NERSCPowering Scientific Discovery Since 1974

Alice Koniges

Alice Evelyn Koniges , Ph.D.
National Energy Research Scientific Computing Center
Maui High Performance Computing Center
550 Lipoa Pkwy # 100
Kihei, HI 96753 US

Biographical Sketch

Alice Koniges is a NERSC affiliate and alumnus of the Application Performance Group at NERSC/Berkeley Lab and is currently at the University of Hawaii where she works on emerging architectures, programming models and applications.

Soon after she became the first woman ever to earn a PhD in Applied and Computational Mathematics at Princeton University, Alice Koniges joined NERSC in 1984 while it was still at Lawrence Livermore Lab. She achieved the first successful parallel code run on the four-processor Cray-2. She began her career researching parallel computing and plasma physics, focusing on the combination of these two fields. Her expertise in the transition from vector to parallel computing culminated in her textbook Industrial Strength Parallel Computing, published by Morgan Kaufmann Publishers in January 2000. Alice re-joined NERSC at the Berkeley Lab in 2009.

Alice's research interests include exascale computing challenges, benchmarking and performance optimization of application codes, development of Adaptive Mesh Refinement (AMR) and Arbitrary Lagrangian Eulerian (ALE) algorithms for time-dependent PDE's, and application supercomputing in plasma physics, laser physics, and energy research. She regularly gives tutorials and short courses on programming models. She served as Principal Investigator of the Computational Science and Engineering Petascale Initiative  which brought the first post-doc program to NERSC.

Previous to joining the Berkeley Lab, she held various positions at the Lawrence Livermore National Laboratory, including management of the Lab's institutional computing. She also led the effort to develop a new 3D multiscale multiphysics code (ALE-AMR) that is used to predict the impacts of target shrapnel and debris on the operation of the National Ignition Facility (NIF) the world's most powerful laser, and model Warm Dense Matter (WDM) experiments at the NDCX facility at LBNL. From 1995 to 1997, Alice led the Parallel Applications Technology Program at LLNL. This was the LLNL portion of the largest (12 million) CRADA (Cooperative Research and Development Agreement) ever undertaken by the Department of Energy. She spent 1998 at the Max-Planck Institute in Garching, Germany (Computer Center and Plasma Physics Institute), where she was a consultant to users at the Institute, assisting in the conversion of applications codes for parallel computers. In addition to her PhD she also holds MSE and MA degrees from Princeton, and a BA from the University of California, San Diego and has published more than 100 refereed technical papers. 

Selected Recent Publications and Presentations

Journal Articles

Thomas Heller, Bryce Adelstein Lelbach, Kevin A. Huck, John Biddiscombe, Patricia Grubel, Alice E. Koniges, Matthias Kretz, Dominic Marcello, David Pfander, Adrian SerioL, Juhan Frank, Geoffrey C. Clayton, Dirk Pflu ̈ger, David Eder, and Hartmut Kaiser, "Harnessing Billions of Tasks for a Scalable Portable Hydrodynamic Simulation of the Merger of Two Stars", The International Journal of High Performance Computing Applications, 2018, Accepted,

Yun (Helen) He, Brandon Cook, Jack Deslippe, Brian Friesen, Richard Gerber, Rebecca Hartman­-Baker, Alice Koniges, Thorsten Kurth, Stephen Leak, Woo­Sun Yang, Zhengji Zhao, Eddie Baron, Peter Hauschildt, "Preparing NERSC users for Cori, a Cray XC40 system with Intel Many Integrated Cores", Concurrency and Computation: Practice and Experience, August 2017, 30, doi: 10.1002/cpe.4291

The newest NERSC supercomputer Cori is a Cray XC40 system consisting of 2,388 Intel Xeon Haswell nodes and 9,688 Intel Xeon‐Phi “Knights Landing” (KNL) nodes. Compared to the Xeon‐based clusters NERSC users are familiar with, optimal performance on Cori requires consideration of KNL mode settings; process, thread, and memory affinity; fine‐grain parallelization; vectorization; and use of the high‐bandwidth MCDRAM memory. This paper describes our efforts preparing NERSC users for KNL through the NERSC Exascale Science Application Program, Web documentation, and user training. We discuss how we configured the Cori system for usability and productivity, addressing programming concerns, batch system configurations, and default KNL cluster and memory modes. System usage data, job completion analysis, programming and running jobs issues, and a few successful user stories on KNL are presented.

Zhaoyi Meng, Ekaterina Merkurjev, Alice Koniges, Andrea L. Bertozzi, "Hyperspectral Image Classification Using Graph Clustering Methods", IPOL Journal · Image Processing On Line, 2017, 2017-08-, doi:

Wangyi Liu, Alice Koniges, Kevin Gott, David Eder, John Barnard, Alex Friedman, Nathan Masters, Aaron Fisher, "Surface tension models for a multi-material ALE code with AMR", Computers & Fluids, January 2017, doi:

A.C. Fisher, D.S. Bailey, T.B. Kaiser, D.C. Eder, B.T.N. Gunney, N.D.
Masters, A.E. Koniges, R.W. Anderson,
"An AMR Capable Finite Element Diffusion Solver for ALE Hydrocodes", Plasma Science and Technology 17, No. 2, 109-116, 2015, doi: 10.1088/1009-0630/17/2/04

Alice Koniges, Nathan Masters, Aaron Fisher, David Eder, Wangyi Liu, Robert Anderson, David Benson,
and Andrea Bertozzi,
"Multi-Material ALE with AMR for Modeling Hot Plasmas and Cold Fragmenting Materials", Plasma Science and Technology 17, No. 2, 117-128, 2015, doi: 10.1088/1009-0630/17/2/05

J.N. Brooks, A. Hassanein, A. Koniges, P.S. Krstic, T.D. Rognlien, T. Sizyuk, V. Sizyuk, and D. P. Stotler, "Scientific and Computational Challenges in Coupled Plasma Edge/Plasma-Material Interactions for Fusion Tokamaks", Contrib. Plasma Phys. 54, No. 4-6, 329 – 340, 2014, doi: 10.1002/ctpp.201410014

Alice Koniges, Wangyi Liu, Steven Lidia, Thomas Schenkel, John Barnard, Alex Friedman, David Eder, Aaron Fisher, and Nathan Masters, "Advanced Target Effects Modeling for Ion Accelerators and other High-Energy-Density Experiments", The Eighth International Conference on Inertial Fusion Sciences and Application (in review), 2014,

JJ Barnard, RM More, M Terry, A Friedman, E Henestroza, A Koniges, JW Kwan, A Ng, PA Ni, W Liu, BG Logan, E Startsev, A Yuen, "NDCX-II target experiments and simulations", Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment Volume 733, January 2014,

Alice Koniges, Wangyi Liu, John Barnard, Alex Friedman, Grant Logan, David Eder, Aaron Fisher, Nathan Masters, and Andrea Bertozzi, "Modeling warm dense matter experiments using the 3D ALE-AMR code and the move toward exascale computing", EPJ Web of Conferences 59, 09006, 2013,

D. Eder, D. Bailey, F. Chambers, I. Darnell, P. Di Nicola, S. Dixit, A. Fisher, G.Gururangan, D. Kalantar, A. Koniges, W. Liu, M. Marinak, N. Masters, V. Mlaker, R. Prasad, S. Sepke, P. Whitman, "Observations and modeling of debris and shrapnel impacts on optics and diagnostics at the National Ignition Facility", EPJ Web of Conferences 59, 08010, 2013,

D.C. Eder, A.C. Fisher, A.E. Koniges and N.D. Masters, "Modelling debris and shrapnel generation in inertial confinement fusion experiments", Nuclear Fusion 53 113037, 2013, doi: 10.1088/0029-5515/53/11/113037

Modelling and mitigation of damage are crucial for safe and economical operation of high-power laser facilities. Experiments at the National Ignition Facility use a variety of targets with a range of laser energies spanning more than two orders of magnitude (~14 kJ to ~1.9 MJ). Low-energy inertial confinement fusion experiments are used to study early-time x-ray load symmetry on the capsule, shock timing, and other physics issues. For these experiments, a significant portion of the target is not completely vaporized and late-time (hundreds of ns) simulations are required to study the generation of debris and shrapnel from these targets. Damage to optics and diagnostics from shrapnel is a major concern for low-energy experiments. We provide the first full-target simulations of entire cryogenic targets, including the Al thermal mechanical package and Si cooling rings. We use a 3D multi-physics multi-material hydrodynamics code, ALE-AMR, for these late-time simulations. The mass, velocity, and spatial distribution of shrapnel are calculated for three experiments with laser energies ranging from 14 to 250 kJ. We calculate damage risk to optics and diagnostics for these three experiments. For the lowest energy re-emit experiment, we provide a detailed analysis of the effects of shrapnel impacts on optics and diagnostics and compare with observations of damage sites.

David E. Keyes, Lois Curfman McInnes, Carol Woodward, William Gropp, Eric Myra, Michael Pernice,
John Bell, Jed Brown, Alain Clo, Jeffrey Connors, Emil Constantinescu, Don Estep, Kate Evans,
Charbel Farhat, Ammar Hakim, Glenn Hammond, Glen Hansen, Judith Hill, Tobin Isaac, Xiaomin Jiao, Kirk Jordan,
Dinesh Kaushik, Efthimios Kaxiras, Alice Koniges, et al.,
"Multiphysics Simulations Challenges and Opportunities", International Journal of High Performance Computing Applications, February 2013, 27:4--83,

Xuefei Yuan, Xiaoye S Li, Ichitaro Yamazaki, Stephen C Jardin, Alice E Koniges, David E Keyes, "Application of PDSLin to the magnetic reconnection problem", Computational Science & Discovery, 2013, 6:014002,

AE Koniges, ND Masters, AC Fisher, RW Anderson, DC Eder, TB Kaiser, DS Bailey, B Gunney, P Wang, B Brown, K Fisher, F Hansen, BR Maddox, DJ Benson, M Meyers, A Geille, "ALE-AMR: A new 3D multi-physics code for modeling laser/target effects", Journal of Physics: Conference Series, 2010, 244:032019,


Gabriele Jost, Alice Koniges, "Special Issue: Exploring languages for expressing medium to massive on-chip parallelism", Scientific Programming, 2010, 18:125--126,

N. Masters, T.B. Kaiser, R.W. Anderson, D.C. Eder, A.C. Fisher, A.E. Koniges, "Laser Ray Tracing in a Parallel Arbitrary Lagrangian Eulerian Adaptive Mesh Refinement Hydrocode", J. Physics, Conf. Ser. 244: 032022, 2010,

AC Fisher, DS Bailey, TB Kaiser, BTN Gunney, ND Masters, AE Koniges, DC Eder, RW Anderson, "Modeling heat conduction and radiation transport with the diffusion equation in NIF ALE-AMR", Journal of Physics: Conference Series, 2010, 244:022075,

Hongzhang Shan, Filip Blagojevic, Seung-Jai Min, Paul Hargrove, Haoqiang Jin, Karl Fuerlinger, Alice Koniges, Nicholas J Wright, "A programming model performance study using the NAS parallel benchmarks", Scientific Programming, 2010, 18:153--167,

Robert Preissl, Alice Koniges, Stephan Ethier, Weixing Wang, Nathan Wichmann, "Overlapping communication with computation using OpenMP tasks on the GTS magnetic fusion code", Scientific Programming, 2010, 18:139--151, doi: 10.3233/SPR-2010-0311

D. C. Eder, R. W. Anderson, D. S. Bailey, P. Bell, D. J. Benson, A. L. Bertozzi, W. Bittle, D, Bradley, C. G. Brown, T. J. Clancy, H. Chen, J. M. Chevalier, P. Combis, L. Dauffy, C. S. Debonnel, M. J. Eckart, A. C. Fisher, A. Geille, V. Y. Glebov, J. Holder, J. P. Jadaud, O. Jones, T. B. Kaiser, D. Kalantar, H. Khater, J. Kimbrough, A. E. Koniges, O. L. Landen, B. J. MacGowan, N. D. Masters, A. MacPhee, B. R. Maddox, M. Meyers, S. Osher, R. Prasad, D. Raffestin, J. Raimbourg, V. Rekow, C. Sangster, P. Song, C. Stoeckl, M. L. Stowell, J. M. Teran, A. Throop, R. Tommasini, J. Vierne, D. White, P. Whitman, "Assessment and Mitigation of Radiation, EMP, Debris and Shrapnel Impacts at Mega-Joule Class Laser Facilities", J. Physics, Conference Series, 2010, 244:0320018,

Subhash Saini, Robert Ciotti, Brian TN Gunney, Thomas E Spelce, Alice Koniges, Don Dossa, Panagiotis Adamidis, Rolf Rabenseifner, Sunil R Tiyyagura, Matthias Mueller, "Performance evaluation of supercomputers using hpcc and imb benchmarks", Journal of Computer and System Sciences, 2008, 74:965--982,

Alice E Koniges, Brian TN Gunney, Robert W Anderson, Aaron C Fisher, Nathan D Masters, "Development Strategies for Modern Predictive Simulation Codes", Advances in Parallel Computing, 2008, 15:697--704,

DC Eder, AE Koniges, OL Landen, ND Masters, AC Fisher, OS Jones, TI Suratwala, LJ Suter, "Debris and shrapnel mitigation procedure for NIF experiments", Journal of Physics: Conference Series, 2008, 112:032023,

ND Masters, RW Anderson, NS Elliott, AC Fisher, BT Gunney, AE Koniges, "Interface reconstruction in two-and three-dimensional arbitrary Lagrangian-Eulerian adaptive mesh refinement simulations", Journal of Physics: Conference Series, 2008, 112:022017,

AC Fisher, ND Masters, P Dixit, DJ Benson, AE Koniges, RW Anderson, BTN Gunney, P Wang, R Becker, "Hierarchical material models for fragmentation modeling in NIF-ALE-AMR", Journal of Physics: Conference Series, 2008, 112:022027,

AE Koniges, C. Debonnel, J. Andrew, D. Eder, D. Kalantar, N. Masters, A. Fisher, R. Anderson, B. Gunney, B. Brown, K. Sain, F. Bonneau, J-L. Bourgade, J-M .Chevalier, P. Combis, A. Geille, J-P. Jadaud, R. Maroni, D. Raffestin, J-L. Ulmer, J. Vierne, M. Tobin, M. Meyers, H. Jarmakani, "Experiments for the validation of debris and shrapnel calculations", Journal of Physics: Conference Series, 2008, 112:032072,

Conference Papers

Yun (Helen) He, Brandon Cook, Jack Deslippe, Brian Friesen, Richard Gerber, Rebecca Hartman­-Baker, Alice Koniges, Thorsten Kurth, Stephen Leak, Woo­Sun Yang, Zhengji Zhao, Eddie Baron, Peter Hauschildt, "Preparing NERSC users for Cori, a Cray XC40 system with Intel Many Integrated Cores", Cray User Group 2017, Redmond, WA. Best Paper First Runner-Up., May 12, 2017,

Alice Koniges, Brandon Cook, Jack Deslippe, Thorston Kurth, Hongzhang Shan, "MPI usage at NERSC: Present and Future", EuroMPI 2016, Edinburgh, Scotland, UK, September 26, 2016,

Zhaoyi Meng, Alice Koniges, Yun (Helen) He, Samuel Williams, Thorsten Kurth, Brandon Cook, Jack Deslippe, Andrea L. Bertozzi, "OpenMP Parallelization and Optimization of Graph-Based Machine Learning Algorithms", Lecture Notes in Computer Science, Springer, 2016, 9903:17-31, doi: 10.1007/978-3-319-45550-1_2

Michael A. Purvis, Alexander Schafgans, Daniel J. W. Brown, Igor Fomenkov, Rob Rafac, Josh Brown, Yezheng Tao, Slava Rokitski, Mathew Abraham, Mike Vargas, Spencer Rich, Ted Taylor, David Brandt, Alberto Pirati, Aaron Fisher, Howard Scott, Alice Koniges, David Eder, Scott Wilks, Anthony Link, Steven Langer, "Advancements in predictive plasma formation modeling", Proc. SPIE 9776, Extreme Ultraviolet (EUV) Lithography VII, 97760K (March 18, 2016); doi:10.1117/12.2221991, March 18, 2016,

This modeling is performed to advance the rate of learning about optimal EUV generation for laser produced plasmas and to provide insights where experimental results are not currently available. The goal is to identify key physical processes necessary for an accurate and predictive model capable of simulating a wide range of conditions. This modeling will help to drive source performance scaling in support of the EUV Lithography roadmap. The model simulates pre-pulse laser interaction with the tin droplet and follows the droplet expansion into the main pulse target zone. Next, the interaction of the expanded droplet with the main laser pulse is simulated. We demonstrate the predictive nature of the code and provide comparison with experimental results. ALE-AMR and other codes are used for the modeling.

Alice Koniges, Shreyas Cholia, Prabhat, Yushu Yao, "Data and Workflow Solutions for Fusion using NERSC", DOE FES/ASCR Workshop on Integrated Simulations for Magnetic Fusion Energy Sciences, June 2, 2015,

Jean-Luc Vay, Leroy Anthony Drummond, Alice Koniges, Brendan Godfrey, Irving Haber, "Scalable Arbitrary-Order Pseudo-Spectral Electromagnetic Solver", SC14, November 17, 2014,

Jean-Luc Vay, Cameron G. R. Geddes, Alice Koniges, Alex Friedman, David P. Grote, David L. Bruhwiler, John P. Verboncoeur, "White Paper on DOE-HEP Accelerator Modeling Science Activities", originally presented at the US Department of Energy workshop: Community Summer Study, October 1, 2013,

Alice Koniges, Jean-Luc Vay, Alex Friedman,Hartmut Kaiser, and Thomas Sterling, "Position Paper: Consideration of Asynchronous Algorithms for Particle-Grid Simulations", 2013,

Thomas Ludwig, Costas Bekas, Alice Koniges, Kengo Nakajima, "Topic 15: High Performance and Scientific Applications", Euro-Par 2012 Parallel Processing, Springer, 2012, Lecture:779--780,

Jihan Kim, Alice Koniges, Richard Martin, Maciej Harancyzk, Joseph Swisher, Berend Smit, "GPU Computational Screening of Carbon Capture Materials - Paper", Proceedings of the 2011 SciDAC Conference, 2011,

Wangyi Liu, John Barnard, Alex Friedman, Nathan Masters, Aaron Fisher, Velemir Mlaker,
Alice Koniges, David Eder,
"Modeling droplet breakup effects in warm dense matter experiments with diffuse interface methods in the ALE-AMR code", Proceedings of the 2011 SciDAC Conference, August 4, 2011,

W. M. Sharp, A. Friedman, D. P. Grote, J. J. Barnard, R. H. Cohen, M. A. Dorf, S. M. Lund, L. J. Perkins, M. R. Terry, B. G. Logan, F. M. Bieniosek, A. Faltens, E. Henestroza, J.-Y. Jung, J. W. Kwan, , A. E. Koniges, E. P. Lee, S. M. Lidia, P. A. Ni, L. L. Reginato, P. K. Roy, P. A. Seidl, J. H. Takakuwa, J.-L. Vay, W. L. Waldron, R. C. Davidson, E. P. Gilson, I. D. Kaganovich, H. Qin, E. Startsev, I. Haber, R. A. Kishek, "Inertial Fusion Driven By Intense Heavy-Ion Beams", Proceedings of 2011 Particle Accelerator Conference, New York, NY, USA, March 2011, 1386-1393,

Robert Preissl, Wichmann, Long, Shalf, Ethier, Alice E. Koniges, "Multithreaded global address space communication techniques for gyrokinetic fusion applications on ultra-scale platforms", SC, 2011, 15,

Praveen Narayanan, Alice Koniges, Leonid Oliker, Robert Preissl, Samuel Williams, Nicholas J Wright, Maxim Umansky, Xueqiao Xu, Benjamin Dudson, Stephane Ethier, Weixing Wang, Jeff Candy, John R. Cary, "Performance Characterization for Fusion Co-design Applications", Proceedings of CUG, 2011,

Alice Koniges, Robert Preissl, Jihan Kim, D Eder, A Fisher, N Masters, V Mlaker, S Ethier, W Wang, M Head-Gordon, N Wichmann, "Application acceleration on current and future Cray platforms,", Proc. Cray User Group Meeting, Edinburgh, Scotland, May 2010,

Hongzhang Shan, Haoqiang Jin, Karl Fuerlinger, Alice Koniges, Nicholas J Wright, "Analyzing the effect of different programming models upon performance and memory usage on cray xt5 platforms", CUG2010, Edinburgh, Scotland, 2010,

MA Meyers, H Jarmakani, BY Cao, CT Wei, B Kad, BA Remington, EM Bringa, B Maddox, D Kalantar, D Eder, A Koniges, "Laser compression and fragmentation of metals", DYMAT 2009-9th International Conference on the Mechanical and Physical Behaviour of Materials under Dynamic Loading, 2009, 2:999--1006,


Timothy G. Mattson, Yun (Helen) He, Alice E. Koniges, The OpenMP Common Core: Making OpenMP Simple Again, Book: Scientific and Engineering Computation Series, edited by William Gropp, Ewing Lusk, (The MPI Press: November 19, 2019) Pages: 320 pp

How to become a parallel programmer by learning the twenty-one essential components of OpenMP.

Book Chapters

Gabriele Jost, Alice Koniges, "Hardware Trends and Implications for Programming Models", Handbook of Research on Computational Science and Engineering: Theory and Practice, ( 2012) Pages: 1-21 doi: 10.4018/978-1-61350-116-0.ch001


Tim Mattson, Alice Koniges, Yun (Helen) He, David Eder, The OpenMP Common Core: A hands-on exploration, SuperComputing 2018 Tutorial, November 11, 2018,

Alice Kong's, Yun (Helen) He, OpenMP Common Core, NERSC Training, February 6, 2018,

Tim Mattson, Alice Koniges, Yun (Helen) He, Barbara Chapman, The OpenMP Common Core: A hands-on exploration, SuperComputing 2017 Tutorial, November 12, 2017,

Barbara Chapman, Alice Koniges, Yun (Helen) He, Oscar Hernandez, and Deepak Eachempati, OpenMP, An Introduction, Scaling to Petascale Institute, XSEDE Training, Berkeley, CA., June 27, 2017,

Tim Mattson, Alice Koniges, Clay Breshears, Programming Irregular Applications with OpenMP: A Hands-On Introduction, SC16 Tutorial, November 14, 2016,

Zhaoyi Meng, Alice Koniges, Yun (Helen) He, Samuel Williams, Thorsten Kurth, Brandon Cook, Jack Deslippe, Andrea L. Bertozzi, OpenMP Parallelization and Optimization of Graph-based Machine Learning Algorithms, IWOMP 2016, October 6, 2016,

Alice Koniges, Brandon Cook, Jack Deslippe, Thorston Kurth, Hongzhang Shan, MPI usage at NERSC: Present and Future, EuroMPI 2016, September 26, 2016,

Alice Koniges, Research on the Path to Exascale at NERSC, Sustainable Research Pathways Workshop, December 8, 2015,

Tim Mattson, Alice Koniges, Simon McIntosh-Smith, Portable Programs for Heterogeneous Computing: A Hands-On Introduction, Tutorial, SC15, November 16, 2015,

Hartmut Kaiser, Steven Brandt, Alice Koniges, Thomas Heller, Sameer Shende, Bryce Lelbach, Massivley Parallel Task-Based Programming with HPX, Tutorial, SC15, November 15, 2015,

Yun (Helen) He, Alice Koniges, Richard Gerber, Katie Antypas, Using OpenMP at NERSC, OpenMPCon 2015, invited talk, September 30, 2015,

Alice Koniges, Tim Mattson, Yun (Helen) He, Richard Gerber, Enabling Application Portability across HPC Platforms: An Application Perspective, OpenMPCon 2015, invited talk, September 29, 2015,

J.-L. Vay, E. Esarey, A. Koniges, J. Barnard, A. Friedman, D. Grote, Predictive Community Computational Tools for Virtual Plasma Science Experiments, Frontiers of Plasma Science Workshops - Town Hall, June 30, 2015,

Alice Koniges, Research Careers in Government Laboratories, Latinos in the Mathematical Sciences Conference, invited talk, April 8, 2015,

J.L. Vay, T. Drummond, A. Koniges, B. Loring, C. Mitchell, J. Qiang, O. Ruebel, R. Ryne, H. Vincent, D. P. Grote, A. Hübl, Advanced Modeling of Particle Accelerators, NERSC Exascale Science Application Program Meeting, December 4, 2014,

Tim Mattson, Alice Koniges, Simon McIntosh-Smith, OpenCL: A Hands-on Introduction, SC14 Tutorial, November 17, 2014,

Alice Koniges, Enabling Physics Insight with Multidimensional Computer Simulations, SC14 Broader Engagement Program, November 16, 2014,

Alice Koniges, Invited Career Seminar, UC Berkeley: Women in Mathematics, October 21, 2014,

Alice Koniges, Applications on HPX: a new runtime for exascale / Summary of recent DOE Exascale Meetings, NERSC Brown Bag, June 13, 2014,

Alice Koniges, APPS on HPX, US Department of Energy, Exascale Software Stack, PI Meeting, Boston MA, May 27-28, 2014,

Alice Koniges, Multimaterial Multiphysics Modeling of Complex Experimental Configurations, LBNL Center for Beam Physics Seminar Series, February 14, 2014,

Pavan Balaji, Alice Koniges, Robert Harrison, Tim Mattson, Nick Wright, David Bernholdt, Application Grand Challenges in the Heterogeneous Accelerator Era, SC13 Birds of a Feather: Invited Panelist, November 21, 2013,

Accelerators have gained prominence as the next disruptive technology with a potential to provide a non-incremental jump in performance. However, the number of applications that have actually moved to accelerators is still limited because of many reasons, arguably the biggest of which is the gap in understanding between accelerator and application developers. This BoF is an application oriented session that aims to bring the two camps of application developers and accelerator developers head-to-head.

Tim Mattson, Alice Koniges, Simon McIntosh-Smith, OpenCL: A Hands-On Introduction, SC13 Tutorial, November 18, 2013,

OpenCL is an open standard for programming heterogeneous parallel computers composed of CPUs, GPUs and other processors. OpenCL consists of a framework to manipulate the host CPU and one or more compute devices (CPUs, GPUs or accelerators), and a C-based programming language for writing programs for the compute devices. Using OpenCL, a programmer can write parallel programs that harness all of the resources of a heterogeneous computer. In this hands-on tutorial, we will introduce OpenCL. For ease of learning we will focus on the easier to use C++ API, but attendees will also gain an understanding of OpenCLs C API. The format will be a 50/50 split between lectures and exercises. Students will use their own laptops (Windows, Linux or OS/X) and log into a remote server running an OpenCL platform on a range of different processors. Alternatively, students can load OpenCL onto their own laptops prior to the course (Intel, AMD and NVIDIA provide OpenCL SDKs. Apple laptops with X-code include OpenCL by default). By the end of the course, attendees will be able to write and optimize OpenCL programs, and will have a collection of example codes to help with future OpenCL program development.

A. Koniges, W. Lui, Y. He, D. Eder, A. Fisher, N. Masters, and R. W. Anderson, Multi-Material Plasma Modeling on HPC Platforms, Invited: 23rd International Conference on Numerical Simulation of Plasmas Beijing, China, September 13, 2013,

A. Koniges, W. Lui, S. Lidia, T. Schenkel, J. Barnard, A. Friedman, D. Eder, A. Fisher, and N. Masters, Advanced Target Effects Modeling for Ion Accelerators and other High-Energy-Density Experiments, 8th International Conference on Inertial Fusion Sciences and Applications, Nara, Japan, September 10, 2013,

Alice Koniges, Jean-Luc Vay, Alex Friedman, Hartmut Kaiser, and Thomas Sterling, Invited Talk: Consideration of Asynchronous Algorithms for Particle-Grid Simulations, DOE Workshop on Applied Mathematics Research for Exascale Computing, Washington DC, August 21-22,, 2013,

Alice Koniges, Praveen Narayanan, Robert Preissl, Xuefei Yuan, Proxy Design and Optimization in Fusion and Accelerator Physics, SIAM Conference on Computational Science and Engineering, February 25, 2013,

J. Barnard, R. M. More, P. A. Ni, A. Friedman, E. Henestroza, I. Kaganovich, A. Koniges, J. W. Kwan, W. Liu, A. Ng,
B.G. Logan, E. Startsev, M. Terry, A. Yuen,
NDCX-II Experimental Plans and Target Simulations, West Coast High Energy Density Science Cooperative Meeting Berkeley and Palo Alto, California, January 2013,

Alice Koniges, Katherine Yelick, Rolf Rabenseifner, Reinhold Bader, David Eder, Filip Blagojevic, Robert Preissl, Paul Hargrove, Introduction to PGAS (UPC and CAF) and Hybrid for Multicore Programming, SC12 Full Day Tutorial, November 2012,

Michael A. Heroux, Alice E. Koniges, David F. Richards, Richard F. Barrett, Thomas Brunner, Using Application Proxies for Co-design of Future HPC Computer Systems and Applications, SC12 Full Day Tutorial, November 2012,

Alice Koniges, Opportunities and Challenges for Domain-Specific Languages in Fusion Applications, ASCR Exascale PI Meeting, October 2012,

Alice Koniges, Mike Heroux, Using Application Proxies for Co-design of Future HPC Computer Systems and Applications, Dagstuhl Co-design Workshop, May 22, 2012,

J. Kim, A. Koniges, R.L. Martin, J. Swisher, M. Haranczyk, B. Smit, Computational Screening of Novel Carbon Capture Materials, 2012 GTC GPU Conference, 2012,

Cherri M. Pancake, Debra Goldfarb, Alice Koniges, Candy Culhane, The View, HPC Edition, SC11 Panel, November 2011,

This panel will be a take-off on ABC's popular morning talk program. A lively format will be used to cover a number of controversial topics in the development and application of HPC. Four women from the HPC world will serve as "co-hosts," discussing topics with international experts associated with specific topics, such as Jean-Yves Berthou (European Exascale Software Initiative), Dave Turek (IBM), Ryan Waite (Microsoft), and Matt Fetes (venture capitalist). The goal is to air a variety of viewpoints in a lively and entertaining way. The panel will raise thought-provoking questions such as why the HPC community has such a hard time converging on standards, whether co-design is really affordable at HPC scales, why efficiency isn't our goal rather than scalability, whether exascale investments can really pay off, and why high-level languages haven't had real impact in HPC. Interactive polling will be used to involve the audience in charting a course for HPC's future - so be sure to bring your laptop or smartphone.

David Eder, David Bailey, Andrea Bertozzi, Aaron Fisher, Alice Koniges, Wangyi Liu, Nathan Masters, Marty Marniak, Late-Time Numerical Simulations of High-Energy-Density (HED) Targets, Twenty Second International Conference on Numerical Simulations of Plasmas, September 7, 2011,

Alice Koniges, Multiphysics Simulations: Challenges and Opportunities -- Insertion Paths, Panel - Institute for Computing in Science, Workshop, August 2011,

Alice Koniges, Challenges and Application Gems on the Path to Exascale, ASCR Programming Challenges Workshop, July 2011,

Alice Koniges, Robert Preissl, Stephan Ethier, John Shalf, What’s Ahead for Fusion Computing?, International Sherwood Fusion Theory Conference, April 2010,

Tim Frazier, Alice Koniges, The National Ignition Facility Data Requirements, SC08 BOF: Computing with Massive and Persistent Data, 2008,


Alice Koniges, "The Petascale Initiative in Computational Science and Engineering", Final Report, October 31, 2013,

A. Friedman, R. H. Cohen, D. P. Grote, W. M. Sharp, I. D. Kaganovich, A. E. Koniges, W. Liu, "Heavy Ion Beams and Interactions with Plasmas and Targets (HEDLP and IFE)", NERSC FES Requirements Workshop: Heavy Ion Fusion and Non-Neutral Plasmas, March 2013,

Saman Amarasinghe, Mary Hall, Richard Lethin, Keshav Pingali, Dan Quinlan, Vivek Sarkar, John Shalf, Robert Lucas, Katherine Yelick, Pavan Balaji, Pedro C. Diniz, Alice Koniges, Marc Snir, Sonia R. Sachs, "Exascale Programming Challenges", 2011,

CH Still, A Arsenlis, RB Bond, MJ Steinkamp, S Swaminarayan, DE Womble, AE Koniges, JR Harrison, JH Chen, "NNSA ASC Exascale Environment Planning, Applications Working Group, Report February 2011", 2011,

A. E. Koniges, N. D. Masters, A. C. Fisher, R. W. Anderson, D. C. Eder, D. Benson, T. B. Kaiser, B. T. Gunney, P. Wang, B. R. Maddox, J. F. Hansen, D. H. Kalantar, P. Dixit, H. Jarmakani, M. A. Meyers, "A Predictive Model of Fragmentation using Adaptive Mesh Refinement and a Hierarchical Material Model", LLNL-TR-411072, March 5, 2009, doi: 10.2172/950085


Alice Koniges, Brandon Cook, Jack Deslippe, Thorston Kurth, Hongzhang Shan, "MPI usage at NERSC: Present and Future", EuroMPI 2016, September 26, 2016,

Jeremy Kemp, Alice Koniges, Yun (Helen) He, and Barbara Chapman, "Advanced Programming Model Constructs Using Tasking on the Latest NERSC (Knights Landing) Hardware", CS Summer Student Poster Session, August 4, 2016,

Ahana Roy Choudhury, Yun (Helen) He, and Alice Koniges, "Advanced OpenMP Constructs, Tuning, and Tools at NERSC", CS Summer Student Poster Session, August 4, 2016,

Nigel Tan, Mathieu Lobet, Alice Koniges, Henri Vicenti, Dong Li, Jean-Luc Vay, "Improving Cache Performance in PICSAR’s Maxwell’s Equations Solver through Field Tiling", SC Summer Student Poster Session, August 4, 2016,

Alice Koniges, Jayashree Ajay Candadai, Hartmut Kaiser, Kevin Huck, Jeremy Kemp, Thomas Heller, Matthew Anderson, Andrew Lumsdaine, Adrian Serio, Michael Wolf, Bryce Adelstein Lelbach, Ron Brightwell, Thomas Sterling, "HPX Applications and Performance Adaptation", SC15, 2015,

Jean-Luc Vay, Leroy Anthony Drummond, Alice Koniges, Brendan Godfrey, Irving Haber, "Scalable Arbitrary-Order Pseudo-Spectral Electromagnetic Solver", SC14, November 17, 2014,

Alice Koniges, David Eder, Aaron Fisher, Wangyi Lui, Nathan Masters, John Barnard, "Multi-Physics Plasma Modeling for a Range of Applications on HPC Platforms", 41st EPS Conference on Plasma Physics, June 23, 2014,

A. Koniges, R. Gerber, D. Skinner, Y. Yao, Y. He, D. Grote, J-L Vay, H. Kaiser, and T. Sterling, "Plasma Physics Simulations on Next Generation Platforms", 55th Annual Meeting of the APS Division of Plasma Physics, Volume 58, Number 16, November 11, 2013,

The current high-performance computing revolution provides opportunity for major increases in computational power over the next several years, if it can be harnessed. This transition from simply increasing the single-processor and network performance to a different architectural paradigms forces application programmers to rethink the basic models of parallel programming from both the language and problem division standpoints. One of the major computing facilities available to researchers in fusion energy is the National Energy Research Scientific Computing Center. As the mission computing center for DOE, Office of Science, NERSC is tasked with helping users to overcome the challenges of this revolution both through the use of new parallel constructs and languages and also by enabling a broader user community to take advantage of multi-core performance. We discuss the programming model challenges facing researchers in fusion and plasma physics in for a variety of simulations ranging from particle-in-cell to fluid-gyrokinetic and MHD models.

Wangyi Liu, John Barnard, Alice Koniges, David Eder, Nathan Masters, Aaron Fisher, Alex Friedman, "A numerical scheme for including surface tension effects in hydrodynamic simulation: a full Korteweg type model without parasitic flows", APS DPP 2012, 2012,

Wangyi Liu, John Barnard, Alex Friedman, Nathan Masters, Aaron Fisher, Alice Koniges, David Eder, "Modeling droplet breakup effects with applications in the warm dense matter NDCX experiment", APS DPP, 2011,

Sean Farley, Ben Dudson, Praveen Narayanan, Lois Curfman McInnes, Maxim Umansky, Xuexiao Xu, Satish Balay, John Cary, Alice Koniges, Carol Woodward, Hong Zhang, "BOUT++: Performance Characterization and Recent Advances in Design", International Conference on Numerical Simulations of Plasmas, Long Beach, New Jersey, 2011, 2011,

J. Kim, A. Koniges, R.L Martin, M. Haranczyk, J. Swisher, B. Smit, "GPU Computational Screening of Carbon Capture Materials", 2011 SciDAC Conference, Denver, CO, 2011,

Wangyi Liu, John Bernard, Alex Friedman, Nathan Masters, Aaron Fisher, Velemir Mlaker, Alice Koniges, David Eder, "Modeling droplet breakup effects in warm dense matter experiments with diffuse interface methods in ALE-AMR code", SciDAC conference, 2011,

Brian Austin, Ji Qiang, Jonathan Wurtele, Alice Koniges, "Influences of architecture and threading on the MPI communication strategies in an accelerator simulation code.", SciDAC 2011, Denver, CO, 2011,

J. Kim, A. Koniges, B. Smit, M. Head-Gordon, "Calculation of RI-MP2 Gradient using Fermi GPUs", Molecular Quantum Mechanics 2010, May 2010,

Alice Koniges,D. Eder,O. Landen,R. Anderson,A. Fisher,B. Gunney,N. Masters,B. Maddox,F. Hansen,B. Brown,K. Fisher,T. Kaiser,A. Geille,J-P. Jadaud,J-M. Chevalier,D. Raffestin,D. Benson,M. Meyers,H. Jarmakani,B. Blue5, "Target Design and Debris Modeling with NIF ALE-AMR", NIF Design Review, 2009,


D C Eder, A E Koniges, N D Masters, A C Fisher, R W Anderson, K R Gaunt and D J Benson, Fragmentation and penetration visualization from the multi-physics ALE-AMR code, SciDAC 2009 J. Phys.: Conf. Ser. 180 013001, June 15, 2009,


On Monday, June 15, 2009, the SciDAC 2009 conference sponsored an Electronic Visualization and Poster Night. Scientists involved in DOE Office of Science research, such as SciDAC, INCITE, and core-funded programs, were encouraged to submit an image or animation to be shown at this event. A DVD of those images and animations is attached to the inside back cover of this proceedings book.