Solving The Protein Folding Problem with HPC

The University of Florida uses high-performance computing to simulate protein folding and help in the fight against disease.

Challenge: The Protein Folding Problem
Just like a road map, there are many ways to fold a protein molecule but only one is right. Misfold a map and the only penalty is inconvenience; but misfold a protein and the penalty can be a bad disease. How does a protein know the shape into which it is supposed to fold? High-performance computing can help answer this question.

Low free energy is good. Laboratory experiments can probe around only the unfolded and folded regions of the energy curve. Computer experiments can probe the whole thing. Professor Adrian Roitberg and Seonah Kim are doing just that on the UF High Performance Computing (HPC) Cluster at the University of Florida. The cluster depends on the high performance and reliability of the Cisco® InfiniBand fabric that connects the AMD Opteron based Rackable servers and storage subsystem. Kim has run more than 45 days on 100 processors and isn't done yet.

The simulation uses the highly parallelized Assisted Model Building with Energy Refinement (AMBER) package of molecular simulation programs. Why so long to study just two proteins? For one thing, biology involves a lot of water. The pinkish cloud is 7000 water molecules (21,000 atoms) surrounding a 14-residue peptide molecule (the bluish "worm" in the middle). The AMBER simulation works by calculating the motions of all these molecules. They bend, rotate, and move through space, avoiding or bouncing off one another. The simulation divides time into little steps and uses Newton's laws of physics to calculate the motion of the thousands of atoms at each step.

The High-Performance Computing Initiative at UF is an innovative approach to such needs. The design is a computing grid, linking specialized research computing clusters to a central parallel cluster over a dedicated high-speed network. Funding from the National Science Foundation and a cooperative agreement with Cisco provided the routers and switches for that grid.

(This news summarized from Cisco and original text can be reach their website)

Penguin Computing Announces Release of New Scyld ClusterWare “Hybrid”

Penguin Computing, experts in high performance computing solutions, announced today that Scyld ClusterWare™ "Hybrid", the newest version of its industry-leading cluster management software, will be released in January of 2010. Scyld ClusterWare Hybrid was developed as a solution for Penguin Computing's Scyld customers who want to provision, monitor and manage heterogeneous operating systems from a single point of control.

Scyld ClusterWare Hybrid is a fully integrated cluster management environment that combines Scyld ClusterWare's industry leading diskless single-system-image architecture with a traditional provisioning architecture that deploys an operating environment to local disk. Combining the "best of both worlds," this hybrid approach provides unmatched flexibility and transparency. Compute nodes can still be booted with Scyld ClusterWare and provisioned extremely rapidly, with a minimal memory footprint and guaranteed consistency, or can be provisioned with a complete operating environment to the local hard drive.

With Scyld ClusterWare Hybrid, target operating environments can be dynamically assigned to cluster nodes at start-up time, allowing for the quick re-purposing of systems according to workload and user demand. Once provisioned, systems can be managed from a single node with a single subset of commands, accelerating the learning curve for new users and reducing the time spent on system management for system administrators and researchers tasked with cluster management.

Click here to access more information.

ScaleMP announces vSMP Foundation for Cluster Structures

The vSMP Foundation for Cluster™ solution provides a simplified compute architecture for high-performance clusters - it hides the InfiniBand fabric, offers built-in high-performance storage as a cluster-filesystem replacement and reduces the number of operating systems to one, making it much easier to administer. This solution is ideally suited for smaller compute implementations in which management tools and skills may not be readily available.

The target customers for the Cluster product are those with initial high performance cluster implementations who are concerned with the complexity of creation and management of the cluster environment.

Key Advantages:

• Simplified install and management of high performance clusters;
  
  
  
  
  • Eliminates multiple nodes, operating systems to one;
  • Eliminates the need for separate cluster-filesystem,
• Stronger entry-level value proposition – scale up growth opportunities with no additional overhead.

You can reach detailed product info at their web pages.