Dryad is a general-purpose distributed execution engine for coarse-grain data-parallel applications. A Dryad applica-tion combines computational “vertices ” with communica-tion “channels ” to form a dataflow graph. Dryad runs the application by executing the vertices of this graph on a set

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

This paper examines simultaneous multithreading, a technique permitting several independent threads to issue instructions to a superscalar’s multiple functional units in a single cycle. We present several models of simultaneous multithreading and compare them with alternative organizations: a wide superscalar, a fine-grain multithreaded processor, and single-chip, multiple-issue multiprocessing architectures. Our results show that both (single-threaded) superscalar and fine-grain multithreaded architectures are limited in their ability to utilize the resources of a wide-issue processor. Simultaneous multithreading has the potential to achieve 4 times the throughput of a superscalar, and double that of fine-grain multithreading. We evaluate several cache configurations made possible by this type of organization and evaluate tradeoffs between them. We also show that simultaneous multithreading is an attractive alternative to single-chip multiprocessors; simultaneous multithreaded processors with a variety of organizations outperform corresponding conventional multiprocessors with similar execution resources. While simultaneous multithreading has excellent potential to increase processor utilization, it can add substantial complexity to the design. We examine many of these complexities and evaluate alternative organizations in the design space.

Abstract: Parallel database machine architectures have evolved from the use of exotic hardware to a software parallel dataflow architecture based on conventional shared-nothing hardware. These new designs provide impressive speedup and scaleup when processing relational database queries. This paper

The U-Net communication architecture provides processes with a virtual view of a network interface to enable userlevel access to high-speed communication devices. The architecture, implemented on standard workstations using offthe-shelf ATM communication hardware, removes the kernel from the communication path, while still providing full protection. The model presented by U-Net allows for the construction of protocols at user level whose performance is only limited by the capabilities of network. The architecture is extremely flexible in the sense that traditional protocols like TCP and UDP, as well as novel abstractions like Active Messages can be implemented efficiently. A U-Net prototype on an 8-node ATM cluster of standard workstations offers 65 microseconds round-trip latency and 15 Mbytes/sec bandwidth. It achieves TCP performance at maximum network bandwidth and demonstrates performance equivalent to Meiko CS-2 and TMC CM-5 supercomputers on a set of Split-C benchmarks. 1

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A number of techniques have been developed for reconstructing surfaces by integrating groups of aligned range images. A desirable set of properties for such algorithms includes: incremental updating, representation of directional uncertainty, the ability to fill gaps in the reconstruction, and robustness in the presence of outliers. Prior algorithms possess subsets of these properties. In this paper, we present a volumetric method for integrating range images that possesses all of these properties. Our volumetric representation consists of a cumulative weighted signed distance function. Working with one range image at a time, we first scan-convert it to a distance function, then combine this with the data already acquired using a simple additive scheme. To achieve space efficiency, we employ a run-length encoding of the volume. To achieve time efficiency, we resample the range image to align with the voxel grid and traverse the range and voxel scanlines synchronously. We generate the f...

for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in pep-tide and side-chain conformations.

Threads are the vehicle,for concurrency in many approaches to parallel programming. Threads separate the notion of a sequential execution stream from the other aspects of traditional UNIX-like processes, such as address spaces and I/O descriptors. The objective of this separation is to make

Paradyn is a performance measurement tool for parallel and distributed programs. Paradyn uses several novel technologies so that it scales to long running programs (hours or days) and large (thousand node) systems, and automates much of the search for performance bottlenecks. It can provide precise