{"id":15,"date":"2015-05-20T17:53:53","date_gmt":"2015-05-20T17:53:53","guid":{"rendered":"https:\/\/cecas.clemson.edu\/fctl\/?page_id=15"},"modified":"2016-05-12T13:12:56","modified_gmt":"2016-05-12T13:12:56","slug":"publications","status":"publish","type":"page","link":"https:\/\/cecas.clemson.edu\/fctl\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

Journal Publications<\/strong><\/p>\n

Pallipuram, V.K., M.C. Smith, N. Raut, and X. Ren, \u201cA Regression-Based Heterogeneous Performance Prediction Framework for GPGPU Clusters,\u201d Concurrency and Computation: Practice and Experience, 26\/2, pp. 27, (2014), DOI: 10.1002\/cpe.3017.<\/p>\n

Feltus, F.A., S.P. Ficklin, S.M. Gibson, and M.C. Smith, \u201cMaximum Capture of an Organism\u2019s Gene Co-Expression Space via Gene Interaction Layer Construction,\u201d BMC Systems Biology, 7\/44, pp. 12, (2013), DOI:10.1186\/1752-0509-7-44.<\/p>\n

Gibson, S.M., S.P. Ficklin, S. Isaacson, F. Luo, F.A. Feltus, and M.C. Smith, \u201cMassive-Scale Gene Co-expression Network Construction and Robustness Testing using Random Matrix Theory,\u201d PLoS ONE 8\/2: e55871, pp. 33, (2013), DOI:10.1371\/journal.pone.0055871.<\/p>\n

Smith, M.C. and G.D. Peterson, \u201cOptimization of Shared High-Performance Reconfigurable Computing Resources,\u201d ACM Transactions on Embedded Computing Systems, 11\/2, pp. 22, (2012), DOI 10.1145\/2220336.2220348.<\/p>\n

Stitt, G., A. George, H. Lam, M.C. Smith, V. Aggarwal, G. Wang, C. Reardon, B. Holland, S. Koehler, and J. Coole, \u201cAn End-to-End Tool Flow for FPGAAccelerated Scientific Computing,\u201d Special Issue of IEEE Design and Test of Computers, Jul\/Aug, pp. 68-77, (2011).<\/p>\n

Holland, B., A.D. George, H. Lam, and M.C. Smith, \u201cAn Analytical Model for Hierarchical Performance Prediction of Multi-FPGA Systems,\u201d ACM Transactions on Reconfigurable Technology and Systems (TRETS), 4\/3, pp. 28, (2011), DOI: 10.1145\/2000832.2000839.<\/p>\n

Pallipuram, V.K., M.C. Smith, and M.A. Bhuiyan, \u201cA Comparative Study of GPU Programming Models and Architectures,\u201d Journal of Supercomputing, May, pp. 46, (2011), DOI: 10.1007\/s11227-011-0631-3.<\/p>\n

Bhuiyan, M.A., M.C. Smith, and V.K. Pallipuram, \u201cPerformance, Optimization and Fitness: Connecting Applications to Architectures,\u201d Concurrency and Computation: Practice and Experience, 23\/10, 1066\u20131100, (2011), DOI: 10.1002\/cpe.1688.<\/p>\n

Alam, S.R., P.K. Agarwal, J.S. Vetter, and M.C. Smith, \u201cThroughput Improvement of Molecular Dynamics Simulations Using Reconfigurable Computing,\u201d Scalable Computing: Practice and Experience – Scientific International Journal for Parallel and Distributed Computing, 8\/4, 395-410,\u00a0(2007).<\/p>\n

Alam, S.R., P.K. Agarwal, M.C. Smith, J.S. Vetter, and D. Caliga, \u201cUsing FPGA Devices to Accelerate Biomolecular Simulations,\u201d IEEE Computer, Vol. 40, No. 3, pp. 66-73, March 2007.<\/p>\n

Smith, M.C. and G.D. Peterson, \u201cParallel Application Performance on Shared High Performance Reconfigurable Computing Resources,\u201d Performance Evaluation: An International Journal, Special Issue on Performance Modeling and Evaluation of High-Performance Parallel and Distributed Systems, Vol. 60\/1-4, pp. 107-125, May 2005.<\/p>\n

Adler, S.S., M. Allen, G. Alley, R. Amirikas, Y. Arai, T.C. Awes, K.N. Barish, F. Barta, S. Batosouli, S. Belikov, M.J. Bennett, et. al., M. Smith, et. al., \u201cPHENIX On-line Systems,\u201d Nuclear Instruments and Methods in Physics Research Section A, Vol. 499, Iss. 2-3, pp. 560-592, March 2003.<\/p>\n

Adcox, K., J. Ajitanand, J. Alexander, J. Barrette, R. Belkin, D. Borland, W.L. Bryan, R. du Rietz, K. El Chanawi, A. Cherlin, et. al., M. Smith, et. al., \u201cConstruction and Performance of the PHENIX Pad Chambers,\u201d Nuclear Instruments and Methods in Physics Research Section A, A497, pp. 263-293, February 2003.<\/p>\n

Nilsson, P., J. Barrette, W. Bryan, Z. Fraenkel, V. Green, S. Garpman, H.A. Gustafsson, U. Jagadish, et. al., M.C. Smith, et. al., \u201cThe Pixel Readout System for the PHENIX Pad Chambers,\u201d Panic99 Nuclear Physics, A661, pp. 665-668, May 1999.<\/p>\n

Smith, M.C., W.L. Bryan, D. Smith, U. Jagadish, D. McMilan, J. Walker, G.R. Young, A. Oskarsson, L. Osterman, V. Greene, and L. Nikkinen, \u201cA Front-End Electronics Module for the PHENIX Pad Chamber,\u201d IEEE Transactions on Nuclear Science, Vol. 46, No. 6, pp. 1998-2002, December 1999.<\/p>\n

Ericson, M.N., M.D. Allen, J. Boissevain, C.L. Britton, M.S. Emery, S.F. Hahn, J.S. Kapustinsky, R.E. Lind, M.S. Musrock, J. Simon-Gillo, D.E. Smith, J.P. Sullivan, H. Van Hecke, G.R. Young, and M.C. Smith, \u201cFront-End Module Readout and Control Electronics for the PHENIX Multiplicity Vertex Detector,\u201d IEEE Transactions on Nuclear Science, Vol. 45, No. 3, pp. 833-837, June 1998.<\/p>\n

Paulus, M.J., J.T. Mihalczo, T.E. Valentine, J.A. Mullens, J.E. Breeding, T. Uckan, J. Mattingly, G. Turner, M.C. Smith, and J.A. McEvers, \u201cA Novel Method for Determining Pulse Counting Circuitry Dead Time Using the Nuclear Weapons Inspection System,\u201d IEEE Transactions on Nuclear Science, Vol. 45, No. 3, pp. 710-714, June 1998.<\/p>\n

Morrison, D.P., Y. Akiba, O. Alford, M. Allen, W. Allen, G. Alley, Y. Arai, J.B. Archuleta, J.R. Archuleta, S.H. Aronson, et. al., M.C. Smith, et. al., \u201cThe PHENIX Experiment at RHIC,\u201d Nuclear Physics, A638, pp. 565-570, April 1998.<\/p>\n

Britton, C.L., W.L. Bryan, M.S. Emery, M.N. Ericson, M.S. Musrock, M.L. Simpson, M.C. Smith, J.W. Walker, A.L. Wintenberg, G.R. Young, M.D. Allen, L.G. Clonts, R.L. Jones, E.J. Kennedy, R.S. Smith, et. al., \u201cDesign and Performance of Beam Test Electronics for the PHENIX Multiplicity Vertex Detector,\u201d IEEE Transactions on Nuclear Science, Vol. 44, No. 3, pp. 283-288, June 1997.<\/p>\n

Mihalczo, J.T., J.A. Mullens, J.E. Breeding, T.E. Valentine, V.K. Pare, D.E. McMillan, T.A. Gafford, R.R. Bentz, G.W. Turner, M.C. Smith, J.A. McEvers, J.K. Mattingly, R.I. Vandermolen, E.D. Blakeman, M.J. Paulus, and T. Uckan, \u201cNew Processor for Subcritical Fissile System Measurements for Nuclear Criticality Safety,\u201d Transactions of American Nuclear Society, Vol. 75, pp. 178-179, 1996.<\/p>\n

 <\/p>\n

Conference Publications<\/span><\/strong><\/p>\n

Husain, B., K. Sapra, R.R. Brooks, and M.C. Smith, \u201cCircumventing Keyloggers and Screendumps,\u201d 8th International Conference on Malicious and Unwanted Software (Malware\u201913), Fajardo, Puerto Rico, USA, October 22-24, 2013.<\/p>\n

Pallipuram, V.K., N. Raut, X. Ren, M.C. Smith, and S. Naik, \u201cA Multi-Node GPU Implementation of Non-Linear Anisotropic Diffusion Filter,\u201d SAAHPC\u201912, pp.8, July 10-12, 2012.<\/p>\n

Goodall, T., S. Gibson, and M.C. Smith, \u201cParallelizing Principle Component Analysis for Robust Facial Recognition using CUDA,\u201d SAAHPC\u201912, pp.4, July10-12-2012.<\/p>\n

Raut, N., V.K. Pallipuram, X. Ren and M.C. Smith, \u201cExploring Multi-Level Parallelism in GPGPU clusters,\u201d XSEDE\u201912 Annual Conference, Chicago, IL, July 16-19, 2012.<\/p>\n

Pallipuram, V.K., M.C. Smith, N. Raut, and X. Ren, \u201cExploring Multi-level Parallelism for Large-scale Spiking Neural Networks,\u201d The 18th International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA’12), pp.7, July 16-19, 2012.<\/p>\n

Pallipuram, V.K., M.A. Bhuiyan and M.C. Smith, \u201cEvaluation of GPU Architectures Using Spiking Neural Networks,\u201d in proceedings of the Symposium on Application Accelerators in High Performance Computing (SAAHPC’11), Knoxville, TN, pp. 10, July 19-20, 2011.<\/p>\n

Bhuiyan, M.A., A. Nallamuthu, M.C. Smith and V.K. Pallipuram, \u201cOptimization and Performance Study of Large-scale Biological Networks for Reconfigurable Computing,\u201d in proceedings of the Fourth International Workshop on High-Performance Reconfigurable Computing Technology and Applications (HPRCTA’10), New Orleans, LA, pp. 9, November 14, 2010.<\/p>\n

Nallamuthu, A., S. Hampton, M.C. Smith, S.R. Alam, P.K. Agarwal, \u201cEnergy Efficient Biomolecular Simulations with FPGA-based Reconfigurable Computing,\u201d in proceedings of ACM Computing Frontiers, Bertinoro, Italy, pp. 8, May 17-19, 2010.<\/p>\n

Bhuiyan, M.A., V.K. Pallipuram, M. C. Smith, and T. Taha, \u201cAcceleration of Spiking Neural Networks in Emerging Multi-core and GPU Architectures,\u201d Workshop on High Performance Computational Biology (HiCOMB) held in conjunction with IPDPS, Atlanta, GA, pp. 12, April 19-23, 2010.<\/p>\n

Rice, K.L., M.A. Bhuiyan, T.M. Taha, C.N. Vutsinas, and M.C. Smith, \u201cFPGA Implementation of Izhikevich Spiking Neural Networks for Character Recognition,\u201d ReConFig 2009, Cancun, Mexico, pp. 6, December 2009.<\/p>\n

Martin, P.M., M.C. Smith, S.R. Alam, and P.K. Agarwal, \u201cImplementation Methodology for Emerging Reconfigurable Systems,\u201d Midwestern Symposium on Circuits and Systems, Knoxville, TN, pp. 4, August 10-13, 2008.<\/p>\n

Merchant, S.G., B.M. Holland, C. Reardon, A.D. George, H. Lam, G. Stitt, N. Alam, M.C. Smith, I. Gonzalez, E. El-Araby, P. Saha, T. El-Ghazawi, and H. Simmler, “Strategic Challenges for Application Development Productivity in Reconfigurable Computing,” 2008 IEEE National Aerospace and Electronics Conference, Dayton, Ohio, USA, pp. 10, July 16-18, 2008.<\/p>\n

Gonzalez, I., E. El-Araby, P. Saha, T. El-Ghazawi, H. Simmler, S.G. Merchant, B.M. Holland, C. Reardon, A.D. George, H. Lam, G. Stitt, N. Alam, and M.C. Smith, “Classification of Application Development for FPGA-Based Systems,” 2008 IEEE National Aerospace and Electronics Conference, Dayton, Ohio, USA, pp. 10, July 16-18, 2008.<\/p>\n

Kruzner, A., J. Merwin, D. Rollend, A. Nallamuthu, C. Gupta, and M.C. Smith, \u201cInquiry: Robust Facial Recognition with Reconfigurable Platforms,\u201d Reconfigurable Systems Summer Institute, University of Illinois at Urbana-Champaign, pp.4, July 7-10, 2008.<\/p>\n

S. Gibson, M.C. Smith, A. Nallamuthu, C. Gupta, D. Rollend, A. Kruzner, and J. Merwin, \u201cCreative Inquiry: Parallel Implementation of Facial Recognition Algorithms,\u201d to appear at Supercomputing 2008 South Carolina Computing Consortium Research Exhibit, Austin, TX, November 15-21, 2008.<\/p>\n

Alam, N., M.C. Smith and M.E. Kurz, \u201cRandom Number Generation on FPGA-based Computing Systems in a Condor Environment,\u201d to appear at Supercomputing 2008 South Carolina Computing Consortium Research Exhibit, Austin, TX, November 15-21, 2008.<\/p>\n

Martin, P.M., M.C. Smith, S.R. Alam, and P.K. Agarwal, \u201cImplementation Methodology for Emerging Reconfigurable Systems,\u201d Midwestern Symposium on Circuits and Systems, Knoxville, TN, August 10-13, 2008.<\/p>\n

Merchant, S.G., B.M. Holland, C. Reardon, A.D. George, H. Lam, G. Stitt, N. Alam, M.C. Smith, I. Gonzalez, E. El-Araby, P. Saha, T. El-Ghazawi, and H. Simmler, “Strategic Challenges for Application Development Productivity in Reconfigurable Computing,” 2008 IEEE National Aerospace and Electronics Conference, Dayton, Ohio, USA, July 16-18, 2008.<\/p>\n

Gonzalez, I., E. El-Araby, P. Saha, T. El-Ghazawi, H. Simmler, S.G. Merchant, B.M. Holland, C. Reardon, A.D. George, H. Lam, G. Stitt, N. Alam, and M.C. Smith, “Classification of Application Development for FPGA-Based Systems,” 2008 IEEE National Aerospace and Electronics Conference, Dayton, Ohio, USA, July 16-18, 2008.<\/p>\n

Kruzner, A., J. Merwin, D. Rollend, A. Nallamuthu, C. Gupta, and M.C. Smith, \u201cInquiry: Robust Facial Recognition with Reconfigurable Platforms,\u201d Reconfigurable Systems Summer Institute, University of Illinois at Urbana- Champaign, July 7-10, 2008.<\/p>\n

Martin, P.M., M.C. Smith, S.R. Alam, and P.K. Agarwal, \u201cAdvances in Reconfigurable Computing Technology Provide New Methods for Application Acceleration,\u201d Supercomputing 2007 South Carolina Computing Consortium Research Exhibit, Reno, NV, November 10-16, 2007.<\/p>\n

Smith, M.C. and G.D. Peterson, \u201cOptimized Resource Usage for High- Performance Reconfigurable Computers,\u201d Engineering of Reconfigurable Systems and Algorithms (ERSA\u201907), Las Vegas, Nevada, June 25-28, 2007.<\/p>\n

Alam, S.R. and M.C. Smith, \u201cAn Application Specific Memory Characterization Technique for Co-processor Accelerators,\u201d IEEE 18th International Conference on Application-specific Systems, Architectures and Processors (ASAP\u201907), Montr\u00e9al, Qu\u00e9bec, Canada, July 9-11, 2007.<\/p>\n

Smith, M.C., J.S. Vetter, and S.R. Alam, \u201cInvestigation of Benchmark Suites for High-Performance Reconfigurable Computing Platforms,\u201d submitted to The 9th annual Military & Aerospace Programmable Logic Device (MAPLD) International Conference, NASA Office of Logic Design, Washington D.C., September 26-28, 2006.<\/p>\n

Smith, M.C., S.R. Alam, P. Agarwal, and J.S. Vetter, \u201cA Task-based Development Model for Accelerating Large-Scale Scientific Applications on FPGA-based Reconfigurable Computing Platforms,\u201d Reconfigurable Systems Summer Institute, RSSI\u201906, Champaign-Urbana, Illinois, July 10-14, 2006.<\/p>\n

Storaasli, O., S. Alam and M. Smith, \u201cCray XD1 Experiences and Comparisons with other FPGA-based Supercomputer Systems,\u201d Cray User Group (CUG) Conference, Ticino, Switzerland, May 8-11, 2006.<\/p>\n

Subramaniyan, R. I. Troxel, A.D. George, and M.C. Smith, \u201cSimulative Analysis of Dynamic Scheduling Heuristics for Reconfigurable Computing of Parallel Applications,\u201d Fourteenth ACM\/SIGDA International Symposium on Field-Programmable Gate Arrays (FPGA\u201906), Monterey, California, February 22-24, 2006.<\/p>\n

Cordova, L., M.C. Smith, S.R. Alam, and J.S. Vetter, \u201cHigh Performance Programming Model for Large-Scale Molecular Dynamics Calculations on Reconfigurable Supercomputers,\u201d The 9th Annual Workshop on High Performance Embedded Computing (HPEC), MIT Lincoln Laboratory, Boston, Massachusetts, September 20-22, 2005.<\/p>\n

Akella, S., M.C. Smith, S.R. Alam, R.T. Mills, R.F. Barrett, and J.S. Vetter, \u201cSparse Matrix-Vector Multiplication Kernel on a Reconfigurable Computer,\u201d The 9th Annual Workshop on High Performance Embedded Computing (HPEC), MIT Lincoln Laboratory, Boston, Massachusetts, September 20-22, 2005.<\/p>\n

Smith, M.C., J. Vetter, and S. Alam, \u201cScientific Computing Beyond CPUs: FPGA implementations of common scientific kernels,\u201d The 8th annual Military & Aerospace Programmable Logic Device (MAPLD) International Conference, NASA Office of Logic Design, Washington D.C., September 7-9, 2005.<\/p>\n

Liang, X., J. Vetter, M.C. Smith, and A. Bland, \u201cBalancing FPGA Resource Utilities,\u201d Engineering of Reconfigurable Systems and Algorithms (ERSA\u201905), Las Vegas, Nevada, June 27-30, 2005.<\/p>\n

Smith, M.C., J. Vetter, and X. Liang, \u201cAccelerating Scientific Applications with the SRC-6 Reconfigurable Computer: Methodologies and Analysis,\u201d Reconfigurable Architectures Workshop (RAW\u201905), Denver, Colorado, April 4-5, 2005.<\/p>\n

Smith, M.C. and G.D. Peterson, \u201cAnalytical Modeling for High Performance Reconfigurable Computers,\u201d International Symposium on Performance Evaluation of Computer and Telecommunication Systems (SPECTS\u201902), San Diego, California, July 14-19, 2002.<\/p>\n

Smith, M.C. and G.D. Peterson, \u201cProgramming High Performance Reconfigurable Computers (HPRC),\u201d SPIE International Symposium ITCom 2001, Denver, Colorado, August 19-24, 2001.<\/p>\n

Peterson, G.D. and M.C. Smith, \u201cProgramming High Performance Reconfigurable Computers,\u201d International Conference on Advances in Infrastructure for Electronic Business, Science, and Education on the Internet (SSGRR\u201901), Rome, Italy, August 6-11, 2001.<\/p>\n

Smith, M.C., S.L. Drager, Lt. L. Pochet, and G.D. Peterson, \u201cHigh Performance Reconfigurable Computing Systems,\u201d Proceedings of 2001 IEEE Midwest Symposium on Circuits and Systems, Fairborn, Ohio, August 14-17, 2001.<\/p>\n

Nilsson, P., J. Barrette, W. Bryan, Z. Fraenkel, V. Green, S. Garpman, H.A. Gustafsson, U.Jagadish, L. Nikkinen, R. Lacey, J. Lauret, et. al., M.C. Smith, et. al., \u201cThe Pixel Readout System for the PHENIX Pad Chambers,\u201d XIV International Conference on Ultra-relativistic Nucleus- Nucleus collisions, Torino, Italy, May 10-15, 1999.<\/p>\n

Vann, J.M., M.C. Smith, C.E. Thomas, M.L. Simpson, M.J. Paulus, J.A. Moore, L.R. Baylor, and J.M. Rochelle, \u201cModeling and Simulation of Weak Inversion Current Sources for Control of Amorphous Diamond Electron Emitters,\u201d Proceeding of the 1998 Midwest Symposium on Circuits and Systems, Notre Dame, Indiana, August 9-12, 1998.<\/p>\n

Britton Jr., C.L., W.L. Bryan, M.S. Emery, S.S. Frank, M.N. Ericson, U. Jagadish, J.A. Moore, M.L. Simpson, M.C. Smith, A.L. Wintenberg, G.R. Young, et. al., \u201cMixed Signal Custom Integrated Circuit Development for Physics Instrumentation,\u201d International Symposium on Optical Science, Engineering, and Instrumentation, San Diego, California July 19-24, 1998.<\/p>\n

Emery, M.S., M.N. Ericson, C.L. Britton, Jr., M.C. Smith, S.S. Frank, G.R. Young, M.D. Allen, and L.G. Clonts, \u201cTiming and Control Requirements for a 32-Channel AMU-ADC ASIC for the PHENIX Detector,\u201d Conference record of the 1997 Nuclear Science Symposium, Albuquerque, New Mexico, November 9-15, 1997.<\/p>\n","protected":false},"excerpt":{"rendered":"

Journal Publications Pallipuram, V.K., M.C. Smith, N. Raut, and X. Ren, \u201cA Regression-Based Heterogeneous Performance Prediction Framework for GPGPU Clusters,\u201d Concurrency and Computation: Practice and Experience, 26\/2, pp. 27, (2014), DOI: 10.1002\/cpe.3017. Feltus, F.A., S.P. Ficklin, S.M. Gibson, and M.C. Smith, \u201cMaximum Capture of an Organism\u2019s Gene Co-Expression Space via Gene Interaction Layer Construction,\u201d BMC Systems Biology, 7\/44, pp. 12,… Read more →<\/a><\/p>\n","protected":false},"author":4,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-15","page","type-page","status-publish","hentry","xfolkentry"],"_links":{"self":[{"href":"https:\/\/cecas.clemson.edu\/fctl\/wp-json\/wp\/v2\/pages\/15","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/cecas.clemson.edu\/fctl\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/cecas.clemson.edu\/fctl\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/cecas.clemson.edu\/fctl\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/cecas.clemson.edu\/fctl\/wp-json\/wp\/v2\/comments?post=15"}],"version-history":[{"count":13,"href":"https:\/\/cecas.clemson.edu\/fctl\/wp-json\/wp\/v2\/pages\/15\/revisions"}],"predecessor-version":[{"id":195,"href":"https:\/\/cecas.clemson.edu\/fctl\/wp-json\/wp\/v2\/pages\/15\/revisions\/195"}],"wp:attachment":[{"href":"https:\/\/cecas.clemson.edu\/fctl\/wp-json\/wp\/v2\/media?parent=15"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}