skip to main content
10.1145/2616498.2616540acmotherconferencesArticle/Chapter ViewAbstractPublication PagesxsedeConference Proceedingsconference-collections
research-article

Gateways to Discovery: Cyberinfrastructure for the Long Tail of Science

Published: 13 July 2014 Publication History

Abstract

NSF-funded computing centers have primarily focused on delivering high-performance computing resources to academic researchers with the most computationally demanding applications. But now that computational science is so pervasive, there is a need for infrastructure that can serve more researchers and disciplines than just those at the peak of the HPC pyramid. Here we describe SDSC's Comet system, which is scheduled for production in January 2015 and was designed to address the needs of a much larger and more expansive science community-- the "long tail of science". Comet will have a peak performance of 2 petaflop/s, mostly delivered using Intel's next generation Xeon processor. It will include some large-memory and GPU-accelerated nodes, node-local flash memory, 7 PB of Performance Storage, and 6 PB of Durable Storage. These features, together with the availability of high performance virtualization, will enable users to run complex, heterogeneous workloads on a single integrated resource.

References

[1]
NSB 93-205 -- NSF Blue Ribbon Panel on High Performance Computing. NSF, Arlington, VA, 1993.
[2]
NSF Advisory Committee for Cyberinfrastructure Task Force on Campus Bridging. Final Report. NSF, Arlington, VA, March 2011.
[3]
Cyberinfrastructure Framework for 21st Century Science and Engineering: Vision. NSF, Arlington, VA, May 2012.
[4]
Cyberinfrastructure Framework for 21st Century Science and Engineering (CIF21), http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504730
[5]
ACCI Task Force reports, available at http://www.nsf.gov/od/oci/taskforces/, NSF, Arlington, VA.
[6]
Stewart, C. A., Katz, D. S., Hart, D. L., Lantrip, D., McCaulay, D. S. and Moore, R. L. Survey of Cyberinfrastructure Needs and Interests of NSF-funded Principal Investigators. Indiana University, Bloomington, IN, January 2011.
[7]
Katz, D. S., Keahey, K. and Jul, S. TeraGrid eXtreme Digital 'Wide Users' Requirements Elicitation Meeting, Computation Institute Technical Report CI-TR-10-0811. University of Chicago and Argonne National Laboratory, 2011.
[8]
XDMoD - XSEDE Metrics on Demand, NSF award OCI-1025159.
[9]
Moore, R. L., Jundt, A., Carson, L. K., Yoshimoto, K., Ghadersohi, A. and Young, W. S. Analyzing throughput and utilization on Trestles, Proceedings of XSEDE12. ACM, (Chicago, IL, 2012).
[10]
Furlani, T. R., Schneider, B. I., Jones, M. D., Towns, J., Hart, D. L., Patra, A. K., DeLeon, R. L., Gallo, S. M., Lu, C.-D. and Ghadersohi, A. Data analytics driven cyberinfrastructure operations, planning and analysis using XDMoD, SC12 Conference, Salt Lake City, UT, 2012.
[11]
Hart, D. Deep and wide metrics for HPC resource capability and project usage, Supercomputing '11, November 2011, Seattle, WA, USA. ACM.
[12]
Schneider, B. A Data History of TeraGrid/XSEDE Usage: Defining a Strategy for Advanced CyberInfrastructure (ACI), April 2012.
[13]
FutureGrid, https://portal.futuregrid.org/.
[14]
SLURM: Simple linux utility for resource management.
[15]
Yoo, A. B., Jette, M. A. and Grondona, M. SLURM: Simple linux utility for resource management. Springer, City, 2003.
[16]
Boyd, E., Newman, H., McKee, S. and Sheldon, P. MRI-R2 Consortium: Development of Dynamic Network System (DYNES), NSF ACI award 0958998, 2010.
[17]
Cortese, J. New Dynamic Circuit Provisioning Available on Pacific Wave, http://pacificwave.net/p=433/, November 26, 2012.
[18]
2012 Annual HPCwire Readers' Choice Awards, November 2012,http://www.hpcwire.com/specialfeatures/2012_Annual_HPCwire_Readers_Choice_Awards.html.
[19]
Jorissen, K., Vila, F. D. and Rehr, J. J. A high performance scientific cloud computing environment for materials simulations. Computer Physics Communications, 183, (9) 2012, 1911--1919.
[20]
Rehr, J. SI2-SSE: Cloud-Computing-Clusters for Scientific Research, NSF ACI award 1048052. NSF, 2010.
[21]
Rehr, J. J., Vila, F. D., Gardner, J. P., Svec, L. and Prange, M. Scientific computing in the cloud. Computing in Science & Engineering, 12, (3) 2010, 34--43.
[22]
Yelick, K., Coghlan, S., Draney, B. and Cannon, R. S. The Magellan Report on Cloud Computing for Science, U.S. Department of Energy, Office of Science, Office of Advanced Scientific Computing Research. December 2011.
[23]
Jackson, K. R., Ramakrishnan, L., Muriki, K., Canon, S., Cholia, S., Shalf, J., Wasserman, H. J. and Wright, N. J. Performance analysis of high performance computing applications on the amazon web services cloud. IEEE 2nd International Conference on Cloud Computing Technology and Science (CloudCom), 2010.
[24]
Mehrotra, P., Djomehri, J., Heistand, S., Hood, R., Jin, H., Lazanoff, A., Saini, S. and Biswas, R. Performance evaluation of Amazon EC2 for NASA HPC applications. Proceedings of the 3rd workshop on Scientific Cloud Computing, ACM, (Delft, The Netherlands, June 2012).
[25]
Overview of Single Root I/O Virtualization (SR-IOV), http://msdn.microsoft.com/enus/library/windows/hardware/hh440148%28v=vs.85%29.aspx.
[26]
Lockwood, G. K., Tatineni, M. and Wagner, R. P. SR-IOV: Performance Benefits for Virtualized Interconnects, Proceedings of XSEDE14, ACM (Atlanta, GA, July 2014).
[27]
Neuroscience Gateway Portal, http://www.nsgportal.org.
[28]
Wagner, R., Tatineni, M., Hocks, E., Yoshimoto, K., Sakai, S., Norman, M. L., Bockelman, B., Sfiligoi, I., Tadel, M. and Letts, J. Using Gordon to accelerate LHC science. Proceedings of XSEDE13, ACM, (San Diego, CA, July, 2013).
[29]
Gaussian, http://www.gaussian.com
[30]
Kong, J., White, C. A., Krylov, A. I., Sherrill, D., Adamson, R. D., Furlani, T. R., Lee, M. S., Lee, A. M., Gwaltney, S. R. and Adams, T. R. Q-Chem 2.0: a high-performance ab initio electronic structure program package. Journal of Computational Chemistry, 21, (16) 2000, 1532--1548.
[31]
Hibbitt, Karlsson and Sorensen ABAQUS/Standard user's manual. Hibbitt, Karlsson & Sorensen, 2001.
[32]
Clean Energy Project, https://cleanenergy.harvard.edu.
[33]
Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q. and Liu, Y. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 1, (1) 2012, 18.
[34]
Zerbino, D. R. and Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome research, 18, (5) 2008, 821--829.
[35]
Götz, A. W., Williamson, M. J., Xu, D., Poole, D., Le Grand, S. and Walker, R. C. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized Born. Journal of chemical theory and computation, 8, (5) 2012, 1542--1555.
[36]
Salomon-Ferrer, R., Götz, A. W., Poole, D., Le Grand, S. and Walker, R. C. Routine microsecond molecular dynamics simulations with Amber on GPUs. 2. Explicit solvent particle mesh Ewald. Journal of Chemical Theory and Computation, 9, (9) 2013, 3878--3888.
[37]
Brooks, B. R., Brooks, C. L., MacKerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C. and Boresch, S. CHARMM: the biomolecular simulation program. Journal of computational chemistry, 30, (10) 2009, 1545--1614.
[38]
Hess, B., Kutzner, C., Van Der Spoel, D. and Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of chemical theory and computation, 4, (3) 2008, 435--447.
[39]
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kale, L. and Schulten, K. Scalable molecular dynamics with NAMD. Journal of computational chemistry, 26, (16) 2005, 1781--1802.
[40]
AMBER (PMEMD) Benchmarks, http://ambermd.org/gpus/benchmarks.htm.
[41]
CIPRES, http://www.phylo.org.
[42]
Drummond, A. J. and Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC evolutionary biology, 7, (1) 2007, 214.
[43]
Huelsenbeck, J. P. and Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17, (8) 2001, 754--755.
[44]
Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, (21) 2006, 2688--2690.
[45]
CyberGIS, http://cybergis.cigi.uiuc.edu.
[46]
Behzad, B., Liu, Y., Shook, E., Finn, M. P., Mattli, D. M. and Wang, S. A Performance Profiling Strategy for High-Performance Map Re-Projection of Coarse-Scale Spatial Raster Data, In Auto-Carto 2012, a cartography and geographic information society research symposium, Columbus, OH, 2012.
[47]
Tarboton, D. G. Terrain analysis using digital elevation models (TauDEM). Utah State University, Logan2005).
[48]
Computational Chemistry Grid, http://www.gridchem.org.
[49]
Bower, J. M. and Beeman, D. The book of GENESIS: exploring realistic neural models with the GEneral NEural SImulation System. The Electronic Library of Science, 1995.
[50]
Carnevale, N. T. and Hines, M. L. The NEURON book. Cambridge University Press, 2006.
[51]
UltraScan Analysis Software, http://ultrascan.uthscsa.edu.
[52]
Wilkins-Diehr, N., Gannon, D., Klimeck, G., Oster, S. and Pamidighantam, S. TeraGrid science gateways and their impact on science. Computer, 41, (11) 2008, 32--41.
[53]
Science Gateway Institute, http://sciencegateways.org.
[54]
Miller, M. A., Pfeiffer, W. and Schwartz, T. The CIPRES science gateway: enabling high-impact science for phylogenetics researchers with limited resources, Proceedings of XSEDE12, ACM, (Chicago, IL, 2012).
[55]
Moore, R. L., Hart, D. L., Pfeiffer, W., Tatineni, M., Yoshimoto, K. and Young, W. S. Trestles: a high-productivity HPC system targeted to modest-scale and gateway users. Proceedings of TeraGrid 11, ACM, (Salt Lake City, UT, 2011).
[56]
Yoshimoto, K., Choi, D., Moore, R., Majumdar, A. and Hocks, E. Implementations of Urgent Computing on Production HPC Systems. Procedia Computer Science, (9) 2012, 1687--1693.

Cited By

View all
  • (2021)HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffoldingBMC Bioinformatics10.1186/s12859-020-03939-y22:1Online publication date: 6-Jan-2021
  • (2021)Expanse: Computing without BoundariesPractice and Experience in Advanced Research Computing 2021: Evolution Across All Dimensions10.1145/3437359.3465588(1-4)Online publication date: 17-Jul-2021
  • (2021)The Hour of Cyberinfrastructure (Hour of CI): Early Findings from Pilot Study to Build Cyber Literacy for GIScience2021 IEEE/ACM Ninth Workshop on Education for High Performance Computing (EduHPC)10.1109/EduHPC54835.2021.00007(9-15)Online publication date: Nov-2021
  • Show More Cited By

Recommendations

Comments

Information & Contributors

Information

Published In

cover image ACM Other conferences
XSEDE '14: Proceedings of the 2014 Annual Conference on Extreme Science and Engineering Discovery Environment
July 2014
445 pages
ISBN:9781450328937
DOI:10.1145/2616498
  • General Chair:
  • Scott Lathrop,
  • Program Chair:
  • Jay Alameda
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

In-Cooperation

  • NSF: National Science Foundation
  • Drexel University
  • Indiana University: Indiana University

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 13 July 2014

Permissions

Request permissions for this article.

Check for updates

Author Tags

  1. GPU
  2. High performance computing
  3. high throughput computing
  4. parallel file system
  5. science gateways
  6. scientific applications
  7. solid-state drive
  8. user support
  9. virtualization

Qualifiers

  • Research-article
  • Research
  • Refereed limited

Conference

XSEDE '14

Acceptance Rates

XSEDE '14 Paper Acceptance Rate 80 of 120 submissions, 67%;
Overall Acceptance Rate 129 of 190 submissions, 68%

Contributors

Other Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

  • Downloads (Last 12 months)4
  • Downloads (Last 6 weeks)0
Reflects downloads up to 01 Mar 2025

Other Metrics

Citations

Cited By

View all
  • (2021)HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffoldingBMC Bioinformatics10.1186/s12859-020-03939-y22:1Online publication date: 6-Jan-2021
  • (2021)Expanse: Computing without BoundariesPractice and Experience in Advanced Research Computing 2021: Evolution Across All Dimensions10.1145/3437359.3465588(1-4)Online publication date: 17-Jul-2021
  • (2021)The Hour of Cyberinfrastructure (Hour of CI): Early Findings from Pilot Study to Build Cyber Literacy for GIScience2021 IEEE/ACM Ninth Workshop on Education for High Performance Computing (EduHPC)10.1109/EduHPC54835.2021.00007(9-15)Online publication date: Nov-2021
  • (2020)Bear: Cyberinfrastructure for Long-Tail Researchers at the Federal Reserve Bank of Kansas CityPractice and Experience in Advanced Research Computing 2020: Catch the Wave10.1145/3311790.3396623(49-55)Online publication date: 26-Jul-2020
  • (2019)Parallel Implementation of a PETSc-Based Framework for the General Curvilinear Coastal Ocean ModelJournal of Marine Science and Engineering10.3390/jmse70601857:6(185)Online publication date: 13-Jun-2019
  • (2019)Mechanical Model for Durotactic Cell MigrationACS Biomaterials Science & Engineering10.1021/acsbiomaterials.8b013655:8(3954-3963)Online publication date: 12-Mar-2019
  • (2019)Electrostatic Spectral Tuning Maps for Biological ChromophoresThe Journal of Physical Chemistry B10.1021/acs.jpcb.9b00489123:23(4813-4824)Online publication date: 14-Mar-2019
  • (2019)Interplay Between the Persistent Random Walk and the Contact Inhibition of Locomotion Leads to Collective Cell BehaviorsBulletin of Mathematical Biology10.1007/s11538-019-00585-1Online publication date: 20-Feb-2019
  • (2019)HDArray: Parallel Array Interface for Distributed Heterogeneous DevicesLanguages and Compilers for Parallel Computing10.1007/978-3-030-34627-0_13(176-184)Online publication date: 13-Nov-2019
  • (2019)The OpenAIRE Research Community Dashboard: On Blending Scientific Workflows and Scientific PublishingDigital Libraries for Open Knowledge10.1007/978-3-030-30760-8_5(56-69)Online publication date: 30-Aug-2019
  • Show More Cited By

View Options

Login options

View options

PDF

View or Download as a PDF file.

PDF

eReader

View online with eReader.

eReader

Figures

Tables

Media

Share

Share

Share this Publication link

Share on social media