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2020 – today
- 2024
[j24]Masha Sosonkina
, Gabriel Mateescu, Peng Xu, Tosaporn Sattasathuchana, Buu Pham, Mark S. Gordon, Sarom S. Leang:
Runtime performance of a GAMESS quantum chemistry application offloaded to GPUs. Concurr. Comput. Pract. Exp. 36(23) (2024)- 2022
- [c22]Giuseppe M. J. Barca, Calum Snowdon, Jorge L. Galvez Vallejo, Fazeleh S. Kazemian, Alistair P. Rendell, Mark S. Gordon:
Scaling Correlated Fragment Molecular Orbital Calculations on Summit. SC 2022: 7:1-7:14 - 2021
- [c21]Giuseppe M. J. Barca, Jorge L. Galvez Vallejo, David L. Poole, Melisa Alkan, Ryan Stocks, Alistair P. Rendell, Mark S. Gordon:
Enabling large-scale correlated electronic structure calculations: scaling the RI-MP2 method on summit. SC 2021: 40 - 2020
- [j23]Vaibhav Sundriyal, Masha Sosonkina, David Poole, Mark S. Gordon:
Runtime power allocation approach for GAMESS hybrid CPU-GPU implementation. Concurr. Comput. Pract. Exp. 32(24) (2020) - [c20]Giuseppe M. J. Barca, David L. Poole, Jorge L. Galvez Vallejo, Melisa Alkan, Colleen Bertoni, Alistair P. Rendell, Mark S. Gordon:
Scaling the hartree-fock matrix build on summit. SC 2020: 81
2010 – 2019
- 2019
- [j22]Vaibhav Sundriyal, Kristopher Keipert, Masha Sosonkina, Mark S. Gordon:
Effect of frequency scaling granularity on energy-saving strategies. Int. J. High Perform. Comput. Appl. 33(4) (2019) - [j21]Nuwan De Silva, Matthew A. Adreance, Mark S. Gordon:
Application of a semi-empirical dispersion correction for modeling water clusters. J. Comput. Chem. 40(2): 310-315 (2019) - 2018
- [c19]Vaibhav Sundriyal, Masha Sosonkina, Bryce M. Westheimer, Mark S. Gordon:
Comparisons of core and uncore frequency scaling modes in quantum chemistry application GAMESS. SpringSim (HPC) 2018: 13:1-13:11 - 2017
- [j20]Federico Zahariev, Nuwan De Silva, Mark S. Gordon, Theresa L. Windus, Marilu Dick-Perez:
ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data. J. Chem. Inf. Model. 57(3): 391-396 (2017) - [c18]Vladimir A. Mironov, Yuri Alexeev, Kristopher Keipert, Michael D'Mello, Alexander A. Moskovsky, Mark S. Gordon:
An efficient MPI/openMP parallelization of the Hartree-Fock method for the second generation of Intel® Xeon Phi™ processor. SC 2017: 39 - [i1]Vladimir A. Mironov, Yuri Alexeev, Kristopher Keipert, Michael D'Mello, Alexander A. Moskovsky, Mark S. Gordon:
An efficient MPI/OpenMP parallelization of the Hartree-Fock method for the second generation of Intel Xeon Phi processor. CoRR abs/1708.00033 (2017) - 2016
- [j19]Yu Harabuchi, Yuriko Ono, Satoshi Maeda, Tetsuya Taketsugu, Kristopher Keipert, Mark S. Gordon:
Nontotally symmetric trifurcation of an SN2 reaction pathway. J. Comput. Chem. 37(5): 487-493 (2016) - [j18]David G. Tomlinson, Andrey Asadchev, Mark S. Gordon:
A new approach for second-order perturbation theory. J. Comput. Chem. 37(14): 1274-1282 (2016) - 2015
- [j17]Caleb Carlin, Mark S. Gordon:
Ab initio calculation of anion proton affinity and ionization potential for energetic ionic liquids. J. Comput. Chem. 36(9): 597-600 (2015) - [j16]Mark S. Gordon, David Ke Hong, Peter M. Chen, Jason Flinn, Scott A. Mahlke, Zhuoqing Morley Mao:
Tango: Accelerating Mobile Applications through Flip-Flop Replication. GetMobile Mob. Comput. Commun. 19(3): 10-13 (2015) - [c17]Mark S. Gordon, David Ke Hong, Peter M. Chen, Jason Flinn, Scott A. Mahlke, Zhuoqing Morley Mao:
Accelerating Mobile Applications through Flip-Flop Replication. MobiSys 2015: 137-150 - [c16]Ananta Tiwari, Kristopher Keipert, Adam Jundt, Joshua Peraza, Sarom S. Leang, Michael Laurenzano, Mark S. Gordon, Laura Carrington:
Performance and energy efficiency analysis of 64-bit ARM using GAMESS. Co-HPC@SC 2015: 8:1-8:10 - 2014
- [j15]Johannes M. Dieterich, David B. Krisiloff, Alexander Gaenko, Florian Libisch, Theresa L. Windus, Mark S. Gordon, Emily A. Carter:
Shared-memory parallelization of a local correlation multi-reference CI program. Comput. Phys. Commun. 185(12): 3175-3188 (2014) - 2012
- [j14]Andrey Asadchev, Mark S. Gordon:
Mixed-precision evaluation of two-electron integrals by Rys quadrature. Comput. Phys. Commun. 183(8): 1563-1567 (2012) - [c15]Lide Zhang, Mark S. Gordon, Robert P. Dick, Zhuoqing Morley Mao, Peter A. Dinda, Lei Yang:
ADEL: an automatic detector of energy leaks for smartphone applications. CODES+ISSS 2012: 363-372 - [c14]Mark S. Gordon, Davoud Anoushe Jamshidi, Scott A. Mahlke, Zhuoqing Morley Mao, Xu Chen:
COMET: Code Offload by Migrating Execution Transparently. OSDI 2012: 93-106 - [c13]Maricris L. Mayes, Graham D. Fletcher, Mark S. Gordon:
Abstract: Towards Highly Accurate Large-Scale Ab Initio Calculations Using Fragment Molecular Orbital Method in GAMESS. SC Companion 2012: 1335 - [c12]Maricris L. Mayes, Graham D. Fletcher, Mark S. Gordon:
Poster: Towards Highly Accurate Large-Scale Ab Initio Calculations Using Fragment Molecular Method in GAMESS. SC Companion 2012: 1336 - 2010
- [j13]Hui Li, Dmitri G. Fedorov, Takeshi Nagata, Kazuo Kitaura, Jan H. Jensen, Mark S. Gordon:
Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation. J. Comput. Chem. 31(4): 778-790 (2010) - [c11]Lakshminarasimhan Seshagiri, Meng-Shiou Wu, Masha Sosonkina, Zhao Zhang, Mark S. Gordon, Michael W. Schmidt:
Enhancing adaptive middleware for quantum chemistry applications with a database framework. IPDPS Workshops 2010: 1-8
2000 – 2009
- 2009
- [c10]Li Li, Joseph P. Kenny, Meng-Shiou Wu, Kevin A. Huck, Alexander Gaenko, Mark S. Gordon, Curtis L. Janssen, Lois C. McInnes, Hirotoshi Mori, Heather Netzloff, Boyana Norris, Theresa L. Windus:
Adaptive Application Composition in Quantum Chemistry. QoSA 2009: 194-211 - [c9]Teena P. Gulabani, Masha Sosonkina, Mark S. Gordon, Curtis L. Janssen, Joseph P. Kenny, Heather Netzloff, Theresa L. Windus:
Development of high performance scientific components for interoperability of computing packages. SpringSim 2009 - 2008
- [j12]Joseph P. Kenny, Curtis L. Janssen, Mark S. Gordon, Masha Sosonkina, Theresa L. Windus:
A component approach to collaborative scientific software development: Tools and techniques utilized by the Quantum Chemistry Science Application Partnership. Sci. Program. 16(4): 287-296 (2008) - [c8]Meng-Shiou Wu, Hirotoshi Mori, Jonathan L. Bentz, Theresa L. Windus, Heather Netzloff, Masha Sosonkina, Mark S. Gordon:
Constructing a performance database for large-scale quantum chemistry packages. SpringSim 2008: 393-400 - 2007
- [j11]Jonathan L. Bentz, Ryan M. Olson, Mark S. Gordon, Michael W. Schmidt, Ricky A. Kendall:
Coupled cluster algorithms for networks of shared memory parallel processors. Comput. Phys. Commun. 176(9-10): 589-600 (2007) - [j10]Lyudmila V. Slipchenko, Mark S. Gordon:
Electrostatic energy in the effective fragment potential method: Theory and application to benzene dimer. J. Comput. Chem. 28(1): 276-291 (2007) - [j9]Yuri Alexeev, Michael W. Schmidt, Theresa L. Windus, Mark S. Gordon:
A parallel distributed data CPHF algorithm for analytic Hessians. J. Comput. Chem. 28(10): 1685-1694 (2007) - [c7]Meng-Shiou Wu, Jonathan L. Bentz, Fang Peng, Masha Sosonkina, Mark S. Gordon, Ricky A. Kendall:
Integrating Performance Tools with Large-Scale Scientific Software. IPDPS 2007: 1-8 - 2006
- [j8]Timothy J. Dudley, Ryan M. Olson, Michael W. Schmidt, Mark S. Gordon:
Parallel coupled perturbed CASSCF equations and analytic CASSCF second derivatives. J. Comput. Chem. 27(3): 352-362 (2006) - [j7]Dmitri G. Fedorov, Kazuo Kitaura, Hui Li, Jan H. Jensen, Mark S. Gordon:
The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO). J. Comput. Chem. 27(8): 976-985 (2006) - [c6]Nurzhan Ustemirov, Masha Sosonkina, Mark S. Gordon, Michael W. Schmidt:
Dynamic Algorithm Selection in Parallel GAMESS Calculations. ICPP Workshops 2006: 489-496 - 2004
- [j6]Dmitri G. Fedorov, Ryan M. Olson, Kazuo Kitaura, Mark S. Gordon, Shiro Koseki:
A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO). J. Comput. Chem. 25(6): 872-880 (2004) - [j5]Heather Netzloff, Mark S. Gordon:
Fast fragments: The development of a parallel effective fragment potential method. J. Comput. Chem. 25(15): 1926-1936 (2004) - 2003
- [j4]William L. Hase, Kihyung Song, Mark S. Gordon:
Direct dynamics simulations. Comput. Sci. Eng. 5(4): 36-44 (2003) - [c5]Mark S. Gordon, Michael W. Schmidt:
Recent Advances in QM and QM/MM Methods. International Conference on Computational Science 2003: 75-83 - [c4]Ryan M. Olson, Michael W. Schmidt, Mark S. Gordon, Alistair P. Rendell:
Enabling the Efficient Use of SMP Clusters: The GAMESS/DDI Model. SC 2003: 41 - 2002
- [c3]Yuri Alexeev, Michael W. Schmidt, Theresa L. Windus, Mark S. Gordon, Ricky A. Kendall:
Performance and Implementation of Distributed Data CPHF and SCF Algorithms. CLUSTER 2002: 135- - [c2]Zhengting Gan, Yuri Alexeev, Ricky A. Kendall, Mark S. Gordon:
A Distributed Data Implementation of Parallel Full CI Program. CLUSTER 2002: 476-479 - 2001
- [j3]Cheol Ho Choi, Klaus Ruedenberg, Mark S. Gordon:
New parallel optimal-parameter fast multipole method (OPFMM). J. Comput. Chem. 22(13): 1484-1501 (2001) - [c1]Jerry A. Boatz, Mark S. Gordon, Gregory A. Voth, Sharon Hammes-Schiffer, Ruth Pachter:
New Materials Design. International Conference on Computational Science (1) 2001: 1108-1116
1990 – 1999
- 1996
- [j2]Takako Kudo, Fujiko Hashimoto, Mark S. Gordon:
Ab initio study of cyclic siloxanes (H2SiO)n: n = 3, 4, 5. J. Comput. Chem. 17(9): 1163-1170 (1996) - 1993
- [j1]Michael W. Schmidt, Kim K. Baldridge, Jerry A. Boatz, Steven T. Elbert, Mark S. Gordon, Jan H. Jensen, Shiro Koseki, Nikita Matsunaga, Kiet A. Nguyen, Shujun Su, Theresa L. Windus, Michel Dupuis, John A. Montgomery Jr.:
General atomic and molecular electronic structure system. J. Comput. Chem. 14(11): 1347-1363 (1993)
Coauthor Index
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