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Investigating the feasibility of making contexts explicit in designing cloud workflow

Investigating the feasibility of making contexts explicit in...

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2013 ieee 37th Annual Computer Software and Applications Conference, COMPSAC 2013

作者： Fan, Xiaoliang Zhang, Ruisheng Brezillon, Patrick School of Information Science and Engineering Lanzhou University Lanzhou Gansu China Laboratory of Computer Sciences of Paris 6 University Pierre and Marie CURIE Paris France

ISBN: (纸本)9780769549798

Cloud workflow allows automating the workflow process through a compilation of known sequences of actions in cloud environment. Current Cloud workflows lack the ability, in the one hand, to capture the contexts during the design phase of Cloud workflows;and in the other hand, to deliver a real-time assistance to help a specific user interact with the system in the selection of the relevant cloud workflow components for his specific need. We propose a context-oriented approach to improve the design phase of cloud workflows. A user-oriented paradigm is presented to make contexts explicit in designing cloud workflows. Context will be made explicit due to the integration of BPEL and Contextual Graphs (CxGs) representation. CxGs representation is the formalism for representing uniformly all the ingredients of design process in cloud workflows, so that users could customize information, formalize their design strategies, and possibly interact with the system to model the cloud workflow. We illustrate our methodology through a case study in virtual screening to testify our investigation study. Finally, we conclude that the method we proposed for making contexts explicit in Cloud workflows could be considered as a successful attempt to address the social and human factors related to the design of Cloud workflows. © 2013 ieee.

关键词： Design

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Network decontamination from a black virus

Network decontamination from a black virus

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2013 ieee 37th Annual Computer Software and Applications Conference, COMPSAC 2013

作者： Cai, Jie Flocchini, Paola Santoro, Nicola School of Computer Science Carleton University Ottawa ON K1S 5B6 Canada School of Electr. Eng. and Comp. Science University of Ottawa Ottawa ON K1N 6N5 Canada

ISBN: (纸本)9780769549798

In this paper, we consider the problem of decontaminating a network from a black virus (BV) using a team of mobile system agents. the BV is a harmful process which, like the extensively studied black hole (BH), destroys any agent arriving at the network site where it resides;when that occurs, unlike a black hole which is static by definition, a BV moves, spreading to all the neighboring sites, thus increasing its presence in the network. If however one of these sites contains a system agent, that clone of the BV is destroyed (i.e., removed permanently from the system). the initial location of the BV is unknown a priori. the objective is to permanently remove any presence of the BVfrom the network with minimum number of site infections (and thus casualties). the main cost measure is the total number of agents needed to solve the problem. this problem integrates in its definition both the harmful aspects of the classical black hole search problem (where however the dangerous elements are static) with the mobility aspects of the classical intruder capture or network decontamination problem(where however there is no danger for the agents). thus, it is the first attempt to model mobile intruders harmful not only forth sites but also for the agents. We start the study of this problem by focusing on some important classes of interconnection networks: grids, tori, and hypercubes. For each class we present solution protocols and strategies for the team of agents, analyze their worst case complexity, and prove their optimality. © 2013 ieee.

关键词： Gravitation

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Cyclops Tensor Framework: Reducing Communication and Eliminating Load Imbalance in Massively parallel Contractions

Cyclops Tensor Framework: Reducing Communication and Elimina...

引用

International symposium on parallel and distributed processing (IPDPS)

作者： Edgar Solomonik Devin Matthews Jeff Hammond James Demmel Department EECS University of California Berkeley USA Department Chemistry and Biochemistry University of Texas Austin USA Leadership Computing Facility Argonne National Laboratory USA

Cyclops (cyclic-operations) Tensor Framework (CTF) 1 is a distributed library for tensor contractions. CTF aims to scale high-dimensional tensor contractions such as those required in the Coupled Cluster (CC) electronic structure method to massively-parallel supercomputers. the framework preserves tensor structure by subdividing tensors cyclically, producing a regular parallel decomposition. An internal virtualization layer provides completely general mapping support while maintaining ideal load balance. the mapping framework decides on the best mapping for each tensor contraction at run-time via explicit calculations of memory usage and communication volume. CTF employs a general redistribution kernel, which transposes tensors of any dimension between arbitrary distributed layouts, yet touches each piece of data only once. Sequential symmetric contractions are reduced to matrix multiplication calls via tensor index transpositions and partial unpacking. the user-level interface elegantly expresses arbitrary-dimensional generalized tensor contractions in the form of a domain specific language. We demonstrate performance of CC with single and double excitations on 8192 nodes of Blue Gene/Q and show that CTF outperforms NWChem on Cray XE6 supercomputers for benchmarked systems.

关键词： Tensile stress Indexes Equations Program processors Chemistry Clustering algorithms Manganese

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A Communication-Optimal N-Body Algorithm for Direct Interactions

A Communication-Optimal N-Body Algorithm for Direct Interact...

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ieee International parallel & distributed processing symposium

作者： Michael Driscoll Evangelos Georganas Penporn Koanantakool Edgar Solomonik Katherine Yelick Computer Science Division University of California Berkeley

ISBN: (纸本)9781467360661

We consider the problem of communication avoid- ance in computing interactions between a set of particles in scenarios with and without a cutoff radius for interaction. Our strategy, which we show to be optimal in communication, divides the work in the iteration space rather than simply dividing the particles over processors, so more than one processor may be responsible for computing updates to a single particle. Similar to a force decomposition in molecular dynamics, this approach requires up to √p times more memory than a particle decomposition, but reduces communication costs by factors up to √p and is often faster in practice than a particle decomposition [1]. We examine a generalized force decomposition algorithm that tolerates the memory limited case, i.e. when memory can only hold c copies of the particles for c = 1,2,...√p. When c = 1, the algorithm degenerates into a particle decomposition;similarly when c = √p, the algorithm uses a force decomposition. We present a proof that the algorithm is communication-optimal and reduces critical path latency and bandwidth costs by factors of c~2 and c, respectively. Performance results from experiments on up to 24K cores of Cray XE-6 and 32K cores of IBM BlueGene/P machines indicate that the algorithm reduces communication in practice. In some cases, it even outperforms the original force decomposition approach because the right choice of c strikes a balance between the costs of collective and point-to- point communication. Finally, we extend the analysis to include a cutoff radius for direct evaluation of force interactions. We show that with a cutoff, communication optimality still holds. We sketch a generalized algorithm for multi-dimensional space and assess its performance for 1D and 2D simulations on the same systems.

关键词： parallel algorithms communication-avoiding algorithms particle methods

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parallel Simulated Annealing for Fragment Based Sequence Alignment

Parallel Simulated Annealing for Fragment Based Sequence Ali...

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26th ieee International parallel and distributed processing symposium (IPDPS) / Workshop on High Performance Data Intensive Computing

作者： Correa, Jan Mendonca Magalhaes Alves de Melo, Alba Cristina Jacobi, Ricardo P. Boukerche, Azzedine Univ Brasilia Dept Comp Sci Brasilia DF Brazil Univ Ottawa SITE Ottawa ON K1N 6N5 Canada Kuwait Univ Safat 13060 Kuwait

ISBN: (纸本)9780769546766

Finding a biologically relevant sequence alignment may be difficult since several sequence alignments are possible, taking different parameters in consideration. A perceptron neuron can be used to associate weights to a set of alignment characteristics and then deciding if two residues should be aligned. Finding a good set of weights can be a hard problem and simulated annealing can be used to find a good set but can take a long time. In this paper, we propose a parallelization strategy for simulated annealing optimizing a Fragment Based Alignment in Linear Space (FBALS). the results were superior to the competing algorithm and the obtained speedups were compatible with the number of processing cores, indicating a good parallel strategy.

关键词： Sequence Alignment Linear Space Algorithms Simulated Annealing Perceptron

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Improved Bounds for Discrete Diffusive Load Balancing

Improved Bounds for Discrete Diffusive Load Balancing

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26th ieee International parallel and distributed processing symposium (IPDPS) / Workshop on High Performance Data Intensive Computing

作者： Adolphs, Clemens P. J. Berenbrink, Petra Rhein Westfal TH Aachen Lehrstuhl Informat 1 Aachen Germany Simon Fraser Univ Dept Comp Sci Burnaby BC V5A 1S6 Canada

ISBN: (纸本)9780769546759

In this paper we consider load balancing in a static and discrete setting where a fixed number of indivisible tasks have to be allocated to processors. We assume uniform tasks but the processors may have different speeds. the load of a processor is the number of tasks assigned to it divided by its speed. We consider diffusion load balancing which works in rounds. In every round the processors are allowed to compare their own load with the load of their neighbors and to balance the load with the neighbors, using their local information only. the question is how many rounds does it take until the whole processor network is balanced, meaning the load discrepancy (difference between maximum load and m/n) is minimized. Our balancing algorithm is deterministic and extends the algorithm studied in [1] from the case of uniform speeds to non-uniform speeds. We use a potential function argument to show that a better load balance can be obtained when the algorithm is allowed to run longer compared to the algorithm of [1].

关键词： load balancing distributed algorithms reallocation

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An SMT-Selection Metric to Improve Multithreaded Applications' Performance

An SMT-Selection Metric to Improve Multithreaded Application...

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26th ieee International parallel and distributed processing symposium (IPDPS) / Workshop on High Performance Data Intensive Computing

作者： Funston, Justin R. El Maghraoui, Kaoutar Jann, Joefon Pattnaik, Pratap Fedorova, Alexandra IBM TJ Watson Res Ctr Yorktown Hts NY 10598 USA Simon Fraser Univ Burnaby BC V5A 1S6 Canada

ISBN: (纸本)9780769546759

Simultaneous multithreading (SMT) increases CPU utilization and application performance in many circumstances, but it can be detrimental when performance is limited by application scalability or when there is significant contention for CPU resources. this paper describes an SMT-selection metric that predicts the change in application performance when the SMT level and number of application threads are varied. this metric is obtained online through hardware performance counters with little overhead, and allows the application or operating system to dynamically choose the best SMT level. We have validated the SMT-selection metric using a variety of benchmarks that capture various application characteristics on two different processor architectures. Our results show that the SMT-selection metric is capable of predicting the best SMT level for a given workload in 90% of the cases. the paper also shows that such a metric can be used with a scheduler or application optimizer to help guide its optimization decisions.

关键词： Operating Systems Performance Optimization SMT

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SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model

SlimCodeML: An Optimized Version of CodeML for the Branch-Si...

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26th ieee International parallel and distributed processing symposium (IPDPS) / Workshop on High Performance Data Intensive Computing

作者： Schabauer, Hannes Valle, Mario Pacher, Christoph Stockinger, Heinz Stamatakis, Alexandros Robinson-Rechavi, Marc Yang, Ziheng Salamin, Nicolas Univ Lausanne Dept Ecol & Evolut CH-1015 Lausanne Switzerland Swiss Natl Supercomp Ctr Swiss Inst Bioinformat CH Sci Comp Grp CH Lugano Switzerland AIT Austrian Inst Technol Safety & Secur Dept Seibersdorf Austria SIB Swiss Inst Bioinformat Vital IT Grp CH Lugano Switzerland Heidelberg Inst Theoret Studies Sci Comp Grp DE Heidelberg Germany UCL Dept Biol London WC1E 6BT England

ISBN: (纸本)9780769546766

CodeML (part of the PAML package) implements a maximum likelihood-based approach to detect positive selection on a specific branch of a given phylogenetic tree. While CodeML is widely used, it is very compute-intensive. We present SlimCodeML, an optimized version of CodeML for the branch-site model. Our performance analysis shows that SlimCodeML substantially outperforms CodeML (up to 9.38 times faster), especially for large-scale genomic analyses.

关键词： scientific computing molecular evolution phylogenetics codon models likelihood computation

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New Scheduling Strategies and Hybrid Programming for a parallel Right-looking Sparse LU Factorization Algorithm on Multicore Cluster Systems

New Scheduling Strategies and Hybrid Programming for a Paral...

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26th ieee International parallel and distributed processing symposium (IPDPS) / Workshop on High Performance Data Intensive Computing

作者： Yamazaki, Ichitaro Li, Xiaoye S. Univ Calif Berkeley Lawrence Berkeley Natl Lab Computat Res Div Berkeley CA 94720 USA

ISBN: (纸本)9780769546759

parallel sparse LU factorization is a key computational kernel in the solution of a large-scale linear system of equations. In this paper, we propose two strategies to address some scalability issues of a factorization algorithm on modern HPC systems. the first strategy is at the algorithmic-level;we schedule independent tasks as soon as possible to reduce the idle time and the critical path of the algorithm. We demonstrate using thousands of cores that our new scheduling strategy reduces the runtime by nearly three-fold from that of a state-of-the-art pipelined factorization algorithm. the second strategy is at both programming-and architecture-levels;we incorporate light-weight OpenMP threads in each MPI process to reduce both memory and time overheads of a pure MPI implementation on manycore NUMA architectures. Using this hybrid programming paradigm, we obtain a significant reduction in memory usage while achieving a parallel efficiency competitive with that of a pure MPI paradigm. As a result, in comparison to a pure MPI paradigm which failed due to the per-core memory constraint, the hybrid paradigm could utilize more cores on each node and reduce the factorization time on the same number of nodes. We show extensive performance analysis of the new strategies using thousands of cores of the two leading HPC systems, a Cray-XE6 and an IBM iDataPlex.

关键词： Factorization

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Investigating Memory Optimization of Hash-index for Next Generation Sequencing on Multi-core Architecture

Investigating Memory Optimization of Hash-index for Next Gen...

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26th ieee International parallel and distributed processing symposium (IPDPS) / Workshop on High Performance Data Intensive Computing

作者： Wang, Wendi Tang, Wen Li, Linchuan Tan, Guangming Zhang, Peiheng Sun, Ninghui Chinese Acad Sci Inst Comp Technol High Performance Comp Res Ctr Beijing 100864 Peoples R China

ISBN: (纸本)9780769546766

Next Generation Sequencing (NGS) is gaining interests due to the increased requirements and the decreased sequencing cost. the important and prerequisite step of most NGS applications is the mapping of short sequences, called reads, to the template reference sequences. Both the explosion of NGS data with over billions of reads generated each day and the data-intensive computations pose great challenges to the capability of existing computing systems. In this paper, we take a hash-index based algorithm (PerM) as an example to investigate the optimization approaches for accelerating NGS reads mapping on multi-core architectures. First, we propose a new parallel algorithm that reorders bucket access in hash index among multiple threads so that data locality in shared cache is improved. Second, in order to reduce the number of empty hash bucket, we propose a serialized hash index compression algorithm, which coincides with the sequential access nature of our new parallel algorithm. With reduced hash index size, it also becomes possible for us to use longer hash keys, which alleviates the hash conflicts and improves the query performance. Our experiment on an 8-socket 8-cores Intel Xeon X7550 SMP with 128 GB memory shows that the new parallel algorithm reduces LLC miss ratio to be 8% similar to 15% of the original algorithm and the overall performance is improved by 4 similar to 11 times (6 times avg.).

关键词： hashing parallel algorithms core construction next generation sequencing locality data reading buckets

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