The proceedings contain 5 papers. The topics discussed include: enabling rapid development of parallel tree search applications;challenges in executing large parameter sweep studies across widely distributed computing...
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ISBN:
(纸本)1595937145
The proceedings contain 5 papers. The topics discussed include: enabling rapid development of parallel tree search applications;challenges in executing large parameter sweep studies across widely distributed computing environments;hyperscaling of plasma turbulence simulations in DEISA;WISDOM-II: a large in silico docking effort for finding novel hits against malaria using computational grid infrastructure;and efficient processing of pathological images using the grid: computer-aided prognosis of neuroblastoma.
Multiprocessor scheduling in a shared multiprogramming environment can be structured as two-level scheduling, where a kernel-level job scheduler allots processors to jobs and a user-level thread scheduler schedules th...
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ISBN:
(纸本)1424409101
Multiprocessor scheduling in a shared multiprogramming environment can be structured as two-level scheduling, where a kernel-level job scheduler allots processors to jobs and a user-level thread scheduler schedules the work of a job on the allotted processors. In this context, the number of processors allotted to a particular job may vary during the job's execution, and the thread scheduler must adapt to these changes in processor resources. For overall system efficiency, the thread scheduler should also provide parallelism feedback to the job scheduler to avoid allotting a job more processors than it can use productively. This paper provides an overview of several adaptive thread schedulers we have developed that provide provably good history-based feedback about the job's parallelism without knowing the future of the job. These thread schedulers complete the job in near-optimal time while guaranteeing low waste. We have analyzed these thread schedulers under stringent adversarial conditions, showing that the thread schedulers are robust to various system environments and allocation policies. To analyze the thread schedulers under this adversarial model, we have developed a new technique, called trim analysis, which can be used to show that the thread scheduler provides good behavior on the vast majority of time steps, and performs poorly on only a few. When our thread schedulers are used with dynamic equipartitioning and other related job scheduling algorithms, they are O(1)-competitive against an optimal offline scheduling algorithm with respect to both mean response time and makespan for batched jobs and nonbatched jobs, respectively. Our algorithms are the first nonclairvoyant scheduling algorithms to offer such guarantees.
We address the problem of optimizing the distribution of partially replicated databases over a computer network. Replication is used to increase data availability in the presence of site or communication failures and ...
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We address the problem of optimizing the distribution of partially replicated databases over a computer network. Replication is used to increase data availability in the presence of site or communication failures and to decrease retrieval costs by local access if possible. We present a new bio-inspired replication management approach which is adaptive, completely decentralized, and based on swarm intelligence. Each node has the autonomy to start at any time, depending on the internal state of its stored data objects, a redistribution process. "Redistribution" means replicate, create, delete, update, or move data objects to other nodes of the network. The redistribution process is a dynamic load-balancing scheme which runs with lower priority in the background. The system is event-driven, but the learning process is not synchronized with the events.
This paper proposes and evaluates a new microarchitecture for out-of-order processors that supports speculative renaming. We call speculative renaming to the speculative omission of physical register allocation along ...
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Profile hidden Markov models (profile HMMs) are used as a popular bioinformatics tool for sensitive database searching, e.g. a set of not annotated protein sequences is compared to a database of profile HMMs to detect...
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Profile hidden Markov models (profile HMMs) are used as a popular bioinformatics tool for sensitive database searching, e.g. a set of not annotated protein sequences is compared to a database of profile HMMs to detect functional similarities. HMMer is a commonly used package for profile HMM-based methods. However, searching large databases with HMMer suffers from long runtimes on traditional computer architectures. These runtime requirements are likely to become even more severe due to the rapid growth in size of both sequence and model databases. In this paper, we present a new reconfigurable architecture to accelerate HMMer database searching. It is described how this leads to significant runtime savings on off-the-shelf field-programmable gate arrays (FPGAs).
As service-oriented architectures become more important in parallel and distributed computing systems, individual service instance reliability as well as appropriate service redundancy becomes an essential necessity i...
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ISBN:
(纸本)9780769528335
As service-oriented architectures become more important in parallel and distributed computing systems, individual service instance reliability as well as appropriate service redundancy becomes an essential necessity in order to increase overall system availability This paper focuses on providing redundancy strategies using service-level replication techniques. Based on previous research using symmetric active/active replication, this paper proposes a transparent symmetric active/active replication approach that allows for more reuse of code between individual service-level replication implementations by using a virtual communication layer. Service- and client-side interceptors are utilized in order to provide total transparency. Clients and servers are unaware of the replication infrastructure as it provides all necessary mechanisms internally.
Modern mobile phones and PDAs are equipped with positioning capabilities (e.g., GPS). Users can access public location-based services (e.g., Google Maps) and ask spatial queries. Although communication is encrypted, p...
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ISBN:
(纸本)9783540735397
Modern mobile phones and PDAs are equipped with positioning capabilities (e.g., GPS). Users can access public location-based services (e.g., Google Maps) and ask spatial queries. Although communication is encrypted, privacy and confidentiality remain major concerns, since the queries may disclose the location and identity of the user. Commonly, spatial K-anonymity is employed to hide the query initiator among a group of K users. However, existing work either fails to guarantee privacy, or exhibits unacceptably long response time. In this paper we propose MOBIHIDE, a Peer-to-Peer system for anonymous location-based queries, which addresses these problems. MOBIHIDE employs the Hilbert space-filling curve to map the 2-D locations of mobile users to 1-D space. The transformed locations are indexed by a Chord-based distributed hash table, which is formed by the mobile devices. The resulting Peer-to-Peer system is used to anonymize a query by mapping it to a random group of K users that are consecutive in the 1-D space. Compared to existing state-of-the-art, MOBIHIDE does not provide theoretical anonymity guarantees for skewed query distributions. Nevertheless, it achieves strong anonymity in practice, and it eliminates system hotspots. Our experimental evaluation shows that MOBIHIDE has good load balancing and fault tolerance properties, and is applicable to real-life scenarios with numerous mobile users.
Grid and distributed public computing schemes has become an essential tool for many scientific fields including bioinformatics, computational biology and systems biology. The adoption of these technologies has given r...
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ISBN:
(纸本)9783540747666
Grid and distributed public computing schemes has become an essential tool for many scientific fields including bioinformatics, computational biology and systems biology. The adoption of these technologies has given rise to a wide range of projects and contributions that provide various ways of setting up these environments and exploiting their potential resources and services for different domains of applications. This paper aims to provide a distilled overview of some of the major projects, technologies and resources employed in the area of structural proteomics. The major emphasis would be to briefly comment on various approaches related to the gridification and parallelization of some flagship legacy applications, tools and data resources related to key structural proteomics problems such as protein structure prediction, folding and comparison. The comments are based on theoretical analysis of some interesting parameters such as performance gain after gridification, user level interaction environments, workload distribution and the choice of deployment infrastructure and technologies. The study of these parameters would provide a basis for some motivating justification needed for further research and development in this domain.
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