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ORCIDBibTeX records: Hasan Metin Aktulga
@article{DBLP:journals/cphysics/AlperenAMY23,
author = {Abdullah Alperen and
Hasan Metin Aktulga and
Pieter Maris and
Chao Yang},
title = {Hybrid eigensolvers for nuclear configuration interaction calculations},
journal = {Comput. Phys. Commun.},
volume = {292},
pages = {108888},
year = {2023},
url = {https://doi.org/10.1016/j.cpc.2023.108888},
doi = {10.1016/J.CPC.2023.108888},
timestamp = {Thu, 09 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cphysics/AlperenAMY23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/ManathungaAGM23,
author = {Madushanka Manathunga and
Hasan Metin Aktulga and
Andreas W. G{\"{o}}tz and
Kenneth M. Merz Jr.},
title = {Quantum Mechanics/Molecular Mechanics Simulations on {NVIDIA} and
{AMD} Graphics Processing Units},
journal = {J. Chem. Inf. Model.},
volume = {63},
number = {3},
pages = {711--717},
year = {2023},
url = {https://doi.org/10.1021/acs.jcim.2c01505},
doi = {10.1021/ACS.JCIM.2C01505},
timestamp = {Sat, 25 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/ManathungaAGM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/CaseABCCCFGGGIKKKKLLLLLMMNOOPPQRR23,
author = {David A. Case and
Hasan Metin Aktulga and
Kellon Belfon and
David S. Cerutti and
G. Andr{\'{e}}s Cisneros and
Vin{\'{\i}}cius Wilian D. Cruzeiro and
Negin Forouzesh and
Timothy J. Giese and
Andreas W. G{\"{o}}tz and
Holger Gohlke and
Saeed Izadi and
Koushik Kasavajhala and
Mehmet Cagri Kaymak and
Edward King and
Tom Kurtzman and
Tai{-}Sung Lee and
Pengfei Li and
Jian Liu and
Tyler Luchko and
Ray Luo and
Madushanka Manathunga and
Mat{\'{\i}}as R. Machado and
Hai Minh Nguyen and
Kurt A. O'Hearn and
Alexey V. Onufriev and
Feng Pan and
Sergio Pantano and
Ruxi Qi and
Ali Rahnamoun and
Ali Risheh and
Stephan Schott{-}Verdugo and
Akhil Shajan and
Jason M. Swails and
Junmei Wang and
Haixin Wei and
Xiongwu Wu and
Yongxian Wu and
Shi Zhang and
Shiji Zhao and
Qiang Zhu and
Thomas E. Cheatham and
Daniel R. Roe and
Adrian E. Roitberg and
Carlos Simmerling and
Darrin M. York and
Maria C. Nagan and
Kenneth M. Merz Jr.},
title = {AmberTools},
journal = {J. Chem. Inf. Model.},
volume = {63},
number = {20},
pages = {6183--6191},
year = {2023},
url = {https://doi.org/10.1021/acs.jcim.3c01153},
doi = {10.1021/ACS.JCIM.3C01153},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/CaseABCCCFGGGIKKKKLLLLLMMNOOPPQRR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/supercomputer/KaymakSCOMA23,
author = {Mehmet Cagri Kaymak and
Samuel S. Schoenholz and
Ekin D. Cubuk and
Kurt A. O'Hearn and
Kenneth M. Merz Jr. and
Hasan Metin Aktulga},
editor = {Abhinav Bhatele and
Jeff R. Hammond and
Marc Baboulin and
Carola Kruse},
title = {End-to-End Differentiable Reactive Molecular Dynamics Simulations
Using {JAX}},
booktitle = {High Performance Computing - 38th International Conference, {ISC}
High Performance 2023, Hamburg, Germany, May 21-25, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13948},
pages = {202--219},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-32041-5\_11},
doi = {10.1007/978-3-031-32041-5\_11},
timestamp = {Sat, 13 May 2023 16:51:19 +0200},
biburl = {https://dblp.org/rec/conf/supercomputer/KaymakSCOMA23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2305-15552,
author = {Abdullah Alperen and
Hasan Metin Aktulga and
Pieter Maris and
Chao Yang},
title = {Hybrid Eigensolvers for Nuclear Configuration Interaction Calculations},
journal = {CoRR},
volume = {abs/2305.15552},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2305.15552},
doi = {10.48550/ARXIV.2305.15552},
eprinttype = {arXiv},
eprint = {2305.15552},
timestamp = {Tue, 06 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2305-15552.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2310-19925,
author = {Shihab Shahriar Khan and
Bryce Palmer and
Christopher Edelmaierd and
Hasan Metin Aktulga},
title = {OpenRAND: {A} Performance Portable, Reproducible Random Number Generation
Library for Parallel Computations},
journal = {CoRR},
volume = {abs/2310.19925},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2310.19925},
doi = {10.48550/ARXIV.2310.19925},
eprinttype = {arXiv},
eprint = {2310.19925},
timestamp = {Fri, 03 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2310-19925.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cphysics/ThompsonABBBCVK22,
author = {Aidan P. Thompson and
Hasan Metin Aktulga and
Richard Berger and
Dan S. Bolintineanu and
W. Michael Brown and
Paul S. Crozier and
Pieter J. in 't Veld and
Axel Kohlmeyer and
Stan G. Moore and
Trung Dac Nguyen and
Ray Shan and
Mark J. Stevens and
Julien Tranchida and
Christian Trott and
Steven J. Plimpton},
title = {{LAMMPS} - a flexible simulation tool for particle-based materials
modeling at the atomic, meso, and continuum scales},
journal = {Comput. Phys. Commun.},
volume = {271},
pages = {108171},
year = {2022},
url = {https://doi.org/10.1016/j.cpc.2021.108171},
doi = {10.1016/J.CPC.2021.108171},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cphysics/ThompsonABBBCVK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tpds/LinggHSA22,
author = {Michael P. Lingg and
Stephen M. Hughey and
Balasubramaniam Shanker and
Hasan Metin Aktulga},
title = {High Performance Evaluation of Helmholtz Potentials Using the Multi-Level
Fast Multipole Algorithm},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {33},
number = {12},
pages = {3651--3666},
year = {2022},
url = {https://doi.org/10.1109/TPDS.2022.3165649},
doi = {10.1109/TPDS.2022.3165649},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tpds/LinggHSA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hipc/RabbiDCA22,
author = {Fazlay Rabbi and
Christopher S. Daley and
{\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and
Hasan Metin Aktulga},
title = {A Portable Sparse Solver Framework for Large Matrices on Heterogeneous
Architectures},
booktitle = {29th {IEEE} International Conference on High Performance Computing,
Data, and Analytics, HiPC 2022, Bengaluru, India, December 18-21,
2022},
pages = {145--155},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/HiPC56025.2022.00030},
doi = {10.1109/HIPC56025.2022.00030},
timestamp = {Wed, 03 May 2023 17:27:40 +0200},
biburl = {https://dblp.org/rec/conf/hipc/RabbiDCA22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpp/AlperenAROCA21,
author = {Abdullah Alperen and
Md. Afibuzzaman and
Fazlay Rabbi and
M. Yusuf {\"{O}}zkaya and
{\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and
Hasan Metin Aktulga},
editor = {Xian{-}He Sun and
Sameer Shende and
Laxmikant V. Kal{\'{e}} and
Yong Chen},
title = {An Evaluation of Task-Parallel Frameworks for Sparse Solvers on Multicore
and Manycore {CPU} Architectures},
booktitle = {{ICPP} 2021: 50th International Conference on Parallel Processing,
Lemont, IL, USA, August 9 - 12, 2021},
pages = {30:1--30:11},
publisher = {{ACM}},
year = {2021},
url = {https://doi.org/10.1145/3472456.3472476},
doi = {10.1145/3472456.3472476},
timestamp = {Thu, 07 Oct 2021 14:37:30 +0200},
biburl = {https://dblp.org/rec/conf/icpp/AlperenAROCA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ijcnn/DikbayirSA21,
author = {Doga Dikbayir and
Balasubramaniam Shanker and
Hasan Metin Aktulga},
title = {Optimizing Data Locality and Termination Criterion for t-SNE},
booktitle = {International Joint Conference on Neural Networks, {IJCNN} 2021, Shenzhen,
China, July 18-22, 2021},
pages = {1--10},
publisher = {{IEEE}},
year = {2021},
url = {https://doi.org/10.1109/IJCNN52387.2021.9534303},
doi = {10.1109/IJCNN52387.2021.9534303},
timestamp = {Wed, 29 Sep 2021 17:00:55 +0200},
biburl = {https://dblp.org/rec/conf/ijcnn/DikbayirSA21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cphysics/MichelAJ20,
author = {Nicolas Michel and
Hasan Metin Aktulga and
Y. Jaganathen},
title = {Toward scalable many-body calculations for nuclear open quantum systems
using the Gamow Shell Model},
journal = {Comput. Phys. Commun.},
volume = {247},
year = {2020},
url = {https://doi.org/10.1016/j.cpc.2019.106978},
doi = {10.1016/J.CPC.2019.106978},
timestamp = {Fri, 21 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cphysics/MichelAJ20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cphysics/HugheyAAGS20,
author = {Stephen M. Hughey and
A. Alsnayyan and
Hasan Metin Aktulga and
T. Gao and
Balasubramaniam Shanker},
title = {Fast and scalable evaluation of pairwise potentials},
journal = {Comput. Phys. Commun.},
volume = {255},
pages = {107248},
year = {2020},
url = {https://doi.org/10.1016/j.cpc.2020.107248},
doi = {10.1016/J.CPC.2020.107248},
timestamp = {Thu, 16 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cphysics/HugheyAAGS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/siamsc/OHearnAA20,
author = {Kurt A. O'Hearn and
Abdullah Alperen and
Hasan Metin Aktulga},
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
journal = {{SIAM} J. Sci. Comput.},
volume = {42},
number = {1},
pages = {C1--C22},
year = {2020},
url = {https://doi.org/10.1137/18M1224684},
doi = {10.1137/18M1224684},
timestamp = {Thu, 30 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/siamsc/OHearnAA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hipc/LinggHDSA20,
author = {Michael P. Lingg and
Stephen M. Hughey and
Doga Dikbayir and
Balasubramaniam Shanker and
Hasan Metin Aktulga},
title = {Exploring Task Parallelism for the Multilevel Fast Multipole Algorithm},
booktitle = {27th {IEEE} International Conference on High Performance Computing,
Data, and Analytics, HiPC 2020, Pune, India, December 16-19, 2020},
pages = {41--50},
publisher = {{IEEE}},
year = {2020},
url = {https://doi.org/10.1109/HiPC50609.2020.00018},
doi = {10.1109/HIPC50609.2020.00018},
timestamp = {Wed, 05 May 2021 09:39:23 +0200},
biburl = {https://dblp.org/rec/conf/hipc/LinggHDSA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pmbs-ws/AfibuzzamanMGOC20,
author = {Md. Afibuzzaman and
Pieter Maris and
Taylor L. Groves and
Dossay Oryspayev and
Brandon Cook and
Chao Yang and
Hasan Metin Aktulga},
title = {Evaluation of the Communication Motif for a Distributed Eigensolver
using the {SST} Network Simulation Tool},
booktitle = {2020 {IEEE/ACM} Performance Modeling, Benchmarking and Simulation
of High Performance Computer Systems, PMBS@SC 2020, Atlanta, GA, USA,
November 12, 2020},
pages = {138--148},
publisher = {{IEEE}},
year = {2020},
url = {https://doi.org/10.1109/PMBS51919.2020.00017},
doi = {10.1109/PMBS51919.2020.00017},
timestamp = {Sat, 18 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/pmbs-ws/AfibuzzamanMGOC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2006-15367,
author = {Michael P. Lingg and
Stephen M. Hughey and
Hasan Metin Aktulga and
Balasubramaniam Shanker},
title = {High Performance Evaluation of Helmholtz Potentials usingthe Multi-Level
Fast Multipole Algorithm},
journal = {CoRR},
volume = {abs/2006.15367},
year = {2020},
url = {https://arxiv.org/abs/2006.15367},
eprinttype = {arXiv},
eprint = {2006.15367},
timestamp = {Wed, 01 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2006-15367.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijhpca/AktulgaKCOSJ19,
author = {Hasan Metin Aktulga and
Chris Knight and
Paul K. Coffman and
Kurt A. O'Hearn and
Tzu{-}Ray Shan and
Wei Jiang},
title = {Optimizing the performance of reactive molecular dynamics simulations
for many-core architectures},
journal = {Int. J. High Perform. Comput. Appl.},
volume = {33},
number = {2},
year = {2019},
url = {https://doi.org/10.1177/1094342017746221},
doi = {10.1177/1094342017746221},
timestamp = {Fri, 04 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ijhpca/AktulgaKCOSJ19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hipc/AfibuzzamanROAC19,
author = {Md. Afibuzzaman and
Fazlay Rabbi and
M. Yusuf {\"{O}}zkaya and
Hasan Metin Aktulga and
{\"{U}}mit V. {\c{C}}ataly{\"{u}}rek},
title = {DeepSparse: {A} Task-Parallel Framework for SparseSolvers on Deep
Memory Architectures},
booktitle = {26th {IEEE} International Conference on High Performance Computing,
Data, and Analytics, HiPC 2019, Hyderabad, India, December 17-20,
2019},
pages = {373--382},
publisher = {{IEEE}},
year = {2019},
url = {https://doi.org/10.1109/HiPC.2019.00052},
doi = {10.1109/HIPC.2019.00052},
timestamp = {Thu, 20 Feb 2020 16:19:46 +0100},
biburl = {https://dblp.org/rec/conf/hipc/AfibuzzamanROAC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/KaymakAFL19,
author = {Mehmet Cagri Kaymak and
Hasan Metin Aktulga and
Ron Fox and
Sean N. Liddick},
editor = {Jo{\~{a}}o M. F. Rodrigues and
Pedro J. S. Cardoso and
J{\^{a}}nio M. Monteiro and
Roberto Lam and
Valeria V. Krzhizhanovskaya and
Michael Harold Lees and
Jack J. Dongarra and
Peter M. A. Sloot},
title = {Data Analysis for Atomic Shapes in Nuclear Science},
booktitle = {Computational Science - {ICCS} 2019 - 19th International Conference,
Faro, Portugal, June 12-14, 2019, Proceedings, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {11537},
pages = {219--233},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-22741-8\_16},
doi = {10.1007/978-3-030-22741-8\_16},
timestamp = {Tue, 11 Jun 2019 12:17:16 +0200},
biburl = {https://dblp.org/rec/conf/iccS/KaymakAFL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ics/OHearnAA19,
author = {Kurt A. O'Hearn and
Abdullah Alperen and
Hasan Metin Aktulga},
editor = {Rudolf Eigenmann and
Chen Ding and
Sally A. McKee},
title = {Performance optimization of reactive molecular dynamics simulations
with dynamic charge distribution models on distributed memory platforms},
booktitle = {Proceedings of the {ACM} International Conference on Supercomputing,
{ICS} 2019, Phoenix, AZ, USA, June 26-28, 2019},
pages = {150--159},
publisher = {{ACM}},
year = {2019},
url = {https://doi.org/10.1145/3330345.3330359},
doi = {10.1145/3330345.3330359},
timestamp = {Tue, 28 Jul 2020 07:46:43 +0200},
biburl = {https://dblp.org/rec/conf/ics/OHearnAA19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sc/RabbiDAW19,
author = {Fazlay Rabbi and
Christopher S. Daley and
Hasan Metin Aktulga and
Nicholas J. Wright},
editor = {Sandra Wienke and
Sridutt Bhalachandra},
title = {Evaluation of Directive-Based {GPU} Programming Models on a Block
Eigensolver with Consideration of Large Sparse Matrices},
booktitle = {Accelerator Programming Using Directives - 6th International Workshop,
{WACCPD} 2019, Denver, CO, USA, November 18, 2019, Revised Selected
Papers},
series = {Lecture Notes in Computer Science},
volume = {12017},
pages = {66--88},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-49943-3\_4},
doi = {10.1007/978-3-030-49943-3\_4},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/sc/RabbiDAW19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cphysics/ShaoAYNMV18,
author = {Meiyue Shao and
Hasan Metin Aktulga and
Chao Yang and
Esmond G. Ng and
Pieter Maris and
James P. Vary},
title = {Accelerating nuclear configuration interaction calculations through
a preconditioned block iterative eigensolver},
journal = {Comput. Phys. Commun.},
volume = {222},
pages = {1--13},
year = {2018},
url = {https://doi.org/10.1016/j.cpc.2017.09.004},
doi = {10.1016/J.CPC.2017.09.004},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cphysics/ShaoAYNMV18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cphysics/AfibuzzamanSA18,
author = {Md. Afibuzzaman and
Bastian Schuetrumpf and
Hasan Metin Aktulga},
title = {Scalable nuclear density functional theory with Sky3D},
journal = {Comput. Phys. Commun.},
volume = {223},
pages = {34--44},
year = {2018},
url = {https://doi.org/10.1016/j.cpc.2017.10.009},
doi = {10.1016/J.CPC.2017.10.009},
timestamp = {Fri, 21 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/cphysics/AfibuzzamanSA18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpp/LinggHA18,
author = {Michael P. Lingg and
Stephen M. Hughey and
Hasan Metin Aktulga},
title = {Optimization of the Spherical Harmonics Transform based Tree Traversals
in the Helmholtz {FMM} Algorithm},
booktitle = {Proceedings of the 47th International Conference on Parallel Processing,
{ICPP} 2018, Eugene, OR, USA, August 13-16, 2018},
pages = {91:1--91:11},
publisher = {{ACM}},
year = {2018},
url = {https://doi.org/10.1145/3225058.3225147},
doi = {10.1145/3225058.3225147},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icpp/LinggHA18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tpds/KylasaAG17,
author = {Sudhir B. Kylasa and
Hasan Metin Aktulga and
Ananth Y. Grama},
title = {Reactive Molecular Dynamics on Massively Parallel Heterogeneous Architectures},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {28},
number = {1},
pages = {202--214},
year = {2017},
url = {https://doi.org/10.1109/TPDS.2016.2548462},
doi = {10.1109/TPDS.2016.2548462},
timestamp = {Fri, 02 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tpds/KylasaAG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tpds/AktulgaAWBSYNMV17,
author = {Hasan Metin Aktulga and
Md. Afibuzzaman and
Samuel Williams and
Aydin Bulu{\c{c}} and
Meiyue Shao and
Chao Yang and
Esmond G. Ng and
Pieter Maris and
James P. Vary},
title = {A High Performance Block Eigensolver for Nuclear Configuration Interaction
Calculations},
journal = {{IEEE} Trans. Parallel Distributed Syst.},
volume = {28},
number = {6},
pages = {1550--1563},
year = {2017},
url = {https://doi.org/10.1109/TPDS.2016.2630699},
doi = {10.1109/TPDS.2016.2630699},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tpds/AktulgaAWBSYNMV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/AktulgaKCOSJ17,
author = {Hasan Metin Aktulga and
Christopher Knight and
Paul K. Coffman and
Kurt A. O'Hearn and
Tzu{-}Ray Shan and
Wei Jiang},
title = {Optimizing the Performance of Reactive Molecular Dynamics Simulations
for Multi-Core Architectures},
journal = {CoRR},
volume = {abs/1706.07772},
year = {2017},
url = {http://arxiv.org/abs/1706.07772},
eprinttype = {arXiv},
eprint = {1706.07772},
timestamp = {Fri, 04 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/AktulgaKCOSJ17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icmla/SalinMA16,
author = {Suleyman Salin and
Murat Manguoglu and
Hasan Metin Aktulga},
title = {Learning the Domain of Sparse Matrices},
booktitle = {15th {IEEE} International Conference on Machine Learning and Applications,
{ICMLA} 2016, Anaheim, CA, USA, December 18-20, 2016},
pages = {800--805},
publisher = {{IEEE} Computer Society},
year = {2016},
url = {https://doi.org/10.1109/ICMLA.2016.0143},
doi = {10.1109/ICMLA.2016.0143},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icmla/SalinMA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sc/OHearnA16,
author = {Kurt A. O'Hearn and
Hasan Metin Aktulga},
title = {Towards Fast Scalable Solvers for Charge Equilibration in Molecular
Dynamics Applications},
booktitle = {7th Workshop on Latest Advances in Scalable Algorithms for Large-Scale
Systems, ScalA@SC 2016, Salt Lake, UT, USA, November 14, 2016},
pages = {9--16},
publisher = {{IEEE} Computer Society},
year = {2016},
url = {https://doi.org/10.1109/ScalA.2016.006},
doi = {10.1109/SCALA.2016.006},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sc/OHearnA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/ShaoAYNMV16,
author = {Meiyue Shao and
Hasan Metin Aktulga and
Chao Yang and
Esmond G. Ng and
Pieter Maris and
James P. Vary},
title = {Accelerating Nuclear Configuration Interaction Calculations through
a Preconditioned Block Iterative Eigensolver},
journal = {CoRR},
volume = {abs/1609.01689},
year = {2016},
url = {http://arxiv.org/abs/1609.01689},
eprinttype = {arXiv},
eprint = {1609.01689},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/ShaoAYNMV16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/concurrency/OryspayevASMV15,
author = {Dossay Oryspayev and
Hasan Metin Aktulga and
Masha Sosonkina and
Pieter Maris and
James P. Vary},
title = {Performance analysis of distributed symmetric sparse matrix vector
multiplication algorithm for multi-core architectures},
journal = {Concurr. Comput. Pract. Exp.},
volume = {27},
number = {17},
pages = {5019--5036},
year = {2015},
url = {https://doi.org/10.1002/cpe.3499},
doi = {10.1002/CPE.3499},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/concurrency/OryspayevASMV15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcc/DittnerMAH15,
author = {Mark Dittner and
Julian M{\"{u}}ller and
Hasan Metin Aktulga and
Bernd Hartke},
title = {Efficient global optimization of reactive force-field parameters},
journal = {J. Comput. Chem.},
volume = {36},
number = {20},
pages = {1550--1561},
year = {2015},
url = {https://doi.org/10.1002/jcc.23966},
doi = {10.1002/JCC.23966},
timestamp = {Wed, 01 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcc/DittnerMAH15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/sp/SauleAYNC15,
author = {Erik Saule and
Hasan Metin Aktulga and
Chao Yang and
Esmond G. Ng and
{\"{U}}mit V. {\c{C}}ataly{\"{u}}rek},
editor = {Samee U. Khan and
Albert Y. Zomaya},
title = {An Out-of-Core Task-based Middleware for Data-Intensive Scientific
Computing},
booktitle = {Handbook on Data Centers},
pages = {647--667},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-1-4939-2092-1\_22},
doi = {10.1007/978-1-4939-2092-1\_22},
timestamp = {Sat, 30 Sep 2023 10:30:29 +0200},
biburl = {https://dblp.org/rec/reference/sp/SauleAYNC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/concurrency/AktulgaYNMV14,
author = {Hasan Metin Aktulga and
Chao Yang and
Esmond G. Ng and
Pieter Maris and
James P. Vary},
title = {Improving the scalability of a symmetric iterative eigensolver for
multi-core platforms},
journal = {Concurr. Comput. Pract. Exp.},
volume = {26},
number = {16},
pages = {2631--2651},
year = {2014},
url = {https://doi.org/10.1002/cpe.3129},
doi = {10.1002/CPE.3129},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/concurrency/AktulgaYNMV14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcphy/KylasaAG14,
author = {Sudhir B. Kylasa and
Hasan Metin Aktulga and
Ananth Grama},
title = {PuReMD-GPU: {A} reactive molecular dynamics simulation package for
GPUs},
journal = {J. Comput. Phys.},
volume = {272},
pages = {343--359},
year = {2014},
url = {https://doi.org/10.1016/j.jcp.2014.04.035},
doi = {10.1016/J.JCP.2014.04.035},
timestamp = {Wed, 19 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcphy/KylasaAG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pc/AktulgaLHNY14,
author = {Hasan Metin Aktulga and
Lin Lin and
Christopher Haine and
Esmond G. Ng and
Chao Yang},
title = {Parallel eigenvalue calculation based on multiple shift-invert Lanczos
and contour integral based spectral projection method},
journal = {Parallel Comput.},
volume = {40},
number = {7},
pages = {195--212},
year = {2014},
url = {https://doi.org/10.1016/j.parco.2014.03.002},
doi = {10.1016/J.PARCO.2014.03.002},
timestamp = {Sat, 22 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/pc/AktulgaLHNY14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sp/JungWCSAYSCK14,
author = {Myoungsoo Jung and
Ellis Herbert Wilson III and
Wonil Choi and
John Shalf and
Hasan Metin Aktulga and
Chao Yang and
Erik Saule and
{\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and
Mahmut T. Kandemir},
title = {Exploring the future of out-of-core computing with compute-local non-volatile
memory},
journal = {Sci. Program.},
volume = {22},
number = {2},
pages = {125--139},
year = {2014},
url = {https://doi.org/10.3233/SPR-140384},
doi = {10.3233/SPR-140384},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/sp/JungWCSAYSCK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ipps/AktulgaBWY14,
author = {Hasan Metin Aktulga and
Aydin Bulu{\c{c}} and
Samuel Williams and
Chao Yang},
title = {Optimizing Sparse Matrix-Multiple Vectors Multiplication for Nuclear
Configuration Interaction Calculations},
booktitle = {2014 {IEEE} 28th International Parallel and Distributed Processing
Symposium, Phoenix, AZ, USA, May 19-23, 2014},
pages = {1213--1222},
publisher = {{IEEE} Computer Society},
year = {2014},
url = {https://doi.org/10.1109/IPDPS.2014.125},
doi = {10.1109/IPDPS.2014.125},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ipps/AktulgaBWY14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sc/JungWCSAYSCK13,
author = {Myoungsoo Jung and
Ellis Herbert Wilson and
Wonil Choi and
John Shalf and
Hasan Metin Aktulga and
Chao Yang and
Erik Saule and
{\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and
Mahmut T. Kandemir},
editor = {William Gropp and
Satoshi Matsuoka},
title = {Exploring the future of out-of-core computing with compute-local non-volatile
memory},
booktitle = {International Conference for High Performance Computing, Networking,
Storage and Analysis, SC'13, Denver, CO, {USA} - November 17 - 21,
2013},
pages = {75:1--75:11},
publisher = {{ACM}},
year = {2013},
url = {https://doi.org/10.1145/2503210.2503261},
doi = {10.1145/2503210.2503261},
timestamp = {Wed, 16 Oct 2019 14:14:57 +0200},
biburl = {https://dblp.org/rec/conf/sc/JungWCSAYSCK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pc/AktulgaFPG12,
author = {Hasan Metin Aktulga and
Joseph C. Fogarty and
Sagar A. Pandit and
Ananth Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic
techniques},
journal = {Parallel Comput.},
volume = {38},
number = {4-5},
pages = {245--259},
year = {2012},
url = {https://doi.org/10.1016/j.parco.2011.08.005},
doi = {10.1016/J.PARCO.2011.08.005},
timestamp = {Sat, 22 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/pc/AktulgaFPG12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/siamsc/AktulgaPDG12,
author = {Hasan Metin Aktulga and
Sagar Pandit and
Adri C. T. van Duin and
Ananth Grama},
title = {Reactive Molecular Dynamics: Numerical Methods and Algorithmic Techniques},
journal = {{SIAM} J. Sci. Comput.},
volume = {34},
number = {1},
year = {2012},
url = {https://doi.org/10.1137/100808599},
doi = {10.1137/100808599},
timestamp = {Thu, 30 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/siamsc/AktulgaPDG12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cluster/ZhouSAYNMVC12,
author = {Zheng Zhou and
Erik Saule and
Hasan Metin Aktulga and
Chao Yang and
Esmond G. Ng and
Pieter Maris and
James P. Vary and
{\"{U}}mit V. {\c{C}}ataly{\"{u}}rek},
title = {An Out-of-Core Eigensolver on SSD-equipped Clusters},
booktitle = {2012 {IEEE} International Conference on Cluster Computing, {CLUSTER}
2012, Beijing, China, September 24-28, 2012},
pages = {248--256},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/CLUSTER.2012.76},
doi = {10.1109/CLUSTER.2012.76},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cluster/ZhouSAYNMVC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/AktulgaYNMV12,
author = {Hasan Metin Aktulga and
Chao Yang and
Esmond G. Ng and
Pieter Maris and
James P. Vary},
editor = {Christos Kaklamanis and
Theodore S. Papatheodorou and
Paul G. Spirakis},
title = {Topology-Aware Mappings for Large-Scale Eigenvalue Problems},
booktitle = {Euro-Par 2012 Parallel Processing - 18th International Conference,
Euro-Par 2012, Rhodes Island, Greece, August 27-31, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7484},
pages = {830--842},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-32820-6\_82},
doi = {10.1007/978-3-642-32820-6\_82},
timestamp = {Tue, 14 May 2019 10:00:46 +0200},
biburl = {https://dblp.org/rec/conf/europar/AktulgaYNMV12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icppw/ZhouSAYNMVC12,
author = {Zheng Zhou and
Erik Saule and
Hasan Metin Aktulga and
Chao Yang and
Esmond G. Ng and
Pieter Maris and
James P. Vary and
{\"{U}}mit V. {\c{C}}ataly{\"{u}}rek},
title = {An Out-of-Core Dataflow Middleware to Reduce the Cost of Large Scale
Iterative Solvers},
booktitle = {41st International Conference on Parallel Processing Workshops, {ICPPW}
2012, Pittsburgh, PA, USA, September 10-13, 2012},
pages = {71--80},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/ICPPW.2012.13},
doi = {10.1109/ICPPW.2012.13},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icppw/ZhouSAYNMVC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/europar/AktulgaYCMVN11,
author = {Hasan Metin Aktulga and
Chao Yang and
{\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and
Pieter Maris and
James P. Vary and
Esmond G. Ng},
editor = {Michael Alexander and
Pasqua D'Ambra and
Adam Belloum and
George Bosilca and
Mario Cannataro and
Marco Danelutto and
Beniamino Di Martino and
Michael Gerndt and
Emmanuel Jeannot and
Raymond Namyst and
Jean Roman and
Stephen L. Scott and
Jesper Larsson Tr{\"{a}}ff and
Geoffroy Vall{\'{e}}e and
Josef Weidendorfer},
title = {On Reducing {I/O} Overheads in Large-Scale Invariant Subspace Projections},
booktitle = {Euro-Par 2011: Parallel Processing Workshops - CCPI, CGWS, HeteroPar,
HiBB, HPCVirt, HPPC, HPSS, MDGS, ProPer, Resilience, UCHPC, VHPC,
Bordeaux, France, August 29 - September 2, 2011, Revised Selected
Papers, Part {I}},
series = {Lecture Notes in Computer Science},
volume = {7155},
pages = {305--314},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-29737-3\_35},
doi = {10.1007/978-3-642-29737-3\_35},
timestamp = {Wed, 19 Feb 2020 14:52:57 +0100},
biburl = {https://dblp.org/rec/conf/europar/AktulgaYCMVN11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ieeehpcs/AktulgaYNMV11,
author = {Hasan Metin Aktulga and
Chao Yang and
Esmond G. Ng and
Pieter Maris and
James P. Vary},
editor = {Waleed W. Smari and
John P. McIntire},
title = {Large-scale parallel null space calculation for nuclear configuration
interaction},
booktitle = {2011 International Conference on High Performance Computing {\&}
Simulation, {HPCS} 2012, Istanbul, Turkey, July 4-8, 2011},
pages = {176--185},
publisher = {{IEEE}},
year = {2011},
url = {https://doi.org/10.1109/HPCSim.2011.5999822},
doi = {10.1109/HPCSIM.2011.5999822},
timestamp = {Tue, 28 Jul 2020 13:09:02 +0200},
biburl = {https://dblp.org/rec/conf/ieeehpcs/AktulgaYNMV11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/parallel/GramaFAP11,
author = {Ananth Grama and
Joseph C. Fogarty and
Hasan Metin Aktulga and
Sagar Pandit},
editor = {David A. Padua},
title = {\emph{N}-Body Computational Methods},
booktitle = {Encyclopedia of Parallel Computing},
pages = {1259--1268},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-0-387-09766-4\_97},
doi = {10.1007/978-0-387-09766-4\_97},
timestamp = {Wed, 12 Jul 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/reference/parallel/GramaFAP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1110-1708,
author = {Esmond G. Ng and
Jason Sarich and
Stefan M. Wild and
Todd S. Munson and
Hasan Metin Aktulga and
Chao Yang and
Pieter Maris and
James P. Vary and
Nicolas Schunck and
M. G. Bertolli and
Markus Kortelainen and
Witold Nazarewicz and
Thomas Papenbrock and
M. V. Stoitsov},
title = {Advancing Nuclear Physics Through {TOPS} Solvers and Tools},
journal = {CoRR},
volume = {abs/1110.1708},
year = {2011},
url = {http://arxiv.org/abs/1110.1708},
eprinttype = {arXiv},
eprint = {1110.1708},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1110-1708.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ejbsb/AktulgaKLSGS07,
author = {Hasan Metin Aktulga and
Ioannis Kontoyiannis and
Leszek Alex Lyznik and
Lukasz Szpankowski and
Ananth Grama and
Wojciech Szpankowski},
title = {Identifying Statistical Dependence in Genomic Sequences via Mutual
Information Estimates},
journal = {{EURASIP} J. Bioinform. Syst. Biol.},
volume = {2007},
year = {2007},
url = {https://doi.org/10.1155/2007/14741},
doi = {10.1155/2007/14741},
timestamp = {Thu, 18 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ejbsb/AktulgaKLSGS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isit/AktulgaKLSGS07,
author = {Hasan Metin Aktulga and
Ioannis Kontoyiannis and
Leszek Alex Lyznik and
Lukasz Szpankowski and
Ananth Y. Grama and
Wojciech Szpankowski},
title = {Statistical Dependence in Biological Sequences},
booktitle = {{IEEE} International Symposium on Information Theory, {ISIT} 2007,
Nice, France, June 24-29, 2007},
pages = {2676--2680},
publisher = {{IEEE}},
year = {2007},
url = {https://doi.org/10.1109/ISIT.2007.4557183},
doi = {10.1109/ISIT.2007.4557183},
timestamp = {Wed, 16 Oct 2019 14:14:48 +0200},
biburl = {https://dblp.org/rec/conf/isit/AktulgaKLSGS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-0710-5190,
author = {Hasan Metin Aktulga and
Ioannis Kontoyiannis and
Leszek Alex Lyznik and
Lukasz Szpankowski and
Ananth Grama and
Wojciech Szpankowski},
title = {Identifying statistical dependence in genomic sequences via mutual
information estimates},
journal = {CoRR},
volume = {abs/0710.5190},
year = {2007},
url = {http://arxiv.org/abs/0710.5190},
eprinttype = {arXiv},
eprint = {0710.5190},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-0710-5190.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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