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Shreyas Cholia
Biographical Sketch
Shreyas Cholia is Group Leader for Integrated Data Systems Group, focused on the data engineering and integration aspects of computational and data analysis systems. He is particularly interested in the interactive aspects of scientific computing at scale. He has extensive experience leading teams and building data systems for scientific projects, including ESS-DIVE, NMDC and the Materials Project. He also worked for over a decade at NERSC, where he led the science gateway and grid computing efforts. Prior to his appointment at LBL, he was a developer and consultant at IBM. He has a Bachelor’s Degree from Rice University, where he double majored in Computer Science and Cognitive Sciences.
Journal Articles
C Varadharajan, S Cholia, C Snavely, V Hendrix, C Procopiou, D Swantek, W Riley, D Agarwal, "Launching an Accessible Archive of Environmental Data", Eos, January 1, 2019, 100, doi: 10.1029/2019eo111263
Dáithí A Stone, Mark D Risser, Oliver M Angélil, Michael F Wehner, Shreyas Cholia, Noel Keen, Harinarayan Krishnan, Travis A O Brien, William D Collins, "A basis set for exploration of sensitivity to prescribed ocean conditions for estimating human contributions to extreme weather in CAM5. 1-1degree", Weather and climate extremes, 2018, 19:10--19,
Patrick Huck, Dan Gunter, Shreyas Cholia, Donald Winston, AT N Diaye, Kristin Persson, "User applications driven by the community contribution framework MPContribs in the Materials Project", Concurrency and Computation: Practice and Experience, 2016, 28:1982--1993,
NJ Wright, SS Dosanjh, AK Andrews, KB Antypas, B Draney, RS Canon, S Cholia, CS Daley, KM Fagnan, RA Gerber, L Gerhardt, L Pezzaglia, A Prabhat, KH Schafer, J Srinivasan, "Cori: A pre-exascale supercomputer for big data and HPC applications", Advances in Parallel Computing, 2015, 26:82--100, doi: 10.3233/978-1-61499-583-8-82
R Madduri, A Rodriguez, T Uram, K Heitmann, T Malik, S Sehrish, R Chard, S Cholia, M Paterno, J Kowalkowski, S Habib, "PDACS: A Portal for Data Analysis Services for Cosmological Simulations", Computing in Science and Engineering, 2015, 17:18--26, doi: 10.1109/MCSE.2015.87
S Cholia, T Sun, "The NEWT platform: An extensible plugin framework for creating ReSTful HPC APIs", Proceedings of GCE 2014: 9th Gateway Computing Environments Workshop, held in conjunction with SC 2014: The International Conference for High Performance Computing, Networking, Storage and Analysis, 2015, 17--20, doi: 10.1109/GCE.2014.14
P Huck, D Gunter, S Cholia, D Winston, A N Diaye, KA Persson, "User Applications Driven by the Community Contribution Framework MPContribs in the Materials Project.", CoRR, 2015, abs/1510,
SP Ong, S Cholia, A Jain, M Brafman, D Gunter, G Ceder, KA Persson, "The Materials Application Programming Interface (API): A simple, flexible and efficient API for materials data based on REpresentational State Transfer (REST) principles", Computational Materials Science, 2015, 97:209--215, doi: 10.1016/j.commatsci.2014.10.037
SP Ong, WD Richards, A Jain, G Hautier, M Kocher, S Cholia, D Gunter, VL Chevrier, KA Persson, G Ceder, "Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis", Computational Materials Science, 2013, 68:314--319, doi: 10.1016/j.commatsci.2012.10.028
O Rübel, A Greiner, S Cholia, K Louie, EW Bethel, TR Northen, BP Bowen, "OpenMSI: A high-performance web-based platform for mass spectrometry imaging", Analytical Chemistry, 2013, 85:10354--103, doi: 10.1021/ac402540a
A Jain, SP Ong, G Hautier, W Chen, WD Richards, S Dacek, S Cholia, D Gunter, D Skinner, G Ceder, KA Persson, "Commentary: The materials project: A materials genome approach to accelerating materials innovation", APL Materials, 2013, 1, doi: 10.1063/1.4812323
MD Pierro, J Hetrick, S Cholia, D Skinner, "Making QCD lattice data accessible and organized through advanced web interfaces", Proceedings of Science, 2011, 139,
M Pala, S Cholia, SA Rea, SW Smith, "Interoperable PKI data distribution in computational grids", International Journal of Grid and High Performance Computing, 2009, 1:56--73, doi: 10.4018/jghpc.2009040105
Conference Papers
B. Enders, D. Bard, C. Snavely, L. Gerhardt, J. Lee, B. Totzke, K. Antypas, S. Byna, R. Cheema, S. Cholia, M. Day, A. Gaur, A. Greiner, T. Groves, M. Kiran, Q. Koziol, K. Rowland, C. Samuel, A. Selvarajan, A. Sim, D. Skinner, R. Thomas, G. Torok, "Cross-facility science with the Superfacility Project at LBNL", 2nd Workshop on Large-scale Experiment-in-the-Loop Computing (XLOOP 2020), in conjunction with the International Conference for High Performance Computing, Networking, Storage, and Analysis (SC 20), 2020, doi: 10.1109/XLOOP51963.2020.00006
Shreyas Cholia, Matthew Henderson, Oliver Evans, Fernando Perez, "Kale: A System for Enabling Human-in-the-loop Interactivity in HPC Workflows", Science Gateways 2018, figshare, September 26, 2018, doi: 10.6084/m9.figshare.7067075.v3
S. Farrell, A. Vose, O. Evans, M. Henderson, S. Cholia, W. Bhimji, R. Thomas, S.
Canon, and Prabhat,,
"Interactive Distributed Deep Learning with Jupyter Notebooks",
ISC Workshop on Interactive High-Performance Computing,
June 28, 2018,
Rollin Thomas, Shane Canon, Shreyas Cholia, Lisa Gerhardt, Evan Racah, "Toward Interactive Supercomputing at NERSC with Jupyter", Cray User Group (CUG) Conference Proceedings, 2017,
R Chard, S Sehrish, A Rodriguez, R Madduri, TD Uram, M Paterno, K Heitmann, S Cholia, J Kowalkowski, S Habib, "PDACS-A portal for data analysis services for cosmological simulations", Proceedings of GCE 2014: 9th Gateway Computing Environments Workshop, held in conjunction with SC 2014: The International Conference for High Performance Computing, Networking, Storage and Analysis, 2015, 30--33, doi: 10.1109/GCE.2014.7
R Cowles, C Jackson, V Welch, S Cholia, "A model for identity management in future scientific collaboratories", Proceedings of Science, 2014, 23-28-Ma,
M Di Pierro, J Hetrick, S Cholia, J Simone, C Deta, "The new Gauge Connection at NERSC", Proceedings of Science, 2013, 29-July-,
D Gunter, S Cholia, A Jain, M Kocher, K Persson, L Ramakrishnan, SP Ong, G Ceder, "Community accessible datastore of high-throughput calculations: Experiences from the materials project", Proceedings - 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, SCC 2012, 2012, 1244--1251, doi: 10.1109/SC.Companion.2012.150
A Jain, G Hautier, SP Ong, C Moore, B Kang, H Chen, X Ma, JC Kim, M Kocher, D Gunter, S Cholia, A Greiner, DH Bailey, D Skinner, K Persson, G Ceder, "Materials Project: A public materials database and its application to lithium ion battery cathode design", ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2012, 243,
Lavanya Ramakrishnan, Keith Jackson, Shane Canon, Shreyas Cholia, John Shalf, "Defining Future Platform Requirements for e-Science Cloud (Position paper)", ACM Symposium on Cloud Computing 2010 (ACM SOCC 2010), Indianapolis, Indiana, 2010,
S Cholia, D Skinner, J Boverhof, "NEWT: A RESTful service for building High: Performance Computing web applications", 2010 Gateway Computing Environments Workshop, GCE 2010, 2010, doi: 10.1109/GCE.2010.5676125
KR Jackson, L Ramakrishnan, K Muriki, S Canon, S Cholia, J Shalf, HJ Wasserman, NJ Wright, "Performance analysis of high performance computing applications on the Amazon Web Services cloud", Proceedings - 2nd IEEE International Conference on Cloud Computing Technology and Science, CloudCom 2010, 2010, 159--168, doi: 10.1109/CloudCom.2010.69
M Pala, S Cholia, SA Rea, SW Smith, "Extending PKI interoperability in computational grids", Proceedings CCGRID 2008 - 8th IEEE International Symposium on Cluster Computing and the Grid, 2008, 645--650, doi: 10.1109/CCGRID.2008.70
S Cholia, RJ Porter, "Publication and protection of sensitive site information in a grid infrastructure", Proceedings CCGRID 2008 - 8th IEEE International Symposium on Cluster Computing and the Grid, 2008, 639--644, doi: 10.1109/CCGRID.2008.86
Book Chapters
Anubhav Jain, Joseph Montoya, Shyam Dwaraknath, Nils ER Zimmermann, John Dagdelen, Matthew Horton, Patrick Huck, Donny Winston, Shreyas Cholia, Shyue Ping Ong, others, "The Materials Project: Accelerating Materials Design Through Theory-Driven Data and Tools", Handbook of Materials Modeling: Methods: Theory and Modeling, (Springer: 2018) Pages: 1--34
Presentation/Talks
D. Bard, C. Snavely, L. Gerhardt, J. Lee, B. Totzke, K. Antypas, S. Byna, R. Cheema, S. Cholia, M. Day, B. Enders, A. Gaur, A. Greiner, T. Groves, M. Kiran, Q. Koziol, K. Rowland, C. Samuel, A. Selvarajan, A. Sim, D. Skinner, R. Thomas, G. Torok, The Superfacility project: automated pipelines for experiments and HPC, International Conference for High Performance Computing, Networking, Storage, and Analysis (SC20), State of the Practice (SOP), 2020,
Shreyas Cholia, Matthew Henderson, Oliver Evans, Demo: Extending Jupyter to Support Interactive High Performance Computing, Science Gateways 2017, October 2017, doi: 10.6084/m9.figshare.5501137.v1
DA Agarwal, C Varadharajan, S Cholia, C Snavely, VC Hendrix, D Gunter, WJ Riley, M jones, AE budden, D Vieglas, Environmental System Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE)-A New US DOE Data Archive, 2017,
Reports
D. Bard, C. Snavely, L. Gerhardt, J. Lee, B. Totzke, K. Antypas, W. Arndt, J. Blaschke, S. Byna, R. Cheema, S. Cholia, M. Day, B. Enders, A. Gaur, A. Greiner, T. Groves, M. Kiran, Q. Koziol, T. Lehman, K. Rowland, C. Samuel, A. Selvarajan, A. Sim, D. Skinner, L. Stephey, R. Thomas, G. Torok, "LBNL Superfacility Project Report", Lawrence Berkeley National Laboratory, 2022, doi: 10.48550/arXiv.2206.11992
Posters
Wahid Bhimji, Steven Farrell, Oliver Evans, Matthew Henderson, Shreyas Cholia, Aaron Vose, Mr Prabhat, Rollin Thomas, Richard Shane Canon, "Interactive HPC Deep Learning with Jupyter Notebooks", Supercomputing 2018, Dallas, TX, November 2018,
A Greiner, E Racah, R Canon, J Liu, Y Liu, D Bard, L Gerhardt, R Thomas, S Cholia, J Porter, W Bhimji, Q Koziol, Prabhat, "Data-Intensive Supercomputing for Science", 2016,
Stone, D., H. Shiogama, P. Wolski, O. Angélil, S. Cholias, N. Christidis, A. Dittus, C. Folland, A. King, J. Kinter, H. Krishnan, S.-K. Min, M. Wehner, "The C20C+ Detection and Attribution Project", Fall Meeting of the American Geophysical Union, 2015,
- Download File: StoneDAGU2015.pdf (pdf: 4.7 MB)
