Mary Thomas

Mary Thomas, Ph.D.
Research Assistant Professor
Office: GMCS 562
Office Hours (Spring, 2017):
      T/Th 12:30-2:00 pm
      GMCS 562 (or EBA110)
Phone: (619) 594-1694
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Mary Thomas, is a member of the faculty in the Department of Computer Science and the Computational Science and Engineering Research Center at San Diego State University.

Ph.D. Computational Science Claremont Graduate University & San Diego State University (2014)
M.S. Computer Science San Diego State University
M.S. Physics San Diego State University
B.S. Physics University of Texas at Austin


SDSU Links:

Current Research:

Thomas' research interests focus on computational science, parallel programming, and advanced computational environments that support high-end scientific applications.

Current projects include investigating parallelization and nesting techniques for 3D staggered grid coastal ocean models, such as the Unified Curvilinear Ocean Atmospheric Model (UCOAM). UCOAM is a non-hydrostatic, large eddie simulation (LES) CFD model capable of running both ocean and atmospheric simulations at very high resolutions (meter-scale). Parallelization approaches include MPI and GPU techniques. For the nested model research, a new model is being developed which nests the UCOAM model within a coarser, global ocean model (kilometer scale). Initial studies will investigate the effects of larger-scale processes influence non-hydrostatic features such as shoaling internal waves and bores which impact diapycnal mixing, transport processes, and a host of biological/ecological processes such as larval connectivity and the transport of low dissolved oxygen/pH waters to the nearshore.

In addition, Thomas works on the development of computational environments (CE's) involve the use of emerging technologies and cyberinfrastructure to integrate advanced computational, data, and networking infrastructure. Research projects include development of the Cyberinfrastructure Web Application Framework (CyberWeb). CyberWeb is designed to facilitate development of virtual environments (VOs), Web services, and portals associated with scientific and high-performance computing. CyberWeb utilizes Cyberinfrastructure (CI) and emerging distributed, Web, and portal technologies.

For more information about her research projects, see

Topics of Interest:
  • Ocean Modeling
  • Parallel Computing
  • Performance
  • Computational Science
  • Cyberinfrastructure for Computational Science
  • Pylons Web Application Frameworks for Computational Grids
  • Cyberinfrastructure-Enabled Portals for Advanced Computing
  • Python Tools for Computational Grids
  • Emerging Technologies
  • Campus Grids
  • CI-enabled Web Services
  • Middleware for Grid Portals
  • XSEDE/TeraGrid
Selected Publications:
P. F. Choboter, M. Garcia, M. Thomas, R. K. Walter, and J. E. Castillo,Nesting Nonhydrostatic GCCOM within Hydrostatic ROMS for Multiscale Coastal Ocean Modeling, in Oceans'16, 2016.
M. Garcia, T. Hoar, M. Thomas, B. Bailey and J. Castillo, "Interfacing an ensemble Data Assimilation system with a 3D nonhydrostatic Coastal Ocean Model, an OSSE experiment," OCEANS 2016 MTS/IEEE Monterey, Monterey, CA, 2016, pp. 1-11. doi: 10.1109/OCEANS.2016.7760992
Thomas, M. P., "Parallel Implementation of the Unified Curvilinear Ocean and Atmospheric (UCOAM) Model and Supporting Computational Environment," Claremont Graduate University and San Diego State University, San Diego, 2014.
P. F. Choboter, M. P. Thomas, and J. E. Castillo, "Nesting nonhydrostatic UCOAM within hydrostatic ROMS," Manuscript in preparation, 2015.
Thomas, M. P., Cheng, C., More, S., Shah, H. Integrating HPC Resources, Services, and Cyberinfrastructure to Develop Science Applications Using Web Application Frameworks. Proceedings of the 2012 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'12), July 16-19, 2012, Las Vegas, Nev., USA, pp 421-427.
Thomas, M. P., Castillo, J. E., Parallelization of the 3D Unified Curvilinear Coastal Ocean Model: Initial Results. The 12th International Conference on Computational Science and Its Applications (ICCSA 2012), June 18-21, 2012, in Salvador de Bahia, Brazil.
Thomas, M. P., Castillo, J. E., Development of a Cyberinfrastructure-based Computational Environment for the General Curvilinear Coastal Ocean Model. Proceedings of the 2010 International Congress on Computer Applications and Computational Science (CACS 2010), December 2010, Singapore.
M. P. Thomas, J. E. Castillo (2009). Development of a Computational Environment for the General Curvilinear Ocean Model. Journal of Physics: Conference Series, v. 180, 2009.
J. Alameda, M. Christie, G. Fox, J. Futrelle, D. Gannon, M. Hategan, G. Kandaswamy, G. von Laszewski, M. A. Nacar, M. Pierce, E. Roberts, C. Severance, M. P. Thomas, The Open Grid Computing Environments collaboration: portlets and services for science gateways. Concurrency and Computation: Practice & Experience, Volume 19 Issue 6, pg.1078, 2007.
M. Pierce, J. Alameda, M. Christie, G. Fox, J. Futrelle, D. Gannon, M. Hategan, G. von Laszewsk, M. A. Nacar, E. Roberts, C. Severance, M. Thomas. The Open Grid Computing Enviroments Collaboration: Portlets and Services for Science Gateways. Accepted for publication in Spec. Edtn, Concurrency & Computation: Practice & Experience, 2005.
M. P. Thomas, J. Burruss, L. Cinquini, G. Fox, D. Gannon, L. Gilbert, G. von Laszewski, K. Jackson, D. Middleton, R. Moore, M. Pierce, B. Plale, A. Rajasekar, R. Regno, E. Roberts, D. Schissel, A. Seth, and W. Schroeder. Grid Portal Architectures for Scientific Applications. Proceedings of SciDAC 2005, 26-30 June 2005, San Francisco, CA, USA. Journal of Physics: Conference Series, Volume 16, 2005.
M. Thomas, J. Boisseau, M. Dahan, C. Mills, S. Mock, K. Mueller. "Development of NPACI Grid Application Portals and Portal Web Services," Journal of Cluster Computing, 6(3), 2003.
M. Thomas, J. Boisseau. Building Grid Computing Portals: The NPACI Grid Portal Toolkit. "Grid Computing: Making the Global Infrastructure a Reality, Ch 28." F. Berman, G. Fox and T. Hey, eds. John Wiley and Sons, Ltd, Chichester (2003). Available from
G. Fox, D. Gannon, M. Thomas. Overview of Grid Computing Environments. "Grid Computing: Making the Global Infrastructure a Reality, Ch 20." F. Berman, G. Fox and T. Hey, eds. John Wiley and Sons, Ltd, Chichester (2003). Available from
G. Fox, D. Gannon, and M. Thomas, "Editorial: A Summary of Grid Computing Environments." Concurrency and Computation: Practice and Experience, Vol. 14, No. 13-15, pp. 1035-1044 (2002).
Organizational Memberships/Professional Affiliations
Dr. Thomas is a Research Assistant Professor in the Department of Computer Science at San Diego State University, an Associated Faculty member of the SDSU Computational Science Research Center, and a member of the General Curvilinear Environmental Modeling Group (GCEM). Her research is focused on parallel computing, coastal ocean modeling, and emerging cyberinfrastructure \& web technologies, including grid portal and middleware technologies. Her current projects include parallelization of the General Coastal Ocean Model (GCOM), and development of the Cyberinfrastructure Web Application Framework (CyberWeb). Before joining SDSU she was a research scientist at the Texas Advanced Computing Center at The University of Texas at Austin, and the San Diego Supercomputer Center, where she led several portal and Web services projects for High Performance Computing infrastructure, including the GridPort Toolkit project, which is part of the Open Grid Computing Environments (OGCE) portal release. Dr. Thomas has published over 30 peer reviewed journal publication and conference proceedings; contributed two chapters to the book “Grid Computing: Making the Global Infrastructure a Reality;” and has given over 40 invited talks, technical presentations and posters at conferences and workshops.

© 2016, Mary Thomas - All rights reserved.
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