High Performance Computation with Amazon EC2

On-demand high performance computation in the genetic and bioinformatic fields led B-Tech Consulting to seek out the expertise of Core IT Pro.

"We've been doing quite a lot of work in computational chemistry, virtual screening and docking to validate a set of compounds identified by a client as potentially binding to a particular receptor. This type of work is very computationally intensive, and a typical run can consume a multiple CPU cluster for days on end. As this project expanded, we simply ran out of CPU cycles. The option to expand the compute server or buy a cluster was evaluated and rejected. It was hard to justify that expense unless the server was running nearly 24/7, which never happens."

As a result, Core IT Pro prepared and deployed Linux instances on Amazon EC2 with the required software to perform the experiments and created management tools to allow quick provisioning and distribution of jobs.

Results:

Task: Run tests on multiple compounds, sequentially, on one system.

Benchmark: A local 2.13ghz quad-core, 4GB RAM rack mounted server running CentOS 5.4.

Time to completion: 17.5 hours

Amazon EC2: High CPU Instance, 8 cores, 7gb memory, CentOS 5.4

Time to completion: 8.75 hours

Task: Run tests on multiple compounds, on multiple systems

Background: "Ligand set was 10,000 compounds from Zinc (subset 3) and same receptor. Use EC2 instances for load balancing across the instances and collate results."

Time to completion:  32.8 hours

Summary:

By using Linux images on Amazon EC2, B-Tech consulting was able to conduct experiments while radically reducing the total cost of ownership of IT resources. The first run on EC2 used $7 worth of compute time, while the second run with multiple machines cost less than $40.

Links:

B-Tech Consulting Newsletter: Virtual screening of chemical libraries using Amazon EC2 Cloud Computing.