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Brandon Cook

Brandon
Brandon Cook Ph.D
Application Performance Specialist
Fax: (510) 486-6459
Application Performance
1 Cyclotron Rd
MS 59R4010A
Berkeley, CA 94720 US

Biographical Sketch

Current projects include the "High Impact Science at Scale on Cori" program, understanding and analyzing performance variability on a system and application level, developing future benchmark suites, analyzing future architectures, developing tools to help NERSC users/staff be more productive, engaging users through consulting, acting as NERSC liaison for several NESAP teams, and exploring future programming models and application/runtime level fault tolerance.

Brandon received his Ph.D. in physics from Vanderbilt University in 2012, where he studied ab initio methods for quantum transport in nanomaterials. Before joining NERSC he was a postdoc at Oak Ridge National Laboratory where he developed and applied electronic structure methods to problems in material science.

Journal Articles

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. 2018;30:e4291. https://doi.org/10.1002/cpe.4291, January 2018,

Uma Tumuluri, Meijun Li, Brandon Cook, Bobby Sumpter, Sheng Dai, Zili Wu, "Surface Structure Dependence of SO2 Interaction with Ceria Nanocrystals with Well-defined Surface Facets", The Journal of Physical Chemistry C, 2015,

Jia-An Yan, Mack A Dela Cruz, Brandon Cook, Kalman Varga, "Structural, electronic and vibrational properties of few-layer 2H-and 1T-TaSe2", Scientific Reports, 2015,

Brandon Cook, Arthur Russakoff, Kálmán Varga, "Coverage dependent work function of graphene on a Cu (111) substrate with intercalated alkali metals", Applied Physics Letters, 2015,

Brandon Cook, William R French, Kálmán Varga, "Electron transport properties of carbon nanotube–graphene contacts", Applied Physics Letters, 2012,

Christopher R Iacovella, William R French, Brandon Cook, Paul RC Kent, Peter T Cummings, "Role of polytetrahedral structures in the elongation and rupture of gold nanowires", ACS Nano, 2011,

Brandon Cook, Peter Dignard, Kálmán Varga, "Calculation of electron transport in multiterminal systems using complex absorbing potentials", Physical Review B, May 16, 2011,

Brandon Cook, John Eric Goff, "Parameter space for successful soccer kicks", European Journal of Physics, 2006,

Conference Papers

C. Yang, B. Friesen, T. Kurth, B. Cook, and S. Williams, "Toward Automated Application Profiling on Cray Systems", Cray User Group (CUG) 2018, May 24, 2018,

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,

Jialin Liu, Quincey Koziol, Houjun Tang, François Tessier, Wahid Bhimji, Brandon Cook, Brian Austin, Suren Byna, Bhupender Thakur, Glenn K. Lockwood, Jack Deslippe, Prabhat, "Understanding the IO Performance Gap Between Cori KNL and Haswell", Proceedings of the 2017 Cray User Group, Redmond, WA, May 10, 2017,

The Cori system at NERSC has two compute partitions with different CPU architectures: a 2,004 node Haswell partition and a 9,688 node KNL partition, which ranked as the 5th most powerful and fastest supercomputer on the November 2016 Top 500 list. The compute partitions share a common storage configuration, and understanding the IO performance gap between them is important, impacting not only to NERSC/LBNL users and other national labs, but also to the relevant hardware vendors and software developers. In this paper, we have analyzed performance of single core and single node IO comprehensively on the Haswell and KNL partitions, and have discovered the major bottlenecks, which include CPU frequencies and memory copy performance. We have also extended our performance tests to multi-node IO and revealed the IO cost difference caused by network latency, buffer size, and communication cost. Overall, we have developed a strong understanding of the IO gap between Haswell and KNL nodes and the lessons learned from this exploration will guide us in designing optimal IO solutions in many-core era.

D Doerfler, B Austin, B Cook, J Deslippe, K Kandalla, P Mendygral, "Evaluating the Networking Characteristics of the Cray XC-40 Intel Knights Landing Based Cori Supercomputer at NERSC", Cray User Group (CUG) 2017, Redmond, WA, May 9, 2017,

T. Barnes, B. Cook, J. Deslippe, D. Doerfler, B. Friesen, Y.H. He, T. Kurth, T. Koskela, M. Lobet, T. Malas, L. Oliker, A. Ovsyannikov, A. Sarje, J.-L. Vay, H. Vincenti, S. Williams, P. Carrier, N. Wichmann, M. Wagner, P. Kent, C. Kerr, J. Dennis, "Evaluating and Optimizing the NERSC Workload on Knights Landing", PMBS 2016: 7th International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems. Supercomputing Conference, Salt Lake City, UT, USA, IEEE, November 13, 2016, LBNL LBNL-1006681, doi: 10.1109/PMBS.2016.010

Douglas Doerfler, Jack Deslippe, Samuel Williams, Leonid Oliker, Brandon Cook, Thorsten Kurth, Mathieu Lobet, Tareq M. Malas, Jean-Luc Vay, Henri Vincenti, "Applying the Roofline Performance Model to the Intel Xeon Phi Knights Landing Processor", ISC Workshops, 2016, doi: 10.1007/978-3-319-46079-6_24

Brandon Cook, Pieter Maris, Meiyue Shao, Nathan Wichmann, Marcus Wagner, John O'Neill, Thanh Phung, Gaurav Bansal, "High Performance Optimizations for Nuclear Physics Code MFDn on KNL", ISC Workshops, October 6, 2016, doi: 10.1007/978-3-319-46079-6_26

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

Presentation/Talks

Yun (Helen) He, Brandon Cook, Jack Deslippe, Brian Friesen, Richard Gerber, Rebecca Hartman-Baker, Alice Koniges, Thorsten Kurth, Stephen Leak, Woo-Sun 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, May 12, 2017,

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,

Posters

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