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Zhengji Zhao

Zhengji-Zhao.jpg
Zhengji Zhao , Ph.D.
HPC Consultant
Phone: (510) 495-2540
Fax: (510) 486-4316
1 Cyclotron Road
Mail Stop 943-256
Berkeley, CA 94720

Biographical Sketch

Zhengji Zhao joined the NERSC Division after working for three years as a postdoc in the Computational Research Division's Scientific Computing Group. In SCG she developed two new methods for computational nanoscience: the linear scaling 3D fragment (LS3DF) method for large-scale electronic structure calculations, and a new motif-based Hessian matrix method to estimate a preconditioner for nanostructures, which speeds up the convergence of atomic relaxation by at least a factor of four. Zhengji received her Ph.D. in computational physics from New York University for developing the reduced density matrix (RDM) method for electronic structure calculations, a highly accurate alternative to wavefunction-based computational chemistry methods. She received an M.S. in computer science from the Courant Institute of Mathematical Sciences, New York University; an M.S. in theoretical physics from Peking University, Beijing, China; and a B.S. in theoretical physics from Jilin University, Changchun, China.

Journal Articles

Zhengji Zhao, Juan Meza, Byounghak Lee, Hongzhang Shan, Erich Strohmaier, David Bailey, "Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations", 2009 J. Phys.: Conf. Ser. 180 012079, July 1, 2009,

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, "A divide and conquer linear scaling three dimensional fragment method for large scale electronic structure calculations", J. Phys.: Condens. Matter 20 (2008) 294203., June 24, 2008,

Maho Nakata, Bastiaan J. Braams, Katsuki Fujisawa, Mituhiro Fukuda, Jerome K. Percus, Makoto Yamashita, and Zhengji Zhao, "Variational calculation of second-order reduced density matrices by strong N-representability conditions and an accurate semidefinite programming solver", J. Chem. Phys., 128, 1, (2008), April 29, 2008,

Lin-Wang Wang, Zhengji Zhao, and Juan Meza, "Linear-scaling three-dimensional fragment method for large-scale electronic structure calculations", Phys. Rev. B 77, 165113 (2008), April 10, 2008,

M.Fukuda, B.J.B.Braams, M.Nakata, M.L.Overton, J.K.Percus, M.Yamashita, and Z. Zhao, "Large-scale semi-definite programs in electronic structure calculations", Mathematical Programming, series B 109, 553-580, Springer Berlin / Heidelberg, (2006)., January 1, 2007,

M. Nakata, B. J. Braams, M. Fukuda, J. K. Percus, M. Yamashita, and Z. Zhao, "Simple Hamiltonians which exhibit drastic failures by variational determination of the 2-RDM with some well known N-representability conditions", J. Chem. Phys., 125, 244109 (2006), December 27, 2006,

Zhengji Zhao , Lin-Wang Wang, and Fengmin Wu, "Wavefunction localizations in bulged CdSe nanowires", J. of Comp. and Theo. Nano., pp.247-251, vol.4, no. 2, (2007)., July 2, 2006,

Zhengji Zhao , Juan Meza, and Michel Van Hove, "Using Pattern Search Methods for Surface Structure Determination", J. Phys.: Condens. Matter 18, 8693-8706 (2006), June 9, 2006,

Zhao, Zhengji, Wang, Lin-Wang and Meza, Juan, "Motif based Hessian matrix for ab initio geometry optimization of nanostructures", Phys. Rev. B 73, 193309 (2006), May 17, 2006,

Zhengji Zhao , Bastiaan J. Braams, Mituhiro Fukuda, Michael L. Overton and Jerome K. Percus, "The Reduced Density Matrix Method for Electronic Structure Calculations and the Role of Three-Index Representability Conditions", J. Chem. Phys. 120, 2095 (2004), February 1, 2004,

Conference Papers

Zhengji Zhao, Katie Antypas, Nicholas J Wright, "Effects of Hyper-Threading on the NERSC workload on Edison", 2013 Cray User Group Meeting, May 9, 2013,

Jack Deslippe, Zhengji Zhao, "Comparing Compiler and Library Performance in Material Science Applications on Edison", Paper. Proceedings of the Cray User Group 2013, 2013,

Megan Bowling, Zhengji Zhao and Jack Deslippe, "The Effects of Compiler Optimizations on Materials Science and Chemistry Applications at NERSC", A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, "Shared Library Performance on Hopper", A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Zhengji Zhao, Yun (Helen) He and Katie Antypas, "Cray Cluster Compatibility Mode on Hopper", A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, Germany., May 1, 2012,

Zhengji Zhao and Nick Wright, "Performance of Density Functional Theory codes on Cray XE6", A paper presented in the Cray User Group meeting, May 23-26, 2011, Fairbanks, Alaska., May 24, 2011,

Zhengji Zhao, and Lin-Wang Wang, "The application of the LS3DF method to CdSe/CdS core/shell structures", A paper presented in the Cray User Group meeting, May 4-7, 2009, Atlanta, GA, May 4, 2009,

Lin-Wang Wang, Byounghak Lee, Hongzhang Shan, Zhengji Zhao, Juan Meza, Erich Strohmaier, David Bailey,, "Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations", An award winning paper (ACM Gordon Bell Prize for algorithm innovation in SC08), Proceedings of the 2008 ACM/IEEE conference on Supercomputing, Article No. 65 (2008)., November 20, 2008,

Book Chapters

David H. Bailey, Lin-Wang Wang, Hongzhang Shan, Zhengji Zhao, Juan Meza, Erich Strohmaier, and Byounghak Lee, "Tuning an Electronic Structure Code", a book chapter in Performance Tuning of Scientific Applications, edited by David H. Bailey, Robert F. Lucas, Samuel W. Williams (2010)., ( November 23, 2010)

Bastiaan Braams, Jerry Percus and Zhengji Zhao, "The T1 and T2 representability conditions", Reduced-Density-Matrix Mechanics -- with applications to many-electron atoms and molecules, A book edited by David Mazziotti, John Wiley Advances in Chemical Physics Series (2007)., ( March 27, 2007)

Presentation/Talks

Zhengji Zhao, NERSC, Best Practices for Best Performance on Edison, February 6, 2014,

Zhengji Zhao, NERSC, Available Software at NERSC, February 3, 2014,

Richard A. Gerber, Tina Declerck. Zhengji Zhao, Edison Update, February 12, 2013,

Overview and update on the installation and configuration of Edison, NERSC's new Cray XC30 supercomputer.

Megan Bowling, Zhengji Zhao and Jack Deslippe, The Effects of Compiler Optimizations on Materials Science and Chemistry Applications at NERSC, A talk in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, Shared Library Performance on Hopper, A talk in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,

Zhengji Zhao, Yun (Helen) He and Katie Antypas, Cray Cluster Compatibility Mode on Hopper, A talk in the Cray User Group meeting, April 29-May-3, 2012, Stuttgart, German., May 1, 2012,

Zhengji Zhao and Helen He, Using Cray Cluster Compatibility Mode on Hopper, A talk NERSC User Group meeting, Feb 2, 2012, Oakland, CA, February 2, 2012,

Zhengji Zhao and Helen He, Cray Cluster Compatibility Mode on Hopper, A Brown Bag Lunch talk at NERSC, Dec. 8, 2011, Oakland, CA, December 8, 2011,

Zhengji Zhao, Mike Davis, Katie Antypas, Rei Lee and Tina Butler, Shared Library Performance on Hopper, Oct. 26, 2011, Cray Quarterly Meeting at St Paul, MN, October 26, 2011,

Zhengji Zhao and Nick Wright, Performance of Density Functional Theory codes on Cray XE6, A talk in Cray User Group meeting 2011, May 23-26, 2011, Fairbanks, Alaska., May 23, 2011,

Zhengji Zhao, Introduction to Materials Science and Chemistry Applications at NERSC, NERSC User Training, April 5, 2011, Oakland, CA, April 5, 2011,

Zhengji Zhao, Tips to Compile Materials Science and Chemistry Codes at NERSC, NERSC User Training, April 5, 2011, Oakland, CA., April 5, 2011,

Rob Cunningham, Zhengji Zhao, Compiling Code on the XE6, A talk at NERSC Cray XE6 user training, Feb 7-8, 2011, Oakland, CA., February 7, 2011,

Zhengji Zhao, Overview NERSC Facilities and Usage, A talk at Workshop on Leadership-class Machines, Petascale Applications, and Performance Strategies, July 19–22, 2010, Snowbird, Utah, July 21, 2010,

Zhengji Zhao, Node mapping and the parallel performance of the LS3DF code on BG/P, An invited talk at ScicomP 16, May10-14, 2010,San Francesco, CA., May 10, 2010,

Zhengji Zhao, Juan Meza, Byounghak Lee, Hongzhang Shan, Erich Strohmaier, David Bailey, Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations, An invited poster presentation in SciDac meeting, June 14-18, 2009, San Diego, CA., June 14, 2009,

Zhengji Zhao, and Lin-Wang Wang, The application of the LS3DF method to CdSe/CdS core/shell structures, A talk at Cray User Group meeting, May 4-7, 2009, Atlanta, GA., May 5, 2009,

Lin-Wang Wang, Byounghak Lee, Zhengji Zhao, Hongzhang Shan, Juan Meza, Erich Strohmaier, David Bailey, Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations, An invited talk at Cray Technical Workshop North America, February 24-25, 2009, Charleston, SC., February 24, 2009,

Lin-Wang Wang, Byounghak Lee, Zhengji Zhao, Hongzhang Shan, Juan Meza, Erich Strohmaier and David Bailey, Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations, A talk in SC08, Nov 20, 2008, Austin, Texas., November 20, 2008,

Zhengji Zhao, Lin-Wang Wang and Juan Meza, A New O(N) Method for Petascale Nanoscience Simulations, the ACM Best poster (SC07) at International Conferences for High Performance Computing, Networking, Storage and Analysis,Nov. 10-16, 2007, Reno, CA., November 10, 2007,

Zhengji Zhao, Third Party Software, A talk at NERSC User Meeting, Sept. 17, 2007, Oakland, CA., September 17, 2007,

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, The linear scaling 3-dimensional fragment method for petascale nanoscience simulations, A poster presented in STANFORD 50: State of the Art & Future Directions of Computational Mathematics & Numerical Computing, March 29-31, 2007, Palo Alto, California., May 29, 2007,

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, A Linear Scaling 3-Dimensional Fragment Method for Petascale Nanoscience Simulations, A poster presented in Office of Advanced Scientific Computing Research (OSCAR) 2007 Applied Mathematics PI Meeting, May 22 - 24, 2007, Livermore, CA., May 22, 2007,

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, Linear Scaling NanoScience Simulations for Petascale Computing, A talk presented in APS March 5-9, 2007, Denver, Colorado., March 5, 2007,

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, Linear Scaling 3D Fragment Method for Petascale Nanoscience Simulations, A poster presented in SIAM Computational Science and Engineering (CSE), Feb 19-23, 2007, Costa Mesa, California., February 19, 2007,

Zhengji Zhao, Lin-Wang Wang, and Juan Meza, Linear Scaling NanoScience Simulations for Petascale Computing,, An invited talk in the HPC for Nano-science and Technology workshop, International Conference for High Performance Computing, Nov. 11-17, 2006, Tampa, FL., November 17, 2006,