Abstract
The current developments in life sciences face a big challenge, with the need of dealing with huge amounts of data and the increasing demand of computational resources, both in hardware and in software, pushing the limits of the available state-of-the-art at an affordable price. This paper introduces a computer cluster whose building blocks are the first commercially available many-core CPU systems: the Tile64 by Tilera Corporation, packed in PCIe cards (TILExpress-20G). We have developed the main software components of the cluster (resource manager and scheduler) and a communication library, in order to offer a high-performance general-purpose platform to speedup bioinformatics applications.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
LinuxHPC.org. Cluster Encyclopedia (2010), http://www.clusterbuilder.org/encyclopedia/alphabetized.php (cited November 4, 2012)
Adaptative-Computing. TORQUE Resource Manager (2012), http://www.adaptivecomputing.com/products/open-source/torque (cited November 4, 2012)
Cluster-Resources. Maui Cluster Scheduler (2012), http://www.clusterresources.com/pages/products/maui-cluster-scheduler.php (cited November 4, 2012)
Gropp, W., Lusk, E., Skjellum, A.: Using MPI: Portable Parallel Programming with the Message Passing Interface. MIT Press (1994)
Gálvez, S., et al.: Next-Generation Bioinformatics: Using Many-Core Processor Architecture to Develop a Web Service for Sequence Alignment. Bioinformatics 26(5), 683–686 (2010)
Esteban, F.J., Díaz, D., Hernández, P., Caballero, J.A., Dorado, G., Gálvez, S.: MC64: A Web Platform to Test Bioinformatics Algorithms in a Many-Core Architecture. In: Rocha, M.P., Rodríguez, J.M.C., Fdez-Riverola, F., Valencia, A., et al. (eds.) PACBB 2011. AISC, vol. 93, pp. 9–16. Springer, Heidelberg (2011)
Diaz, D., et al.: Parallelizing and optimizing a bioinformatics pairwise sequence alignment algorithm for many-core architecture. Parallel Computing 37(4-5), 244–259 (2011)
Esteban, F.J., et al.: Direct approaches to exploit many-core architecture in bioinformatics. Future Generation Computer System 29(1), 15–26 (2013)
Esteban, F.J., Díaz, D., Hernández, P., Caballero, J.A., Dorado, G., Gálvez, S.: Many-Core Processor Bioinformatics and Next-Generation Sequencing. In: Liñán Reyes, M., Flores Arias, J.M., González de la Rosa, J.J., Langer, J., Bellido Outeiriño, F.J., Moreno-Munñoz, A., et al. (eds.) IT Revolutions. LNICST, vol. 82, pp. 172–188. Springer, Heidelberg (2012)
Sunderam, V.S.: PVM: a framework for parallel distributed computing. Concurrency: Pract. Exper. 2(4), 315–339 (1990)
IEEE Standard for IT-Telecom. and Information Exchange Between Systems-LAN and MAN-Specific Requirements. Part 3: CSMA With Method and Physical Layer Specifications. Amendment: Physical Layer and Management Parameters for 10 Gb/S Operation, Type 10 GBASE-CX4. IEEE Std 802.3ak-2004 (Amendment to IEEE Std 802.3-2002 as amended by IEEE Stds 802.3ae-2002, 802.3af-2003 and 802.3aj-2003), p. 0_1 (2004)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Esteban, F.J., Díaz, D., Hernández, P., Caballero, J.A., Dorado, G., Gálvez, S. (2013). MC64-Cluster: A Many-Core CPU Cluster for Bioinformatics Applications. In: Rocha, Á., Correia, A., Wilson, T., Stroetmann, K. (eds) Advances in Information Systems and Technologies. Advances in Intelligent Systems and Computing, vol 206. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-36981-0_76
Download citation
DOI: https://doi.org/10.1007/978-3-642-36981-0_76
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-36980-3
Online ISBN: 978-3-642-36981-0
eBook Packages: EngineeringEngineering (R0)