HPCwire: Scali Cluster Software Used in Bioinformatics Research

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April 21, 2006

Scali Cluster Software Used in Bioinformatics Research

Institut de Biologie et Chimie des Proteines (IBCP) is now using Scali Manage 5 from Scali, Inc. to maximize the availability and effectiveness of their cluster. IBCP, located in Lyon, France, relies on a high performance cluster to analyze and predict protein sequence, structure and function. The IBCP Structural NMR and Bioinformatics team is currently focused on gaining a deeper understanding of the Hepatitis C virus' resistance to drugs.

IBCP's research is focused on deciphering the three-dimensional organization and properties of proteins to understand their biological function. An essential role of the cluster running at IBCP is to provide a powerful, integrated and easy-to-use Web resource that is accessible to a world wide community of scientists to further their research.

Ensuring the performance and availability of the cluster is integral to the success of the group and its research. The cluster processes an average of 4,000 bioinformatics requests from around the world per day and downtime can create a backload of jobs that can reach into the thousands in only a few hours. The cluster is accessed 24x7 by internal and external researchers, which includes requests from various parts of the world with 25 percent coming from France, 33 percent from elsewhere in Europe, 33 percent from North America and the remainder from other geographic areas.

"Ensuring that the cluster is available and working properly is imperative to moving our research forward," said Gilbert Deleage who is the head of the Bioinformatics team at IBCP. "Low utilization rates and downtime is not an option and using Scali Manage reduces our risk significantly. Scali's support for heterogeneous cluster configurations is also a key factor for us because we are running a mix of architectures and brands for compute, storage and web servers. Prior to installing Scali Manage, we tried both open source and commercial management applications but neither was successful due to lack of support for the required platforms."

"Computing demands at research organizations like IBCP can be enormous with very large datasets dealing with complicated software codes," stated Hakon Bugge, Chief Technical Officer of Scali. "The cluster at IBCP has the added complexity of being a heterogeneous integration of compute servers, NFS servers, storage firewalls, databases and web servers that are orchestrated into a single high performance cluster. Scali is unique in its ability to deliver management for such complex Linux environments."

With incoming requests varying from jobs that take seconds to 24 hours to complete, intelligent job management is imperative in order to prioritize requests and server allocation to ensure the highest rates of resource utilization. Scali's out-of-the-box integration with workload management applications, in this case PBS Pro from Altair, was another necessity for IBCP.

The cluster at IBCP consists of 16 servers processing 2.6 TB of data. The cluster includes 11 Dell Power Edge 2650 as compute nodes, 2 Dell Power Edge 2850 file servers attached to a DELL EMC CX400 SAN storage, 1 NEC 120 Rf-1 (PostgreSQL) server attached to a NEC ST 1430 storage, 1 120 Rf-1 (Web) server and 1 NEC 120-Rh2 server running the Scali Manage configuration server and a PBSPro server.

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