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

Cloud Computing, the long-held dream of computing as a utility, has the potential to transform a large part of the IT industry, making software even more attractive as a service and shaping the way IT hardware is designed and purchased. Developers with innovative ideas for new Internet services no longer require the large capital outlays in hardware to deploy their service or the human expense to operate it. They need not be concerned about overprovisioning for a service whose popularity does not meet their predictions, thus wasting costly resources, or underprovisioning for one that becomes wildly popular, thus missing potential customers and revenue. Moreover, companies with large batch-oriented tasks can get results as quickly as their programs can scale, since using 1000 servers for one hour costs no more than using one server for 1000 hours. This elasticity of resources, without paying a premium for large scale, is unprecedented in the history of IT. Cloud Computing refers to both the applications delivered as services over the Internet and the hardware and systems software in the datacenters that provide those services. The services themselves have long been referred to as Software as a Service (SaaS). The datacenter hardware and software is what we will call a Cloud. When a Cloud is made available in a pay-as-you-go manner to the general public, we call it a Public Cloud; the service being sold is Utility Computing. We use the term Private Cloud to refer to internal datacenters of a business or other organization, not made available to the general public. Thus, Cloud Computing is the sum of SaaS and Utility Computing, but does not include Private Clouds. People can be users or providers of SaaS, or users or providers of Utility Computing. We focus on SaaS Providers (Cloud Users) and Cloud Providers, which have received less attention than SaaS Users. From a hardware point of view, three aspects are new in Cloud Computing.

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Above the Clouds: A Berkeley View of Cloud Computing

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

物件導向軟體之架構(Object-Oriented Software Construction)探討

The availability of powerful microprocessors and high-speed networks as commodity components has enabled high-performance computing on distributed systems (wide-area cluster computing). In this environment, as the resources are usually distributed geographically at various levels (department, enterprise or worldwide), there is a great challenge in integrating, coordinating and presenting them as a single resource to the user, thus forming a computational grid. Another challenge comes from the distributed ownership of resources, with each resource having its own access policy, cost and mechanism. The proposed Nimrod/G grid-enabled resource management and scheduling system builds on our earlier work on Nimrod (D. Abramson et al., 1994, 1995, 1997, 2000) and follows a modular and component-based architecture enabling extensibility, portability, ease of development, and interoperability of independently developed components. It uses the GUSTO (GlobUS TOolkit) services and can be easily extended to operate with any other emerging grid middleware services. It focuses on the management and scheduling of computations over dynamic resources scattered geographically across the Internet at department, enterprise or global levels, with particular emphasis on developing scheduling schemes based on the concept of computational economy for a real testbed, namely the Globus testbed (GUSTO).

/pdf/nimrod-g-an-architecture-for-a-resource-management-and-44df3lztxs.pdf

Nimrod/G: an architecture for a resource management and scheduling system in a global computational grid

The accelerated development in peer-to-peer and Grid computing has positioned them as promising next-generation computing platforms. They enable the creation of virtual enterprises for sharing resources distributed across the world. However, resource management, application development and usage models in these environments is a complex undertaking. This is due to the geographic distribution of resources that are owned by different organizations or peers. The resource owners of each of these resources have different usage or access policies and cost models, and varying loads and availability. In order to address complex resource management issues, we have proposed a computational economy framework for resource allocation and for regulating supply and demand in Grid computing environments. This framework provides mechanisms for optimizing resource provider and consumer objective functions through trading and brokering services. In a real world market, there exist various economic models for setting the price of services based on supply-and-demand and their value to the user. They include commodity market, posted price, tender and auction models. In this paper, we discuss the use of these models for interaction between Grid components to decide resource service value, and the necessary infrastructure to realize each model. In addition to usual services offered by Grid computing systems, we need an infrastructure to support interaction protocols, allocation mechanisms, currency, secure banking and enforcement services. We briefly discuss existing technologies that provide some of these services and show their usage in developing the Nimrod-G grid resource broker. Furthermore, we demonstrate the effectiveness of some of the economic models in resource trading and scheduling using the Nimrod/G resource broker, with deadline and cost constrained scheduling for two different optimization strategies, on the World-Wide Grid testbed that has resources distributed across five continents.

Economic models for resource management and scheduling in Grid computing

The evolution of a particular tool, Nimrod, from a local computing environment to the global computational grid is discussed. The various services of Globus and how these were applied in building a grid aware application are described. The algorithm used is both simple and adaptive to changes in the workload distribution on the grid and incorporates user requirements as well as system ones. Results show that it is possible to build an application which takes account of the highly dynamic and unpredictable nature of the grid.

High performance parametric modeling with Nimrod/G: Killer application for the global grid?

This work identifies challenges in managing resources in a Grid computing environment and proposes computational economy as a metaphor for effective management of resources and application scheduling. It identifies distributed resource management challenges and requirements of economy-based Grid systems, and discusses various representative economy-based systems, both historical and emerging, for cooperative and competitive trading of resources such as CPU cycles, storage, and network bandwidth. It presents an extensive, service-oriented Grid architecture driven by Grid economy and an approach for its realization by leveraging various existing Grid technologies. It also presents commodity and auction models for resource allocation. The use of commodity economy model for resource management and application scheduling in both computational and data grids is also presented.

The Grid Economy

Computational grids that couple geographically distributed resources such as PCs, workstations, clusters, and scientific instruments, have emerged as a next generation computing platform for solving large-scale problems in science, engineering, and commerce. However, application development, resource management, and scheduling in these environments continue to be a complex undertaking. In this article, we discuss our efforts in developing a resource management system for scheduling computations on resources distributed across the world with varying quality of service (QoS). Our service-oriented grid computing system called Nimrod-G manages all operations associated with remote execution including resource discovery, trading, scheduling based on economic principles and a user-defined QoS requirement. The Nimrod-G resource broker is implemented by leveraging existing technologies such as Globus, and provides new services that are essential for constructing industrial-strength grids. We present the results of experiments using the Nimrod-G resource broker for scheduling parametric computations on the World Wide Grid (WWG) resources that span five continents.

David Abramson

Papers

Nimrod/G: an architecture for a resource management and scheduling system in a global computational grid

Economic models for resource management and scheduling in Grid computing

High performance parametric modeling with Nimrod/G: Killer application for the global grid?

The Grid Economy

A computational economy for grid computing and its implementation in the Nimrod-G resource broker