ExMatEx | Publications and Resources

Publications & Resources Everything All of our research products are listed on this page—sorted by year.

A project as large as ExMatEx produces a lot of “stuff”. This poses a challenge to organize it efficiently for convenient access by others. At some point we may incorporate a searchable, database-backed, solution on this site. For the time being we'll try and organize our output into a structure of HTML pages.

There are five pages listed in the menu to the left:

Everything (this page): one page with all of our output on it, ordered by year. Within each year we have categories for papers, presentations, reports, and software.
Papers: Computer scientists typically publish at conferences, physicists in journals. We make no distinction and gather all published papers on one page, sorted by year of publication.
Talks: Same deal—no distinction on where, or to whom, the talk was given. All presented talks are on one page, sorted by when presented. Where possible, we try to cross-link between related talks and papers.
Reports: This is a catchall category for things that don't fit in the bins above. Examples include unpublished technical reports, position papers, review documents, software documentation, web posts, etc.
Software: links to our open source software. This page may also include pointers to partner (e.g. vendor, academia) software if it's used in ExMatEx proxies or for analysis.

You may note that there are no specific categories for proxies or research areas. We do list, on each project and research area page, all of the publications (in each category above) related to that particular project.

Finally, where possible, we provide a link to the actual content. Pointers to the external source of the content (e.g. journal or conference site) is preferred. If necessary, we store content on this site and serve it from here.

2015

Papers

Presentations

M. McKerns, “Modern optimization methods in python”, EuroPython, Bilbao, ESP, July 2015.

M. McKerns, “klepto: Unified persistent storage to memory, disk, or database”, the 14th Python in Science Conference, Austin, TX, July 2015.

M. McKerns, “Modern optimization methods in python”, the 14th Python in Science Conference, Austin, TX, July 2015.

M. McKerns, “Efficient python for high-performance parallel computing”, the 14th Python in Science Conference, Austin, TX, July 2015.

M. McKerns, “Are rigorous predictions in the stock market, battlefield scenarios, engineering design, and natural disasters possible?”, ASME Verification & Validation Symposium, Las Vegas, NV, May 2015.

M. McKerns, “Living with ‘dirty’ data while avoiding exascale ‘garbage in, garbage out’”, Salishan Conference on High-Speed Computing, Gleneden Beach, OR, April 2015.

M. McKerns, “Redesigning optimization and UQ for exascale”, ASCR Exascale Co-Design Program Meeting, Livermore, CA, February 2015.

Software

M. McKerns, “Modern optimization methods in python”, EuroPython, Bilbao, ESP, July 2015.

M. McKerns, “klepto: Unified persistent storage to memory, disk, or database”, the 14th Python in Science Conference, Austin, TX, July 2015.

M. McKerns, “Modern optimization methods in python”, the 14th Python in Science Conference, Austin, TX, July 2015.

M. McKerns, “Efficient python for high-performance parallel computing”, the 14th Python in Science Conference, Austin, TX, July 2015.

M. McKerns, “Living with ‘dirty’ data while avoiding exascale ‘garbage in, garbage out’”, Salishan Conference on High-Speed Computing, Gleneden Beach, OR, April 2015.

M. McKerns, “Redesigning optimization and UQ for exascale”, ASCR Exascale Co-Design Program Meeting, Livermore, CA, February 2015.

2014

Papers

B. Rouet-Leduc, K. Barros, E. Cieren, V. Elango, C. Junghans, T. Lookman, J. Mohd-Yusof, R. S. Pavel, A. Y. Rivera, D. Roehm, A. L. McPherson and T. C. Germann , “ Spatial adaptive sampling in multiscale simulation ” Comp. Phys. Comm. 185, 1857 (2014).

P. Cicotto, S. M. Mniszewski, L. Carrington, , “ An Evaluation of Threaded Models for a Classical MD Proxy Application, ” First International Workshop on Hardware-Software Co-Design for High Performance Computing (Co-HPC 2014).

R. S. Pavel, D. Roehm, C. Mitchell, C. Junghans, K. Barros, J. Mohd-Yusof, T. C. Germann and A. L. McPherson , “ Cloud+X: a Service-Based HPC Software Stack ”, submitted.

I. Laguna, D. F. Richards, T. Gamblin, M. Schulz, B. R. de Supinski, "Evaluating User-Level Fault Tolerance for MPI Applications", Proceedings of the 21st European MPI Users' Group Meeting (EuroMPI/ASIA), ACM, Kyoto, Japan, Sep 9-12, 2014.

Presentations

J. Mohd-Yusof, and N. Sakharnykh, “ Optimizing CoMD: A Molecular Dynamics Proxy Application Study ”, GPU Technology Conference 2014, San Jose, CA, March 2014, accepted for presentation

Allen McPherson, Christopher Mitchell, Kipton Barros, “Non-Traditional Approaches to Developing Multi-Scale Simulation Codes”, 16th SIAM Conference on Parallel Processing for Scientific Computing, Portland, Oregon, Feb. 18-21, 2014 [accepted]

M. Schulz and I. Laguna, “Evaluating the Impact of Faults and Recovery Mechanisms in Exascale Applications”, Mini-Symposium “ Toward Resilient Applications for Extreme-Scale Systems” at SIAM-PP 2014, Portland, OR, February 2014 accepted for presentation [external link]

[1/14/14] T. C. Germann, “ Semi‐coherent Ramblings on Future Computing and Co‐design”, New Computational Paradigms (New CoPa) Workshop, LANL, Los Alamos, NM, Jan. 14, 2014

[2/27/14] T. C. Germann, “Exploiting Asynchrony for Materials in Extreme Environments”, 19th Annual Mardi Gras Conference on Application Development for Exascale Computing, 27 February - 1 March 2014, Baton Rouge, LA

[3/5/14] T. C. Germann, “Integrating Simulation and Data for Materials in Extreme Environments”, American Physical Society (APS) March Meeting, 3-7 March 2014, Denver, CO

[3/18/14] T. C. Germann, “ExMatEx: Exascale Co-design Center for Materials in Extreme Environments”, SOS 18 Workshop, 17-20 March 2014, St. Moritz, Switzerland

[3/19/14] A. L. McPherson, “ExMatEx: Non-Traditional Approaches to HPC Software Development” SOS 18 Workshop, 17-20 March 2014, St. Moritz, Switzerland

[4/22/14] T. C. Germann, “Exploiting Asynchrony for Materials in Extreme Environments: Programming Models and Runtime Requirements”, The Salishan Conference on High-Speed Computing, 21-24 April 2014, Gleneden Beach, OR

[4/23/14] J. Belak, “Exascale Co-Design for Materials in Extreme Environments: Applications in Viscosity, Nucleation, and Kinetics”, Materials Research Society (MRS) Spring Meeting, 21-25 April 2014, San Francisco, CA

[4/24/14] T. C. Germann, “Exascale Co-Design for Materials in Extreme Environments”, Materials Research Society (MRS) Spring Meeting, 21-25 April 2014, San Francisco, CA

[5/7/14] T. C. Germann, “ExMatEx: Exascale Co-design Center for Materials in Extreme Environments”, National Science Foundation (NSF), Arlington, VA May 7, 2014

[5/27/14] J. Belak, “Exascale Co-Design for Materials in Extreme Environments”, Center for Hierarchical Materials Design, Northwestern University, Evanston, IL, May 27, 2014

[5/29/14] J. Belak, “DOE Co-design Center - X-Stack Post-docs”, X-Stack PI Meeting, 28-29 May 2014, Cambridge, MA

[6/9/14] J. Belak, “Exascale Co-Design for Materials in Extreme Environments”, UK Consortium for Computational Structural Mechanics, Oxford University, Oxford, UK, June 9, 2014

[6/12/14] J. Belak, “Exascale Co-Design for Materials in Extreme Environments”, Barcelona Supercomputer Center, Barcelona, Spain, May 12, 2014.

[7/4/14] T. C. Germann, “Exascale Co-design for Modeling Materials in Extreme Environments”, Laboratoire Univers et Théories;, l'Observatoire de Paris, Paris, France, July 4, 2014

[7/8/14] T. C. Germann, “Co-design of future computational materials science applications”, Commissariat à l'énergie; atomique (CEA-DIF) Workshop on modelling and simulation in material sciences, Bruyères-le-Ch;âtel;, France, July 8, 2014

[7/28/14] T. C. Germann, “Atomistic simulation studies of microstructural effects on the shock response of metals: bicrystals to exascale computing”, 10th ÍInternational Conference on New Models and Hydrocodes for Shock Wave Processes, 27 July - 1 Aug 2014, Pardubice, Czech Republic

[10/1/14] T. C. Germann, “Atomistic studies of material dynamics: from petascale to exascale”, Society of Engineering Science (SES) 51st Annual Technical Meeting, 1-3 Oct 2014, West Lafayette, IN

[10/2/14] J. Belak, “Preparing for the Future of Computing: Bridging Meso- and Continuum within the Exascale (KEYNOTE)”, Society of Engineering Science (SES) 51st Annual Technical Meeting, 1-3 Oct 2014, West Lafayette, IN

[10/21/14] J. Belak, “Exascale Co-Design Center for Materials in Extreme Environments (ExMatEx): Preparing for the Future of Computing”, Center for Computational Innovations, Computer Science Department, Rensselaer Polytechnic Institute, Troy, NY, Oct. 21, 2014.

[11/7/14] T. C. Germann, “Exascale Co-design for Materials in Extreme Environments”, Graduate Aerospace Laboratories of the California Institute of Technology (GALCIT) Colloquium, Pasadena, CA, Nov. 7, 2014.

[11/17/14] T. C. Germann, “Exascale Co-design for Materials in Extreme Environments (KEYNOTE)”, First International Workshop on Hardware-Software Co-Design for High Performance Computing (Co-HPC 2014), New Orleans, LA, Nov. 17, 2014.

[11/17/14] J. Belak, “The Exascale Materials Co-design Center and Lessons Learned from the 2014 LLNL Co-design Summer School (KEYNOTE)”, WOLFHPC: Fourth International Workshop on Domain-Specific Languages and High-Level Frameworks for High Performance Computing, New Orleans, LA Nov. 17, 2014.

[12/10/14] J. Belak, “Preparing for the Future of Computing: The Exascale Materials Co-design Center”, International Workshop on Dislocation Dynamics Simulations, 10-12 Dec 2014, Saclay, FRANCE

[12/19/14] J. Belak, “Preparing for the Future of Computing: The Exascale Materials Co-design Center”, Mechanical and Aerospace Engineering Department Seminar, UCLA, Los Angeles, CA, Dec. 19, 2014.

M. McKerns, “The failure of python object serialization”, PyCon Ireland, Dublin, IRL, October 2014.

M. McKerns, “The lack of reproducibility in statistical science, and how to fix it”, PyCon Ireland, Dublin, IRL, October 2014.

M. McKerns, “The failure of python object serialization”, PyCon UK, Coventry, GBR, September 2014.

M. McKerns, “The lack of reproducibility in statistical science, and how to fix it”, PyCon UK, Coventry, GBR, September 2014.

M. McKerns, “The failure of python object serialization”, the 7th European Conference on Python in Science, Cambridge, GBR, August 2014.

M. McKerns, “The failure of python object serialization”, the 13th Python in Science Conference, Austin, TX, July 2014.

M. McKerns, “Don’t be a lemming, statistically speaking”, the 13th Python in Science Conference, Austin, TX, July 2014.

M. McKerns, T. Sullivan, C. Scovel, H. Owhadi, “OUQ+mystic: a framework for uncertainty quantification and predictive science”, Information Science for Materials Discovery and Design Workshop, Santa Fe, NM, April 2014.

Software

M. McKerns, “The failure of python object serialization”, PyCon Ireland, Dublin, IRL, October 2014.

M. McKerns, “The lack of reproducibility in statistical science, and how to fix it”, PyCon Ireland, Dublin, IRL, October 2014.

M. McKerns, “The failure of python object serialization”, PyCon UK, Coventry, GBR, September 2014.

M. McKerns, “The lack of reproducibility in statistical science, and how to fix it”, PyCon UK, Coventry, GBR, September 2014.

M. McKerns, “The failure of python object serialization”, the 7th European Conference on Python in Science, Cambridge, GBR, August 2014.

M. McKerns, “The failure of python object serialization”, the 13th Python in Science Conference, Austin, TX, July 2014.

M. McKerns, “Don’t be a lemming, statistically speaking”, the 13th Python in Science Conference, Austin, TX, July 2014.

2013

Papers

R. A. Lebensohn, J. P. Escobedo, E. K. Cerreta, D. Dennis-Koller, C. A. Bronkhorst, and J. F. Bingert, “Modeling void growth in polycrystalline materials” Acta Materialia 61, 6918-6932 (2013) [external link]

M. Schulz, J. Belak, A. Bhatele, P.-T. Bremer, G. Bronevetsky, M. Casas, T. Gamblin, K. Isaacs, I. Laguna, J. Levine, V. Pascucci, D. Richards and B. Rountree, "Performance Analysis Techniques for the Exascale Co-Design Process", Proceedings of PARCO 2013, Munich, Germany, September 2013.

Patki, Tapysa, D. K. Lowenthal, B. Rountree, M. Schulz and B. R. de Supinski, “Exploring Hardware Overprovisioning in Power-Constrained, High Performance Computing”, Twenty Seventh International Conference on Supercomputing (ICS 2013), Eugene, Oregon, June 10–14, 2013. [external link]

I. Karlin, A. Bhatele, Jeff, Bradford L. Chamberlain, J. Cohen, Z. DeVito, R. Haque, D. Laney, E. Luke, F. Wang, D. Richards, M. Schulz and C. Still, “Exploring Traditional and Emerging Parallel Programming Models using a Proxy Application”, IPDPS 2013, Cambridge, MA, May 2013 (best paper, software track) [PDF]

B. Rountree, T. Gamblin, B. R. de Supinski, M. Schulz, D. K. Lowenthal, G. Cobb and H. Tufo, “Parallelizing heavyweight debugging tools with mpiecho”, Parallel Computing, Volume 39, Issue 3, March 2013, Pages 156-166, ISSN 0167-8191, http://dx.doi.org/10.1016/j.parco.2012.11.002 [external link]

Spafford, K., Vetter, J. S., Benson, T., & Parker, M., “Modeling synthetic aperture radar computation with Aspen”, International Journal of High Performance Computing Applications, 27(3), 255-262, 2013 [external link]

Z. DeVito, J. Hegarty, A. Aiken, P. Hanrahan, and J. Vitek, “Terra: a multi-stage language for high-performance computing”, 34th annual ACM SIGPLAN conference on Programming Language Design and Implementation (PLDI 2013), Seattle WA, June 16-22, 2013 [external link]

Presentations

Christopher Sewell, La-Ti Lo, James Ahrens, “Portable Data-Parallel Visualization and Analysis in Distributed Memory Environments”, IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV), Atlanta, Georgia, October 2013 (LA-UR-13-23809) [external link]

Christopher Sewell, “Analysis and Visualization Capabilities on Multi-core/Many-core Emerging Architectures”, NNSA - CEA Collaboration Meeting, Santa Fe, New Mexico, June 2013 (LA-UR-13-23729) [external link]

S. Mniszewski, and J. Mohd-Yusof, “CoDesign Molecular Dynamics (CoMD) Proxy Application”, PGI OpenACC WorkShop, Oct. 9-10, 2013 (LA-UR-13-27831)

J. Mohd-Yusof, “CoDesign Molecular Dynamics (CoMD) Overview”, ExMatEx All-Hands Meeting, March 12-14, 2013 Santa Ana Pueblo, New Mexico (LA-UR-13-21655)

C. Mitchell, A. McPherson, “Leveraging the Cloud for Materials Proxy Applications”, SIAM Conference on Computational Science and Engineering, Boston, MA, February 25–March 1, 2013, [external link]

I. Laguna, E. Leon, M. Schulz and M. Stephenson, “A Study of Application-Level Recovery Methods for Transient Network Faults”, Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems (ScalA) 2013, Denver, CO, November 2013

M. Schulz, J. Belak, G. Bronevetsky, I. Laguna, D. Richards, B. Rountree, “Emulating Exascale Conditions on Today’s Platforms”, ASCR Workshop on Modeling and Simulation, Seattle, WA, September 2013. File: attached

I. Laguna, M. Schulz, J. Keasler, D. Richards, J. Belak, “Optimal Placement of Retry-Based Fault Recovery Annotations in HPC Applications”, SC2013, Denver, Colorado, November, 2013.

M. Schulz, J. Belak, G. Bronevetsky, M. Casas, I. Laguna, D. Richards, B. Rountree, “Analyzing Future Exascale Platforms on Today's Machines”, Workshop on Extreme-Scale Programming Tools, Denver, CO, November 2013. File: attached

M. Schulz, “Performance Analysis Techniques for the Exascale Co-Design Process”, Invited Keynote Talk at ParCo 2013, Munich, Germany, September 2013 [external link]

C. D. Carothers, M. Mubarak, R. B. Ross, P. Carns, J. S. Vetter and J. S. Meredith, “Combining Aspen with Massively Parallel Simulation for Effective Exascale Co-Design”, DOE Workshop on Modeling and Simulation of Exascale Systems and Applications, 2013 [external link]

ExMatEx Team, “Presentations to Year 2 review committee”, Second annual ExMatEx project review, LLNL, December 4, 2013 [PDF] (LLNL-PRES-647492)

T. C. Germann, “Co-Design Centers in the US: Exascale Co-design for Materials in Extreme Environments”, International Workshop on CODESIGN (COllaborative DEvelopment of SImulation software of next GeNeration), Guilin CHINA, October 29-31, 2013 [external link]

T. C. Germann, “Integrating Simulation and Data for Materials in Extreme Environments”, 2013 Smoky Mountains Computational Sciences and Engineering Conference, Gatlinburg TN, September 3-5, 2013 [external link]

T. C. Germann, “Shock Response of Nanostructured Metals: Reconciling Large-Scale Molecular Dynamics Simulations and Experiments”, 7th International Conference on Materials for Advanced Technologies (ICMAT 2013), SINGAPORE, July 1-5, 2013

Reports

ExMatEx Team, “Exascale Co-Design Center for Materials in Extreme Environments (ExMatEx) Annual Report—Year 2”, Second annual ExMatEx project review, LLNL, December 4, 2013 [PDF, external link] (LA-UR-13-29322)

Software

“CoGL: Ginzburg-Landau Proxy Application, Version 1.0” (September 2013), [open source at GitHub]

“CoMD: Classical Molecular Dynamics Proxy Application, Version 1.1” (February 2013) [open source at GitHub , alternate entry point]

“VPFFT: Crystal Viscoplasticity Proxy Application Version 1.0” (February 14, 2013) [open source at GitHub]

“Terra: A low-level counterpart to Lua”, [open source at GitHub, see also terralang.org]

“Liszt: A DSL for solving mesh-based PDEs”, [older version of Liszt at liszt.stanford.edu]

“pyina: a MPI-based parallel mapper and launcher”, [open source at GitHub]

2012

Papers

Presentations

J. Mohd-Yusof, “CoDesign Molecular Dynamics (CoMD) Proxy App Deep Dive”, Exascale Research Conference, Oct. 1-3, 2012 Arlington, Virginia (LA-UR-12-25066)

J. Mohd-Yusof, “CoDesign Molecular Dynamics (CoMD) Proxy App”, ExMatEx All-Hands Meeting, May 30- June 1, 2012 Pacific Grove, California (LA-UR-12-21782)

Allen McPherson, Christopher Mitchell, James Ahrens, “Cloud+X: Exploring Asynchronous Concurrent Applications”, Los Alamos Unclassified Report. LA-UR-12-20511 (slides for LA-UR-12-10472), Presented at DoE Exascale Research Conference, Portland, Oregon, April 16-18, 2012 [PDF]

T. C. Germann, “Molecular Dynamics Studies of Material Dynamics: From Petascale to Exascale”, The 3rd Workshop on Computational and Statistical Physics (CSP3), Kyoto JAPAN, October 19-20, 2012

T. C. Germann, “Molecular Dynamics Studies of Material Dynamics: From Petascale to Exascale”, Conference on Computational Physics (CCP2012), Kobe JAPAN, October 14-18, 2012

Reports

A. McPherson, C. Mitchell, J. Ahrens, “Cloud+X: Exploring Asynchronous Concurrent Applications”, Los Alamos Unclassified Report. LA-UR-12-10472, 2012 [PDF]

Software

“CoMD: Classical Molecular Dynamics Proxy Application, Version 1.0”