Hasan Metin Aktulga

Publication Activity (10 Years)

Years Active: 2007-2024
Publications (10 Years): 33

Top Topics

Distributed Memory

Molecular Dynamics

Parallel Computation

Top Venues

Comput. Phys. Commun.

IEEE Trans. Parallel Distributed Syst.

Concurr. Comput. Pract. Exp.

Publications

Doga Dikbayir, Abdel Alsnayyan, Vishnu Naresh Boddeti, Balasubramaniam Shanker, Hasan Metin Aktulga
A Deep Learning Framework for Three Dimensional Shape Reconstruction from Phaseless Acoustic Scattering Far-field Data. CoRR (2024)
Shihab Shahriar Khan, Bryce Palmer, Christopher Edelmaier, Hasan Metin Aktulga
OpenRAND: A performance portable, reproducible random number generation library for parallel computations. SoftwareX 27 (2024)
Abdullah Alperen, Hasan Metin Aktulga, Pieter Maris, Chao Yang
Hybrid eigensolvers for nuclear configuration interaction calculations. Comput. Phys. Commun. 292 (2023)
David A. Case, Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro, Negin Forouzesh, Timothy J. Giese, Andreas W. Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet Cagri Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matías R. Machado, Hai Minh Nguyen, Kurt A. O'Hearn, Alexey V. Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason M. Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E. Cheatham, Daniel R. Roe, Adrian E. Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz Jr.
AmberTools. J. Chem. Inf. Model. 63 (20) (2023)
Shihab Shahriar Khan, Bryce Palmer, Christopher Edelmaierd, Hasan Metin Aktulga
OpenRAND: A Performance Portable, Reproducible Random Number Generation Library for Parallel Computations. CoRR (2023)
Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Götz, Kenneth M. Merz Jr.
Quantum Mechanics/Molecular Mechanics Simulations on NVIDIA and AMD Graphics Processing Units. J. Chem. Inf. Model. 63 (3) (2023)
Abdullah Alperen, Hasan Metin Aktulga, Pieter Maris, Chao Yang
Hybrid Eigensolvers for Nuclear Configuration Interaction Calculations. CoRR (2023)
Mehmet Cagri Kaymak, Samuel S. Schoenholz, Ekin D. Cubuk, Kurt A. O'Hearn, Kenneth M. Merz Jr., Hasan Metin Aktulga
End-to-End Differentiable Reactive Molecular Dynamics Simulations Using JAX. ISC (2023)
Fazlay Rabbi, Christopher S. Daley, Ümit V. Çatalyürek, Hasan Metin Aktulga
A Portable Sparse Solver Framework for Large Matrices on Heterogeneous Architectures. HIPC (2022)
Michael P. Lingg, Stephen M. Hughey, Balasubramaniam Shanker, Hasan Metin Aktulga
High Performance Evaluation of Helmholtz Potentials Using the Multi-Level Fast Multipole Algorithm. IEEE Trans. Parallel Distributed Syst. 33 (12) (2022)
Aidan P. Thompson, Hasan Metin Aktulga, Richard Berger, Dan S. Bolintineanu, W. Michael Brown, Paul S. Crozier, Pieter J. in 't Veld, Axel Kohlmeyer, Stan G. Moore, Trung Dac Nguyen, Ray Shan, Mark J. Stevens, Julien Tranchida, Christian Trott, Steven J. Plimpton
LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Comput. Phys. Commun. 271 (2022)
Abdullah Alperen, Md. Afibuzzaman, Fazlay Rabbi, M. Yusuf Özkaya, Ümit V. Çatalyürek, Hasan Metin Aktulga
An Evaluation of Task-Parallel Frameworks for Sparse Solvers on Multicore and Manycore CPU Architectures. ICPP (2021)
Doga Dikbayir, Balasubramaniam Shanker, Hasan Metin Aktulga
Optimizing Data Locality and Termination Criterion for t-SNE. IJCNN (2021)
Stephen M. Hughey, A. Alsnayyan, Hasan Metin Aktulga, T. Gao, Balasubramaniam Shanker
Fast and scalable evaluation of pairwise potentials. Comput. Phys. Commun. 255 (2020)
Nicolas Michel, Hasan Metin Aktulga, Y. Jaganathen
Toward scalable many-body calculations for nuclear open quantum systems using the Gamow Shell Model. Comput. Phys. Commun. 247 (2020)
Kurt A. O'Hearn, Abdullah Alperen, Hasan Metin Aktulga
Fast Solvers for Charge Distribution Models on Shared Memory Platforms. SIAM J. Sci. Comput. 42 (1) (2020)
Md. Afibuzzaman, Pieter Maris, Taylor Groves, Dossay Oryspayev, Brandon Cook, Chao Yang, Hasan Metin Aktulga
Evaluation of the Communication Motif for a Distributed Eigensolver using the SST Network Simulation Tool. PMBS@SC (2020)
Michael P. Lingg, Stephen M. Hughey, Doga Dikbayir, Balasubramaniam Shanker, Hasan Metin Aktulga
Exploring Task Parallelism for the Multilevel Fast Multipole Algorithm. HiPC (2020)
Michael P. Lingg, Stephen M. Hughey, Hasan Metin Aktulga, Balasubramaniam Shanker
High Performance Evaluation of Helmholtz Potentials usingthe Multi-Level Fast Multipole Algorithm. CoRR (2020)
Fazlay Rabbi, Christopher S. Daley, Hasan Metin Aktulga, Nicholas J. Wright
Evaluation of Directive-Based GPU Programming Models on a Block Eigensolver with Consideration of Large Sparse Matrices. WACCPD@SC (2019)
Md. Afibuzzaman, Fazlay Rabbi, M. Yusuf Özkaya, Hasan Metin Aktulga, Ümit V. Çatalyürek
DeepSparse: A Task-Parallel Framework for SparseSolvers on Deep Memory Architectures. HiPC (2019)
Hasan Metin Aktulga, Chris Knight, Paul K. Coffman, Kurt A. O'Hearn, Tzu-Ray Shan, Wei Jiang
Optimizing the performance of reactive molecular dynamics simulations for many-core architectures. Int. J. High Perform. Comput. Appl. 33 (2) (2019)
Kurt A. O'Hearn, Abdullah Alperen, Hasan Metin Aktulga
Performance optimization of reactive molecular dynamics simulations with dynamic charge distribution models on distributed memory platforms. ICS (2019)
Mehmet Cagri Kaymak, Hasan Metin Aktulga, Ron Fox, Sean N. Liddick
Data Analysis for Atomic Shapes in Nuclear Science. ICCS (2) (2019)
Michael P. Lingg, Stephen M. Hughey, Hasan Metin Aktulga
Optimization of the Spherical Harmonics Transform based Tree Traversals in the Helmholtz FMM Algorithm. ICPP (2018)
Md. Afibuzzaman, Bastian Schuetrumpf, Hasan Metin Aktulga
Scalable nuclear density functional theory with Sky3D. Comput. Phys. Commun. 223 (2018)
Meiyue Shao, Hasan Metin Aktulga, Chao Yang, Esmond G. Ng, Pieter Maris, James P. Vary
Accelerating nuclear configuration interaction calculations through a preconditioned block iterative eigensolver. Comput. Phys. Commun. 222 (2018)
Sudhir B. Kylasa, Hasan Metin Aktulga, Ananth Y. Grama
Reactive Molecular Dynamics on Massively Parallel Heterogeneous Architectures. IEEE Trans. Parallel Distributed Syst. 28 (1) (2017)
Hasan Metin Aktulga, Md. Afibuzzaman, Samuel Williams, Aydin Buluç, Meiyue Shao, Chao Yang, Esmond G. Ng, Pieter Maris, James P. Vary
A High Performance Block Eigensolver for Nuclear Configuration Interaction Calculations. IEEE Trans. Parallel Distributed Syst. 28 (6) (2017)
Hasan Metin Aktulga, Christopher Knight, Paul K. Coffman, Kurt A. O'Hearn, Tzu-Ray Shan, Wei Jiang
Optimizing the Performance of Reactive Molecular Dynamics Simulations for Multi-Core Architectures. CoRR (2017)
Suleyman Salin, Murat Manguoglu, Hasan Metin Aktulga
Learning the Domain of Sparse Matrices. ICMLA (2016)
Meiyue Shao, Hasan Metin Aktulga, Chao Yang, Esmond G. Ng, Pieter Maris, James P. Vary
Accelerating Nuclear Configuration Interaction Calculations through a Preconditioned Block Iterative Eigensolver. CoRR (2016)
Kurt A. O'Hearn, Hasan Metin Aktulga
Towards Fast Scalable Solvers for Charge Equilibration in Molecular Dynamics Applications. ScalA@SC (2016)
Mark Dittner, Julian Müller, Hasan Metin Aktulga, Bernd Hartke
Efficient global optimization of reactive force-field parameters. J. Comput. Chem. 36 (20) (2015)
Dossay Oryspayev, Hasan Metin Aktulga, Masha Sosonkina, Pieter Maris, James P. Vary
Performance analysis of distributed symmetric sparse matrix vector multiplication algorithm for multi-core architectures. Concurr. Comput. Pract. Exp. 27 (17) (2015)
Hasan Metin Aktulga, Chao Yang, Esmond G. Ng, Pieter Maris, James P. Vary
Improving the scalability of a symmetric iterative eigensolver for multi-core platforms. Concurr. Comput. Pract. Exp. 26 (16) (2014)
Hasan Metin Aktulga, Lin Lin, Christopher Haine, Esmond G. Ng, Chao Yang
Parallel eigenvalue calculation based on multiple shift-invert Lanczos and contour integral based spectral projection method. Parallel Comput. 40 (7) (2014)
Myoungsoo Jung, Ellis Herbert Wilson III, Wonil Choi, John Shalf, Hasan Metin Aktulga, Chao Yang, Erik Saule, Ümit V. Çatalyürek, Mahmut T. Kandemir
Exploring the future of out-of-core computing with compute-local non-volatile memory. Sci. Program. 22 (2) (2014)
Sudhir B. Kylasa, Hasan Metin Aktulga, Ananth Grama
PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs. J. Comput. Phys. 272 (2014)
Hasan Metin Aktulga, Aydin Buluç, Samuel Williams, Chao Yang
Optimizing Sparse Matrix-Multiple Vectors Multiplication for Nuclear Configuration Interaction Calculations. IPDPS (2014)
Myoungsoo Jung, Ellis Herbert Wilson, Wonil Choi, John Shalf, Hasan Metin Aktulga, Chao Yang, Erik Saule, Ümit V. Çatalyürek, Mahmut T. Kandemir
Exploring the future of out-of-core computing with compute-local non-volatile memory. SC (2013)
Zheng Zhou, Erik Saule, Hasan Metin Aktulga, Chao Yang, Esmond G. Ng, Pieter Maris, James P. Vary, Ümit V. Çatalyürek
An Out-of-Core Dataflow Middleware to Reduce the Cost of Large Scale Iterative Solvers. ICPP Workshops (2012)
Hasan Metin Aktulga, Chao Yang, Esmond G. Ng, Pieter Maris, James P. Vary
Topology-Aware Mappings for Large-Scale Eigenvalue Problems. Euro-Par (2012)
Zheng Zhou, Erik Saule, Hasan Metin Aktulga, Chao Yang, Esmond G. Ng, Pieter Maris, James P. Vary, Ümit V. Çatalyürek
An Out-of-Core Eigensolver on SSD-equipped Clusters. CLUSTER (2012)
Hasan Metin Aktulga, Joseph C. Fogarty, Sagar A. Pandit, Ananth Grama
Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques. Parallel Comput. 38 (4-5) (2012)
Hasan Metin Aktulga, Sagar Pandit, Adri C. T. van Duin, Ananth Grama
Reactive Molecular Dynamics: Numerical Methods and Algorithmic Techniques. SIAM J. Sci. Comput. 34 (1) (2012)
Hasan Metin Aktulga, Chao Yang, Ümit V. Çatalyürek, Pieter Maris, James P. Vary, Esmond G. Ng
On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections. Euro-Par Workshops (1) (2011)
Hasan Metin Aktulga, Chao Yang, Esmond G. Ng, Pieter Maris, James P. Vary
Large-scale parallel null space calculation for nuclear configuration interaction. HPCS (2011)
Esmond G. Ng, Jason Sarich, Stefan M. Wild, Todd S. Munson, Hasan Metin Aktulga, Chao Yang, Pieter Maris, James P. Vary, Nicolas Schunck, M. G. Bertolli, Markus Kortelainen, Witold Nazarewicz, Thomas Papenbrock, M. V. Stoitsov
Advancing Nuclear Physics Through TOPS Solvers and Tools CoRR (2011)
Hasan Metin Aktulga, Ioannis Kontoyiannis, Leszek Alex Lyznik, Lukasz Szpankowski, Ananth Grama, Wojciech Szpankowski
Identifying Statistical Dependence in Genomic Sequences via Mutual Information Estimates. EURASIP J. Bioinform. Syst. Biol. 2007 (2007)
Hasan Metin Aktulga, Ioannis Kontoyiannis, Leszek Alex Lyznik, Lukasz Szpankowski, Ananth Grama, Wojciech Szpankowski
Identifying statistical dependence in genomic sequences via mutual information estimates CoRR (2007)
Hasan Metin Aktulga, Ioannis Kontoyiannis, Leszek Alex Lyznik, Lukasz Szpankowski, Ananth Y. Grama, Wojciech Szpankowski
Statistical Dependence in Biological Sequences. ISIT (2007)