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

Today's data centers may contain tens of thousands of computers with significant aggregate bandwidth requirements. The network architecture typically consists of a tree of routing and switching elements with progressively more specialized and expensive equipment moving up the network hierarchy. Unfortunately, even when deploying the highest-end IP switches/routers, resulting topologies may only support 50% of the aggregate bandwidth available at the edge of the network, while still incurring tremendous cost. Non-uniform bandwidth among data center nodes complicates application design and limits overall system performance.In this paper, we show how to leverage largely commodity Ethernet switches to support the full aggregate bandwidth of clusters consisting of tens of thousands of elements. Similar to how clusters of commodity computers have largely replaced more specialized SMPs and MPPs, we argue that appropriately architected and interconnected commodity switches may deliver more performance at less cost than available from today's higher-end solutions. Our approach requires no modifications to the end host network interface, operating system, or applications; critically, it is fully backward compatible with Ethernet, IP, and TCP.

/pdf/a-scalable-commodity-data-center-network-architecture-5evikm9tu4.pdf

A scalable, commodity data center network architecture

Cities and regions have long captured the imagination of sociologists, economists, and urbanists. From Alfred Marshall to Robert Park and Jane Jacobs, cities have been seen as cauldrons of diversit...

http://www.iranshahrsaz.com/attachment.php?aid=17733

Cities and the Creative Class

The Rise of the Creative Class

Crossing the great divide: Coproduction, synergy, and development

New forms of social stratification are emerging. Much of our thinking about stratification - from Marx, Weber, and others - must be recast to capture these new developments. Social class was the key theme of past stratification work. Yet class is an increasingly outmoded concept. Class stratification implies that people can be differentiated hierarchically on one or more criteria into distinct layers, classes. Class analysis has grown increasingly inadequate in recent decades as traditional hierarchies have declined and new social differences have emerged. The cumulative impact of these changes is fundamentally altering the nature of social stratification - placing past theories in need of substantial modification. This paper outlines first some general propositions about the sources of class stratification and its decline. The decline of hierarchy, and its spread across situses, is emphasised. The general propositions are applied to political parties and ideological cleavages, the economy, the family, an...

Are social classes dying

Introduction: Taking entertainment seriously ; Political theory of consumption ; Urban amenities: lakes, opera, and juice bars: do they drive development? / Terry Nichols Clark -- Globalization and the liminal: transgression, identity and the urban primitive / Lauren Langman and Katie Cangemi -- Consumers and cities: Edward L. Glaeser, Jed Kolko and Albert Saiz -- New political culture and local government in England / Anne Bartlett with Terry Nichols Clark and Dennis Merritt -- Technology and tolerance: the importance of diversity to high-technology growth / Richard Florida and Gary Gates -- Gays and urban development: how are they linked? / Terry Nichols Clark -- Amenities: recent economic studies / Alexei Zelenev -- International mayor / Terry Nichols Clark with Dennis Merritt and Lenka Siroky -- Starbucks, bicycle paths, and urban growth machines: emails among members of urban and community sections of American Sociological Association / compiled by Terry Nichols Clark -- Amenities drive urban growth: a new paradigm and policy linkages / Terry Nichols Clark ... [et al.].

The city as an entertainment machine

Studies of the city traditionally posit a division between a city’s economy and its culture, with culture subordinate in explanatory power to work. However, post–industrial and globalizing trends are dramatically elevating the importance of culture. Cultural activities are increasingly crucial to urban economic vitality. Models to explain the growth of cities from the era of industrial manufacturing are outmoded. Citizens in the postindustrial city increasingly make quality of life demands, treating their own urban location as if tourists, emphasizing aesthetic concerns. These practices impact considerations about the proper nature of amenities that post–industrial cities can sustain.

Amenities Drive Urban Growth

We have analyzed a systematic flaw in the current system of gene identification: the oligo(dT) primer widely used for cDNA synthesis generates a high frequency of truncated cDNAs through internal poly(A) priming. Such truncated cDNAs may contribute to 12% of the expressed sequence tags in the current dbEST database. By using a synthetic transcript and real mRNA templates as models, we characterized the patterns of internal poly(A) priming by oligo(dT) primer. We further demonstrated that the internal poly(A) priming can be effectively diminished by replacing the oligo(dT) primer with a set of anchored oligo(dT) primers for reverse transcription. Our study indicates that cDNAs designed for genomewide gene identification should be synthesized by use of the anchored oligo(dT) primers, rather than the oligo(dT) primers, to diminish the generation of truncated cDNAs caused by internal poly(A) priming.

https://www.pnas.org/content/pnas/99/9/6152.full.pdf

Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription

The New Political Culture: An Analytical Framework To Interpret What Has Changed, Where, And Why Overview of the Book (Terry Nichols Clark) The New Political Culture: Changing Dynamics of Support for the Welfare State and Other Policies in Postindustrial Societies (T. N. Clark and Ronald Inglehart. ) Where Has The New Political Culture Emerged And Why? Is There Really a New Political Culture: Evidence from Major Historical Developments of Recent Decades. (T. N. Clark. ) Assessing the New Political Culture by Comparing Cities Around the World ( T. N. Clark, with Jerzy Bartkowski, Zhiyue Bo, Lincoln Quillian, Doug Huffer, Ziad Munson, Eric Fong, Yun-Ji-Qian, Mark Gromala, Michael Rempel, and Dennis Merritt ) How Hierarchies And Parties Specifically Redirect Politics And Policy Priorities Urban Political Parties: Role and Transformation (Vincent Hoffmann-Martinot. ) Transformations in Policy Preferences of Local Officials (Oscar Gabriel, Katja Ahlstich, Frank Brettschneider, and Volker Kunz. ) Toward a One-Dimensional Ideological Culture? Evidence from Swiss Local Parties (Hans Geser.) Citizen Preferences for Local Growth Controls: Trends in U.S. Suburban Support for a New Political Culture Movement (Mark Baldassare. )

Terry Nichols Clark

Papers

Are social classes dying

The city as an entertainment machine

Amenities Drive Urban Growth

Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription

The New Political Culture