/pdf/scalable-molecular-dynamics-with-namd-3j7xyc70g4.pdf

Scalable Molecular Dynamics with NAMD

In the past few years several major reports highlighted the gap between our knowledge of effective treatments and services currently being received by consumers. These reports agree that we know much about interventions that are effective but make little use of them to help achieve important behavioral health outcomes for children families and adults nationally. This theme is repeated in reports by the Surgeon General (United States Department of Health and Human Services 1999; 2001) the National Institute of Mental Health [NIMH] National Advisory Mental Health Council Workgroup on Child and Adolescent Mental Health Intervention Development and Deployment (2001) Bernfeld Farrington & Leschied (2001) Institute of Medicine (2001) and the Presidents New Freedom Commission on Mental Health (2003). The authors call for applied research to better understand service delivery processes and contextual factors to improve the efficiency and effectiveness of program implementation at local state and national levels. Our understanding of how to develop and evaluate evidence-based intervention programs has been furthered by on-going efforts to research and refine programs and practices to define "evidence bases" and to designate and catalogue "evidence-based programs or practices". However the factors involved in successful implementation of these programs are not as well understood. Current views of implementation are based on the scholarly foundations prepared by Pressman & Wildavskys (1973) study of policy implementation Havelock & Havelocks (1973) classic curriculum for training change agents and Rogers (1983; 1995) series of analyses of factors influencing decisions to choose a given innovation. These foundations were tested and further informed by the experience base generated by pioneering attempts to implement Fairweather Lodges and National Follow-Through education models among others. Petersilia (1990) concluded that "The ideas embodied in innovative social programs are not self-executing." Instead what is needed is an "implementation perspective on innovation--an approach that views postadoption events as crucial and focuses on the actions of those who convert it into practice as the key to success or failure". (excerpt)

Implementation research: a synthesis of the literature.

Migrating operating system instances across distinct physical hosts is a useful tool for administrators of data centers and clusters: It allows a clean separation between hard-ware and software, and facilitates fault management, load balancing, and low-level system maintenance.By carrying out the majority of migration while OSes continue to run, we achieve impressive performance with minimal service downtimes; we demonstrate the migration of entire OS instances on a commodity cluster, recording service downtimes as low as 60ms. We show that that our performance is sufficient to make live migration a practical tool even for servers running interactive loads.In this paper we consider the design options for migrating OSes running services with liveness constraints, focusing on data center and cluster environments. We introduce and analyze the concept of writable working set, and present the design, implementation and evaluation of high-performance OS migration built on top of the Xen VMM.

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Live migration of virtual machines

Systems and methods for navigating hypermedia using multiple coordinated input/output device sets. Disclosed systems and methods allow a user and/or an author to control what resources are presented on which device sets (whether they are integrated or not), and provide for coordinating browsing activities to enable such a user interface to be employed across multiple independent systems. Disclosed systems and methods also support new and enriched aspects and applications of hypermedia browsing and related business activities.

Method and apparatus for browsing using multiple coordinated device sets

Disk arrays were proposed in the 1980s as a way to use parallelism between multiple disks to improve aggregate I/O performance. Today they appear in the product lines of most major computer manufacturers. This article gives a comprehensive overview of disk arrays and provides a framework in which to organize current and future work. First, the article introduces disk technology and reviews the driving forces that have popularized disk arrays: performance and reliability. It discusses the two architectural techniques used in disk arrays: striping across multiple disks to improve performance and redundancy to improve reliability. Next, the article describes seven disk array architectures, called RAID (Redundant Arrays of Inexpensive Disks) levels 0–6 and compares their performance, cost, and reliability. It goes on to discuss advanced research and implementation topics such as refining the basic RAID levels to improve performance and designing algorithms to maintain data consistency. Last, the article describes six disk array prototypes of products and discusses future opportunities for research, with an annotated bibliography disk array-related literature.

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RAID: high-performance, reliable secondary storage

Process migration is the act of transferring a process between two machines. It enables dynamic load distribution, fault resilience, eased system administration, and data access locality. Despite these goals and ongoing research efforts, migration has not achieved widespread use. With the increasing deployment of distributed systems in general, and distributed operating systems in particular, process migration is again receiving more attention in both research and product development. As high-performance facilities shift from supercomputers to networks of workstations, and with the ever-increasing role of the World Wide Web, we expect migration to play a more important role and eventually to be widely adopted.This survey reviews the field of process migration by summarizing the key concepts and giving an overview of the most important implementations. Design and implementation issues of process migration are analyzed in general, and then revisited for each of the case studies described: MOSIX, Sprite, Mach, and Load Sharing Facility. The benefits and drawbacks of process migration depend on the details of implementation and, therefore, this paper focuses on practical matters. This survey will help in understanding the potentials of process migration and why it has not caught on.

Process migration

Process migration is the act of transferring a process between two machines. It enables dynamic load distribution, fault resilience, eased system administration, and data access locality. Despite these goals and ongoing research efforts, migration has not achieved widespread use. With the increasing deployment of distributed systems in general, and distributed operating systems in particular, process migration is again receiving more attention in both research and product development. As high-performance facilities shift from supercomputers to networks of workstations, and with the ever-increasing role of the World Wide Web, we expect migration to play a more important role and eventually to be widely adopted.
This survey reviews the field of process migration by summarizing the key concepts and giving an overview of the most important implementations. Design and implementation issues of process migration are analyzed in general, and then revisited for each of the case studies described: MOSIX, Sprite, Mach, and Load Sharing Facility. The benefits and drawbacks of process migration depend on the details of implementation and, therefore, this paper focuses on practical matters. This survey will help in understanding the potentials of process migration and why it has not caught on.

Overview of MOSIX- The UNIX file system- Distributed UNIX file systems- The UNIX process- The MOSIX process- The MOSIX linker- Load balancing- Scaling considerations- System performance- Distributed applications

The MOSIX Distributed Operating System: Load Balancing for UNIX

Preface. I. INTRODUCTION. 1. Introduction. Benefits, Deployment Challenges, and Technical Issues. Overview of the Book. II. MOBILITY IN A CLUSTER: PROCESS MIGRATION. 2. Process Migration. Benefits and Challenges of Process Migration. Applications. Myths and Facts. 3. Early Work. J. Shoch and UeJ. Hupp, The Worm Programs - Early Experience with Distributed Computing. M. Powell and B. Miller, Process Migration in DEMOS/MP. 4. Kernel Supported Migration. A. Barak and R. Wheeler, MOSIX: An Integrated Multiprocessor UNIX. F. Douglis and J. Ousterhout, Transparent Process Migration: Design Alternatives and the Sprite Implementation. Y. Artsy and R. Finkel, Designing a Process Migration Facility: The Charlotte Experience. E. Zayas, Attacking the Process Migration Bottleneck. M. Theimer, K. Lantz, and D. Cheriton, Preemptable Remote Execution Facilities for the V System. D.S. Milojicic, W. Zint, A. Dangel, and P. Giese, Task Migration on the top of the Mach Microkernel. 5. User-Space Migration. M. Litzkow and M. Solomon, Supporting Checkpointing and Process Migration Outside the UNIX Kernel. E. Jul, H. Levy, N. Hutchinson, and A. Black, Fine-Grained Mobility in the Emerald System. P. Smith and N.C. Hutchinson, Heterogeneous Process Migration: The Tui System. 6. Migration Policies. Luis-Felipe Cabrera, The Influence of Workload on Load Balancing Strategies. Exploiting Process Lifetime Distributions for Dynamic Load Balancing. 7. Other Sources of Information. III. PHYSICAL MOBILITY: MOBILE COMPUTING. 8. Mobile Computing. Benefits and Challenges of Mobile Computing. Applications. Myths and Facts. Overview. G.H. Forman and J. Zahorjan, The Challenges of Mobile Computing. 9. Limits on Connectivity. J.J. Kistler and M. Satyanarayanan, Disconnected Operation in the Coda File System. L. Mummert, M. Ebling, and M. Satyanarayanan, Exploiting Weak Connectivity for Mobile File Access. D. Terry, M. Theimer, K. Petersen, A. Demers, M. Spreitzer, and C. Hauser, Managing Update Conflicts in a Weakly Connected Replicated Storage System. A.D. Joseph, J.A. Tauber, and M.F. Kaashoek, Mobile Computing with the Rover Toolkit. B.C. Housel and D.B. Lindquist, WebExpress: A System for Optimizing Web Browsing in a Wireless Environment. 10. Mobile IP. J. Ioannidis and G.Q. Maguire, Jr., The Design and Implementation of a Mobile Internetworking Architecture. C.E. Perkins, Mobile Networking with Mobile IP. S. Cheshire and M. Baker, Internet Mobility 4x4. H. Balakrishnan, V.N. Padmanabhan, S. Seshan, and R.H. Katz, A Comparison of Mechanisms for Improving TCP Performance over Wireless Links. 11. Ubiquitous Computing. M. Weiser, Some Computer Science Issues in Ubiquitous Computing. A. Fox, S.D. Gribble, Y. Chawathe, and E.A. Brewer, Adapting to Network and Client Variation Using Active Proxies: Lessons and Perspectives. 12. Other Sources of Information. IV. MOBILITY ON THE INTERNET: MOBILE AGENTS. 13. Mobility on the Internet. Benefits and Challenges of Mobile Agents. Applications. Myths and Facts. 14. Mobile Agent Systems. J.E. White, Telescript Technology: Mobile Agents. D. Lange and M. Oshima, Mobile Agents with Java: The Aglet API. D. Kotz, R. Gray, S. Nog, D. Rus, S. Chawla, and G. Cybenko, AGENT TCL: Targeting the Needs of Mobile Computers. T. Walsh, N. Paciorek, and D. Wong, Security and Reliability in Concordia. J. Baumann, F. Hohl, K. Rothermel, and M. Straber, Mole - Concepts of a Mobile Agent System. D. Johansen, R. van Renesse, and F.B. Schneider, Operating System Support for Mobile Agents. M. Ranganathan, A. Acharya, S.D. Sjharma, and J. Saltz, Network-Aware Mobile Programs. H. Peine and T. Stolpmann, The Architecture of the Area Platform for Mobile Agents. D.S. Milojicic, D. Chauhan, and W. LaForge, Mobile Objects and Agents (MOA). G. Glass, ObjectSpace Voyager Core Package Technical Overview. D.S. Milojicic, B. Breugst, I. Busse, J. Campbell, S. Covaci, B. Friedman, K. Kosaka, D. Lange, K. Ono, M. Oshima, C. Tham, S. Virdhagriswaran, and J. White, MASIF, The OMG Mobile Agent System Interoperability Facility. 15. Other Sources of Information. V. SUMMARY. 16. Summary. Comparison. Looking into the Future. Summary. References. 0201379287T04062001

Richard Wheeler

Papers

Process migration

Process migration

The MOSIX Distributed Operating System: Load Balancing for UNIX

Mobility: Processes, Computers, and Agents

The MOSIX Distributed Operating System