Journal: IJHPCA

Volume 37, Issue 6

649 -- 0Edmond Chow. Editorial
650 -- 665Jie Chen, Zhiwei Nie, Yu Wang, Kai Wang, Fan Xu, Zhiheng Hu, Bing Zheng, Zhennan Wang, Guoli Song, Jingyi Zhang, Jie Fu, Xiansong Huang, Zhongqi Wang, Zhixiang Ren, Qiankun Wang, Daixi Li, Dongqing Wei, Bin Zhou, Chao Yang, Yonghong Tian 0001. Running ahead of evolution - AI-based simulation for predicting future high-risk SARS-CoV-2 variants
666 -- 682Darren J. Hsu, Hao Lu 0001, Aditya Kashi, Michael A. Matheson, John Gounley, Feiyi Wang, Wayne Joubert, Jens Glaser. TwoFold: Highly accurate structure and affinity prediction for protein-ligand complexes from sequences
683 -- 705Maxim Zvyagin, Alexander Brace, Kyle Hippe, Yuntian Deng, Bin Zhang, Cindy Orozco Bohorquez, Austin Clyde, Bharat Kale, Danilo Perez-Rivera, Heng Ma, Carla M. Mann, Michael W. Irvin, Defne G. Ozgulbas, Natalia Vassilieva, J. Gregory Pauloski, Logan T. Ward, Valérie Hayot-Sasson, Murali Emani, Sam Foreman, Zhen Xie, Diangen Lin, Maulik Shukla, Weili Nie, Josh Romero, Christian Dallago, Arash Vahdat, Chaowei Xiao, Thomas Gibbs, Ian T. Foster, James J. Davis 0002, Michael E. Papka, Thomas S. Brettin, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, Arvind Ramanathan. GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics

Volume 37, Issue 5

465 -- 486Philipp Grete, Joshua C. Dolence, Jonah M. Miller, Joshua Brown 0006, Ben Ryan, Andrew Gaspar, Forrest Wolfgang Glines, Sriram Swaminarayan, Jonas Lippuner, Clell J. Solomon, Galen M. Shipman, Christoph Junghans, Daniel Holladay, James M. Stone, Luke F. Roberts. Parthenon - a performance portable block-structured adaptive mesh refinement framework
487 -- 502Martin Karp, Daniele Massaro, Niclas Jansson, Alistair Hart, Jacob Wahlgren, Philipp Schlatter, Stefano Markidis. Large-Scale direct numerical simulations of turbulence using GPUs and modern Fortran
503 -- 515Sergio Iserte, Alejandro González-Barberá, Paloma Barreda, Krzysztof Rojek. A study on the performance of distributed training of data-driven CFD simulations
516 -- 529He Bai 0005, Changjun Hu, Yuhan Zhu, Dandan Chen, Genshen Chu, Shuai Ren. Accelerating cluster dynamics simulation of fission gas behavior in nuclear fuel on deep computing unit-based heterogeneous architecture supercomputer
530 -- 538Robert Schade, Tobias Kenter, Hossam Elgabarty, Michael Lass, Thomas D. Kühne, Christian Plessl. ab-initio molecular dynamics
539 -- 559Megan Hickman Fulp, Dakota Fulp, Changfeng Zou, Cooper Sanders, Ayan Biswas, Melissa C. Smith, Jon C. Calhoun. Accelerated dynamic data reduction using spatial and temporal properties
560 -- 577Noel Chalmers, Abhishek Mishra, Damon McDougall, Tim Warburton. HipBone: A performance-portable graphics processing unit-accelerated C++ version of the NekBone benchmark
578 -- 599Will Pazner, Tzanio V. Kolev, Jean-Sylvain Camier. End-to-end GPU acceleration of low-order-refined preconditioning for high-order finite element discretizations
600 -- 625Jerry Watkins, Max Carlson, Kyle Shan, Irina Tezaur, Mauro Perego, Luca Bertagna, Carolyn Kao, Matthew J. Hoffman 0004, Stephen F. Price. Performance portable ice-sheet modeling with MALI
626 -- 646Marc González 0001, Enric Morancho. Heterogeneous programming using OpenMP and CUDA/HIP for hybrid CPU-GPU scientific applications

Volume 37, Issue 3-4

211 -- 212Jack J. Dongarra, Bernard Tourancheau. Guest editors note: Special issue on clusters, clouds, and data for scientific computing
213 -- 228Emmanuel Jeannot, Guillaume Pallez, Nicolas Vidal. IO-aware Job-Scheduling: Exploiting the Impacts of Workload Characterizations to select the Mapping Strategy
229 -- 244Piotr Luszczek, Wissam M. Sid-Lakhdar, Jack J. Dongarra. Combining multitask and transfer learning with deep Gaussian processes for autotuning-based performance engineering
245 -- 259Satoshi Matsuoka, Jens Domke, Mohamed Wahib, Aleksandr Drozd, Torsten Hoefler. Myths and legends in high-performance computing
260 -- 271Naweiluo Zhou, Giorgio Scorzelli, Jakob Lüttgau, Rahul R. Kancharla, Joshua J. Kane, Robert Wheeler, Brendan P. Croom, Pania Newell, Valerio Pascucci, Michela Taufer. Orchestration of materials science workflows for heterogeneous resources at large scale
272 -- 287Jorge Ejarque, Rosa M. Badia. Automatizing the creation of specialized high-performance computing containers
288 -- 305Sadaf R. Alam, Miguel Gila, Mark Klein, Maxime Martinasso, Thomas C. Schulthess. Versatile software-defined HPC and cloud clusters on Alps supercomputer for diverse workflows
306 -- 327Sanjukta Bhowmick, Patrick Bell, Michela Taufer. A Survey of Graph Comparison Methods with Applications to Nondeterminism in High-Performance Computing
328 -- 350Vladimir Ostapenco, Laurent Lefèvre, Anne-Cécile Orgerie, Benjamin Fichel. Modeling, evaluating, and orchestrating heterogeneous environmental leverages for large-scale data center management
351 -- 379Jeffrey S. Vetter, Prasanna Date, Farah Fahim, Shruti R. Kulkarni, Petro Maksymovych, A. Alec Talin, Marc González Tallada, Pruek Vanna-Iampikul, Aaron R. Young, David Brooks 0001, Yu Cao 0001, Gu-Yeon Wei, Sung Kyu Lim, Frank Liu 0001, Matthew J. Marinella, Bobby G. Sumpter, Narasinga Rao Miniskar. Abisko: Deep codesign of an architecture for spiking neural networks using novel neuromorphic materials
380 -- 393Andrés E. Tomás, Enrique S. Quintana-Ortí, Hartwig Anzt. Fast truncated SVD of sparse and dense matrices on graphics processors
394 -- 411Hongwei Jin, Krishnan Raghavan, George Papadimitriou 0002, Cong Wang 0014, Anirban Mandal, Mariam Kiran, Ewa Deelman, Prasanna Balaprakash. Graph neural networks for detecting anomalies in scientific workflows
412 -- 433Robert Underwood, Julie Bessac, David Krasowska, Jon C. Calhoun, Sheng Di, Franck Cappello. Black-box statistical prediction of lossy compression ratios for scientific data
434 -- 441Olga Pearce, Stephanie Brink. Finding the forest in the trees: Enabling performance optimization on heterogeneous architectures through data science analysis of ensemble performance data
442 -- 461Sabra Ossen, Jeremy Musser, Luke Dalessandro, Martin Swany. INDIANA - In-Network Distributed Infrastructure for Advanced Network Applications

Volume 37, Issue 2

61 -- 81Martin Kronbichler 0002, Dmytro Sashko, Peter Munch. Enhancing data locality of the conjugate gradient method for high-order matrix-free finite-element implementations
82 -- 100José Ignacio Aliaga, Hartwig Anzt, Thomas Grützmacher, Enrique S. Quintana-Ortí, Andrés E. Tomás. Compressed basis GMRES on high-performance graphics processing units
101 -- 114John M. Dennis, Allison H. Baker, Brian Dobbins, Michael M. Bell, Jian Sun, Youngsung Kim, Ting-Yu Cha. Enabling efficient execution of a variational data assimilation application
115 -- 131Marc T. Henry de Frahan, Jon S. Rood, Marcus S. Day, Hariswaran Sitaraman, Shashank Yellapantula, Bruce A. Perry, Ray W. Grout, Ann S. Almgren, Weiqun Zhang, John B. Bell, Jacqueline H. Chen. PeleC: An adaptive mesh refinement solver for compressible reacting flows
132 -- 150Long Qu, Rached Abdelkhalak, Hatem Ltaief, Issam Said, David E. Keyes. Exploiting temporal data reuse and asynchrony in the reverse time migration
151 -- 164Jakub Sístek, Tomás Oberhuber. Acceleration of a parallel BDDC solver by using graphics processing units on subdomains
165 -- 179Florent Lopez, Théo Mary. Mixed precision LU factorization on GPU tensor cores: reducing data movement and memory footprint
180 -- 196Lukas Einkemmer, Alexander Moriggl. Semi-Lagrangian 4d, 5d, and 6d kinetic plasma simulation on large-scale GPU-equipped supercomputers
197 -- 208Jacques Middlecoff, Yonggang G. Yu, Mark W. Govett. Performance comparison of the A-grid and C-grid shallow-water models on icosahedral grids

Volume 37, Issue 1

3 -- 0Mark Parsons. Special issue: Introduction
4 -- 27Parantapa Bhattacharya, Jiangzhuo Chen, Stefan Hoops, Dustin Machi, Bryan L. Lewis, Srinivasan Venkatramanan, Mandy L. Wilson, Brian Klahn, Aniruddha Adiga, Benjamin Hurt, Joseph Outten, Abhijin Adiga, Andrew S. Warren, Young Yun Baek, Przemyslaw J. Porebski, Achla Marathe, Dawen Xie, Samarth Swarup, Anil Vullikanti, Henning S. Mortveit, Stephen G. Eubank, Christopher L. Barrett, Madhav Vinayak Marathe. Data-driven scalable pipeline using national agent-based models for real-time pandemic response and decision support
28 -- 44Abigail C. Dommer, Lorenzo Casalino, Fiona L. Kearns, Mia Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John Russo, A. Sofia F. Oliveira, Clare Morris, Anthony T. Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, S. Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders S. Christensen, Daniel G. A. Smith, Zhuoran Qiao, Sai K. Sirumalla, Michael O'Connor, Frederick R. Manby, Anima Anandkumar, David J. Hardy, James C. Phillips, Abraham C. Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang 0019, John D. McCalpin, Christopher J. Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John E. Stone, Daniel M. Zuckerman, Adrian J. Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T. Chong, Rommie E. Amaro. #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol
45 -- 57Zhe Li, Chengkun Wu, Yishui Li, Runduo Liu, Kai Lu, Ruibo Wang, Jie Liu, Chunye Gong, Canqun Yang, Xin Wang, Chang-Guo Zhan, Hai-Bin Luo. Free energy perturbation-based large-scale virtual screening for effective drug discovery against COVID-19