CRPL -- Computational Research Programming Lab | Publications, Posters and Talks

Conferences and Workshops

Vineeth Gutta, Satish Ranganathan Ganakammal, Sara Jones, Matthew Beyers, Sunita Chandrasekaran. UNNT: A novel Utility for comparing Neural Net and Tree-based models. bioRxiv - https://www.biorxiv.org/content/10.1101/2023.09.12.557300v1 (Will be published with PLOS Computational Biology) 2023
Eric Wright, Cena Brown, Damien Przybylski, Matthias Rempel, Supreet Suresh, Sunita Chandrasekaran. Analysis of MURaM, a Solar Physics Application, for Scalability, Performance and Portability. In Proceedings of the SC'23 Workshops of The International Conference on High Performance Computing, Network, Storage, and Analysis (pp. 1929-1938). 2023
Wael Elwasif, William Godoy, Nick Hagerty, J Austin Harris, Oscar Hernandez, Balint Joo, Paul Kent, Damien Lebrun-Grandie, Elijah Maccarthy, Veronica Melesse Vergara, Bronson Messer, Ross Miller, Sarp Oral, Sergei Bastrakov, Michael Bussmann, Alexander Debus, Klaus Steiniger, Jan Stephan, Rene Widera, Spencer Bryngelson, Henry Le Berre, Anand Radhakrishnan, Jeffrey Young, Sunita Chandrasekaran, Florina Ciorba, Osman Simsek, Kate Clark, Filippo Spiga, Jeff Hammond, Stone John, David Hardy, Sebastian Keller, Jean-Guillaume Piccinali, Christian Trott. Application experiences on a gpu-accelerated arm-based hpc testbed. In Proceedings of the HPC Asia 2023 Workshops (pp. 35-49). 2023
Atchley, S., Zimmer, C., Lange, J., Bernholdt, D., Melesse Vergara, V., Beck, T., Brim, M., Budiardja, R., Chandrasekaran, S., Eisenbach, M. and Evans, T., 2023, November. Frontier: Exploring Exascale. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, SC (pp. 1-16). 2023
Meyer, Felix, Benjamin Hernandez, Richard Pausch, René Widera, David Groß, Sergei Bastrakov, Axel Huebl et al. “Hardware-Agnostic Interactive Exascale In Situ Visualization of Particle-In-Cell Simulations.” In Proceedings of the Platform for Advanced Scientific Computing Conference, pp. 1-14. 2023.
Eric Wright, Johannes Doerfert, Shilei Tian, Barbara Chapman, Sunita Chandrasekaran. Implementing OpenMP’s SIMD Directive in LLVM’s GPU Runtime. DOI:10.1145/3605573.3605640 2023 ACM International Conference on Parallel Processing (ICPP), 2023
Thomas Huber, Swaroop Pophale, Nolan Baker, Michael Carr, Nikhil Rao, Jaydon Reap, Kristina Holsapple, Joshua Hoke Davis, Tobias Burnus, Seyong Lee, David E. Bernholdt, Sunita Chandrasekaran. ECP SOLLVE: Validation and Verification Testsuite Status Update and Compiler Insight for OpenMP. DOI:10.1109/P3HPC56579.2022.0001 2022 IEEE/ACM International Workshop on Performance, Portability and Productivity in HPC (P3HPC), 2022
Matt Stack, Paul Macklin, Robert Searles. Sunita Chandrasekaran (2022). OpenACC acceleration of an agent-based biological simulation framework. IEEE Computing in Science & Engineering (CiSE), 24(5), 53-63. 2022
Jarmusch, A. M., Liu, A., Munley, C., Horta, D.,Ravichandran, V., Denny, J., & Chandrasekaran, S. (2022). Analysis of Validating and Verifying OpenACC Compilers 3.0 and Above, 2022 Workshop on Accelerator Programming Using Directives (WACCPD) DOI: 10.1109/WACCPD56842.2022.00006
Holger Brunst, Sunita Chandrasekaran, Florina Ciorba, Nick Hagerty, Robert Henschel, Guido Juckeland, Junjie Li, Veronica G. Melesse Vergara, Sandra Wienke, Miguel Zavala., “First Experiences in Performance Benchmarking with the New SPEChpc 2021 Suites” In 2022 22nd IEEE International Symposium on Cluster, Cloud and Internet Computing (CCGrid) (pp. 675-684). IEEE https://ieeexplore.ieee.org/abstract/document/9826013 (arXiv: https://arxiv.org/pdf/2203.06751.pdf)
Kelling, J., Bastrakov, S., Debus, A., Kluge, T., Leinhauser, M., Pausch, R., Steiniger, K., Stephan, J., Widera, R., Young, J., Bussman, M., Chandrasekaran, S., & Juckeland, G. (2021). Challenges Porting a C++ Template-Metaprogramming Abstraction Layer to Directive-based Offloading. In International Workshop on Accelerator Programming Using Directives, pp. 92-111. Springer, Cham, 2022 (arXiv preprint arXiv:2110.08650)
Wright, Eric, Damien Przybylski, Matthias Rempel, Cena Miller, Supreeth Suresh, Shiquan Su, Richard Loft, and Sunita Chandrasekaran. “Refactoring the MPS/University of Chicago Radiative MHD (MURaM) model for GPU/CPU performance portability using OpenACC directives.” In Proceedings of the Platform for Advanced Scientific Computing Conference (PASC), pp. 1-12. 2021. https://dl.acm.org/doi/abs/10.1145/3468267.3470576
Davis J.H., Daley C., Pophale S., Huber T., Chandrasekaran S., Wright N.J. (2021) Performance Assessment of OpenMP Compilers Targeting NVIDIA V100 GPUs. In: Bhalachandra S., Wienke S., Chandrasekaran S., Juckeland G. (eds) Accelerator Programming Using Directives at SC2020. WACCPD 2020. Lecture Notes in Computer Science, vol 12655. Springer, Cham. https://doi.org/10.1007/978-3-030-74224-9_2
Wright, E., Ferrato, M., Bryer, A., Searles, R., Perilla, J. R., & Chandrasekaran, S. (2020). Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC. PLoS Comput Biol 16(5): e1007877. DOI: https://doi.org/10.1371/journal.pcbi.1007877, May 2020
Millad Ghane, Sunita Chandrasekaran, and Margaret S. Cheung. Towards A Portable Hierarchical View of Distributed Shared Memory Systems: Challenges and Solutions In The 11th International Workshop on Programming Models and Applications for Multicores and Manycores (PMAM’20 ). Article No.: 5. pp 1-10 DOI: https://doi.org/10.1145/3380536.3380542
Millad Ghane, Sunita Chandrasekaran, and Margaret S. Cheung. Gecko: Hierarchical Distributed View of Heterogeneous Shared Memory Architectures. In The 10th International Workshop on Programming Models and Applications for Multicores and Manycores (PMAM’19 ), February 17, 2019, https://doi.org/10.1145/3303084.3309489 NY, 2019
Sunita Chandrasekaran, Guido Juckeland, Meifeng Lin et. Al., Best Practices in Running Collaborative GPU Hackathons. In Proceedings of IEEE Computing in Science and Engineering (CiSE) Journal, 10.1109/MCSE.2018.042781332, NSPEC Accession Number: 17916295, pg. 95-106, 2018
Jose Monsalve Diaz, Swaroop Pophale, Oscar Hernandez, David E. Bernholdt, and Sunita Chandrasekaran. OpenMP 4.5 Validation and Verification Suite for Device offloading, In Proceedings of the International Workshop on OpenMP (IWOMP), Volume 11128, pages 82, 2018
Jose Monsalve Diaz, Swaroop Pophale, Kyle Friedline, Oscar Hernandez, David E. Bernholdt, and Sunita Chandrasekaran. 2018. Evaluating Support for OpenMP Offload Features. In the 47th International Conference on Parallel Processing Companion (ICPP ‘18). ACM, New York, NY, USA, Article 31, 10 pages. DOI: 10.1145/ 3229710.3229717
Robert Searles, Sunita Chandrasekaran, Wayne Joubert, and Oscar Hernandez. 2018. MPI + OpenACC: Accelerating Radiation Transport Mini-Application, Minisweep, on Heterogeneous Systems. In Journal of Computer Physics Communications (CPC 2018). DOI: 10.1016/j.cpc.2018.10.007
Robert Searles, Sunita Chandrasekaran, Wayne Joubert, Oscar Hernandez. 2018. Abstractions and Directives for Adapting Wavefront Algorithms to Future Architectures. In ACM proceedings of 5th Platform for Advanced Scientific Computing (PASC). DOI: 10.1145/3218176.3218228
Millad Ghane, Sunita Chandrasekaran, Robert Searles, Margaret Cheung, Oscar Hernandez, “Path forward for softwarization to tackle evolving hardware”, Proc. SPIE 10652, Disruptive Technologies in Information Sciences, 106520O, 2018, DOI: 10.1117/ 12.2304813; https://doi.org/10.1117/12.2304813
Kyle Friedline, Sunita Chandrasekaran, Graham Lopex, Oscar Hernandez. 2017. OpenACC 2.5 Validation Testsuite targeting multiple architectures. In LNCS Proceedings of 2nd International Workshop on Performance Portable Programming Models for Accelerators, LNCS, volume 10524, pp 557-575, 2017
Sergio Pino, Lori Pollock, and Sunita Chandrasekaran. Exploring translation of OpenMP to OpenACC 2.5: Lessons learned. Proceedings of the Seventh International Workshop on Accelerators and Hybrid Exascale Systems (AsHES). IEEE Press, 2017. DOI: 10.1109/IPDPSW.2017.84.
Michael Wolfe, Seyong Lee, Jungwon Kim, Xiaonan Tian, Rengan Xu, Sunita Chandrasekaran and Barbara Chapman. Implementing the OpenACC Data Model. Proceedings of the Seventh International Workshop on Accelerators and Hybrid Exascale Systems (AsHES). IEEE Press, 2017. DOI: 10.1109/IPDPSW.2017.85.
Robert Searles, Stephen Herbein, and Sunita Chandrasekaran. 2016. A Portable, High-Level Graph Analytics Framework Targeting Distributed, Heterogeneous Systems. In Proceedings of the Third International Workshop on Accelerator Programming Using Directives (WACCPD ‘16). IEEE Press, Piscataway, NJ, USA, 79-88. DOI: 10.1109/WACCPD.2016.012.

JOURNALS

Mauricio H Ferrato, Adam G Marsh, Karl R Franke, Benjamin J Huang, E Anders Kolb, Deborah DeRyckere, Douglas K Graham, Sunita Chandrasekaran, Erin L Crowgey, Machine learning classifier approaches for predicting response to RTK-Type-III Inhibitors demonstrates high accuracy using transcriptomic signatures and ex vivo data, Bioinformatics Advances, 2023;, vbad034, https://doi.org/10.1093/bioadv/vbad034
Steiniger, Klaus, Rene Widera, Sergei Bastrakov, Michael Bussmann, Sunita Chandrasekaran, Benjamin Hernandez, Kristina Holsapple et al. “EZ: An efficient, charge conserving current deposition algorithm for electromagnetic particle-in-cell simulations.” Computer Physics Communications 291 (2023): 108849.
Matt Leinhauser, Rene Widera, Sergi Bastrakov, Alex Debus, Michael Bussmann, and Sunita Chandrasekaran, Metrics and Design of an Instruction Roofline Model for AMD GPUs. ACM Transactions on Parallel Computing, Volume 9, Issue 1, March 2022, Article No.:1, pp 1–14 https://doi.org/10.1145/3505285
Eric Wright, Mauricio Ferrato, Alex Bryer, Robert Searles, Juan Perilla, Sunita Chandrasekaran. Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC. PLoS computational biology. 2020 May 13;16(5):e1007877
Diaz, J. M., Friedline, K., Pophale, S., Hernandez, O., Bernholdt, D. E., & Chandrasekaran, S. (2019). Analysis of OpenMP 4.5 Offloading in Implementations: Correctness and Overhead. Parallel Computing, 89, 102546.
Robert Searles, Sunita Chandrasekaran, Wayne Joubert, Oscar Hernandez. 2018. MPI + OpenACC: Accelerating Radiation Transport Mini-Application, Minisweep, on Heterogeneous Systems. Journal of Computer Physics Communications (CPC), https://doi.org/10.1016/j.cpc.2018.10.007, 2018
Michael Wolfe, Jungwon Kim, Xiaonan Tian, Rengan Xu, Barbara Chapman, Sunita Chandrasekaran. The OpenACC Data Model: Preliminary Study on Its Major Challenges and Implementations. Special Issue in the Journal of Parallel Computing (PARCO), Parallel Computing, \ https://doi.org/10.1016/j.parco.2018.07.003, 2018
Robert Searles, Stephen Herbein, Travis Johnston, Michela Taufer, Sunita Chandrasekaran. 2017. Creating a portable, high-level graph analytics paradigm for compute and data-intensive applications. International Journal of High Performance Computing and Networking (IJHPCN). Special Issue of High Level Programming Approaches for Accelerators. Vol. 10. DOI: 10.1504/IJHPCN.2017.10007922

TECHNICAL REPORTS

Jarmusch, A., Baker, N. & Chandrasekaran, Su. (2021). Using Jetstream for OpenMP Offloading and OpenACC Testsuites. Presentation given at the Jetstream Research Experience for Undergraduates Program Presentation Session. Link to ScholarWorks
Ferrato, Mauricio, Crowgey, Erin, Chandrasekaran, Sunita. Proposing a Machine Learning Framework for Classification of Patient Cohorts Using Genomics Data. American Medical Informatics Association (AMIA) 2020 Annual Symposium. Link to AMIA
Jarmusch, A., Baker, N., Eigenmann, R., & Chandrasekaran, S. HPC Rankings Based on Real Applications. Link to ScholarWorks
Leinhauser, M., Bastrakov, S., Widera, R., Debus, A., Bussmann, M., Juckeland, G., Arghya Chatterjee, & Chandrasekaran, S. (2020). CAAR for Frontier -An ORNL Project Jan 2020 TECHNICAL REPORT Analysis of PIConGPU’s Three Most Intensive Kernels from NVProf on Summit. University of Delaware. https://doi.org/10.13140/RG.2.2.30951.80802
Leinhauser, M., Young, J., Bastrakov, S., Widera, R., Debus, A., Bussmann, M., Juckeland, G., Arghya Chatterjee, & Chandrasekaran, S. (2020). CAAR for Frontier -An ORNL Project Analysis of PIConGPU’s Three Most Intensive Kernels from NSight Systems and NSight Compute on Summit. https://doi.org/10.13140/RG.2.2.28095.33448
Leinhauser, Matthew, Young, Jeffrey, Bastrakov, Sergei, Widera, Rene, Chatterjee, Ronnie, & Chandrasekaran, Sunita. Performance Analysis of PIConGPU: Particle-in-Cell on GPUs using NVIDIA’s NSight Systems and NSight Compute. United States. Link to PDF on OSTI

POSTERS

Jarmusch, A. M., Liu, A., Munley, C., Horta, D., Ravichandran, V., Denny, J., & Chandrasekaran, S. (2022). Analysis of Validating and Verifying OpenACC Compilers 3.0 and Above. Presented at Super Computing Conference 2022
Baker, N., Rao, N., Holsapple, K., Carr, M., Reap, J., Pophale, S., Lee, S., Bernholdt, Chandrasekaran, S., D.E., 2022. ECP SOLLVE Validation and Verification OpenMP Offloading Testsuite. Presented at Super Computing Conference 2022.
Jarmusch, A., Baker, N. & Chandrasekaran, Su. (2021). Using Jetstream for OpenMP Offloading and OpenACC Testsuites. Presentation given at the Jetstream Research Experience for Undergraduates Program Presentation Session. Presented at Super Computing Conference 2021. (Virtual)
Jarmusch, A., Baker, N., Chandrasekaran, Su., Eigenmann, R. (2020). HPC Rankings Based on Real Applications. Presentation given at the Jetstream Research Experience for Undergraduates Program Presentation Session. Presented at Super Computing Conference 2020. (Virtual)
Robert Searles, Sunita Chandrasekaran, “Abstractions and Directives for Adapting Wavefront Algorithms to Future Architectures”, GTC 2019
Mauricio Ferrato, Erin L. Crowgey, Sunita Chandrasekaran. Proposing a Machine Learning Framework for Classification of Patient Cohorts Using Genomics Data. AMIA. November 2020
Eric Wright and Mauricio Ferrato, Sunita Chandrasekaran, “Accelerating Chemical Shift Prediction for LArge-scale Biomolecular Modeling” GTC 2019
Joel Bricker, Sunita Chandrasekaran, “OpenACC Enabled Benchmark Suite on Intel Ivy Bridge” GTC 2016

TALKS (by students)

Fabian Mora, XBLang: an extensible MLIR frontend, EuroLLVM, Vienna, Austria, 2024
Eric Wright, Implementing OpenMP’s SIMD Directive in LLVM’s GPU Runtime, ICPP, Utah, 2023
Christian Munley, Aaron Jarmusch, OpenACC Validation & Verification Testsuite, OpenACC Webinar, Dec 2023
Aaron Jarmusch, OpenACC Validation & Verification Testsuite, WACCPD workshop and ACM poster competition @ SC22, Dallas, 2022
Eric Wright, Refactoring the MPS/University of Chicago Radiative MHD (MURaM) Model for GPU/CPU Performance Portability Using OpenACC Directives, PASC 2021 (Virtual)
Matthew Leinhauser, Designing an Instruction Roofline Model for AMD GPUs, Center for Accelerated Systems Understanding (CASUS), Görlitz, Germany, July 2021 (Virtual)
Eric Wright, Accelerating Solar Physics Application MURaM for GPU, National Center for Atmospheric Research (NCAR), Boulder, CO, September 2019
Robert Searles, Creating Language Extensions For Complex Parallel Patterns, National Center for Atmospheric Research (NCAR), Boulder, CO, March 2019
Sanhu Li, Sunita Chandrasekaran, Using OpenACC for NGS Techniques to create a portable and easy-to-use code base. GTC 2017 link.
Arnov Sinha, Sunita Chandrasekaran. Using OpenACC to Parallelize Irregular Algorithms on GPUs! GTC 2017 link.