On Being Close to the Data : Executing Code in a Replica Management System

The goal of scientific grid computing is to enable researchers to attack problems that were previously impossible. Cooperative storage systems have been assembled to provide users with access to surprisingly large amounts of useful space, but locating, accessing, and efficiently employing such distributed data sets in scientific simulation or analysis is another monumental problem. In this paper, we describe simple techniques compatible with existing software that may be used on clusters or grids to access catalogued, replicated data sets: software tools that allow user code to use a replica system as a scientific file system. The importance of operating in-place, close to the data, is demonstrated by the performance improvements gained by using data locations as a guide when scheduling computation. A new replica management system, called GEMS 1 , is proposed to improve the research capabilities of two important computing infrastructures: university networks (groups of clusters) and volunteer computer resources (Internet computing).

[1]  Ian T. Foster,et al.  Globus: a Metacomputing Infrastructure Toolkit , 1997, Int. J. High Perform. Comput. Appl..

[2]  Michael R. Shirts,et al.  Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. , 2003, Biopolymers.

[3]  Francine Berman,et al.  Adaptive Computing on the Grid Using AppLeS , 2003, IEEE Trans. Parallel Distributed Syst..

[4]  J. Howard Et El,et al.  Scale and performance in a distributed file system , 1988 .

[5]  Thierry Matthey,et al.  ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics , 2004, TOMS.

[6]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[7]  Thierry Matthey,et al.  Framework Design, Parallelization and Force Computation in Molecular Dynamics , 2002 .

[8]  Carl Kesselman,et al.  Performance and scalability of a replica location service , 2004, Proceedings. 13th IEEE International Symposium on High performance Distributed Computing, 2004..

[9]  Miron Livny,et al.  Condor-a hunter of idle workstations , 1988, [1988] Proceedings. The 8th International Conference on Distributed.

[10]  Reagan Moore,et al.  Data grids, collections, and grid bricks , 2003, 20th IEEE/11th NASA Goddard Conference on Mass Storage Systems and Technologies, 2003. (MSST 2003). Proceedings..

[11]  Remzi H. Arpaci-Dusseau,et al.  Gathering at the Well: Creating Communities for Grid I/O , 2001, ACM/IEEE SC 2001 Conference (SC'01).

[12]  David A. Goldberg,et al.  Design and Implementation of the Sun Network Filesystem , 1985, USENIX Conference Proceedings.

[13]  Stuart Murdock,et al.  BioSimGrid: towards a worldwide repository for biomolecular simulations. , 2004, Organic & biomolecular chemistry.

[14]  David P. Anderson,et al.  BOINC: a system for public-resource computing and storage , 2004, Fifth IEEE/ACM International Workshop on Grid Computing.

[15]  David A. Patterson,et al.  A case for intelligent disks (IDISKs) , 1998, SGMD.

[16]  Andrea C. Arpaci-Dusseau,et al.  Flexibility, manageability, and performance in a Grid storage appliance , 2002, Proceedings 11th IEEE International Symposium on High Performance Distributed Computing.

[17]  Ian T. Foster,et al.  GASS: a data movement and access service for wide area computing systems , 1999, IOPADS '99.

[18]  Carl Kesselman,et al.  A Metadata Catalog Service for Data Intensive Applications , 2003, SC.

[19]  D. Thain,et al.  Applying feedback control to a replica management system , 2006, 2006 Proceeding of the Thirty-Eighth Southeastern Symposium on System Theory.

[20]  Douglas Thain,et al.  Separating Abstractions from Resources in a Tactical Storage System , 2005, ACM/IEEE SC 2005 Conference (SC'05).

[21]  Douglas Thain,et al.  Generosity and gluttony in GEMS: grid enabled molecular simulations , 2005, HPDC-14. Proceedings. 14th IEEE International Symposium on High Performance Distributed Computing, 2005..

[22]  Andrew S. Grimshaw,et al.  LegionFS: A Secure and Scalable File System Supporting Cross-Domain High-Performance Applications , 2001, International Conference on Software Composition.

[23]  H. Wilson,et al.  Flexibility , 1911, Encyclopedia of Autism Spectrum Disorders.

[24]  David P. Anderson,et al.  SETI@home: an experiment in public-resource computing , 2002, CACM.