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78,142
Fast Parallel Algorithms for ShortRange Molecular Dynamics
 JOURNAL OF COMPUTATIONAL PHYSICS
, 1995
"... 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 interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dyn ..."
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Cited by 622 (6 self)
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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 interatomic 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 shortrange forces where the neighbors of each atom change rapidly. They can be implemented on any distributedmemory parallel machine which allows for messagepassing of data between independently executing processors. The algorithms are tested on a standard LennardJones 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 YMP and C90 algorithm shows that the current generation of parallel machines is competitive with conventi...
Basic concepts and taxonomy of dependable and secure computing
 IEEE TDSC
, 2004
"... This paper gives the main definitions relating to dependability, a generic concept including as special case such attributes as reliability, availability, safety, integrity, maintainability, etc. Security brings in concerns for confidentiality, in addition to availability and integrity. Basic defin ..."
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Cited by 758 (6 self)
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This paper gives the main definitions relating to dependability, a generic concept including as special case such attributes as reliability, availability, safety, integrity, maintainability, etc. Security brings in concerns for confidentiality, in addition to availability and integrity. Basic definitions are given first. They are then commented upon, and supplemented by additional definitions, which address the threats to dependability and security (faults, errors, failures), their attributes, and the means for their achievement (fault prevention, fault tolerance, fault removal, fault forecasting). The aim is to explicate a set of general concepts, of relevance across a wide range of situations and, therefore, helping communication and cooperation among a number of scientific and technical communities, including ones that are concentrating on particular types of system, of system failures, or of causes of system failures.
StackGuard: Automatic adaptive detection and prevention of bufferoverflow attacks
 In Proceedings of the 7th USENIX Security Symposium
, 1998
"... 1 ..."
Evolving Neural Networks through Augmenting Topologies
 Evolutionary Computation
"... An important question in neuroevolution is how to gain an advantage from evolving neural network topologies along with weights. We present a method, NeuroEvolution of Augmenting Topologies (NEAT), which outperforms the best fixedtopology method on a challenging benchmark reinforcement learning task ..."
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Cited by 524 (113 self)
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An important question in neuroevolution is how to gain an advantage from evolving neural network topologies along with weights. We present a method, NeuroEvolution of Augmenting Topologies (NEAT), which outperforms the best fixedtopology method on a challenging benchmark reinforcement learning task. We claim that the increased efficiency is due to (1) employing a principled method of crossover of different topologies, (2) protecting structural innovation using speciation, and (3) incrementally growing from minimal structure. We test this claim through a series of ablation studies that demonstrate that each component is necessary to the system as a whole and to each other. What results is significantly faster learning. NEAT is also an important contribution to GAs because it shows how it is possible for evolution to both optimize and complexify solutions simultaneously, offering the possibility of evolving increasingly complex solutions over generations, and strengthening the analogy with biological evolution.
Good ErrorCorrecting Codes based on Very Sparse Matrices
, 1999
"... We study two families of errorcorrecting codes defined in terms of very sparse matrices. "MN" (MacKayNeal) codes are recently invented, and "Gallager codes" were first investigated in 1962, but appear to have been largely forgotten, in spite of their excellent properties. The ..."
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Cited by 741 (23 self)
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We study two families of errorcorrecting codes defined in terms of very sparse matrices. "MN" (MacKayNeal) codes are recently invented, and "Gallager codes" were first investigated in 1962, but appear to have been largely forgotten, in spite of their excellent properties. The decoding of both codes can be tackled with a practical sumproduct algorithm. We prove that these codes are "very good," in that sequences of codes exist which, when optimally decoded, achieve information rates up to the Shannon limit. This result holds not only for the binarysymmetric channel but also for any channel with symmetric stationary ergodic noise. We give experimental results for binarysymmetric channels and Gaussian channels demonstrating that practical performance substantially better than that of standard convolutional and concatenated codes can be achieved; indeed, the performance of Gallager codes is almost as close to the Shannon limit as that of turbo codes.
Static Scheduling of Synchronous Data Flow Programs for Digital Signal Processing
 IEEE TRANSACTIONS ON COMPUTERS
, 1987
"... Large grain data flow (LGDF) programming is natural and convenient for describing digital signal processing (DSP) systems, but its runtime overhead is costly in real time or costsensitive applications. In some situations, designers are not willing to squander computing resources for the sake of pro ..."
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Cited by 592 (37 self)
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Large grain data flow (LGDF) programming is natural and convenient for describing digital signal processing (DSP) systems, but its runtime overhead is costly in real time or costsensitive applications. In some situations, designers are not willing to squander computing resources for the sake of programmer convenience. This is particularly true when the target machine is a programmable DSP chip. However, the runtime overhead inherent in most LGDF implementations is not required for most signal processing systems because such systems are mostly synchronous (in the DSP sense). Synchronous data flow (SDF) differs from traditional data flow in that the amount of data produced and consumed by a data flow node is specified a priori for each input and output. This is equivalent to specifying the relative sample rates in signal processing system. This means that the scheduling of SDF nodes need not be done at runtime, but can be done at compile time (statically), so the runtime overhead evaporates. The sample rates can all be different, which is not true of most current datadriven digital signal processing programming methodologies. Synchronous data flow is closely related to computation graphs, a special case of Petri nets. This selfcontained paper develops the theory necessary to statically schedule SDF programs on single or multiple processors. A class of static (compile time) scheduling algorithms is proven valid, and specific algorithms are given for scheduling SDF systems onto single or multiple processors.
SNOPT: An SQP Algorithm For LargeScale Constrained Optimization
, 2002
"... Sequential quadratic programming (SQP) methods have proved highly effective for solving constrained optimization problems with smooth nonlinear functions in the objective and constraints. Here we consider problems with general inequality constraints (linear and nonlinear). We assume that first deriv ..."
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Cited by 582 (23 self)
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Sequential quadratic programming (SQP) methods have proved highly effective for solving constrained optimization problems with smooth nonlinear functions in the objective and constraints. Here we consider problems with general inequality constraints (linear and nonlinear). We assume that first derivatives are available, and that the constraint gradients are sparse. We discuss
An introduction to software architecture
 Advances in Software Engineering and Knowledge Engineering
, 1993
"... ..."
Stochastic Inversion Transduction Grammars and Bilingual Parsing of Parallel Corpora
, 1997
"... ..."
UNet: A UserLevel Network Interface for Parallel and Distributed Computing
 In Fifteenth ACM Symposium on Operating System Principles
, 1995
"... The UNet communication architecture provides processes with a virtual view of a network interface to enable userlevel access to highspeed communication devices. The architecture, implemented on standard workstations using offtheshelf ATM communication hardware, removes the kernel from the communi ..."
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Cited by 596 (17 self)
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The UNet communication architecture provides processes with a virtual view of a network interface to enable userlevel access to highspeed communication devices. The architecture, implemented on standard workstations using offtheshelf ATM communication hardware, removes the kernel from the communication path, while still providing full protection. The model presented by UNet 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 UNet prototype on an 8node ATM cluster of standard workstations offers 65 microseconds roundtrip latency and 15 Mbytes/sec bandwidth. It achieves TCP performance at maximum network bandwidth and demonstrates performance equivalent to Meiko CS2 and TMC CM5 supercomputers on a set of SplitC benchmarks. 1
Results 11  20
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78,142