14860992
Scalable Time-Parallelization of Molecular Dynamics Simulations in Nano Mechanics
Molecular dynamics (MD) is an important atomistic simulation technique, with widespread use in computational chemistry, biology, and materials. An important limitation of MD is that the time step size is small, requiring a large number of iterations to simulate realistic time spans. Conventional parallelization is not very effective for this. We recently introduced a new approach to parallelization, where data from related prior simulations are used to parallelize a new computation along the time domain. In our prior work, the size of the physical system in the current simulation needed to be identical to that of the prior simulations. The significance of this paper lies in demonstrating a strategy that enables this approach to be used even when the physical systems differ in size. Furthermore, this method scaled up to almost 1000 processors with close to ideal speedup in one case, where conventional methods scale to only 2-3 processors
17105049
Data-Driven Time-Parallelization in the AFM Simulation of Proteins
Molecular dynamics is a popular technique to simulate the behavior of physical systems, with resolution at the atomic scale. One of its limitations is that an enormous computational effort is required to simulate to realistic time spans. Conventional parallelization strategies have limited effectiveness in dealing with this difficulty. We recently introduced a more scalable approach to parallelization, where data from prior, related, simulations are used to parallelize a simulation in the time domain. We demonstrated its effectiveness in nano-mechanics simulations. In this paper, we develop our approach so that it can be used in a soft-matter application involving the atomic force microscopy simulation of proteins. We obtain an order of magnitude improvement in performance when we combine time parallelization with conventional parallelization. The significance of this work lies in demonstrating the promise of data-driven time parallelization in soft-matter applications, which are more challenging than the hard-matter applications considered earlier.
83148
Latency tolerance through parallelization of time in scientific applications
Summary form only given. Distributed computing environments, such as the grid, promise enormous raw computational power, but involve high communication overheads. It is therefore considered that they are ideally suited for "embarrassingly parallel" applications, such as Monte Carlo, and for certain applications where the loosely-coupled nature of the science involved in the simulations leads to a coarse grained computation. In a typical application, this is not feasible. We discuss our solution strategy, based on scalable functional decomposition, which can be used to keep the computation coarse grained, even on a large number of processors. Such decomposition can be attempted through a variety of means. We discuss the use of time parallelization to achieve this. We demonstrate results with a model problem, and then discuss its implementation for an important problem in nanomaterials simulation. We also show that this technique can be extended to make it inherently fault-tolerant.
16971481
Image compression for fast wavelet-based subregion retrieval
In an image browsing environment there is need for progressively viewing image subregions at various resolutions. We describe a storage scheme that accomplishes good image compression, while supporting fast image subregion retrieval. We evaluate analytically and experimentally the compression performance of our algorithm. We also provide results on the speed of the algorithm to demonstrate its effectiveness, and present an extension to a client/server environment.
36642411
Parameterizing parallel multiplicative lagged-Fibonacci generators
Monte Carlo computations are commonly considered to be naturally parallel. However, one needs to exercise care in parallelizing the underlying pseudorandom number generator (PRNG) to avoid correlations within, and between, random number streams. PRNGs are normally parallelized using one of the following two paradigms: (i) cycle division and (ii) parameterization. Most of the popular PRNGs based on linear recurrences, such as linear congruential generators (LCGs), generalized feedback shift-register generators (GFSRs), and additive lagged-Fibonacci generators (ALFGs) have been parallelized using both these paradigms. While the (nonlinear) multiplicative lagged-Fibonacci generators (MLFG) is considered superior to the ALFG in quality, it had so far been parallelized only via the cycle division paradigm, which has its limitations. In this paper, we describe parallelization of the MLFG using parameterization, and discuss its implementation in the Scalable Parallel Random Number Generators (SPRNG) [ACM Trans. Math. Software 26 (2000) 436] parallel pseudorandom number generation software. We also present empirical results demonstrating the quality, and quantitatively compare the parallel ALFGs and MLFGs quality.
36878064
A Compact Storage Scheme for Fast Wavelet-Based Subregion Retrieval
In an image browsing environment there is need for progressively viewing image subregions at various resolutions. We describe a storage scheme that accomplishes good image compression, while supporting fast image subregion retrieval. We evaluate analytically and experimentally the compression performance of our algorithm. We also provide results on the speed of the algorithm to demonstrate its effectiveness, and present an extension to a client/server environment.
2380498
Improved bounds and algorithms for hypergraph two-coloring
We show that for all large n, every n-uniform hypergraph with at most 0.7/spl radic/(n/lnn)/spl times/2/sup n/ edges can be two-colored. We, in fact, present fast algorithms that output a proper two-coloring with high probability for such hypergraphs. We also derandomize and parallelize these algorithms, to derive NC/sup 1/ versions of these results. This makes progress on a problem of Erdos (1963), improving the previous-best bound of n/sup 1/3-0(1)//spl times/2/sup n/ due to Beck (1978). We further generalize this to a "local" version, improving on one of the first applications of the Lovasz Local Lemma.
5519685
Efficient scheduling of soft real-time applications on multiprocessors
In this paper, we consider fair scheduling of soft real-time applications on multiprocessors using the earliest pseudo deadline first (EPDF) Pfair algorithm. Our main contributions are twofold. First, we establish a condition for ensuring a tardiness of at most one quantum under EPDF. This condition is very liberal and should often hold in practice. Second, we present simulation results involving randomly-generated task sets, including those that do not satisfy our condition. In these experiments, deadline misses were rare, and no misses by more than one quantum ever occurred.
18206354
Optimal design of signaling networks for Internet telephony
We present an approach for efficient design of a signaling network for a network of software switches supporting Internet telephony. While one may take an integer programming approach to solve this problem, it quickly becomes intractable even for modest-sized networks. Instead, our topology design uses random graphs that we show to be nearly optimal in cost, highly connected, and computationally efficient even for large networks. We then formulate a quadratic assignment problem (QAP) to map the abstract topology into the physical network to achieve optimal load balancing for given demand forecasts, which we solve using randomized heuristics. Numerical results on several example networks illustrate the performance and computational efficiency of our method. A graphical design tool has been developed based on our algorithms.
18165537
Application-layer broker for scalable Internet services with resource reservation
Scalability is a very important issue in providing Internet services, especially in view of the explosive growth in the number of Web users. When using the phrase Internet services, we consider text as well as multimedia presentations over the Internet, since accessing video and audio have become an integral part of the Web browsing activity. While this task of scalability can be considered as one of finding the best server or resource, the key issue of interest here is providing such a service in a transparent manner to the client. One such transparent approach is the Domain Name Server (DNS) proposed in [5]. This approach uses a modified DNS to distribute incoming client requests to different servers in a round-robin manner or based on a weighted classification. This allocation of client requests is done at the time of name-to-IP address translation carried out by the DNS. One limitation of this approach is that a translation request can go through a chain of intermediate DNSs that may cache the translation results. This caching might defeat the purpose of load balancing since an intermediate DNS can potentially allocate clients without the knowledge of the DNS in charge of load balancing. Another approach is to use a transparent front-end to forward requests to servers [4, 51. Cisco’s LocalDirector [4] is a product that uses address translation to forward requests to appropriate servers. The LocalDirector translates the headers of all data packets
7812373
Improved bounds on the sample complexity of learning
We present a new general upper bound on the number of examples required to estimate all of the expectations of a set of random variables uniformly well. The quality of the estimates is measured using a variant of the relative error proposed by Haussler and Pollard. We also show that our bound is within a constant factor of the best possible. Our upper bound implies improved bounds on the sample complexity of learning according to Haussler's decision theoretic model.