Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

"Grid" computing has emerged as an important new field, distinguished from conventional distributed computing by its focus on large-scale resource sharing, innovative applications, and, in some cases, high performance orientation. In this article, the authors define this new field. First, they review the "Grid problem," which is defined as flexible, secure, coordinated resource sharing among dynamic collections of individuals, institutions, and resources--what is referred to as virtual organizations. In such settings, unique authentication, authorization, resource access, resource discovery, and other challenges are encountered. It is this class of problem that is addressed by Grid technologies. Next, the authors present an extensible and open Grid architecture, in which protocols, services, application programming interfaces, and software development kits are categorized according to their roles in enabling resource sharing. The authors describe requirements that they believe any such mechanisms must satisfy and discuss the importance of defining a compact set of intergrid protocols to enable interoperability among different Grid systems. Finally, the authors discuss how Grid technologies relate to other contemporary technologies, including enterprise integration, application service provider, storage service provider, and peer-to-peer computing. They maintain that Grid concepts and technologies complement and have much to contribute to these other approaches.

The Anatomy of the Grid: Enabling Scalable Virtual Organizations

http://cloud.pubs.dbs.uni-leipzig.de/sites/cloud.pubs.dbs.uni-leipzig.de/files/Brandic2008CloudcomputingandemergingITplatformsVisionhypeand.pdf

Cloud computing and emerging IT platforms: Vision, hype, and reality for delivering computing as the 5th utility

"Grid" computing has emerged as an important new field, distinguished from conventional distributed computing by its focus on large-scale resource sharing, innovative applications, and, in some cases, high-performance orientation. In this article, we define this new field. First, we review the "Grid problem," which we define as flexible, secure, coordinated resource sharing among dynamic collections of individuals, institutions, and resources-what we refer to as virtual organizations. In such settings, we encounter unique authentication, authorization, resource access, resource discovery, and other challenges. It is this class of problem that is addressed by Grid technologies. Next, we present an extensible and open Grid architecture, in which protocols, services, application programming interfaces, and software development kits are categorized according to their roles in enabling resource sharing. We describe requirements that we believe any such mechanisms must satisfy, and we discuss the central role played by the intergrid protocols that enable interoperability among different Grid systems. Finally, we discuss how Grid technologies relate to other contemporary technologies, including enterprise integration, application service provider, storage service provider, and peer-to-peer computing. We maintain that Grid concepts and technologies complement and have much to contribute to these other approaches.

The Anatomy of the Grid - Enabling Scalable Virtual Organizations

In both e-business and e-science, we often need to integrate services across distributed, heterogeneous, dynamic “virtual organizations” formed from the disparate resources within a single enterprise and/or from external resource sharing and service provider relationships. This integration can be technically challenging because of the need to achieve various qualities of service when running on top of different native platforms. We present an Open Grid Services Architecture that addresses these challenges. Building on concepts and technologies from the Grid and Web services communities, this architecture defines a uniform exposed service semantics (the Grid service); defines standard mechanisms for creating, naming, and discovering transient Grid service instances; provides location transparency and multiple protocol bindings for service instances; and supports integration with underlying native platform facilities. The Open Grid Services Architecture also defines, in terms of Web Services Description Language (WSDL) interfaces and associated conventions, mechanisms required for creating and composing sophisticated distributed systems, including lifetime management, change management, and notification. Service bindings can support reliable invocation, authentication, authorization, and delegation, if required. Our presentation complements an earlier foundational article, “The Anatomy of the Grid,” by describing how Grid mechanisms can implement a service-oriented architecture, explaining how Grid functionality can be incorporated into a Web services framework, and illustrating how our architecture can be applied within commercial computing as a basis for distributed system integration—within and across organizational domains. This is a DRAFT document and continues to be revised. The latest version can be found at http://www.globus.org/research/papers/ogsa.pdf. Please send comments to foster@mcs.anl.gov, carl@isi.edu, jnick@us.ibm.com, tuecke@mcs.anl.gov Physiology of the Grid 2

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The Physiology of the Grid An Open Grid Services Architecture for Distributed Systems Integration

Describes work in progress to develop a standard for interoperability among high-performance scientific components. This research stems from the growing recognition that the scientific community needs to better manage the complexity of multidisciplinary simulations and better address scalable performance issues on parallel and distributed architectures. The driving force for this is the need for fast connections among components that perform numerically intensive work and for parallel collective interactions among components that use multiple processes or threads. This paper focuses on the areas we believe are most crucial in this context, namely an interface definition language that supports scientific abstractions for specifying component interfaces and a port connection model for specifying component interactions.

/pdf/toward-a-common-component-architecture-for-high-performance-4q69vjsuff.pdf

Toward a common component architecture for high-performance scientific computing

This paper explores the use of cloud computing for scientific workflows, focusing on a widely used astronomy application-Montage. The approach is to evaluate from the point of view of a scientific workflow the tradeoffs between running in a local environment, if such is available, and running in a virtual environment via remote, wide-area network resource access. Our results show that for Montage, a workflow with short job runtimes, the virtual environment can provide good compute time performance but it can suffer from resource scheduling delays and widearea communications.

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On the Use of Cloud Computing for Scientific Workflows

The Science Clouds provide EC2-style cycles to scientific projects. This document contains a description of technologies enabling this project and an early summary of its experiences.

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Science Clouds: Early Experiences in Cloud Computing for Scientific Applications

By defining standardized protocols for discovering, accessing, monitoring, and managing remote computers, storage systems, networks, and other resources, Grid technologies make it possible—in principle—to allocate resources to applications dynamically, in an on-demand fashion [1]. However, while Grids offer users access to many diverse and powerful resources, they do little to ensure that once a resource is accessed, it fulfills user expectations for

/pdf/virtual-workspaces-achieving-quality-of-service-and-quality-i96jxif2v6.pdf

Virtual workspaces: Achieving quality of service and quality of life in the Grid

Infrastructure-as-a-Service (IaaS) cloud computing offers new possibilities to scientific communities. One of the most significant is the ability to elastically provision and relinquish new resources in response to changes in demand. In our work, we develop a model of an “elastic site” that efficiently adapts services provided within a site, such as batch schedulers, storage archives, or Web services to take advantage of elastically provisioned resources. We describe the system architecture along with the issues involved with elastic provisioning, such as security, privacy, and various logistical considerations. To avoid over- or under-provisioning the resources we propose three different policies to efficiently schedule resource deployment based on demand. We have implemented a resource manager, built on the Nimbus toolkit to dynamically and securely extend existing physical clusters into the cloud. Our elastic site manager interfaces directly with local resource managers, such as Torque. We have developed and evaluated policies for resource provisioning on a Nimbus-based cloud at the University of Chicago, another at Indiana University, and Amazon EC2. We demonstrate a dynamic and responsive elastic cluster, capable of responding effectively to a variety of job submission patterns. We also demonstrate that we can process 10 times faster by expanding our cluster up to 150 EC2 nodes.

Kate Keahey

Papers

Toward a common component architecture for high-performance scientific computing

On the Use of Cloud Computing for Scientific Workflows

Science Clouds: Early Experiences in Cloud Computing for Scientific Applications

Virtual workspaces: Achieving quality of service and quality of life in the Grid

Elastic Site: Using Clouds to Elastically Extend Site Resources