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Generalizable coordination of large multiscale workflows: challenges and learnings at scale

Published: 13 November 2021 Publication History

Abstract

The advancement of machine learning techniques and the heterogeneous architectures of most current supercomputers are propelling the demand for large multiscale simulations that can automatically and autonomously couple diverse components and map them to relevant resources to solve complex problems at multiple scales. Nevertheless, despite the recent progress in workflow technologies, current capabilities are limited to coupling two scales. In the first-ever demonstration of using three scales of resolution, we present a scalable and generalizable framework that couples pairs of models using machine learning and in situ feedback. We expand upon the massively parallel Multiscale Machine-Learned Modeling Infrastructure (MuMMI), a recent, award-winning workflow, and generalize the framework beyond its original design. We discuss the challenges and learnings in executing a massive multiscale simulation campaign that utilized over 600,000 node hours on Summit and achieved more than 98% GPU occupancy for more than 83% of the time. We present innovations to enable several orders of magnitude scaling, including simultaneously coordinating 24,000 jobs, and managing several TBs of new data per day and over a billion files in total. Finally, we describe the generalizability of our framework and, with an upcoming open-source release, discuss how the presented framework may be used for new applications.

Supplementary Material

MP4 File (Generalizable Coordination of Large Multiscale Ensembles_ Challenges and Learnings at Scale.mp4.mp4)
Presentation video

References

[1]
Mark James Abraham, Teemu Murtola, Roland Schulz, Szilárd Páll, Jeremy C. Smith, Berk Hess, and Erik Lindahl. 2015. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1--2 (Sept. 2015), 19--25.
[2]
Brian M. Adams, Lara E. Bauman, William J. Bohnhoff, Keith R. Dalbey, Mohamed S. Ebeida, John P. Eddy, Michael S. Eldred, Patricia D. Hough, Kenneth T. Hu, John D. Jakeman, J. Adam Stephens, Laura P. Swiler, Dena M. Vigil, and Timothy M. Wildey. 2009. Dakota, A Multilevel Parallel Object-Oriented Framework for Design Optimization, Parameter Estimation, Uncertainty Quantification, and Sensitivity Analysis: Version 6.0 User's Manual. Sandia National Laboratory.
[3]
Dong H. Ahn, Ned Bass, Albert Chu, Jim Garlick, Mark Grondona, Stephen Herbein, Helgi I. Ingólfsson, Joseph Koning, Tapasya Patki, Thomas R.W. Scogland, Becky Springmeyer, and Michela Taufer. 2020. Flux: Overcoming scheduling challenges for exascale workflows. Future Generation Computer Systems 110 (2020), 202--213.
[4]
Riccardo Alessandri, Paulo C. T. Souza, Sebastian Thallmair, Manuel N. Melo, Alex H. de Vries, and Siewert J. Marrink. 2019. Pitfalls of the Martini Model. Journal of Chemical Theory and Computation 15, 10 (2019), 5448--5460. 31498621.
[5]
Ilkay Altintas, Chad Berkley, Efrat Jaeger, Matthew Jones, Bertram Ludascher, and Steve Mock. 2004. Kepler: an extensible system for design and execution of scientific workflows. In Proceedings of the 16th International Conference on Scientific and Statistical Database Management, 2004. IEEE, 423--424.
[6]
Nojood A. Altwaijry, Michael Baron, David W. Wright, Peter V. Coveney, and Andrea Townsend-Nicholson. 2017. An Ensemble-Based Protocol for the Computational Prediction of Helix-Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics. Journal of Chemical Theory and Computation 13, 5 (2017), 2254--2270.
[7]
Argonne National Laboratory. 2021. Aurora. Retrieved March, 2021 from https://www.alcf.anl.gov/aurora
[8]
Yadu Babuji, Anna Woodard, Zhuozhao Li, Daniel S. Katz, Ben Clifford, Rohan Kumar, Lukasz Lacinski, Ryan Chard, Justin Wozniak, Ian Foster, Mike Wilde, and Kyle Chard. 2019. Parsl: Pervasive Parallel Programming in Python. In 28th ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC).
[9]
Tal Ben-Nun, Todd Gamblin, D. S. Hollman, Hari Krishnan, and Chris J. Newburn. 2020. Workflows are the New Applications: Challenges in Performance, Portability, and Productivity. In IEEE/ACM International Workshop on Performance, Portability and Productivity in HPC (P3HPC). 57--69.
[10]
Robert B. Best, Xiao Zhu, Jihyun Shim, Pedro E. M. Lopes, Jeetain Mittal, Michael Feig, and Alexander D. MacKerell. 2012. Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone Φ, Ψ and Side-Chain χ1 and χ2 Dihedral Angles. Journal of Chemical Theory and Computation 8, 9 (2012), 3257--3273. 23341755.
[11]
Abhinav Bhatele, Jayaraman J. Thiagarajan, Taylor Groves, Rushil Anirudh, Staci A. Smith, Brandon Cook, and David K. Lowenthal. 2020. The Case of Performance Variability on Dragonfly-based Systems. In 2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS). 896--905.
[12]
Harsh Bhatia, Timothy S. Carpenter, Helgi I. Ingólfsson, Gautham Dharuman, Piyush Karande, Shusen Liu, Tomas Oppelstrup, Chris Neale, Felice C. Lightstone, Brian Van Essen, James N. Glosli, and Peer-Timo Bremer. 2021. Machine Learning Based Dynamic-Importance Sampling for Adaptive Multiscale Simulations. Nature Machine Intelligence 3 (2021), 401--409.
[13]
Harsh Bhatia, Nikhil Jain, Abhinav Bhatele, Yarden Livnat, Jens Domke, Valerio Pascucci, and Peer-Timo Bremer. 2018. Interactive Investigation of Traffic Congestion on Fat-Tree Networks Using TreeScope. Computer Graphics Forum 37, 3 (2018), 561--572.
[14]
Harsh Bhatia and Joseph Y. Moon. 2020. Dynamic-Importance Sampling. https://github.com/LLNL/dynim.
[15]
J. Borgdorff, M. Ben Belgacem, C. Bona-Casas, L. Fazendeiro, D. Groen, O. Hoenen, A. Mizeranschi, J.L. Suter, D. Coster, P.V. Coveney, W. Dubitzky, A.G. Hoekstra, P. Strand, and B. Chopard. 2014. Performance of distributed multiscale simulations. Phil. Trans. R. Soc. A 372 (2014), 20130407.
[16]
Hans-Joachim Bungartz, Florian Lindner, Bernhard Gatzhammer, Miriam Mehl, Klaudius Scheufele, Alexander Shukaev, and Benjamin Uekermann. 2016. preCICE - A fully parallel library for multi-physics surface coupling. Computers & Fluids 141 (2016), 250--258.
[17]
Lorenzo Casalino, Abigail Dommer, Zied Gaieb, Emilia P. Barros, Terra Sztain, Surl-Hee Ahn, Anda Trifan, Alexander Brace, Anthony Bogetti, Heng Ma, Hyungro Lee, Matteo Turilli, Syma Khalid, Lillian Chong, Carlos Simmerling, David J. Hardy, Julio D. C. Maia, James C. Phillips, Thorsten Kurth, Abraham Stern, Lei Huang, John McCalpin, Mahidhar Tatineni, Tom Gibbs, John E. Stone, Shantenu Jha, Arvind Ramanathan, and Rommie E. Amaro. 2020. AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics. bioRxiv (2020).
[18]
David A. Case, Thomas E. Cheatham III, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M. Merz Jr., Alexey Onufriev, Carlos Simmerling, Bing Wang, and Robert J. Woods. 2005. The Amber biomolecular simulation programs. Journal of Computational Chemistry 26, 16 (2005), 1668--1688.
[19]
Bastien Chopard, Joris Borgdorff, and Alfons Hoekstra. 2014. A framework for multi-scale modelling. Philosophical Transactions of The Royal Society A 372 (2014), 20130378.
[20]
Anthony Craig, Sophie Valcke, and Laure Coquart. 2017. Development and performance of a new version of the OASIS coupler, OASIS3-MCT_3.0. Geoscientific Model Development 10, 9 (2017), 3297--3308.
[21]
Tamara L. Dahlgren, David Domyancic, Scott Brandon, Todd Gamblin, John Gyllenhaal, Rao Nimmakayala, and Richard Klein. 2015. Poster: Scaling uncertainty quantification studies to millions of jobs. In Proceedings of the 27th ACM/IEEE International Conference for High Performance Computing and Communications Conference (SC).
[22]
Ewa Deelman, Karan Vahi, Gideon Juve, Mats Rynge, Scott Callaghan, Philip J. Maechling, Rajiv Mayani, Weiwei Chen, Rafael Ferreira Da Silva, Miron Livny, and Kent Wenger. 2015. Pegasus: a Workflow Management System for Science Automation. Future Generation Computer Systems 46 (2015), 17--35.
[23]
Francesco Di Natale. 2017. Maestro Workflow Conductor. https://github.com/LLNL/maestrowf.
[24]
Francesco Di Natale, Harsh Bhatia, Timothy S. Carpenter, Chris Neale, Sara Kokkila Schumacher, Tomas Oppelstrup, Liam Stanton, Xiaohua Zhang, Shiv Sundram, Thomas R. W. Scogland, Gautham Dharuman, Michael P. Surh, Yue Yang, Claudia Misale, Lars Schneidenbach, Carlos Costa, Changhoan Kim, Bruce D'Amora, Sandrasegaram Gnanakaran, Dwight V. Nissley, Fred Streitz, Felice C. Lightstone, Peer-Timo Bremer, James N. Glosli, and Helgi I. Ingólfsson. 2019. A Massively Parallel Infrastructure for Adaptive Multiscale Simulations: Modeling RAS Initiation Pathway for Cancer. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC '19). ACM, New York, NY, USA, Article 57, 16 pages.
[25]
Jack Dongarra, Pete Beckman, Terry Moore, Patrick Aerts, Giovanni Aloisio, Jean-Claude Andre, David Barkai, Jean-Yves Berthou, Taisuke Boku, Bertrand Braunschweig, Franck Cappello, Barbara Chapman, Xuebin Chi, Alok Choudhary, Sudip Dosanjh, Thom Dunning, Sandro Fiore, Al Geist, Bill Gropp, Robert Harrison, Mark Hereld, Michael Heroux, Adolfy Hoisie, Koh Hotta, Zhong Jin, Yutaka Ishikawa, Fred Johnson, Sanjay Kale, Richard Kenway, David Keyes, Bill Kramer, Jesus Labarta, Alain Lichnewsky, Thomas Lippert, Bob Lucas, Barney Maccabe, Satoshi Matsuoka, Paul Messina, Peter Michielse, Bernd Mohr, Matthias S. Mueller, Wolfgang E. Nagel, Hiroshi Nakashima, Michael E Papka, Dan Reed, Mitsuhisa Sato, Ed Seidel, John Shalf, David Skinner, Marc Snir, Thomas Sterling, Rick Stevens, Fred Streitz, Bob Sugar, Shinji Sumimoto, William Tang, John Taylor, Rajeev Thakur, Anne Trefethen, Mateo Valero, Aad van der Steen, Jeffrey Vetter, Peg Williams, Robert Wisniewski, and Kathy Yelick. 2011. The International Exascale Software Project roadmap. The International Journal of High Performance Computing Applications 25, 1 (2011), 3--60.
[26]
Florent Duchaine, Stéphan Jauré, Damien Poitou, Eric Quémerais, Gabriel Staffelbach, Thierry Morel, and Laurent Gicquel. 2015. Analysis of high performance conjugate heat transfer with the OpenPALM coupler. Computational Science & Discovery 8, 1 (July 2015), 015003.
[27]
Ernest J. Friedman-Hill, Edward L. Hoffman, Marcus J. Gibson, Robert L. Clay, and Kevin H. Olson. 2015. Incorporating Workflow for V&V/UQ in the Sandia Analysis Workbench. Technical Report. Sandia National Lab.(SNL-NM), Albuquerque, NM (United States).
[28]
Todd Gamblin, Matthew LeGendre, Michael R. Collette, Gregory L. Lee, Adam Moody, Bronis R. de Supinski, and Scott Futral. 2015. The Spack Package Manager: Bringing Order to HPC Software Chaos. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (Austin, Texas) (SC '15). ACM, New York, NY, USA, Article 40, 12 pages.
[29]
Todd Gamblin and The Spack Team. 2020. Spack. https://github.com/spack/spack.
[30]
James N. Glosli, David F. Richards, Kyle J. Caspersen, Robert E. Rudd, John A. Gunnels, and Frederick H. Streitz. 2007. Extending Stability Beyond CPU Millennium: A Micron-scale Atomistic Simulation of Kelvin-Helmholtz Instability. In Proceedings of the 2007 ACM/IEEE Conference on Supercomputing (Reno, Nevada). ACM, New York, NY, USA, Article 58, 11 pages.
[31]
John M.A. Grime, James F. Dama, Barbie K. Ganser-Pornillos, Cora L. Woodward, Grant J. Jensen, Mark Yeager, and Gregory A. Voth. 2016. Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly. Nature Communications 7 (2016), 11568.
[32]
Alfons Hoekstra, Bastien Chopard, and Peter Coveney. 2014. Multiscale modelling and simulation: A position paper. Philosophical Transactions of The Royal Society A 372 (2014), 20130377.
[33]
Tsuyoshi Ichimura, Kohei Fujita, Takuma Yamaguchi, Akira Naruse, Jack C. Wells, Thomas C. Schulthess, Tjerk P. Straatsma, Christopher J. Zimmer, Maxime Martinasso, Kengo Nakajima, Muneo Hori, and Lalith Maddegedara. 2018. A Fast Scalable Implicit Solver for Nonlinear Time-evolution Earthquake City Problem on Low-ordered Unstructured Finite Elements with Artificial Intelligence and Transprecision Computing. In Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis (SC '18). IEEE Press, Piscataway, NJ, USA, 627--637.
[34]
Helgi I. Ingólfsson, Harsh Bhatia, Talia Zeppelin, W. F. Drew Bennett, Kristy A. Carpenter, Pin-Chia Hsu, Gautham Dharuman, Peer-Timo Bremer, Birgit Schiøtt, Felice C. Lightstone, and Timothy S. Carpenter. 2020. Capturing Biologically Complex Tissue-Specific Membranes at Different Levels of Compositional Complexity. The Journal of Physical Chemistry B 124, 36 (2020), 7819--7829. 32790367.
[35]
Helgi I. Ingólfsson, Timothy S. Carpenter, Harsh Bhatia, Peer-Timo Bremer, Siewert J. Marrink, and Felice C. Lightstone. 2017. Computational Lipidomics of the Neuronal Plasma Membrane. Biophysical Journal 113, 10 (Nov. 2017), 2271--2280.
[36]
Helgi I. Ingólfsson, Cesar A. Lopez, Jaakko J. Uusitalo, Djurre H. de Jong, Srinivasa M. Gopal, Xavier Periole, and Siewert J. Marrink. 2014. The power of coarse graining in biomolecular simulations. WIREs Computational Molecular Science 4, 3 (2014), 225--248.
[37]
Helgi I. Ingólfsson, Chris Neale, Timothy S. Carpenter, Rebika Shrestha, Cesar A López, Timothy H. Tran, Tomas Oppelstrup, Harsh Bhatia, Liam G. Stanton, Xiaohua Zhang, Shiv Sundram, Francesco Di Natale, Animesh Agarwal, Gautham Dharuman, Sara I. L. Kokkila Schumacher, Thomas Turbyville, Gulcin Gulten, Que N. Van, Debanjan Goswami, Frantz Jean-Francios, Constance Agamasu, De Chen, Jeevapani J. Hettige, Timothy Travers, Sumantra Sarkar, Michael P. Surh, Yue Yang, Adam Moody, Shusen Liu, Brian C. Van Essen, Arthur F. Voter, Arvind Ramanathan, Nicolas W. Hengartner, Dhirendra K. Simanshu, Andrew G. Stephen, Peer-Timo Bremer, S. Gnanakaran, James N. Glosli, Felice C. Lightstone, Frank McCormick, Dwight V. Nissley, and Frederick H. Streitz. 2020. Machine Learning-driven Multiscale Modeling Reveals Lipid-Dependent Dynamics of RAS Signaling Proteins. (2020). Preprint.
[38]
Sam Ade Jacobs, Tim Moon, Kevin McLoughlin, Derek Jones, David Hysom, Dong H. Ahn, John Gyllenhaal, Pythagoras Watson, Felice C. Lightstone, Jonathan E. Allen, Ian Karlin, and Brian Van Essen. 2020. Enabling Rapid COVID-19 Small Molecule Drug Design Through Scalable Deep Learning of Generative Models. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC '20). ACM, New York, NY, USA. Finalist for the 2020 Gordon Bell Special Prize.
[39]
Anubhav Jain, Shyue Ping Ong, Wei Chen, Bharat Medasani, Xiaohui Qu, Michael Kocher, Miriam Brafman, Guido Petretto, Gian-Marco Rignanese, Geoffroy Hautier, Daniel Gunter, and Kristin A. Persson. 2015. FireWorks: a dynamic workflow system designed for high-throughput applications. Concurrency and Computation: Practice and Experience 27, 17 (2015), 5037--5059. CPE-14-0307.R2.
[40]
Nikhil Jain, Abhinav Bhatele, Sam White, Todd Gamblin, and Laxmikant V. Kale. 2016. Evaluating HPC Networks via Simulation of Parallel Workloads. In SC '16: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis. 154--165.
[41]
Hervé Jégou, Matthijs Douze, Jeff Johnson, and Lucas Hosseini. [n.d.]. FAISS. https://github.com/facebookresearch/faiss.
[42]
Jeff Johnson, Matthijs Douze, and Hervé Jégou. 2019. Billion-scale similarity search with GPUs. IEEE Transactions on Big Data (2019).
[43]
Dirk Kessler, Michael Gmachl, Andreas Mantoulidis, Laetitia J. Martin, Andreas Zoephel, Moriz Mayer, Andreas Gollner, David Covini, Silke Fischer, Thomas Gerstberger, Teresa Gmaschitz, Craig Goodwin, Peter Greb, Daniela Häring, Wolfgang Hela, Johann Hoffmann, Jale Karolyi-Oezguer, Petr Knesl, Stefan Kornigg, Manfred Koegl, Roland Kousek, Lyne Lamarre, Franziska Moser, Silvia Munico-Martinez, Christoph Peinsipp, Jason Phan, Jörg Rinnenthal, Jiqing Sai, Christian Salamon, Yvonne Scherbantin, Katharina Schipany, Renate Schnitzer, Andreas Schrenk, Bernadette Sharps, Gabriella Siszler, Qi Sun, Alex Waterson, Bernhard Wolkerstorfer, Markus Zeeb, Mark Pearson, Stephen W. Fesik, and Darryl B. McConnell. 2019. Drugging an undruggable pocket on KRAS. Proceedings of the National Academy of Sciences 116, 32 (2019), 15823--15829.
[44]
Kai J. Kohlhoff, Diwakar Shukla, Morgan Lawrenz, Gregory R. Bowman, David E. Konerding, Dan Belov, Russ B. Altman, and Vijay S. Pande. 2014. Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nature Chemistry 6, 1 (2014), 15--21.
[45]
V.V. Krzhizhanovskaya, D. Groen, B. Bozak, and A.G. Hoekstra. 2015. Multiscale Modelling and Simulation Workshop: 12 Years of Inspiration. Procedia Computer Science 51 (2015), 1082--1087. International Conference On Computational Science, ICCS 2015.
[46]
Redis Labs. 2018. Redis. https://redis.io.
[47]
Lawrence Livermore National Laboratory. 2019. Lassen. Retrieved March, 2021 from https://hpc.llnl.gov/hardware/platforms/lassen
[48]
Lawrence Livermore National Laboratory. 2021. El Capitan. https://www.llnl.gov/news/llnl-and-hpe-partner-amd-el-capitan-projected-worlds-fastest-supercomputer
[49]
Boyang Li, Sudheer Chunduri, Kevin Harms, Yuping Fan, and Zhiling Lan. 2019. The Effect of System Utilization on Application Performance Variability. In Proceedings of the 9th International Workshop on Runtime and Operating Systems for Supercomputers (Phoenix, AZ, USA) (ROSS '19). Association for Computing Machinery, New York, NY, USA, 11--18.
[50]
Umberto M.B. Marconi and Pedro Tarazona. 1999. Dynamic density functional theory of fluids. The Journal of chemical physics 110, 16 (1999), 8032--8044.
[51]
Siewert J. Marrink, H. Jelger Risselada, Serge Yefimov, D. Peter Tieleman, and Alex H. de Vries. 2007. The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations. The Journal of Physical Chemistry B 111, 27 (July 2007), 7812--7824.
[52]
Manuel N. Melo, Clément Arnarez, Hendrik Sikkema, Neeraj Kumar, Martin Walko, Herman J. C. Berendsen, Armagan Kocer, Siewert J. Marrink, and Helgi I. Ingólfsson. 2017. High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating. Journal of the American Chemical Society 139, 7 (Feb. 2017), 2664--2671.
[53]
Misako Nagasaka, Yiwei Li, Ammar Sukari, Sai-Hong Ignatius Ou, Mohammed Najeeb Al-Hallak, and Asfar S. Azmi. 2020. KRAS G12C Game of Thrones, which direct KRAS inhibitor will claim the iron throne? Cancer Treatment Reviews 84 (2020), 101974.
[54]
Oak Ridge National Laboratory. 2019. Summit. Retrieved March, 2021 from https://www.olcf.ornl.gov/olcf-resources/compute-systems/summit
[55]
Alexander J. Pak, John M. A. Grime, Prabuddha Sengupta, Antony K. Chen, Aleksander E.P. Durumeric, Anand Srivastava, Mark Yeager, John A.G. Briggs, Jennifer Lippincott-Schwartz, and Gregory A. Voth. 2017. Immature HIV-1 lattice assembly dynamics are regulated by scaffolding from nucleic acid and the plasma membrane. Proceddings of the National Academy of Sciences 114, 47 (2017), E10056--E10065.
[56]
Albert C. Pan, Daniel Jacobson, Konstantin Yatsenko, Duluxan Sritharan, Thomas M. Weinreich, and David E. Shaw. 2019. Atomic-level characterization of protein-protein association. Proceedings of the National Academy of Sciences 116, 10 (2019), 4244--4249.
[57]
J. Luc Peterson, Ben Bay, Joe Koning, Peter Robinson, Jessica Semler, Jeremy White, Rushil Anirudh, Kevin Athey, Peer-Timo Bremer, Francesco Di Natale, David Fox, Jim A. Gaffney, Sam A. Jacobs, Bogdan Kustowski Bhavya Kailkhura, Steven Langer, Brian Spears, Jayaraman J. Thiagarajan, Brian Van Essen, and Jae-Seung Yeom. 2019. Merlin: Enabling Machine Learning-Ready HPC Ensembles. https://arxiv.org/abs/1912.02892
[58]
Jayson L. Peterson, Kelli D. Humbird, John E. Field, Scott T. Brandon, Steve H. Langer, Ryan C. Nora, Brian K. Spears, and Paul T. Springer. 2017. Zonal Flow Generation in Inertial Confinement Fusion Implosions. Physics of Plasmas 24, 3 (2017), 032702.
[59]
Ian A. Prior, Fiona E. Hood, and James L. Hartley. 2020. The Frequency of Ras Mutations in Cancer. Cancer Research 80, 14 (2020), 2969--2974.
[60]
Benedict J. Reynwar, Gregoria Illya, Vagelis A. Harmandaris, Martin M. Müller, Kurt Kremer, and Markus Deserno. 2007. Aggregation and vesiculation of membrane proteins by curvature-mediated interactions. Nature 447, 7143 (2007), 461.
[61]
Rob Farber. 2020. Workflow Technologies impact SC20 Gorden Bell COVID-19 Award Winner and Two of the Three Finalists. Retrieved May, 2021 from https://www.exascaleproject.org/workflow-technologies-impact-sc20-gordon-bell-covid-19-award-winner-and-two-of-the-three-finalists/
[62]
Romelia Salomon-Ferrer, Andreas W. Götz, Duncan Poole, Scott Le Grand, and Ross C. Walker. 2013. Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald. Journal of Chemical Theory and Computation 9, 9 (2013), 3878--3888. 26592383.
[63]
Marissa G. Saunders and Gregory A. Voth. 2013. Coarse-Graining Methods for Computational Biology. Annual Review of Biophysics 42, 1 (2013), 73--93.
[64]
David E. Shaw, Ron O. Dror, John K. Salmon, J.P. Grossman, Kenneth M. Mackenzie, Joseph A. Bank, Cliff Young, Martin M. Deneroff, Brannon Batson, Kevin J. Bowers, Edmond Chow, Michael P. Eastwood, Douglas J. Ierardi, John L. Klepeis, Jeffrey S. Kuskin, Richard H. Larson, Kresten Lindorff-Larsen, Paul Maragakis, Mark A. Moraes, Stefano Piana, Yibing Shan, and Brian Towles. 2009. Millisecond-scale Molecular Dynamics Simulations on Anton. In Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis (Portland, Oregon) (SC '09). New York, NY, USA, 1--11.
[65]
Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, and Ellen D. Zhong. 2017. Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset. Journal of Computer-Aided Molecular Design 31, 1 (2017), 147--161.
[66]
Dhirendra K. Simanshu, Dwight V. Nissley, and Frank McCormick. 2017. RAS Proteins and Their Regulators in Human Disease. Cell 170, 1 (June 2017), 17--33.
[67]
James Smith. 2017. IBM Spectrum LSF. IBM Corporation. https://www.ibm.com/support/knowledgecenter/en/SSWRJV_10.1.0/lsf_welcome/lsf_welcome.html
[68]
Frederick H Streitz, James N Glosli, and Mehul V Patel. 2006. Beyond finite-size scaling in solidification simulations. Physical Review Letters 96, 22 (2006), 225701.
[69]
Frederick H. Streitz, James N. Glosli, Mehul V. Patel, Bor Chan, Robert K. Yates, Bronis R. de Supinski, James Sexton, and John A. Gunnels. 2005. 100+ TFlop Solidification Simulations on BlueGene/L. In Proceedings of the 2005 ACM/IEEE Conference on Supercomputing (Seattle, Washington) (SC '05). ACM, New York, NY, USA.
[70]
TOP500. 2020. TOP500 Supercomputer Sites / November 2020. Retrieved March, 2021 from https://www.top500.org/lists/top500/2020/11/
[71]
Timothy Travers, Cesar A. López, Que N. Van, Chris Neale, Marco Tonelli, Andrew G. Stephen, and Sandrasegaram Gnanakaran. 2018. Molecular recognition of RAS/RAF complex at the membrane: Role of RAF cysteine-rich domain. Scientific Reports 8, 1 (May 2018), 8461.
[72]
Vincent A. Voelz, Marcus Jäger, Shuhuai Yao, Yujie Chen, Li Zhu, Steven A. Waldauer, Gregory R. Bowman, Mark Friedrichs, Olgica Bakajin, Lisa J. Lapidus, Shimon Weiss, and Vijay S. Pande. 2012. Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment. Journal of the American Chemical Society 134, 30 (2012), 12565--12577.
[73]
Gregory A. Voth. 2017. A Multiscale Description of Biomolecular Active Matter: The Chemistry Underlying Many Life Processes. Accounts of Chemical Research 50, 3 (March 2017), 594--598.
[74]
Tsjerk A. Wassenaar, Helgi I. Ingólfsson, Rainer A. Böckmann, D. Peter Tieleman, and Siewert J. Marrink. 2015. Computational Lipidomics with insane : A Versatile Tool for Generating Custom Membranes for Molecular Simulations. Journal of Chemical Theory and Computation 11, 5 (May 2015), 2144--2155.
[75]
Tsjerk A. Wassenaar, Kristyna Pluhackova, Rainer A. Böckmann, Siewert J. Marrink, and D. Peter Tieleman. 2014. Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models. Journal of Chemical Theory and Computation 10, 2 (2014), 676--690. 26580045.
[76]
Tsjerk A. Wassenaar, Kristyna Pluhackova, Anastassiia Moussatova, Durba Sengupta, Siewert J. Marrink, D. Peter Tieleman, and Rainer A. Böckmann. 2015. High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach. Journal of Chemical Theory and Computation 11, 5 (May 2015), 2278--2291.
[77]
Andy B. Yoo, Morris A. Jette, and Mark Grondona. 2002. SLURM: Simple Linux Utility for Resource Management. In In Lecture Notes in Computer Science: Proceedings of Job Scheduling Strategies for Parallel Processing (JSSPP) 2003. Springer-Verlag, 44--60.
[78]
Xiaohua Zhang, Shiv Sundram, Tomas Oppelstrup, Sara I. L. Kokkila-Schumacher, Timothy S. Carpenter, Helgi I. Ingólfsson, Frederick H. Streitz, Felice C. Lightstone, and James N. Glosli. 2020. ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field. The Journal of Chemical Physics 153, 4 (2020), 045103.

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  • (2023)Graph3PO: A Temporal Graph Data Processing Method for Latency QoS Guarantee in Object Cloud Storage SystemProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/3581784.3607075(1-16)Online publication date: 12-Nov-2023
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cover image ACM Conferences
SC '21: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis
November 2021
1493 pages
ISBN:9781450384421
DOI:10.1145/3458817
This work is licensed under a Creative Commons Attribution International 4.0 License.

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Publication History

Published: 13 November 2021

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Author Tags

  1. adaptive simulations
  2. cancer research
  3. heterogenous architecture
  4. machine learning
  5. massively parallel
  6. multiscale simulations

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Overall Acceptance Rate 1,516 of 6,373 submissions, 24%

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  • (2024)The Flux OperatorF1000Research10.12688/f1000research.147989.113(203)Online publication date: 21-Mar-2024
  • (2023)Orchestration of materials science workflows for heterogeneous resources at large scaleInternational Journal of High Performance Computing Applications10.1177/1094342023116780037:3-4(260-271)Online publication date: 1-Jul-2023
  • (2023)Graph3PO: A Temporal Graph Data Processing Method for Latency QoS Guarantee in Object Cloud Storage SystemProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/3581784.3607075(1-16)Online publication date: 12-Nov-2023
  • (2023)An Empirical Study of High Performance Computing (HPC) Performance Bugs2023 IEEE/ACM 20th International Conference on Mining Software Repositories (MSR)10.1109/MSR59073.2023.00037(194-206)Online publication date: May-2023
  • (2023)Enabling Scalability in the Cloud for Scientific Workflows: An Earth Science Use Case2023 IEEE 16th International Conference on Cloud Computing (CLOUD)10.1109/CLOUD60044.2023.00052(383-393)Online publication date: Jul-2023
  • (2023)Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation InfrastructureJournal of Chemical Theory and Computation10.1021/acs.jctc.2c0101819:9(2658-2675)Online publication date: 19-Apr-2023
  • (2023)Mesoscale simulations: An indispensable approach to understand biomembranesBiophysical Journal10.1016/j.bpj.2023.02.017122:11(1883-1889)Online publication date: Jun-2023
  • (2023)Asynchronous Execution of Heterogeneous Tasks in ML-Driven HPC WorkflowsJob Scheduling Strategies for Parallel Processing10.1007/978-3-031-43943-8_2(27-45)Online publication date: 19-May-2023
  • (2022)Ubique: A New Model for Untangling Inter-task Data Dependence in Complex HPC Workflows2022 IEEE 18th International Conference on e-Science (e-Science)10.1109/eScience55777.2022.00068(421-422)Online publication date: Oct-2022
  • (2022)HPC Extensions to the OpenKIM Processing Pipeline2022 IEEE 18th International Conference on e-Science (e-Science)10.1109/eScience55777.2022.00041(278-283)Online publication date: Oct-2022
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