# 2017 Publications

### 2017

### B Mohammed, S Moyo, KM Maiyama, S Kinteh, ANMK Al-Shaidy, MA Kamala, M Kiran, "Technical Report on Deploying a highly secured OpenStack Cloud Infrastructure using BradStack as a Case Study", 2017,

### George Michelogiannakis, John Shalf, "Last Level Collective Hardware Prefetching For Data-Parallel Applications", IEEE 24th International Conference on High Performance Computing, IEEE, December 2017,

### George Michelogiannakis, John Shalf, Last Level Collective Hardware Prefetching For Data-Parallel Applications, IEEE 24th International Conference on High Performance Computing, December 18, 2017,

- Download File: hipc.pptx (pptx: 357 KB)

### J. Wang, A. Sim, K. Wu, S. Hwangbo, "Accurate Signal Timing from High Frequency Streaming Data", 2017 IEEE International Conference on Big Data (Big Data 2017), 2017, doi: 10.1109/bigdata.2017.8258565

### A. Lazar, L. Jin, A. Spurlock, A. Todd, K. Wu, A. Sim, "Data Quality Challenges with Missing Values and Mixed Types in Joint Sequence Analysis", Workshop in Data Quality Issues in Big Data and Machine Learning Applications: Going Beyond Data Cleaning and Transformations, in conjunction with the 2017 IEEE International Conference on Big Data (Big Data 2017), 2017, doi: 10.1109/BigData.2017.8258222

### J. Wang, K. Wu, A. Sim, S. Hwangbo, "Feature Engineering and Classification Models for Partial Discharge Events in Power Transformers", 10th IEEE/ACM International Conference on Utility and Cloud Computing (UCC 2017), 2017, doi: 10.1145/3148055.3149270

### Shashanka Ubaru, Kesheng Wu, Kristofer E. Bouchard, "UoI-NMF Cluster: A Robust Nonnegative Matrix Factorization Algorithm for Improved Parts-Based Decomposition and Reconstruction of Noisy Data", the 16th IEEE International Conference on Machine Learning and Applications (ICMLA 2017), 2017, 241-248, doi: 10.1109/ICMLA.2017.0-152

### John Bachan, Scott Baden, Dan Bonachea, Paul Hargrove, Steven Hofmeyr, Khaled Ibrahim, Mathias Jacquelin, Amir Kamil, Brian Van Straalen, "UPC++: a PGAS C++ Library", ACM/IEEE Conference on Supercomputing, SC'17, November 2017,

### P. Harrington, W. Yoo (Advisor), A. Sim (Advisor), K. Wu (Advisor), "Diagnosing Parallel I/O Bottlenecks in HPC Applications", International Conference for High Performance Computing, Networking, Storage and Analysis (SC’17), ACM Student Research Competition (SRC), First place winner, 2017,

### Glenn Lockwood, Shane Snyder, Wucherl Yoo, Kevin Harms, Zachary Nault, Suren Byna, Philip Carns, Nicholas Wright, "UMAMI: A Recipe for Generating Meaningful Metrics through Holistic I/O Performance Analysis", 2nd Joint International Workshop on Parallel Data Storage & Data Intensive Scalable Computing Systems (PDSW-DISCS), 2017 (Held in conjunction with SC17), November 14, 2017,

### Tzu-Hsien Wu, Jerry Chou, Shyng Hao, Bin Dong, KeshengWu, Scott Klasky, "Optimizing the Query Performance of Block Index Through Data Analysis and I/O Modeling", The International Conference for High Performance Computing, Networking, Storage and Analysis (SC'17), November 13, 2017,

### John Bachan, Dan Bonachea, Paul H Hargrove, Steve Hofmeyr, Mathias Jacquelin, Amir Kamil, Brian van Straalen, Scott B Baden, "The UPC++ PGAS library for Exascale Computing", Proceedings of the Second Annual PGAS Applications Workshop (PAW17), November 13, 2017, 7, doi: 10.1145/3144779.3169108

We describe UPC++ V1.0, a C++11 library that supports APGAS programming. UPC++ targets distributed data structures where communication is irregular or fine-grained. The key abstractions are global pointers, asynchronous programming via RPC, and futures. Global pointers incorporate ownership information useful in optimizing for locality. Futures capture data readiness state, are useful for scheduling and also enable the programmer to chain operations to execute asynchronously as high-latency dependencies become satisfied, via continuations. The interfaces for moving non-contiguous data and handling memories with different optimal access methods are composable and closely resemble those used in modern C++. Communication in UPC++ runs at close to hardware speeds by utilizing the low-overhead GASNet-EX communication library.

### E. Georganas, S. Hofmeyr, L. Oliker, R. Egan, D. Rokhsar, A. Buluc, K. Yelick, "Extreme-scale de novo genome assembly", Exascale Scientific Applications: Scalability and Performance Portability, edited by T.P. Straatsma, K. B. Antypas, T. J. Williams, ( November 13, 2017) doi: https://doi.org/10.1201/b21930

### Brian Van Straalen, David Trebotich, Andrey Ovsyannikov, Daniel T. Graves, "Scalable Structured Adaptive Mesh Refinement with Complex Geometry", Exascale Scientific Applications: Scalability and Performance Portability, edited by Tjerk P. Straatsma, Katerina B. Antypas, Timothy J. Williams, (Chapman and Hall/CRC: November 13, 2017) doi: 10.1201/b21930

- Download File: 10.1201-b21930-14.pdf (pdf: 604 KB)

### Yang You, Aydin Buluc, James Demmel, "Scaling deep learning on GPU and Knights Landing clusters", Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC'17), 2017,

### Samuel Williams, Introduction to the Roofline Model, Roofline Training, November 2017,

- Download File: roofline-intro.pptx (pptx: 3.1 MB)
- Download File: roofline-intro.pdf (pdf: 3.6 MB)

### Erik Paulson, Dan Bonachea, Paul Hargrove, GASNet ofi-conduit, Presentation at the Open Fabrics Interface BoF at Supercomputing 2017, November 2017,

### Haohuan Fu, Junfeng Liao, Nan Ding, Xiaohui Duan, Lin Gan,Yishuang Liang,Xinliang Wang,Jinzhe Yang,Yan Zheng,Weiguo Liu,Lanning Wang,Guangwen Yang, "Redesigning CAM-SE for peta-scale climate modeling performance and ultra-high resolution on Sunway TaihuLight (ACM Gordon Bell Prize Finalist)", SC'17, November 12, 2017,

- Download File: redesign.pdf (pdf: 4.8 MB)

### J. Wang, K. Wu, A. Sim, S. Hwangbo, "Convolutional Filtering for Accurate Signal Timing from Noisy Streaming Data", 3rd IEEE International Conference on Big Data Intelligence and Computing (DataCom2017), 2017, doi: 10.1109/DASC-PICom-DataCom-CyberSciTec.2017.157

### B. Van Straalen, D. Trebotich, A. Ovsyannikov and D.T. Graves, "Scalable Structured Adaptive Mesh Refinement with Complex Geometry", Exascale Scientific Applications: Programming Approaches for Scalability, Performance, and Portability, edited by Straatsma, T., Antypas, K., Williams, T., (Chapman and Hall/CRC: November 9, 2017)

### E. J. Bylaska, E. Apra, K. Kowalski, M. Jacquelin, W.A. de Jong, A. Vishnu, B. Palmer, J. Daily, T.P. Straatsma, J.R. Hammond, M. Klemm, "Transitioning NWChem to the Next Generation of Many Core Machines", Exascale Scientific Applications Scalability and Performance Portability, edited by Tjerk P. Straatsma, Katerina B. Antypas, Timothy J. Williams, (Taylor & Francis: November 9, 2017)

### M. Jacquelin, L. Lin and C. Yang, "PSelInv – A distributed memory parallel algorithm for selected inversion : the symmetric case", Parallel Computing, November 9, 2017, 74:84-98, doi: 10.1016/j.parco.2017.11.009

### David Hatchell, Patrick Miller, Michael Coleman, Sean Peisert, Cybersecurity for the Electricity Grid", Bits & Watts Annual Conference, November 6, 2017,

### Tze Meng Low, Varun Nagaraj Rao, Matthew Lee, Doru Thom Popovici, Franz Franchetti Scott McMillan, "First look: Linear algebra-based triangle counting without matrix multiplication", HPEC, 2017,

### Doru Thom Popovici, Franz Franchetti, Tze Meng Low, "Mixed data layout kernels for vectorized complex arithmetic", HPEC, 2017,

### N. Sanderson, E. Shugerman, S. Molnar, J. Meiss E. Bradley, "Computational Topology Techniques for Characterizing Time-Series Data", Advances in Intelligent Data Analysis XVI 16th International Symposium, IDA 2017, London, UK, October 26–28, 2017, Proceedings, October 2017, pp.284-296, doi: 10.1007/978-3-319-68765-0_24

Topological data analysis (TDA), while abstract, allows a characterization of time-series data obtained from nonlinear and complex dynamical systems. Though it is surprising that such an abstract measure of structure—counting pieces and holes—could be useful for real-world data, TDA lets us compare different systems, and even do membership testing or change-point detection. However, TDA is computationally expensive and involves a number of free parameters. This complexity can be obviated by coarse-graining, using a construct called the witness complex. The parametric dependence gives rise to the concept of persistent homology: how shape changes with scale. Its results allow us to distinguish time-series data from different systems—e.g., the same note played on different musical instruments.

### Philip C. Roth, Hongzhang Shan, David Riegner, Nikolas Antolin, Sarat Sreepathi, Leonid Oliker, Samuel Williams, Shirley Moore, Wolfgang Windl, "Performance Analysis and Optimization of the RAMPAGE Metal Alloy Potential Generation Software", SIGPLAN International Workshop on Software Engineering for Parallel Systems (SEPS), October 2017,

### E.J. Bylaska, J. Hammond, M. Jacquelin, W.A. de Jong, M. Klemm, "Performance Evaluation of NWChem Ab-Initio Molecular Dynamics (AIMD) Simulations on the Intel® Xeon Phi© Processor", High Performance Computing. ISC High Performance 2017. Lecture Notes in Computer Science, Springer, Cham, October 21, 2017, 404-418, doi: 10.1007/978-3-319-67630-2_30

### Shreyas Cholia, Matthew Henderson, Oliver Evans, Demo: Extending Jupyter to Support Interactive High Performance Computing, Science Gateways 2017, October 2017, doi: 10.6084/m9.figshare.5501137.v1

### W. Hu, L. Lin, R. Zhang, C. Yang, J. Yang, "Highly efficient photocatalytic water splitting over edge-modified phosphorene nanoribbons", J. Am. Chem. Soc., October 13, 2017, 139:15429–1543, doi: 10.1021/jacs.7b08474

### Lorenzo Di Tucci, Giulia Guidi, Sara Notargiacomo, Luca Cerina, Alberto Scolari, Marco D. Santambrogio, "HUGenomics: A Support to Personalized Medicine Research", 2017 IEEE 3rd International Forum on Research and Technologies for Society and Industry (RTSI), October 12, 2017,

### Sean Peisert, Security in High Performance Computing Environments, Computing Sciences/NERSC Security Seminar, October 5, 2017,

### Meiyue Shao and Chao Yang, "Properties of Definite Bethe--Salpeter Eigenvalue Problems", Eigenvalue Problems: Algorithms, Software and Applications in Petascale Computing. EPASA 2015. Lecture Notes in Computational Science and Engineering, vol 117., 2017, 91--105, doi: 10.1007/978-3-319-62426-6_7

### Sean Peisert, Matt Bishop, Ed Talbot,, "A Model of Owner Controlled, Full-Provenance, Non-Persistent, High-Availability Information Sharing", Proceedings of the 2017 New Security Paradigms Workshop (NSPW), Santa Cruz, CA, October 2017, 80-89, doi: 10.1145/3171533.3171536

### Sean Peisert, Security and Privacy in Data-Intensive, High-Performance Computing Contexts, Berkeley Institute for Data Science (BIDS), October 2, 2017,

### Jean-Philippe Peraud, Andrew J. Nonaka, John B. Bell, Aleksandar Donev, Alejandro L. Garcia, "Fluctuation-enhanced electric conductivity in electrolyte solutions", Proceedings of the National Academy of Sciences, 2017, 114:10829--108, doi: 10.1073/pnas.1714464114

### John Bachan, Scott Baden, Dan Bonachea, Paul Hargrove, Steven Hofmeyr, Khaled Ibrahim, Mathias Jacquelin, Amir Kamil, Brian van Straalen, "UPC++ Programmer’s Guide, v1.0-2017.9", Lawrence Berkeley National Laboratory Tech Report, September 2017, LBNL 2001065, doi: 10.2172/1398522

UPC++ is a C++11 library that provides Asynchronous Partitioned Global Address Space (APGAS) programming. It is designed for writing parallel programs that run efficiently and scale well on distributed-memory parallel computers. The APGAS model is single program, multiple-data (SPMD), with each separate thread of execution (referred to as a rank, a term borrowed from MPI) having access to local memory as it would in C++. However, APGAS also provides access to a global address space, which is allocated in shared segments that are distributed over the ranks. UPC++ provides numerous methods for accessing and using global memory. In UPC++, all operations that access remote memory are explicit, which encourages programmers to be aware of the cost of communication and data movement. Moreover, all remote-memory access operations are by default asynchronous, to enable programmers to write code that scales well even on hundreds of thousands of cores.

### W. Hu, L. Lin, C. Yang, "Interpolative Separable Density Fitting Decomposition for Accelerating Hybrid Density Functional Calculations with Applications to Defects in Silicon", J. Chem. Theory Comput., September 29, 2017, 13:5420–5431, doi: 10.1021/acs.jctc.7b00807

### J Bachan, S Baden, D Bonachea, P Hargrove, S Hofmeyr, K Ibrahim, M Jacquelin, A Kamil, B Lelbach, B van Straalen, "UPC++ Specification v1.0, Draft 4", Lawrence Berkeley National Laboratory Tech Report, September 27, 2017, LBNL 2001066, doi: 10.2172/1398521

UPC++ is a C++11 library providing classes and functions that support Asynchronous Partitioned Global Address Space (APGAS) programming. We are revising the library under the auspices of the DOE’s Exascale Computing Project, to meet the needs of applications requiring PGAS support. UPC++ is intended for implementing elaborate distributed data structures where communication is irregular or fine-grained. The UPC++ interfaces for moving non-contiguous data and handling memories with different optimal access methods are composable and similar to those used in conventional C++. The UPC++ programmer can expect communication to run at close to hardware speeds. The key facilities in UPC++ are global pointers, that enable the programmer to express ownership information for improving locality, one-sided communication, both put/get and RPC, futures and continuations. Futures capture data readiness state, which is useful in making scheduling decisions, and continuations provide for completion handling via callbacks. Together, these enable the programmer to chain together a DAG of operations to execute asynchronously as high-latency dependencies become satisfied.

### Matthew S. Barclay, Timothy J. Quincy, David B. Williams-Young, Marco Caricato, Christopher G. Elles, "Accurate Assignments of Excited-State Resonance Raman Spectra: A Benchmark Study Combining Experiment and Theory", Journal of Physical Chemistry A, 2017, 121:7937-7946, doi: 10.1021/acs.jpca.7b09467

### Jonathan Ganz, Sean Peisert, "ASLR: How Robust is the Randomness", Proceedings of the IEEE Secure Development Conference (SecDev), Cambridge, MA, IEEE Computer Society, September 24, 2017, doi: 10.1109/SecDev.2017.19

### W. Hu, L. Lin, C. Yang, "Projected Commutator DIIS Method for Accelerating Hybrid Functional Electronic Structure Calculations", J. Chem. Theory Comput, September 22, 2017, 13:5458–5467, doi: 10.1021/acs.jctc.7b00892

### Mahdi Jamei, Anna Scaglione, Ciaran Roberts, Emma Stewart, Sean Peisert, Chuck McParland, Alex McEachern, "Anomaly Detection Using μPMU Measurements in Distribution Grids", IEEE Transactions on Power Systems, 2017, doi: 10.1109/TPWRS.2017.2764882

### V. Yu. F. Corsetti, A. García, W. P. Huhn, M. Jacquelin, W. Jia, B. Lange, L. Lin, J. Lu, W. Mi, A. Seifitokaldan, Á. Vazquez-Mayagoitia, C. Yang, H. Yang, V. Blum, "ELSI: A unified software interface for Kohn–Sham electronic structure solvers", Computer Physics Communications, September 7, 2017, 222:267-285, doi: 10.1016/j.cpc.2017.09.007

### Houjun Tang, Suren Byna, Bin Dong, Jialin Liu, and Quincey Koziol, "SoMeta: Scalable Object-centric Metadata Management for High Performance Computing", IEEE Cluster 2017, September 5, 2017,

### Sean Peisert, "Security in High-Performance Computing Environments", Communications of the ACM (CACM), September 2017, 60(9):72-80, doi: 10.1145/3096742

### Jose Oñorbe, Joseph F. Hennawi, Zarija Lukić, and Michael Walther, "Constraining Reionization with the z ~ 5-6 Lyman-alpha Forest Power Spectrum: the Outlook after Planck", The Astrophysical Journal, 2017,

### Robert Saye, "Implicit mesh discontinuous Galerkin methods and interfacial gauge methods for high-order accurate interface dynamics, with applications to surface tension dynamics, rigid body fluid-structure interaction, and free surface flow: Part I", Journal of Computational Physics, September 1, 2017,

### Robert Saye, "Implicit mesh discontinuous Galerkin methods and interfacial gauge methods for high-order accurate interface dynamics, with applications to surface tension dynamics, rigid body fluid-structure interaction, and free surface flow: Part II", Journal of Computational Physics, September 1, 2017,

### R. Van Beeumen, D.B. Williams-Young, J.M. Kasper, C. Yang, E.G. Ng, X. Li, "Model order reduction algorithm for estimating the absorption spectrum", Journal of Chemical Theory and Computation, 2017, 13:4950-4961, doi: 10.1021/acs.jctc.7b00402

### Frederick B. Davies, Joseph F. Hennawi, Anna-Christina Eilers, and Zarija Lukić, "A New Method to Measure the Post-Reionization Ionizing Background from the Joint Distribution of Lyman-α and Lyman-β Forest Transmission", The Astrophysical Journal, 2017,

### Jack Deslippe, Doug Doerfler, Brandon Cook, Tareq Malas, Samuel Williams, Sudip Dosanjh, "Optimizing science applications for the Cori, Knights Landing, System at NERSC", Advances in Parallel Computing, New Frontiers in High Performance Computing and Big Data, August 2017, 30, doi: 10.3233/978-1-61499-816-7-235

### Dan Bonachea, Paul Hargrove, "GASNet Specification, v1.8.1", Lawrence Berkeley National Laboratory Tech Report, August 31, 2017, LBNL 2001064, doi: 10.2172/1398512

GASNet is a language-independent, low-level networking layer that provides network-independent, high-performance communication primitives tailored for implementing parallel global address space SPMD languages and libraries such as UPC, UPC++, Co-Array Fortran, Legion, Chapel, and many others. The interface is primarily intended as a compilation target and for use by runtime library writers (as opposed to end users), and the primary goals are high performance, interface portability, and expressiveness. GASNet stands for "Global-Address Space Networking".

### Muammar El Khatib, Alireza Khorshidi, Andrew A Peterson, Acceleration of Saddle-Point Searches Assisted by Machine Learning, 68 th Annual Meeting of the International Society of Electro-chemistry, August 31, 2017,

### Daniel Martin, Stephen Cornford, Antony Payne, Millennial-Scale Vulnerability of the Antarctic Ice Sheet to localized subshelf warm-water forcing, International Symposium on Polar Ice, Polar Climate, Polar Change, August 18, 2017,

- Download File: Martin-IGS-2017.pdf (pdf: 6.9 MB)

### K. Wu, D. Lee, A. Sim, J. Choi, "Statistical Data Reduction for Streaming Data", 2017 New York Scientific Data Summit (NYSDS), Data-Driven Discovery in Science and Industry, 2017, doi: 10.1109/NYSDS.2017.8085035

### Seher Acer, R. Oguz Selvitopi, Cevdet Aykanat, "Addressing Volume and Latency Overheads in 1D-parallel Sparse Matrix-Vector Multiplication", European Conference on Parallel Processing (Euro-Par), Springer, August 2017, 625-637, doi: 10.1007/978-3-319-64203-1_45

### Jinoh Kim, Alex Sim, "A New Approach to Online, Multivariate Network Traffic Analysis", 2nd Workshop on Network Security Analytics and Automation (NSAA), in conjunction with the 26th International Conference on Computer Communications and Networks (ICCCN 2017), 2017, doi: 10.1109/ICCCN.2017.8038520

### J Muller, "SOCEMO: Surrogate Optimization of Computationally Expensive Multiobjective Problems", INFORMS Journal on Computing, July 31, 2017, 29:581-596,

### Alireza Khorshidi, Muammar El Khatib, Andrew A Peterson*, Amp: The Atomistic Machine-learning Package v0.6, https://bitbucket.org/andrewpeterson/amp, July 31, 2017,

### Dilip Vasudevan, George Michelogiannakis, John Shalf, "CASPER - Configurable Design Space Exploration of Programmable Architectures for Machine Learning using Beyond Moore Devices", IEEE/ACM International Symposium on Nanoscale Architectures (NANOARCH), July 2017,

### E. Vecharynski, J. Brabec, M. Shao, N. Govind, C. Yang, "Efficient Block Preconditioned Eigensolvers for Linear Response Time-dependent Density Functional Theory", Computer Physics Communications, 2017, 221:42-52, doi: https://doi.org/10.1016/j.cpc.2017.07.017

We present two efficient iterative algorithms for solving the linear response eigenvalue problem arising fromthe time dependent density functional theory. Although the matrix to be diagonalized is nonsymmetric, it has a special structure that can be exploited to save both memory and floating point operations. In particular, the nonsymmetric eigenvalue problem can be transformed into a product eigenvalue problem that is self-adjoint with respect to a K-inner product. This product eigenvalue problem can be solved efficiently by a modified Davidson algorithm and a modified locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm that make use of the K-inner product. The solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. However, the other component of the eigenvector can be easily recovered in a postprocessing procedure. Therefore, the algorithms we present here are more efficient than existing algorithms that try to approximate both components of the eigenvectors simultaneously.The efficiency of the new algorithms is demonstrated by numerical examples.

### Mahdi Jamei, Anna Scaglione, Ciaran Roberts, Alex McEachern, Emma Stewart, Sean Peisert, Chuck McParland, "Online Thevenin Parameter Tracking Using Synchrophasor Data", Proceedings of the 2017 IEEE Power Engineering Society (PES) General Meeting (GM), Chicago, IL, IEEE, July 2017, doi: 10.1109/PESGM.2017.8273818

### Sugeerth Murugesan, Kristofer Bouchard, Jesse A. Brown, Bernd Hamann, William W. Seeley, Andrew Trujillo, Gunther H. Weber, "Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity", IEEE Transactions on Computational Biology and Bioinformatics, 2017, 14(4):805-818, LBNL 1005732, doi: 10.1109/TCBB.2016.2564970

### Nishant Nangia, Hans Johansen, Neelesh A. Patankar, Amneet Pal Singh Bhalla, "A moving control volume approach to computing hydrodynamic forces and torques on immersed bodies", Journal of Computational Physics, June 29, 2017, doi: 10.1016/j.jcp.2017.06.047

### Dongeun Lee, Alex Sim, Jaesik Choi, Kesheng Wu, "Improving Statistical Similarity Based Data Reduction for Non-Stationary Data", 29th International Conference on Scientific and Statistical Database Management (SSDBM2017), 2017, doi: 10.1145/3085504.3085583

Updated experiment version: https://sdm.lbl.gov/oapapers/ssdbm17-lee-upd.pdf

Original version: http://dl.acm.org/citation.cfm?doid=3085504.3085583

### Bin Dong, Kesheng Wu, Surendra Byna, Jialin Liu, Weijie Zhao, Florin Rusu, "ArrayUDF: User-Defined Scientific Data Analysis on Arrays", The ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC) 2017 (Acceptance rate:19%), June 26, 2017,

- Download File: hpdc02.pdf (pdf: 921 KB)

### Devarshi Ghoshal, Lavanya Ramakrishnan, "MaDaTS: Managing Data on Tiered Storage for Scientific Workflows", Proceedings of the 26th International Symposium on High-Performance Parallel and Distributed Computing (HPDC '17), ACM, 2017, 41--52, doi: 10.1145/3078597.3078611

### Alberto Gonzalez, Jason Leigh, Sean Peisert, Brian Tierney, Edward Balas, Predrag Radulovic, Jennifer M. Schopf, "Big Data and Analysis of Data Transfers for International Research Networks Using NetSage", Proceedings of IEEE BigData Congress 2017, Honolulu, Hawaii, June 2017, doi: 10.1109/BigDataCongress.2017.51

### Anastasiia Butko, Florent Bruguier, Abdoulaye Gamatié, Gilles Sassatelli, "Efficient Programming for Multicore Processor Heterogeneity: OpenMP versus OmpSs", Open Source Supercomputing Workshop, Frankfurt, Germany, Springer’s Lecture Notes in Computer Science (LNCS), June 22, 2017,

ARM single-ISA heterogeneous multicore processors combine high-performance big cores with power-efficient small cores. They aim at achieving a suitable balance between performance and energy. How- ever, a main challenge is to program such architectures so as to efficiently exploit their features. In this paper, we study the impact on performance and energy trade-offs of single-ISA architecture according to OpenMP 3.0 and the OmpSs programming models. We consider different symmetric/asymmetric architecture configura- tions in terms of core frequency and core count between big and LITTLE clusters. Experiments are conducted on both a real Samsung Exynos 5 Octa system-on-chip and the gem5/McPAT simulation frameworks. Results show that OmpSs implementations are more sensitive to loop scheduling parameters than OpenMP 3.0. In most cases, best OmpSs configurations significantly outperform OpenMP ones. While cluster frequency asym- metry provides uninteresting results, asymmetric cluster configuration with single high-performance core and multiple low-power cores provides better performance/energy trade-offs in many cases.

### Sean Peisert, Mike Corn, Dewight Kramer, David Rusting, Tye Stallard, The Role of the WAN and the Community to Improve Security, 2017 UC Information Security Symposium,, June 21, 2017,

### Galen Rasche, Jenna Goodward, Sheeraz Haji, Gabriel Paun, Sean Peisert, Managing Energy: Role of Data and Security, Prospect Silicon Valley 2017 Innovation and Impact Symposium, June 14, 2017,

### X. Zhang, A. Kucharski, S.R. Ellingson, W.A. de Jong, "Towards a better understanding of on and off target effects of the lymphocyte-specific kinase LCK for the development of novel and safer pharmaceuticals", Procedia Computer Science, June 9, 2017, 108:1222-1231, doi: 10.1016/j.procs.2017.05.268

### Sugeerth Murugesan, Kristofer Bouchard, Edward Chang, Dougherty, Bernd Hamann, Gunther H. Weber, "Multi-scale Visual Analysis of Time-varying Electrocorticography Data Clustering of Brain Regions", BMC Bioinformatics, 2017, 18:236, doi: 10.1186/s12859-017-1633-9

### Hongzhang Shan, Samuel Williams, Calvin Johnson, Kenneth McElvain, "A Locality-based Threading Algorithm for the Configuration-Interaction Method", Parallel and Distributed Scientific and Engineering Computing (PDSEC), June 2017,

- Download File: pdsec17-bigstick.pdf (pdf: 715 KB)

### Bryce Adelstein Lelbach, Hans Johansen, Samuel Williams, "Simultaneously Solving Swarms of Small Sparse Systems on SIMD Silicon", Parallel and Distributed Scientific and Engineering Computing (PDSEC), June 2017,

### Brandon Cook, Thorsten Kurth, Brian Austin, Samuel Williams, Jack Deslippe, "Performance Variability on Xeon Phi", Intel Xeon Phi Users Group (IXPUG), June 2017,

### Thorsten Kurth, William Arndt, Taylor Barnes, Brandon Cook, Jack Deslippe, Doug Doerfler, Brian Friesen, Yun (Helen) He, Tuomas Koskela, Mathieu Lobet, Tareq Malas, Leonid Oliker, Andrey Ovsyannikov, Samuel Williams, Woo-Sun Yang, and Zhengji Zhao, "Analyzing Performance of Selected NESAP Applications on the Cori HPC System", Intel Xeon Phi Users Group (IXPUG), June 2017,

- Download File: ixpug17-nesap.pdf (pdf: 395 KB)

### Jonas Lukasczyk, Ross Maciejewski, Gunther H. Weber, Garth, Heike Leitte, "Nested Tracking Graphs", Computer Graphics Forum (Special Issue, Proceedings Symposium on Visualization), 2017, 36 (3):12--22, doi: 10.1111/cgf.13164

### SM Martin, MJ Berger, SB Baden, "Toucan-A Translator for Communication Tolerant MPI Applications", Proceedings - 2017 IEEE 31st International Parallel and Distributed Processing Symposium, IPDPS 2017, June 2017, 998-1007, doi: 10.1109/IPDPS.2017.44

We discuss early results with Toucan, a source-to-source translator that automatically restructures C/C++ MPI applications to overlap communication with computation. We co-designed the translator and runtime system to enable dynamic, dependence-driven execution of MPI applications, and require only a modest amount of programmer annotation. Co-design was essential to realizing overlap through dynamic code block reordering and avoiding the limitations of static code relocation and inlining. We demonstrate that Toucan hides significant communication in four representative applications running on up to 24K cores of NERSC's Edison platform. Using Toucan, we have hidden from 33% to 85% of the communication overhead, with performance meeting or exceeding that of painstakingly hand-written overlap variants. © 2017 IEEE.

### Ariful Azad, Aydin Buluc, "Towards a GraphBLAS Library in Chapel", IPDPS Workshops, Orlando, FL, May 2017,

- Download File: GraphBLAS-Chapel.pdf (pdf: 368 KB)

### Aydin Buluc, Tim Mattson, Scott McMillan, Jose Moreira, Carl Yang, "Design of the GraphBLAS API for C", IEEE Workshop on Graph Algorithm Building Blocks, IPDPSW, 2017,

- Download File: GABB17.pdf (pdf: 359 KB)

### Ariful Azad, Aydin Buluc, "A work-efficient parallel sparse matrix-sparse vector multiplication algorithm", IEEE International Parallel & Distributed Processing Symposium (IPDPS), Orlando, FL, May 2017,

- Download File: SpMSpV-ipdps17.pdf (pdf: 422 KB)

### Nathan Zhang, Michael Driscoll, Armando Fox, Charles Markley, Samuel Williams, Protonu Basu, "Snowflake: A Lightweight Portable Stencil DSL", High-level Parallel Programming Models and Supportive Environments (HIPS), May 2017,

- Download File: hips17-snowflake.pdf (pdf: 475 KB)

### Jonathan Wang, Wucherl Yoo, Alex Sim, Peter Nugent, K. John Wu, "Parallel Variable Selection for Effective Performance Prediction", the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid2017), 2017, doi: 10.1109/CCGRID.2017.47

### George Michelogiannakis, Khaled Z. Ibrahim, John Shalf, Jeremiah J. Wilke, Samuel Knight, Joseph P. Kenny, "APHiD: Hierarchical Task Placement to Enable a Tapered Fat Tree Topology for Lower Power and Cost in HPC Networks", 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, IEEE, May 2017, LBNL 1007126,

### Weijie Zhao, Florin Rusu, Bin Dong, Kesheng Wu, and Peter Nugent, "Incremental View Maintenance over Array Data", In Proceedings of the 2017 ACM International Conference on Management of Data (SIGMOD '17) (Acceptance rate: 20%). ACM, New York, NY, USA, May 14, 2017,

### Dai Wang, Junyu Gaob, Pan Li, Bin Wang, Cong Zhang, Samveg Saxena, "Modeling of plug-in electric vehicle travel patterns and charging load based on trip chain generation", Journal of Power Sources, May 13, 2017, 359:468 - 479, doi: 10.1016/j.jpowsour.2017.05.036

Modeling PEV travel and charging behavior is the key to estimate the charging demand and further explore the potential of providing grid services. This paper presents a stochastic simulation methodology to generate itineraries and charging load profiles for a population of PEVs based on real-world vehicle driving data. In order to describe the sequence of daily travel activities, we use the trip chain model which contains the detailed information of each trip, namely start time, end time, trip distance, start location and end location. A trip chain generation method is developed based on the Naive Bayes model to generate a large number of trips which are temporally and spatially coupled. We apply the proposed methodology to investigate the multi-location charging loads in three different scenarios. Simulation results show that home charging can meet the energy demand of the majority of PEVs in an average condition. In addition, we calculate the lower bound of charging load peak on the premise of lowest charging cost. The results are instructive for the design and construction of charging facilities to avoid excessive infrastructure.

### Dharshi Devendran, Daniel T. Graves, Hans Johansen,Terry Ligocki, "A Fourth Order Cartesian Grid Embedded Boundary Method for Poisson's Equation", Communications in Applied Mathematics and Computational Science, edited by Silvio Levy, May 12, 2017, 12:51-79, doi: DOI 10.2140/camcos.2017.12.51

- Download File: poisson-eb-4th-order.pdf (pdf: 1.1 MB)

### Suren Byna, Mohamad Chaarawi, Quincey Koziol, John Mainzer, and Frank Willmore,, "Tuning HDF5 subfiling performance on parallel file systems", Cray User Group (CUG) meeting 2017, May 10, 2017,

### Cong Xu, Shane Snyder, Omkar Kulkarni, Vishwanath Venkatesan, Philip Carns, Suren Byna, Robert Sisneros, and Kalyana Chadalavada,, "DXT: Darshan eXtended Tracing", Cray User Group (CUG) meeting 2017, May 10, 2017,

### Chaplin, Christopher, Colella, Phillip, "A single-stage flux-corrected transport algorithm for high-order finite-volume methods", Communications in Applied Mathematics and Computational Science, May 8, 2017, 12:1-24, doi: 10.2140/camcos.2017.12.1

### Alessio Petrone, David B. Williams-Young, David B. Lingerfelt, Xiaosong Li, "Ab Initio Transient Raman Analysis", Journal of Physical Chemistry A, 2017, 121:3958-3965, doi: 10.1021/acs.jpca.7b02905

### M. de Raad, T. de Rond, O. Rübel, J. D. Keasling, T. R. Northen, B. P. Bowen, "OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging", ACS Analytical Chemistry, May 3, 2017, doi: 10.1021/acs.analchem.6b05004

### Anna-Christina Eilers, Frederick B. Davies, Joseph F. Hennawi, J. Xavier Prochaska, Zarija Lukić, and Chiara Mazzucchelli, "Implications of z ~ 6 Quasar Proximity Zones for the Epoch of Reionization and Quasar Lifetimes", The Astrophsyical Journal, 2017, 840:24,

### Bei Wang, Stephane Ethier, William Tang, Khaled Ibrahim, Kamesh Madduri, Samuel Williams, Leonid Oliker, "Modern Gyrokinetic Particle-in-cell Simulation of Fusion Plasmas on Top Supercomputers", International Journal of High-Performance Computing Applications (IJHPCA), May 2017, doi: https://doi.org/10.1177/1094342017712059

### Jialin Liu, Quincey Koziol, Houjun Tang, François Tessier, Wahid Bhimji, Brandon Cook, Brian Austin, Suren Byna, Bhupender Thakur, Glenn Lockwood, Jack Deslippe, Prabhat, "Understanding the I/O Performance Gap Between Cori KNL and Haswell", Cray User Group Conference 2017 (CUG 2017), May 1, 2017,

### Franco Egidi, David B. Williams-Young, Alberto Baiardi, Julien Bloino, Giovanni Scalmani, Michael J. Frisch, Xiaosong Li, Vincenzo Barone, "Effective Inclusion of MEchanical and Electrical Anharmonivity in Excited Electronic States: VPT2-TDDFT Route", Journal of Chemical Theory and Computation, 2017, 13:2789-2803, doi: 10.1021/acs.jctc.7b00218

### Gunther H. Weber, Sheelagh Carpendale, David Ebert, Brian Fisher Hans Hagen, Ben Shneiderman, Anders Ynnerman, "Apply or Die: On the Role and Assessment of Application Papers in", IEEE Computer Graphics \& Applications, 2017, 37 (3):96--104, doi: 10.1109/MCG.2017.51

### Gilberto Z. Pastorello, Dario Papale, Housen Chu, Carlo Trotta, Deb A. Agarwal, Eleonora Canfora, Dennis D. Baldocchi, M. S. Torn, "A new data set to keep a sharper eye on land-air exchanges", Eos, 2017, 98:28-32, doi: 10.1029/2017EO071597

### Sergi Molins, David Trebotich, Gregory H. Miller, Carl I. Steefel, "Mineralogical and transport controls on the evolution of porous media texture using direct numerical simulation", Water Resources Research, April 7, 2017, doi: 10.1002/2016WR020323

### Protonu Basu, Samuel Williams, Brian Van Straalen, Leonid Oliker, Phillip Colella, Mary Hall, "Compiler-Based Code Generation and Autotuning for Geometric Multigrid on GPU-Accelerated Supercomputers", Parallel Computing (PARCO), April 2017, doi: 10.1016/j.parco.2017.04.002

### Dongeun Lee, Alex Sim, Jaesik Choi, Kesheng Wu, "Expanding Statistical Similarity Based Data Reduction to Capture Diverse Patterns", Data Compression Conference (DCC 2017), 2017,

### Stone, D. A., H. Krishnan, R. Lance, S. Sippel, and M. F. Wehner, "The First and Second Hackathons of the International CLIVAR C20C+ Detection and Attribution Project", CLIVAR Exchanges, 2017,

- Download File: StoneDA-KrishnanH-etalii-2017.pdf (pdf: 636 KB)

### Sean Peisert, Greg Bell, Anita Nikolich, Von Welch, Cybersecurity: New Directions for Research and Education - Your own safety is at stake when your neighbor's wall is ablaze. (—Horace), CENIC Annual Conference — The Right Connection ¦ CENIC 2.0, March 22, 2017,

### Hannah E. Ross, Keri L. Dixon, Ilian T. Iliev, Garrelt Mellema, "Simulating the impact of X-ray heating during the cosmic dawn", Montly Notices of the Royal Astronomical Society, March 22, 2017,

### Hannah E. Ross, Keri L. Dixon, Ilian T. Iliev, Garrelt Mellema, "Simulating the impact of X-ray heating during the cosmic dawn", Monthly Notices of the Royal Astronomical Society, March 2017, 468:3785-3797, doi: 10.1093/mnras/stx649

### Yingqi Xiong, Bin Wang, Chi-cheng Chu, Rajit Gadh, "Distributed Optimal Vehicle Grid Integration Strategy with User Behavior Prediction", IEEE PES General Meeting 2017, March 13, 2017,

With the increasing of electric vehicle (EV) adoption in recent years, the impact of EV charging activities to the power grid becomes more and more significant. In this article, an optimal scheduling algorithm which combines smart EV charging and V2G gird service is developed to integrate EVs into power grid as distributed energy resources, with improved system cost performance. Specifically, an optimization problem is formulated and solved at each EV charging station according to control signal from aggregated control center and user charging behavior prediction by mean estimation and linear regression. The control center collects distributed optimization results and updates the control signal, periodically. The iteration continues until it converges to optimal scheduling. Experimental result shows this algorithm helps fill the valley and shave the peak in electric load profiles within a microgrid, while the energy demand of individual driver can be satisfied.

### Leon J. Osterweil, Matt Bishop, Heather M. Conboy, Huong Phan, Borislava I. Simidchieva, George S. Avrunin, Lori A. Clarke, Sean Peisert, "A Comprehensive Framework for Using Iterative Analysis to Improve Human-Intensive Process Security: An Election Example", ACM Transactions on Privacy and Security (TOPS), 2017, 20(2), doi: https://doi.org/10.1145/3041041

### Alex Krolewski, Khee-Gan Lee, Zarija Lukić, and Martin White, "Measuring Alignments between Galaxies and the Cosmic Web at z ~ 2-3 Using IGM Tomography", The Astrophysical Journal, 2017, 837:31,

### B. Sprinkle, R. Bale, A.P.S. Bhalla, M.A. MacIver, N.A. Patankar, "Hydrodynamic optimality of balistiform and gymnotiform locomotion", European Journal of Computational Mechanics, February 27, 2017, doi: 10.1080/17797179.2017.1305160

### Alireza Khorshidi, Zachary Ulissi, Muammar El Khatib, Andrew A Peterson, Amp: The Atomistic Machine-learning Package v0.5, https://bitbucket.org/andrewpeterson/amp, February 24, 2017,

### Khaled Z. Ibrahim, Evgeny Epifanovsky, Samuel Williams, Anna I. Krylov, "Cross-scale efficient tensor contractions for coupled cluster computations through multiple programming model backends", Journal of Parallel and Distributed Computing (JPDC), February 2017, doi: 10.1016/j.jpdc.2017.02.010

### Tan Nguyen, Pietro Cicotti, Eric Bylaska, Dan Quinlan, and Scott Baden, "Automatic Translation of MPI Source into a Latency-tolerant, Data-driven Form", Journal of Parallel and Distributed Computing, February 21, 2017,

### Ma, S., T. Zhou, D. A. Stone, D. Polson, A. Dai, P. A. Stott, H. von Storch, Y. Qian, C. Burke, P. Wu, L. Zou, and A. Ciavarella, "Detectable anthropogenic shift toward heavy precipitation over eastern China", Journal of Climate, 2017, 30:1381-1396, doi: 10.1175/JCLI-D-16-0311.1

### Saverio E Spagnolie, Colin Wahl, Joseph Lukasik, Jean-Luc Thiffeault, "Microorganism billiards", Physica D: Nonlinear Phenomena, February 15, 2017, 341:33 - 44, doi: https://doi.org/10.1016/j.physd.2016.09.010

### Timmermans, B., D. Stone, M. Wehner, and H. Krishnan, "Impact of tropical cyclones on modeled wind-wave climate", Geophysical Research Letters, 2017, 44:1393-1401, doi: 10.1002/2016GL071681

### Sean Peisert, Von Welch, Andrew Adams, Michael Dopheide, Susan Sons, RuthAnne Bevier, Rich LeDuc, Pascal Meunier, Stephen Schwab, and Karen Stocks, Ilkay Altintas, James Cuff, Reagan Moore, Warren Raquel, "Open Science Cyber Risk Profile", February 10, 2017, doi: 2022/21259

### Mitchell, D., K. AchutaRao, M. Allen, I. Bethke, U. Beyerle, A. Ciavarella, P. M. Forster, J. Fuglestvedt, N. Gillett, K. Haustein, W. Ingram, T. Iverson, V. Kharin, N. Klingaman, N. Massey, E. Fischer, C.-F. Schleussner, J. Scinocca, O. Seland, H. Shiogama, E. Shuckburgh, S. Sparrow, D. Stone, P. Uhe, D. Wallom, M. Wehner, and R. Zaaboul, "Half a degree additional warming, prognosis and projected impacts (HAPPI): background and experimental design", Geoscientific Model Development, 2017, 10:571-583, doi: 10.5194/gmd-10-571-2017

### W. Hu, L. Lin, A. Banerjee, E. Vecharynski, C. Yang, "Adaptively compressed exchange operator for large scale hybrid density functional calculations with applications to the adsorption of water on silicene", J. Chem. Theory Comput., February 8, 2017, 13:1188–1198,

### Ling Jin, Doris Lee, Alex Sim, Sam Borgeson, John Wu, Anna Spurlock, Annika Todd, "Comparison of Clustering Techniques for Residential Energy Behavior using Smart Meter Data", 2nd International Workshop on Artificial Intelligence for Smart Grids and Smart Buildings, In conjunction with AAAI 2017, 2017,

### R. Oguz Selvitopi, Seher Acer, Cevdet Aykanat, "A Recursive Hypergraph Bipartitioning Framework for Reducing Bandwidth and Latency Costs Simultaneously", IEEE Transactions on Parallel and Distributed Systems (TPDS), February 2017, 28, 2:345-358, doi: 10.1109/TPDS.2016.2577024

### Yubo Wan, Wenbo Shi, Bin Wang, Chi-Cheng Ch, Rajit Gadh, "Optimal operation of stationary and mobile batteries in distribution grids", Applied Energy, January 28, 2017, 190:1289 - 130, doi: 10.1016/j.apenergy.2016.12.139

The trending integrations of Battery Energy Storage System (BESS, stationary battery) and Electric Vehicles (EV, mobile battery) to distribution grids call for advanced Demand Side Management (DSM) technique that addresses the scalability concerns of the system and stochastic availabilities of EVs. Towards this goal, a stochastic DSM is proposed to capture the uncertainties in EVs. Numerical approximation is then used to make the problem tractable. To accelerate the computational speed, the proposed DSM is tightly relaxed to a convex form using second-order cone programming. Furthermore, in light of the continuous increasing problem size, a distributed method with a guaranteed convergence is applied to shift the centralized computational burden to distributed controllers. To verify the proposed DSM, real-life EV data collected on UCLA campus is used to test the proposed DSM in an IEEE benchmark test system. Numerical results demonstrate the correctness and merits of the proposed approach.

### J. Kim, A. Sim, S.C. Suh, I. Kim, "An Approach to Online Network Monitoring Using Clustered Patterns", International Conference on Computing, Networking and Communications (ICNC 2017), 2017, doi: 10.1109/ICCNC.2017.7876207

### J. Kim, W. Yoo, A. Sim, S.C. Suh, I. Kim, "A Lightweight Network Anomaly Detection Technique", International Workshop on Computing, Networking and Communications (CNC 2017), 2017, doi: 10.1109/ICCNC.2017.7876251

### Richard LeDuc, Sean Peisert, Karen Stocks, Von Welch, Open Science Cyber Risk Profile (OSCRP), National Science Foundation Cybersecurity Center of Excellence (CCoE) Webinar Series, January 23, 2017,

### F. Balboa Usabiaga, B. Kallemov, B. Delmotte, A.P.S Bhalla, B. E. Griffith, A. Donev, "Hydrodynamics of suspensions of passive and active rigid particles: A rigid multiblob approach", Communications in Applied Mathematics and Computational Science, 2017, 11(2):217-296, doi: 10.2140/camcos.2016.11.217

### K. Meerbergen, W. Michiels, R. Van Beeumen, E. Mengi, "Computation of pseudospectral abscissa for large-scale nonlinear eigenvalue problems", IMA Journal of Numerical Analysis, 2017, 37:1831-1863, doi: 10.1093/imanum/drw065

### Mahdi Jamei, Anna Scaglione, Ciaran Roberts, Emma Stewart, Sean Peisert, Chuck McParland, Alex McEachern, "Automated Anomaly Detection in Distribution Grids Using µPMU Measurements", Proceedings of the 50th Hawaii International Conference on System Sciences (HICSS), Electric Energy Systems Track, Resilient Networks Minitrack, IEEE, January 2017, doi: http://hdl.handle.net/10125/41543

### John Bachan, Scott Baden, Dan Bonachea, Paul Hargrove, Steven Hofmeyr, Khaled Ibrahim, Mathias Jacquelin, Amir Kamil, Brian van Straalen, "UPC++ and GASNet: PGAS Support for Exascale Apps and Runtimes", Poster at Exascale Computing Project (ECP) Annual Meeting 2017., January 2017,

### T Nguyen, D Unat, W Zhang, A Almgren, N Farooqi, J Shalf, "Perilla: Metadata-Based Optimizations of an Asynchronous Runtime for Adaptive Mesh Refinement", International Conference for High Performance Computing, Networking, Storage and Analysis, SC, January 1, 2017, 945--956, doi: 10.1109/SC.2016.80

### P Oesterling, C Heine, GH Weber, D Morozov, G Scheuermann, "Computing and visualizing time-varying merge trees for high-dimensional data", Mathematics and Visualization, ( 2017) Pages: 87--101 doi: 10.1007/978-3-319-44684-4_5

### O Angélil, D Stone, M Wehner, CJ Paciorek, H Krishnan, W Collins, "An independent assessment of anthropogenic attribution statements for recent extreme temperature and rainfall events", Journal of Climate, 2017, 30:5--16, doi: 10.1175/JCLI-D-16-0077.1

### E. Vecharynski and C. Yang, "Preconditioned iterative methods for eigenvalue counts", Lecture Notes in Computational Science, January 1, 2017,

### Esmond Ng, Katherine J. Evans, Peter Caldwell, Forrest M. Hoffman, Charles Jackson, Kerstin Van Dam, Ruby Leung, Daniel F. Martin, George Ostrouchov, Raymond Tuminaro, Paul Ullrich, Stefan Wild, Samuel Williams, "Advances in Cross-Cutting Ideas for Computational Climate Science (AXICCS)", January 2017, doi: 10.2172/1341564

- Download File: AXICCS-Report.pdf (pdf: 4 MB)

### Ariful Azad, Mathias Jacquelin, Aydin Bulu\cc, Esmond G Ng, "The reverse Cuthill-McKee algorithm in distributed-memory", Parallel and Distributed Processing Symposium (IPDPS), 2017 IEEE International, January 2017, 22--31,

- Download File: RCM-ipdps17.pdf (pdf: 1.1 MB)

### MN Farooqi, D Unat, T Nguyen, W Zhang, A Almgren, J Shalf, "Nonintrusive AMR asynchrony for communication optimization", Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), January 1, 2017, 10417 LN:682--694, doi: 10.1007/978-3-319-64203-1_49

### J. O\ norbe, J. F. Hennawi, Z. Luki\ c, "Self-consistent Modeling of Reionization in Cosmological Hydrodynamical Simulations", Astrophysical Journal, 2017, 837:106, doi: 10.3847/1538-4357/aa6031

### A. Rorai, J. F. Hennawi, J. O\ norbe, M. White, J. X., G. Kulkarni, M. Walther, Z. Luki\ c, K.-G. Lee, "Measurement of the small-scale structure of the intergalactic medium using close quasar pairs", Science, 2017, 356:418-422, doi: 10.1126/science.aaf9346

### U Ayachit, A Bauer, EPN Duque, G Eisenhauer, N Ferrier, J Gu, KE Jansen, B Loring, Z Lukic, S Menon, D Morozov, P O Leary, R Ranjan, M Rasquin, CP Stone, V Vishwanath, GH Weber, B Whitlock, M Wolf, KJ Wu, EW Bethel, "Performance Analysis, Design Considerations, and Applications of Extreme-Scale in Situ Infrastructures", International Conference for High Performance Computing, Networking, Storage and Analysis, SC, 2017, 921--932, LBNL 1007264, doi: 10.1109/SC.2016.78

### U Ayachit, B Whitlock, M Wolf, B Loring, B Geveci, D Lonie, EW Bethel, "The SENSEI generic in situ interface", Proceedings of ISAV 2016: 2nd Workshop on In Situ Infrastructures for Enabling Extreme-Scale Analysis and Visualization - Held in conjunction with SC 2016: The International Conference for High Performance Computing, Networking, Storage and Analysis, 2017, 40--44, doi: 10.1109/ISAV.2016.13

### E. Wes Bethel, In Situ Processing Overview and Relevance to the HPC Community, SIAM Conference on Computational Science and Engineering, MS74: In Situ Methods and Infrastructures: Faster Insight Through Smarter Computing, 2017,

### M Ellis, E Georganas, R Egan, S Hofmeyr, A Buluç, B Cook, L Oliker, K Yelick, "Performance characterization of de novo genome assembly on leading parallel systems", Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2017, 10417 LN:79--91, doi: 10.1007/978-3-319-64203-1_6

### Y. Liu, A. C. Yucel, H. Bagci, A. C. Gilbert, and E. Michielssen, "Wavelet-enhanced plane-wave time-domain algorithm for analysis of transient scattering from electrically large conducting objects", IEEE Trans. Antennas Propag., 2017,

### H. Guo, Y. Liu, J. Hu, and E. Michielssen, "A butterfly-based direct integral equation solver using hierarchical LU factorization for analyzing scattering from electrically large conducting objects", IEEE Trans. Antennas Propag., 2017,

### Y. Liu, H. Guo, and E. Michielssen, "A HSS matrix-inspired butterfly-based direct solver for analyzing scattering from two-dimensional objects", IEEE AntennasWireless Propag. Lett., 2017,

### D Vasudevan, A Butko, G Michelogiannakis, D Donofrio, J Shalf, "Towards an Integrated Strategy to Preserve Digital Computing Performance Scaling Using Emerging Technologies", Springer International Publishing, January 1, 2017, 115--123, doi: 10.1007/978-3-319-67630-2_10

With the decline and eventual end of historical rates of lithographic scaling, we arrive at a crossroad where synergistic and holistic decisions are required to preserve Moore's law technology scaling. Numerous emerging technologies aim to extend digital electronics scaling of performance, energy efficiency, and computational power/density,

ranging from devices (transistors), memories, 3D integration capabilities, specialized architectures, photonics, and others.

The wide range of technology options creates the need for an integrated strategy to understand the impact of these emerging technologies on future large-scale digital systems for diverse application requirements and optimization metrics.

In this paper, we argue for a comprehensive methodology that spans the different levels of abstraction -- from materials, to devices, to complex digital systems and applications. Our approach integrates compact models of low-level characteristics of the emerging technologies to inform higher-level simulation models to evaluate their responsiveness to application requirements.

The integrated framework can then automate the search for an optimal architecture using available emerging technologies to maximize a targeted optimization metric.