Skip to main content
Disciplines
Automotive Business IT + Informatics Construction + Real Estate Electrical Engineering + Electronics Energy + Sustainability Insurance + Risk Finance + Banking Management + Leadership Marketing + Sales Mechanical Engineering + Materials
Events
DE
EN
Books
Journals
Topic Page
Marketing
Start single access now
Access for companies
EXTENDED SEARCH
Log in
Top
International Journal of Parallel Programming
Published in: International Journal of Parallel Programming 4/2013

01-08-2013

GPU-Friendly Parallel Genome Matching with Tiled Access and Reduced State Transition Table

Authors: Yunho Oh, Doohwan Oh, Won W. Ro

Published in: International Journal of Parallel Programming | Issue 4/2013

Log in

Activate our intelligent search to find suitable subject content or patents.

search-config
loading …

Abstract

In this paper, we propose a new parallel genome matching algorithm using graphics processing units (GPUs). Our proposed approach is based on the Aho–Corasick algorithm and it was developed based on a consideration of the architectural features of existing GPUs with a hundred or more cores. Thus, we provide an appropriate task partitioning method that runs on multiple threads and we fully utilize the cache memory and the shared memory structures available in GPUs. Especially, we propose a tiled access method for rapid data transfer from the global memory to the shared memory. We also provide new models for cache-friendly state transition table to improve performance of pattern matching operations on GPUs. The maximum throughput we achieved in various experiments was 15.3 Gbps. Moreover, we showed that our proposed design outperformed an earlier approach with a 15.4 % performance improvement.
previous article Analytical Performance Models for MapReduce Workloads
next article Online Mesh Refinement for Parallel Atmospheric Models

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

inform now
Literature
1.
2.
3.
NVIDIA CUDA Programming Guide 3.0. NVIDIA (2009)
4.
5.
6.
Baker, Z.K., Prasanna, V.K.: A Methodology for Synthesis of Efficient Intrusion Detection Systems on FPGAs. In: Proceedings of 12th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM ’04), pp. 135–144. IEEE Computer Society (2004)
7.
Bakhoda, A., Yuan, G.L., Fung, W.W.L., Wong, H., Aamodt, T.M.: Analyzing CUDA Workloads Using a Detailed GPU Simulator. In: Proceedings of IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS 2009), pp. 163–174. IEEE Computer Society (2009)
8.
Boeva, V., Clement, J., Regnier, M., Roytberg, M., Makeev, V.: Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. Algorithms Mol Biol 2(1), 13 (2007)CrossRef
9.
Bos, H., Huang, K.: A Network Intrusion Detection System on IXP1200 Network Processors with Support for Large Rule Sets. Leiden Universiteit, Technical report (2004)
10.
Boyer, R.S., Moore, J.S.: A fast string searching algorithm. Commun. ACM 20(10), 762–772 (1977)MATHCrossRef
11.
Brudno, M., Morgenstern, B.: Fast and sensitive alignment of large genomic sequences. In: Proceedings of 2002 Bioinformatics Conference, pp. 138–147. IEEE Computer Society (2002)
12.
Buhler, J., Keich, U., Sun, Y.: Designing seeds for similarity search in genomic DNA. In: Proceedings of 7th Annual International Conference on Research in Computational Molecular Biology, RECOMB ’03, pp. 67–75. ACM (2003)
13.
Castelo, A.T., Martins, W., Gao, G.R.: TROLL-tandem repeat occurrence locator. Bioinformatics 18(4), 634–636 (2002)CrossRef
14.
Dandass, Y., Burgess, S., Lawrence, M., Bridges, S.: Accelerating string set matching in FPGA hardware for bioinformatics research. BMC Bioinformatics 9(1), 197–207 (2008)CrossRef
15.
Hong, S., Kim, H.: An analytical model for a gpu architecture with memory-level and thread-level parallelism awareness. In: Proceedings of the 36th Annual International Symposium on Computer Architecture, ISCA ’09, pp. 152–163. ACM, New York (2009)
16.
17.
Majumder, A., Rastogi, R., Vanama, S.: Scalable regular expression matching on data streams. In: Proceedings of 2008 ACM SIGMOD International Conference on Management of Data (SIGMOD ’08), pp. 161–172. ACM (2008)
18.
Michael, M., Dieterich, C., Vingron, M.: Siteblast-rapid and sensitive local alignment of genomic sequences employing motif anchors. Bioinformatics 21(9), 2093–2094 (2005)CrossRef
19.
20.
NVIDIA: Tuning CUDA Applications for Fermi 1.3 (2010)
21.
Scarpazza, D.: Top-performance tokenization and small-ruleset regular expression matching. Int. J. Parallel Program. 39(1), 3–32 (2011)CrossRef
22.
Scarpazza, D., Villa, O., Petrini, F.: High-speed string searching against large dictionaries on the cell/B.E. Processor. In: Proceedings of IEEE International Symposium on Parallel and Distributed Processing, 2008 (IPDPS 2008), pp. 1–12. IEEE Computer Society (2008)
23.
Tan, L., Sherwood, T.: A high throughput string matching architecture for intrusion detection and prevention. In: Proceedings of 32nd Annual International Symposium on Computer Architecture (ISCA ’05), pp. 112–122. IEEE Computer Society (2005)
24.
Trapnell, C., Schatz, M.C.: Optimizing data intensive GPGPU computations for DNA sequence alignment. Parallel Comput. 35(8–9), 429–440 (2009)CrossRef
25.
Tumeo, A., Villa, O.: Accelerating DNA analysis applications on GPU clusters. In: Proceedings of 2010 IEEE 8th Symposium on Application Specific Processors (SASP), pp. 71–76. IEEE Computer Society (2010)
26.
Tumeo, A., Villa, O., Sciuto, D.: Efficient pattern matching on GPUs for intrusion detection systems. In: Proceedings of 7th ACM International Conference on Computing Frontiers, CF ’10, pp. 87–88. ACM (2010)
27.
28.
Vasiliadis, G., Antonatos, S., Polychronakis, M., Markatos, E.P., Ioannidis, S.: Gnort: high performance network intrusion detection using graphics processors. In: Proceedings of 11th International Symposium on Recent Advances in Intrusion Detection (RAID ’08), pp. 116–134. Springer-Verlag (2008)
29.
Vespa, L., Weng, N., Ramaswamy, R.: MS-DFA: multiple-stride pattern matching for scalable deep packet inspection. Comput J 54(2), 285–303 (2011)CrossRef
30.
Villa, O., Chavarria-Miranda, D., Maschhoff, K.: Input-independent, scalable and fast string matching on the cray XMT. In: Proceedings of IEEE International Symposium on Parallel Distributed Processing, 2009. IPDPS 2009, pp. 1–12 (2009)
31.
Wu, S., Manber, U.: Agrep - A fast approximate pattern-matching tool. In: Proceedings of USENIX Technical Conference, pp. 153–162. USENIX (1992)
32.
Xu, C., Kirk, S., Jenkins, S.: Tiling for performance tuning on different models of GPUs. In: Proceedings of 2009 Second International Symposium on Information Science and Engineering (ISISE), pp. 500–504 (2009)
33.
Yang, Y.H.E., Jiang, W., Prasanna, V.K.: Compact architecture for high-throughput regular expression matching on FPGA. In: Proceedings of 4th ACM/IEEE Symposium on Architectures for Networking and Communications Systems (ANCS ’08), pp. 30–39. ACM (2008)
34.
Zhongqiang, C., Yuan, Z., Zhongrong, C., Alex, D.: A digest and pattern matching-based intrusion detection engine. Comput. J. 52(6), 699–723 (2009)CrossRef
Metadata
Title
GPU-Friendly Parallel Genome Matching with Tiled Access and Reduced State Transition Table
Authors
Yunho Oh
Doohwan Oh
Won W. Ro
Publication date
01-08-2013
Publisher
Springer US
Published in
International Journal of Parallel Programming / Issue 4/2013
Print ISSN: 0885-7458
Electronic ISSN: 1573-7640
DOI
https://doi.org/10.1007/s10766-012-0234-5

Premium Partner

    Image Credits