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Shared Memory and Hardware Utilizations for the Parallelization of Local Sequences Alignment using SW Algorithm: A Review

Manhal ElfadilEltayeeb, Muhammad S. Abd Latiff, Ismail Fuzi Isnin
2015 International Journal of Computer Applications  
Many studies in recent years have focused on different implementations of Sequences Alignment Problems (SAP). However, researcher confused with the ambiguous classification of the SAP.  ...  This paper is set out mainly to review, investigate, and analysis current trends in shared memory and hardware implementation of local SAP using Smith-Waterman algorithm.  ...  To reduce the time of sequences comparisons a multi-core system is considered in the implementation phase.  ... 
doi:10.5120/20141-2257 fatcat:arg4ddbqsfbolbfdag6gwz75yy

Hardware-Conscious Stream Processing: A Survey [article]

Shuhao Zhang, Feng Zhang, Yingjun Wu, Bingsheng He, Paul Johns
2020 arXiv   pre-print
In this paper, we conduct a systematic survey of recent work in the field, particularly along with the following three directions: 1) computation optimization, 2) stream I/O optimization, and 3) query  ...  Data stream processing systems (DSPSs) enable users to express and run stream applications to continuously process data streams.  ...  This work is supported by a MoE Tier 1 grant (T1 251RES1824) and a MoE Tier 2 grant (MOE2017-T2-1-122) in Singapore.  ... 
arXiv:2001.05667v1 fatcat:hga7siyyzvbavilpxvxjofvtii

Posting list intersection on multicore architectures

Shirish Tatikonda, B. Barla Cambazoglu, Flavio P. Junqueira
2011 Proceedings of the 34th international ACM SIGIR conference on Research and development in Information - SIGIR '11  
In practice, the intersection operation takes a significant fraction of the query processing time, for some queries dominating the total query latency.  ...  In this work, we focus on improving the performance of posting list intersection by leveraging the compute capabilities of recent multicore systems.  ...  Strohman and Croft [28] present a preliminary evaluation of in-memory query processing techniques on multicore systems.  ... 
doi:10.1145/2009916.2010045 dblp:conf/sigir/TatikondaCJ11 fatcat:s2v44wbv4vhs5cgwoiekpe7ke4

APSkyline: Improved Skyline Computation for Multicore Architectures [chapter]

Stian Liknes, Akrivi Vlachou, Christos Doulkeridis, Kjetil Nørvåg
2014 Lecture Notes in Computer Science  
In this paper, we present APSkyline, a new approach for multicore skyline query processing, which adheres to the partition-execute-merge framework.  ...  This need is particularly evident in the case of CPU-intensive query operators. One example of such a query with applicability in data analytics is the skyline query.  ...  Since multicore skyline processing differs from skyline processing in other parallel environments, we apply all necessary adaptations of the partitioning technique for a multicore system, which combined  ... 
doi:10.1007/978-3-319-05810-8_21 fatcat:6vgdrfz4lzfspglbdh5nfbzufa

Palette

Fei Chen, Tere Gonzalez, Jun Li, Manish Marwah, Jim Pruyne, Krishnamurthy Viswanathan, Mijung Kim
2014 Proceedings of the 2014 ACM SIGMOD international conference on Management of data - SIGMOD '14  
Hadoop and its variants have been widely used for processing large scale analytics tasks in a cluster environment.  ...  feature, and (3) monitor and compare different operator implementations.  ...  For example, 90% of analytics tasks in a production system have input sizes under 100 GB [11] . Similar studies have reported a median task size of only 14 GB [2] .  ... 
doi:10.1145/2588555.2594509 dblp:conf/sigmod/ChenGLMPVK14 fatcat:ezdrp7vi5zauvdyik3qc2kdxmu

Efficient Wavelet Tree Construction and Querying for Multicore Architectures [chapter]

José Fuentes-Sepúlveda, Erick Elejalde, Leo Ferres, Diego Seco
2014 Lecture Notes in Computer Science  
We also present a querying technique based on batch processing that improves on simple domain-decomposition techniques.  ...  This paper introduces two practical multicore algorithms for wavelet tree construction that run in O(n) time using lg σ processors, where n is the size of the input and σ the alphabet size.  ...  In order to exploit multicore architectures, we also investigated techniques to speed up range queries and propose BQA (batch-queryanswering), a hybrid domain-decomposition/parallel batch processing technique  ... 
doi:10.1007/978-3-319-07959-2_13 fatcat:3ri2tqxejnbozoxqjorjy3uzza

Multicore SIMD ASIP for Next-Generation Sequencing and Alignment Biochip Platforms

Nuno Neves, Nuno Sebastiao, David Matos, Pedro Tomas, Paulo Flores, Nuno Roma
2015 IEEE Transactions on Very Large Scale Integration (vlsi) Systems  
Targeting the development of new biochip platforms capable of autonomously sequencing and aligning biological sequences, a new multicore processing structure is proposed in this manuscript.  ...  The complete system was prototyped on different field-programmable gate array platforms and synthesized with a 90-nm CMOS process technology.  ...  With such a technique, a vector of cells parallel to the query sequence can be simultaneously processed by each SIMD instruction [ Fig. 1(a) ].  ... 
doi:10.1109/tvlsi.2014.2333757 fatcat:twsa7irxnjhkxl3mhqktxdsb4e

Cache-Conscious Data Access for DBMS in Multicore Environments

Fang XI, Takeshi MISHIMA, Haruo YOKOTA
2015 IEICE transactions on information and systems  
In this paper, we propose CARIC-DA, middleware for achieving higher performance in DBMSs on multicore processors, by reducing cache misses with a new cache-conscious dispatcher for concurrent queries.  ...  In particular, the number of cores on a chip has been growing exponentially, enabling an ever-increasing number of processes to be executed in parallel.  ...  A study on MCC-DB [7] pointed out the conflicts in the shared cache for concurrent queries on the multicore platform and solved the problem by integrating the OS facility of cache partitioning into DBMS  ... 
doi:10.1587/transinf.2014dap0004 fatcat:sliycbq2erbezj4xz56l277p2u

Cache-conscious graph collaborative filtering on multi-socket multicore systems

Lifeng Nai, Yinglong Xia, Ching-Yung Lin, Bo Hong, Hsien-Hsin S. Lee
2014 Proceedings of the 11th ACM Conference on Computing Frontiers - CF '14  
Based on these observations, we present a cache-conscious system for collaborative filtering on modern multi-socket multicore platforms.  ...  In this system, we propose a cache-conscious query scheduling technique and an in-memory graph representation, and to maximize cache performance and minimize cross-core/socket communication overhead, we  ...  The main contributions of this paper are as follows: • To the best of our knowledge, this is the first study of data locality of a collaborative filtering system on modern multi-socket multicore platforms  ... 
doi:10.1145/2597917.2597935 dblp:conf/cf/NaiXLHL14 fatcat:mxhc2q2y5jam3kxossw6bxhikq

Compact graph representations and parallel connectivity algorithms for massive dynamic network analysis

K. Madduri, D.A. Bader
2009 2009 IEEE International Symposium on Parallel & Distributed Processing  
We present the first study of novel highperformance combinatorial techniques for analyzing largescale information networks, encapsulating dynamic interaction data in the order of billions of entities.  ...  With these new approaches, we achieve an average performance rate of 25 million structural updates per second and a parallel speedup of nearly 28 on a 64-way Sun UltraSPARC T2 multicore processor, for  ...  We design parallel approaches for tree construction, updates, as well as query processing. The implementations scale quite well on multicore architectures.  ... 
doi:10.1109/ipdps.2009.5161060 dblp:conf/ipps/MadduriB09 fatcat:zmhf354mznharab6dkuzqrj55q

Cache Hierarchy-Aware Query Mapping on Emerging Multicore Architectures

Ozcan Ozturk, Umut Orhan, Wei Ding, Praveen Yedlapalli, Mahmut Taylan Kandemir
2017 IEEE transactions on computers  
Our proposed scheme distributes a given batch of queries across the cores of a target multicore architecture based on the affinity relations among the queries.  ...  Most of current commercial multicore systems on the market have on-chip cache hierarchies with multiple layers (typically, in the form of L1, L2 and L3, the last two being either fully or partially shared  ...  ACKNOWLEDGMENTS A preliminary 2-page version of this paper appears in the Proceedings of 2014 IEEE International Symposium on Workload Characterization (IISWC) [27] . This work has been done when U.  ... 
doi:10.1109/tc.2016.2605682 fatcat:fdfe4mhddrhyfk4isdwak2tkd4

Parallel quadtree coding of large-scale raster geospatial data on GPGPUs

Jianting Zhang, Simin You, Le Gruenwald
2011 Proceedings of the 19th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems - GIS '11  
In this study, we have developed an efficient spatial data structure called BQ-Tree to code raster geospatial data by exploiting the uniform distributions of quadrants of bitmaps at the bitplanes of a  ...  The performance achieves a 5.9X speedup when compared with the best dual quadcore CPU implementation and a 36.9X speedup compared with a highly optimized single core CPU implementation.  ...  Second, while the GPGPU-based design and implementation are compared against CPU-based ones in this study, from a practical perspective, it is more useful to integrate multicore CPU and GPGPU implementations  ... 
doi:10.1145/2093973.2094047 dblp:conf/gis/ZhangYG11 fatcat:zwr7obnjozcwvdmsbquydic5fm

An Improved Distance Matrix Computation Algorithm for Multicore Clusters

Mohammed W. Al-Neama, Naglaa M. Reda, Fayed F. M. Ghaleb
2014 BioMed Research International  
Further it also achieves speedups more than 9 orders of magnitude compared to the publicly available parallel implementation utilized in ClustalW-MPI.  ...  However, the multicore cluster systems, which are available now, with their scalability and performance/cost ratio, meet the need for more powerful and efficient performance.  ...  Acknowledgments The authors would like to thank Bibliotheca Alexandria for granting the access for running their computations on its platform.  ... 
doi:10.1155/2014/406178 pmid:25013779 pmcid:PMC4074972 fatcat:qqnwu2aamvb4zmclnc6nqjmpyq

Database engines on multicores scale

Joao Soares, Nuno Preguica
2015 Proceedings of the 30th Annual ACM Symposium on Applied Computing - SAC '15  
This paper presents a practical study on In-Memory DBMS and shows that contention imposed by concurrency control mechanisms, such as locking, are limiting factors for both performance and scalability of  ...  Multicore processors are available for over a decade, being the norm for current computer systems, but general purpose database management systems (DBMS) still cannot fully explore the computational resources  ...  IN-MEMORY DBMS OVERVIEW In this section we provide an overview on the components of a DBMS, focusing on how these are implemented on the studied systems and discussing their interactions during transaction  ... 
doi:10.1145/2695664.3200145 fatcat:ytpt6ce4cbbkfizz3qhphseajy

Empirical Evaluation of the Parallel Distribution Sweeping Framework on Multicore Architectures [article]

Deepak Ajwani, Nodari Sitchinava
2013 arXiv   pre-print
While modern processors consist of sophisticated memory systems (multiple levels of caches, set associativity, TLB, prefetching), we empirically show that algorithms designed in simple models, that focus  ...  In particular, we implement the parallel distribution sweeping framework of Ajwani, Sitchinava and Zeh to solve batched 1-dimensional stabbing max problem.  ...  We would also like to thank Dennis Luxen and Dennis Schieferdecker for their extensive help with our implementations and getting perf and papi to run on our systems.  ... 
arXiv:1306.4521v1 fatcat:l52zhgubxzhslfsl7bkltnvdu4
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