HPC Publications

  • Weeks, Nathan T.; Luecke, Glenn R.; Groth, Brandon M.; Kraeva, Marina; Ma, Li; Kramer, Luke M., Koltes, James E.; Reecy, James M. "High Performance Epistasis Detection in Quantitative Trait GWAS". International Journal of High Performance Computing, vol. doi: 10.1177/1094342016658110. July 2016.
  • Tony Pan, Patrick Flick, Chirag Jain, Yongchao Liu and Srinivas Aluru "Kmerind: A flexible parallel library for k-mer indexing of biological sequences on distributed memory systems". 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB 2016), 2016.
  • Sharma, A., Singh, P., Johnson, D. D., Liaw, P. K. & Balasubramanian, G. "Atomistic clustering-ordering and high strain deformation of Al0.1CrCoFeNi high-entropy alloy". Scientific Reports, Accepted July 2016, 2016.
  • Yongchao Liu, Tony Pan, and Srinivas Aluru "Parallel pairwise correlation computation On Intel Xeon Phi clusters". 28th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD 2016), under review, 2016.
  • Kramer, L. M.; Abdel Ghaffar, M.A.; Koltes, J. E.; Fritz-Waters E.R.; Mayes M.; Sewell A.D.; Weeks, N.T.; Garrick, D.; Fernando R.; Reecy, J.M. "Epistatic Interactions associated with Fatty Acid concentrations of beef from Angus Sired Beef Cattle". BMC Genomics, In Review, 2016.
  • Malekpour, Hoda and Ramnani, Pankaj and Srinivasan, Srilok and Balasubramanian, Ganesh and Nika, Denis L. and Mulchandani, Ashok and Lake, Roger K. and Balandin, Alexander A. "Thermal conductivity of graphene with defects induced by electron beam irradiation". Nanoscale, vol. The Royal Society of Chemistry, doi 10.1039/C6NR03470E. 2016.
  • Yongchao Liu and Srinivas Aluru "LightScan: faster scan primitive on CUDA compatible manycore processors". Journal of Parallel and Distributed Computing, under review, 2016.
  • Srilok Srinivasan, Upamanyu Ray, and Ganesh Balasubramanian "Thermal conductivity reduction in analogous 2D nanomaterials with isotope substitution: Graphene and silicene". Chemical Physics Letters, vol. 650 pp. 88 - 93. vol. issn 0009-2614 http://dx.doi.org/10.1016/j.cplett.2016.02.073. 2016.
  • N. Jammula, S. Chockalingam, and S. Aluru "Parallel Read Error Correction for Big Genomic Datasets". 2015 IEEE 22nd International Conference on High Performance Computing (HiPC), pp. 446-455. vol. 10.1109/HiPC.2015.47. December 2015.
  • Luecke, Glenn R.; Weeks, Nathan T.; Groth, Brandon M.; Kraeva, Marina; Ma, Li; Kramer, Luke M.; Koltes, James E.; Reecy, James M. "Fast Epistasis Detection in Large-Scale GWAS for Intel Xeon Phi Clusters". Trustcom/BigDataSE/ISPA, vol. 3 pp. 228-235. vol. doi: 10.1109/Trustcom.2015.637. August 2015.
  • Alex Travesset "Binary nanoparticle superlattices of soft-particle systems". Proceedings of the National Academy of Sciences of the United States of America, vol. doi: 10.1073/pnas.1504677112. June 2015.
  • P. Flick, C. Jain, T. Pan, S. Aluru "A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications". Proc. ACM/IEEE Supercomputing Conference (SC), 2015.
  • P. Flick, S. Aluru "Parallel distributed memory construction of suffix and longest common prefix arrays". Proc. ACM/IEEE Supercomputing Conference (SC), 2015.
  • Sines, T.R., C.J. Anderson and R.W. Arritt "A simple modification to improve interaction between convective parameterization and grid scale microphysics". 16th WRF Users Workshop, 15-18 June 2015, Boulder, Colorado, 2015.
  • Sines, T.R., C.J. Anderson and R.W. Arritt "Improving prediction of mesoscale convective systems with convective parameterization". 16th Conference on Mesoscale Processes, American Meteorological Society, 3-6 August 2015, Boston, Massachusetts, 2015.
  • Scott Broderick, Upamanyu Ray, Srikant Srinivasan, Krishna Rajan, and Ganesh Balasubramanian "An informatics based analysis of the impact of isotope substitution on phonon modes in graphene". APPLIED PHYSICS LETTERS 104, 243110 (2014), July 2014.
  • Hu, X., Passalacqua, A., Fox, R.O "Application of quadrature-based uncertainty quantification to the NETL small-scale challenge problem SSCP-I". Powder Technology, July 2014.
  • Panicker, N.S., Passalacqua, A., Fox, R. O "Analysis and Closure Verification of Multiphase Turbulence Models for Gas -Liquid Flows". AIChE Annual Meeting, Atlanta, 2014, July 2014.
  • Khaitan, S. and McCalley, J. "SCALE: A hybrid MPI and Multithreading Based Work Stealing Approach for Massive Contingency Analysis in Power Systems". Electric Power Systems Research, vol. 114 pp. 118-125. June 2014.
  • Hu, X., Passalacqua, A., Fox, R.O "Quadrature-Based Uncertainty Quantification Approach in a Multiphase Gas-Particle Flow Simulation in a Riser". AIChE Annual Meeting, Atlanta, 2014, June 2014.
  • Pruitt, Spencer; Bertoni, Colleen; Brorsen, Kurt; Gordon, Mark "Efficient and Accurate Fragmentation Methods". Accounts of Chemical Research, May 2014.
  • Siddhartha Kumar Khaitan∗, James D. McCalley "SCALE: A hybrid MPI and multithreading based work stealing approach for massive contingency analysis in power systems". Elsevier, April 2014.
  • Capecelatro, Jesse; Desjardins, Olivier; Fox, Rodney O "Numerical study of collisional particle dynamics in cluster-induced turbulence". Journal of Fluid Mechanics vol 747, pp. R2. vol. Cambridge University Press. April 2014.
  • Koesterke, L., Koltes, J. E., Weeks, N. T., Milfeld, K., Vaughn, M. W., Reecy, J. M. and Stanzione, D. "Discovery of biological networks using an optimized partial correlation coefficient with information theory algorithm on Stampede's Xeon and Xeon Phi processors. ". Concurrency Computat.: Pract. Exper., vol. doi: 10.1002/cpe.3252. March 2014.
  • Nathan T. Weeks, Marina Kraeva, Glenn R. Luecke "ipcmd: A command-line interface to System V semaphores and message queues". Concurrency and Computation: Practice and Experience, vol. 26 no. 2 pp. 396-411. vol. John Wiley & Sons Ltd.. February 2014.
  • J. M. Carraher, D. Galvin, S. G. Hartke, A. J. Radcliffe, D. Stolee "On the independence ratio of distance graphs". February 2014.
  • Sarom S. Leang, Alistair P. Rendell, Mark S. Gordon "Quantum Chemical Calculations Using Accelerators: Migrating Matrix Operations to the NVIDIA Kepler GPU and the Intel Xeon Phi". Journal of Chemical Theory and Computation, vol. ACS Publications. February 2014.
  • Cheng Y, Rachagani S, Canovas A, Mayes MS, Tait Jr. RG, Dekkers JCM, and Reecy JM "Body composition and geneexpression QTL mapping in mice reveals imprinting and interaction effects.". BMC Genetics, vol. 14 no. 103 vol. doi: 10.1186/1471-2156-14-103.. January 2014.
  • S. K. Khaitan and J. McCalley "PARAGON: an approach for parallelization of power system contingency analysis using go programming language". International Transactions on Electrical Energy Systems, vol. doi: 10.1002/etep.1999. 2014.
  • Sines, T.R. and R.W. Arritt "WRF-ARW physics parameterizations influence on mesoscale convective system (MCS) forecasts and development of process-oriented verification for WRF-ARW output". American Geophysical Union 2014 Fall Meeting, 15-19 December 2014, San Francisco, California, 2014.
  • Jahn, D. E., W. A. Gallus, E. S. Takle "Evaluation of the MYNN PBL scheme closure constants for Low-Level Jet events in a stable boundary layer". 21st Symposium on Boundary Layers and Turbulence, 9-13 June, Amer. Meteor. Soc., Leeds, UK, 2014.
  • Hu, X., A. Passalacqua and R. O. Fox "Multiphase flow research-Uncertainty quantification tools for multiphase gas-solid flow simulations using MFIX". Crosscutting Research Review Meeting, Pittsburgh, PA, 2014.
  • Hu, X., A. Passalacqua and R. O. Fox "Validation of a quadrature-based uncertainty quantification approach using NETL small scale challenge problem SSCP-1". ASME 2014 Verification & Validation Symposium, Las Vegas, NV, 2014.
  • Fox, R. O., J. Capecelatro and O. Desjardins "Multiphase turbulence in vertical wall-bounded collisional gas-particle flows". APS-DFD Annual Meeting, San Francisco, CA, 2014.
  • Fox, R. O., J. Capecelatro and O. Desjardins "The role of granular temperature in turbulent gas-particle flows". AIChE Annual Meeting, Atlanta, GA, 2014.
  • Fox, R. O., J. Capecelatro and O. Desjardins "Numerical investigation of particle dynamics in cluster-induced turbulence". 17th U.S. National Congress on Theoretical and Applied Mechanics, East Lansing, MI, 2014.
  • A Fontanini, M Olsen, A Passalacqua, B. Ganapathysubramanian "High-Resolution Performance Analysis of a Large Building with Linear Dispersion Ductwork System". ASHRAE Transactions, 2014.
  • Desjardins, O., J. Capecelatro and R. O. Fox "An adaptive filter strategy for extracting multiphase flow statistics from Euler-Lagrange simulations". NETL Workshop on Multiphase Flow Science, Morgantown, WV, 2014.
  • Capecelatro, J., O. Desjardins and R. O. Fox "Fluid-particle characteristics in fully-developed cluster-induced turbulence". APS-DFD Annual Meeting, San Francisco, CA, 2014.
  • Capecelatro, J., O. Desjardins and R. O. Fox "Turbulence modeling of collisional gas-particle flows in wall-bounded risers". AIChE Annual Meeting, Atlanta, GA, 2014.
  • Capecelatro, J., O. Desjardins, and R. O. Fox "Investigating multiphase turbulence statistics of large-scale two-way coupled gravity-driven flows". Proceedings of the ASME 2014 4th Joint US-European Fluids Engineering Division Summer Meeting, Chicago, IL, 2014.
  • Baes C, Dolezal M, Fritz-Waters E, Koltes JE, Bapst B, Flury C, Signer-Hasler H, Stricker C, Fernando R, Reecy J, Garrick D, Schmitz-Hsu F, Fries R, Gredler B "Comparison of variant calling methods for whole genome sequencing data in dairy cattle". Proc. of Plant and Animal Genome XXII. San Diego, CA, USA, 2014.
  • Baes C, von Rohr P, Dolezal MA, Fritz-Waters E, Koltes JE, Bapst B, Flury C, Signer-Hasler H, Stricker C, Fernando R, Reecy J, Garrick D, Schmitz-Hsu F, Gredler B. "Assessing genomic variation in Swiss dairy cattle breeds using annotated whole genome sequence information". Proc. of the EAAP. Copehhagen, Denmark, 2014.
  • Baes C, von Rohr P, Dolezal MA, Fritz-Waters E, Koltes JE, Bapst B, Flury C, Signer-Hasler H, Stricker C, Fernando R, Reecy J, Garrick D, Schmitz-Hsu F, Gredler B "The effect of genome coverage in whole genome sequencing data". Proc. of the EAAP. Copehhagen, Denmark, 2014.
  • Baes C.F., Dolezal M.A., Bapst B., Fritz-Waters E., Koltes J.E., Jansen S., Flury C., Signer-Hasler H., Stricker C., Fernando R., Fries R., Moll J., Garrick D.J., Reecy J.M., and Gredler B. "Evaluation of variant identification methods for whole genome sequencing data in dairy cattle". BMC Genomics. Nov 1; 15:948, 2014.
  • Khaitan, S., McCalley, J. D., and Somani, A "Proactive Task Scheduling and Stealing in Master-Slave Based Load Balancing for Parallel Contingency Analysis". Electric Power Systems Research, vol. 103 pp. 9-15. October 2013.
  • Selvaraj, S., A. Chaves, E. Takle and A. Sharma "Numerical Prediction of Surface Flow Convergence Phenomenon in Windfarms". Proc. of the Conference on Wind Energy Science and Technology, RUZGEM, Ankara, Turkey, October 2013.
  • Saatchi, M, Garrick DJ, Tait Jr. RG, Mayes MS, Drewnoski M, Schoonmaker J, Diaz C, Beitz DC and Reecy JM "Genome-wide association and prediction of direct genomic breeding values for composition of fatty acids in Angus beef cattle. BMC Genomics.". BMC Genomics. 2013 Oct 25;, vol. 14 no. 730 vol. doi: 10.1186/1471-2164-14-730.. October 2013.
  • Week, N; Kraeva, M; Luecke, G.R. "Parallelization of software pipelines using the mpififo Tool". Cluster Computing (CLUSTER), 2013 IEEE International Conference on, pp. 1-3. September 2013.
  • Nathan T. Weeks, Marina Kraeva, Glenn R. Luecke "Parallelization of software pipelines using the mpififo tool". Cluster Computing (CLUSTER) 2013 IEEE International Conference on, 23-27 Sept. 2013., September 2013.
  • Khaitan, S. and McCalley, J "Parallelizing Power System Contingency Analysis Using D Programming Language". IEEE PES GM 2013, Vancouver, BC, pp. 1-5, 21-25. June 2013.
  • Khaitan, S. and McCalley, J "“Achieving Load-Balancing in Power System Parallel Contingency Analysis Using X10 Programming Language”". Proceedings of the third ACM SIGPLAN X10 Workshop, Seattle, pp. 20-28. June 2013.
  • Hu, X., Passalacqua, A., Fox, R.O. "A Quadrature-Based Uncertainty Quantification Approach with Reconstruction of the Probability Distribution Function of the System Response in Bubbling Fluidized Beds". AIChE Annual Meeting, San Francisco, 2013, May 2013.
  • S. G. Hartke, D. Stolee "A linear programming approach to the Manickam-Miklós-Singhi Conjecture, ". European Journal of Combinatorics 36, pp. 53-70. February 2013.
  • Koesterke L, Milfeld M, Vaughn MW, Stanzione D, Koltes JE, Weeks NT, Reecy JM. "Optimizing the PCIT algorithm on Stampede's Xeon and Xeon Phi processors for faster discovery of biological networks.". Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery (XSEDE '13)., January 2013.
  • Bai, W., N. K. G. Keller, T. J. Heindel, and R. O. Fox "Numerical study of mixing and segregation in a biomass fluidized bed". Powder Technology, vol. 237 pp. 355-366. 2013.
  • Capecelatro, J., O. Desjardins and R. O. Fox "Evaluating multiphase turbulence statistics using mesoscale DNS of gravity-driven particle-laden flows". AIChE Annual Meeting, San Francisco, CA, 2013.
  • Fox, R. O., J. Capecelatro and O. Desjardins "Validation of a multiphase turbulence model using mesoscale DNS of gravity-driven gas-particle flows". NETL Workshop on Multiphase Flow Science, Morgantown, WV, 2013.
  • Fox, R. O., J. Capecelatro and O. Desjardins "Evaluating multiphase turbulence statistics using mesoscale DNS of gravity-driven particle-laden flows". APS-DFD Annual Meeting, Pittsburgh, PA, 2013.
  • Khaitan, S. and McCalley, J. "Optimizing cache energy efficiency in multicore power system simulations". Energy Systems, vol. doi 10.1007/s12667-013-0090-4. 2013.
  • Kong, B., and R. O. Fox "Extended conditional quadrature-based moment methods for polydisperse gas-particle flows with size-conditioned velocity". NETL Workshop on Multiphase Flow Science, Morgantown, WV, 2013.
  • Kong, B., A. Passalacqua and R. O. Fox "Extended conditional quadrature-based moment methods for polydisperse gas-particle flows with size-conditioned velocity". AIChE Annual Meeting, San Francisco, CA, 2013.
  • Olsen, M., Y. Shi, G. Iaccarino and R. O. Fox "CFD predictions of confined turbulent swirling flows in a microscale multi-inlet vortex reactor". APS-DFD Annual Meeting, Pittsburgh, PA, 2013.
  • Panicker, N., A. Passalacqua and R. O. Fox "Mesoscale direct numerical simulations of monodisperse bubbly flow". AIChE Annual Meeting, San Francisco, CA, 2013.
  • Passalacqua, A., X. Hu and R. O. Fox "Uncertainty quantification tools for multiphase flow simulations using MFIX". NETL 2013 NETL Workshop on Multiphase Flow Science, Morgantown, WV, 2013.
  • Rokkam, R. G., A. Sowinski, R. O. Fox, P. Mehrani, and M. E. Muhle "Computational and experimental study of electrostatics in gas-solid polymerization fluidized beds". Chemical Engineering Science, vol. 92 pp. 146-156. 2013.
  • Yuan, C., V. Vikas, R. O. Fox, and Z. J. Wang "An extended quadrature-based velocity-mass Euler-Euler model for 2-D bubbly flows". Proceedings of 8th International Conference on Multiphase Flow (ICMF 2013), Jeju, Korea, pp. 1-7. 2013.
  • Khaitan, S. and McCalley, J "EmPower: An Efficient Load Balancing Approach For Massive Dynamic Contingency Analysis in Power Systems". 2nd International Workshop on High Performance Computing, Networking and Analytics for the Power Grid, SC12, Salt Lake City, UT, USA, November 2012.
  • S. G. Hartke, D. Stolee "Uniquely Kr-saturated graph ". Electronic Journal of Combinatorics 19(4), September 2012.
  • Marina Kraeva, James Coyle, Glenn R. Luecke, Indranil Roy, Elizabeth Kleiman, James Hoekstra "CompilerCheck: A tool for Evaluating Error Detection Capabilities of UPC Compilers". Conference Proceedings, Computational Tools 2012, July 2012.
  • James Coyle, Indranil Roy, Marina Kraeva, Glenn R. Luecke "UPC-CHECK: A scalable tool for detecting run-time errors in Unified Parallel C". Conference Proceedings, ISC 2012, Hamburg, Germany, June 17-21, 2012, June 2012.
  • S. G. Hartke, D. Stolee, D. B. West, M. Yancey "On extremal graphs with a given number of perfect matchings". Journal of Graph Theory, 73(4), pp. 449-468. April 2012.
  • D. Stolee "Generating p-extremal graphs". August 2011.
  • Glenn R. Luecke, Olga Weiss, Marina Kraeva, James Coyle, James Hoekstra "Performance Analysis of Pure MPI Versus MPI+OpenMP for Jacobi Iteration and a 3D FFT on the Cray XT5". Cray Users Group 2010, Edinburgh, Scotland, May 2010, May 2010.
  • Glenn R. Luecke, James Coyle, James Hoekstra, Marina Kraeva, Ying Xu, Elizabeth Kleiman, Olga Weiss "Evaluating Error Detection Capabilities of UPC Run-time Systems". Third Conference on Partitioned Global Address Space (PGAS) Programming Models, October 2009, October 2009.
  • Glenn R. Luecke, James Coyle, James Hoekstra, Marina Kraeva, Ying Xu, Mi-Young Park, Elizabeth Kleiman, Olga Weiss, Andre Wehe, Melissa Yahya "The Importance of Run-time Error Detection". Tools for High Performance Computing 2009, Proceedings of the 3rd International Workshop on Parallel Tools for High Performance Computing, September 2009, ZIH, Dresden, Springer 2009, September 2009.
  • Glenn R. Luecke, James Coyle, James Hoekstra, Marina Kraeva, Ying Xu, Mi-Young Park, Elizabeth Kleiman, Olga Weiss, Andre Wehe, Melissa Yahya "Evaluating the Capability of Compilers and Tools to Detect Serial and Parallel Run-time Errors". Supercomputing 2009, July 2009.
  • Glenn R. Luecke, James Coyle, Jim Hoekstra, Marina Kraeva, Ying Li, Olga Taborskaia, and Yanmei Wang "A Survey of Systems for Detecting Serial Run-Time Errors". Concurrency and Computation: Practice and Experience, vol. 18 pp. 1885-1907. March 2006.
  • Glenn R. Luecke, Silvia Spanoyannis and Marina Kraeva "The Performance and Scalability of SHMEM and MPI-2 One-Sided Routines on a SGI Origin 2000 and a Cray T3E-600". Concurrency and Computation: Practice and Experience. 2004, vol. 16 pp. 1037-1060. June 2004.
  • Glenn R. Luecke, Marina Kraeva, Jing Yuan and Silvia Spanoyannis "Performance and Scalability of MPI on PC Clusters". Concurrency and Computation: Practice and Experience, vol. 16 pp. 79-107. January 2004.
  • Glenn R. Luecke, Marina Kraeva and Lili Ju "Comparing the Performance of MPICH with Cray's MPI and with SGI's MPI". Concurrency and Computation: Practice and Experience, vol. 15 pp. 779-802. January 2003.
  • Glenn R. Luecke, Hua Chen, James Coyle, Jim Hoekstra, Marina Kraeva and Yan Zou "MPI-CHECK: a Tool for Checking Fortran 90 MPI Programs". Concurrency and Computation: Practice and Experience., vol. 15 pp. 93-100. January 2003.
  • Glenn R. Luecke, Yan Zou, James Coyle, Jim Hoekstra and Marina Kraeva "Deadlock Detection In MPI Programs". Concurrency and Computation: Practice and Experience, vol. 14 pp. 911-932. January 2002.