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2020 – today
- 2025
[c14]JaeHyuk Kwack
, Colleen Bertoni, Umesh Unnikrishnan, Riccardo Balin, Khalid Hossain, Yasaman Ghadar, Timothy J. Williams, Abhishek Bagusetty, Mathialakan Thavappiragasam, Väinö Hatanpää, Archit Vasan, John R. Tramm, Scott Parker:
AI and HPC Applications on Leadership Computing Platforms: Performance and Scalability Studies. IPDPS 2025: 210-222- [c13]Dikshant Pratap Singh, Mathialakan Thavappiragasam, Brice Videau:
Efficient Intra-node Hierarchical Parallelisms And Dynamic Load Balancing Strategies On Heterogeneous Systems. IPDPS (Workshops) 2025: 543-552 - 2024
- [c12]Colleen Bertoni, JaeHyuk Kwack, Thomas Applencourt, Abhishek Bagusetty, Yasaman Ghadar, Brian Homerding, Christopher Knight, Ye Luo, Mathialakan Thavappiragasam, John R. Tramm, Esteban Rangel, Umesh Unnikrishnan, Timothy J. Williams, Scott Parker:
Early Application Experiences on Aurora at ALCF: Moving From Petascale to Exascale Systems. CUG 2024: 12-23 - [c11]Mathialakan Thavappiragasam, James Austin Harris, Eirik Endeve, Brice Videau:
Performance Porting the ExaStar Multi-Physics App Thornado On Heterogeneous Systems - A Fortran-OpenMP Code-Base Evaluation. IWOMP 2024: 16-30 - 2023
- [c10]Mathialakan Thavappiragasam, Vivek Kale:
CPU-GPU Tuning for Modern Scientific Applications using Node-Level Heterogeneity. HiPC 2023: 179-183 - 2022
- [j4]Russell B. Davidson, Jess Woods, T. Chad Effler, Mathialakan Thavappiragasam, Julie C. Mitchell, Jerry M. Parks, Ada Sedova:
OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances. Bioinform. 38(12): 3297-3298 (2022) - [c9]Mathialakan Thavappiragasam, Wael R. Elwasif, Ada Sedova:
Portability for GPU-accelerated molecular docking applications for cloud and HPC: can portable compiler directives provide performance across all platforms? CCGRID 2022: 975-984 - [c8]Mathialakan Thavappiragasam, Vivek Kale:
OpenMP's Asynchronous Offloading for All-pairs Shortest Path Graph Algorithms on GPUs. HiPar@SC 2022: 1-11 - [i2]Mathialakan Thavappiragasam, Wael R. Elwasif, Ada Sedova:
Portability for GPU-accelerated molecular docking applications for cloud and HPC: can portable compiler directives provide performance across all platforms? CoRR abs/2203.02096 (2022) - 2021
- [j3]Jens Glaser, Josh Vincent Vermaas, David M. Rogers, Jeff Larkin, Scott LeGrand, Swen Boehm, Matthew B. Baker, Aaron Scheinberg, Andreas F. Tillack, Mathialakan Thavappiragasam, Ada Sedova, Oscar R. Hernandez:
High-throughput virtual laboratory for drug discovery using massive datasets. Int. J. High Perform. Comput. Appl. 35(5) (2021) - [j2]Andrew J. Christlieb, Pierson T. Guthrey, William A. Sands, Mathialakan Thavappiragasam:
Parallel Algorithms for Successive Convolution. J. Sci. Comput. 86(1): 1 (2021) - [c7]Russell B. Davidson, Mathialakan Thavappiragasam, T. Chad Effler, Jess Woods, Dwayne A. Elias, Jerry M. Parks, Ada Sedova:
Modeling protein structures from predicted contacts with modern molecular dynamics potentials: accuracy, sensitivity, and refinement. BCB 2021: 21:1-21:10 - [c6]Mathialakan Thavappiragasam, Vivek Kale, Oscar R. Hernandez, Ada Sedova:
Addressing Load Imbalance in Bioinformatics and Biomedical Applications: Efficient Scheduling across Multiple GPUs. BIBM 2021: 1992-1999 - 2020
- [j1]Atanu Acharya, Rupesh Agarwal, Matthew B. Baker, Jérôme Baudry, Debsindhu Bhowmik, Swen Böhm, Kendall G. Byler, Sam Yen-Chi Chen, Leighton Coates, Connor J. Cooper, Omar Demerdash, Isabella Daidone, John D. Eblen, Sally R. Ellingson, Stefano Forli, Jens Glaser, James C. Gumbart, John A. Gunnels, Oscar R. Hernandez, Stephan Irle, Daniel W. Kneller, Andrey Kovalevsky, Jeffrey M. Larkin, Travis J. Lawrence, Scott LeGrand, Shih-Hsien Liu, Julie C. Mitchell, Gilchan Park, Jerry M. Parks, Anna Pavlova, Loukas Petridis, Duncan Poole, Line Pouchard, Arvind Ramanathan, David M. Rogers, Diogo Santos-Martins, Aaron Scheinberg, Ada Sedova, Yue Shen, Jeremy C. Smith, Micholas Dean Smith, Carlos Soto, Aristides Tsaris, Mathialakan Thavappiragasam, Andreas F. Tillack, Josh Vincent Vermaas, Van Quan Vuong, Junqi Yin, Shinjae Yoo, Mai Zahran, Laura Zanetti Polzi:
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J. Chem. Inf. Model. 60(12): 5832-5852 (2020) - [c5]Scott LeGrand, Aaron Scheinberg, Andreas F. Tillack, Mathialakan Thavappiragasam, Josh Vincent Vermaas, Rupesh Agarwal, Jeff Larkin, Duncan Poole, Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas Koch, Stefano Forli, Oscar R. Hernandez, Jeremy C. Smith, Ada Sedova:
GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research. BCB 2020: 43:1-43:10 - [c4]Mathialakan Thavappiragasam, Aaron Scheinberg, Wael R. Elwasif, Oscar R. Hernandez, Ada Sedova:
Performance Portability of Molecular Docking Miniapp On Leadership Computing Platforms. P3HPC@SC 2020: 36-44 - [i1]Andrew J. Christlieb, Pierson T. Guthrey, William A. Sands, Mathialakan Thavappiragasam:
Parallel Algorithms for Successive Convolution. CoRR abs/2007.03041 (2020)
2010 – 2019
- 2015
- [c3]Etienne Z. Gnimpieba, Mathialakan Thavappiragasam, Abalo Chango, Bill Conn, Carol M. Lushbough:
SBMLDock: Docker Driven Systems Biology Tool Development and Usage. CMSB 2015: 282-285 - 2014
- [c2]Mathialakan Thavappiragasam, Carol M. Lushbough, Etienne Z. Gnimpieba:
Heuristic parallelizable algorithm for similarity based biosystems comparison. BCB 2014: 782-789 - [c1]Mathialakan Thavappiragasam, Carol M. Lushbough, Etienne Z. Gnimpieba:
Automatic biosystems comparison using semantic and name similarity. BCB 2014: 790-796
Coauthor Index
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