up in every case.

As the number of processor goes well beyond 140 chips, mpiBLAST tends to drift back toward reality and performance suffers.

The scientists found that "the master" will wait until all "workers" have completed their jobs before formatting the results. This means the cluster can be slowed as a result of the least efficient worker.

Solutions to this problem are proposed in their paper PDF , but regardless of some slowdowns, mpiBLAST performs like a champ up to 120 processors.

What needs to be done?

The researchers have some suggestions for where they think mpiBLAST needs to go.

One of the preferred additions to the code would be a fault tolerance mechanism to account for server failures. Having each server signal back to a master system should do the trick. If no alive and kicking signal comes in, the master switches the workload to another system.

The group also hopes to develop a way to automatically determine the number of servers that should be used on a given query to get the best performance.

The project caught the eye of Microsoft earlier this year. A Redmond worker contacted Los Alamos to see if some other license other than the GPL could be used with mpiBLAST. Microsoft wanted to take a peek at the code but couldn't bring itself to do so with the cancerous GPL hanging over its head.

Nonetheless, mpiBLAST runs on Unix, Linux and Windows.

For those interested in helping out with mipBLAST, there is a SourceForge project underway here. ®

Related Link

Homepage for mpiBLAST

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