Sciences and Exploration Directorate

Brief Bio


Dr. Thomas Clune is a senior computational scientist at NASA GSFC and leads the Software Infrastructure Team within the Global Modeling and Assimilation Office. Dr. Clune has ongoing software collaborations for the development of numerous models across several disciplines. 


Dr. Clune serves as the NASA representative on the Fortran language committee, where he currently leads the subgroup focused on introducing generic programming features into Fortran.


Dr. Clune is a strong advocate for open source software and best practices for development of scientific software, and in particular for test driven development. He is the lead developer of pFUnit, an open source unit testing framework for parallel Fortran Software. This highly-extensible framework has successfully been used in testing and development of several software packages within NASA, and is also being used at several prestigious institutions including \ac{ECMWF} and \ac{NCAR}. Other open source packages developed by Dr. Clune include gFTL, a templating library for Fortran, pFlogger, a logging utility for Fortran, and yaFyaml a YAML parser with customized Fortran interfaces..


Current Projects


A Framework for Global Cloud Resolving OSSEs.

Analysis

Dr. Clune serves on this project which is funded by NASA's Advanced Information Systems Technology program. The project aims too reduce the cost and complexity of simulating instrument observations within the context of a high-resolution nature run. The project will achieve this by developing a pluggable framework that allows researchers to separately provide their own instrument simulator, observation geometry, and output collections.

Positions/Employment


Acting Office Head

NASA - NASA Goddard Space Flight Center, Greenbelt, MD

2008 - 2009

  • Managed the Software Integration and Visualization Office (SIVO). SIVO is an organization of over 40 staff providing cross-cutting support for Goddard's Earth Sciences Division, primarily in information technology. Suborganizations within the office include the Advanced Software Technology Group which provides high-end computing and software engineering support, the Scientific Visualization Studio which provides awared-winning visualizations from NASA's satellite date and scientific models, and the Education and Public Outreach group which brings NASA's scientific results to students and society via the web.
  • Managed the $7M budget from multiple NASA funding sources. Established organizational priorities in coordination with NASA Headquarters, Goddard's Earth Sciences Division, and the NASA Center for Computational Sciences.

 


Group Lead

NASA - Goddard Space Flight Center, Greenbelt, MD

2002 - Present

  • Managed the Advanced Software Technology Group (ASTG), a team of 15 contractor staff to provide support to NASA's High End Computing Program and NASA's Modeling and Prediction Program. ASTG was responsible for help desk and level 2 support for the NASA Center for Computational Sciences (NCCS). Maintained and extended GMI, an atmospheric chemistry model. Created MPI implementation of ModelE, the GISS climate Model.
  • Provided government oversight for the development of the Earth System Modeling Framework (ESMF), and later sered on the Change Review Board for ESMF.
  • Developed open source framework for unit testing to support development of parallel Fortran software. Advocated for increased emphasis on software quality and productivity within NASA's scientific modeling community.
  • Presented occasional seminars on topics relevant to the development of scientific software. Representative topics include technology trends, software refactoring, test driven development, and the Fortran 2003 standard.


Applications Analyst/Consultant

SGI Professional Services - NASA Goddard Space Flight Center, Greenbelt, MD

2000 - 2002

  • Provided optimization and software engineering support to in-house scientific models at NASA Goddard Space Flight Center.
  • Provided over 10 fold performance increase for a mission-critical 3D variational analysis code via a combination of customized communication kernels, hybrid parallelism, and cache-based optimizations.
  • Presented lectures on optimization and scientific best practices for NASA summer school program.


Applications Analyst

Cray Research (SGI) - NASA Goddard Space Flight Center, Greenbelt, MD

1997 - 2000

  • Provided computational optimizations to NASA' s High Performance Computing and Communications (HPCC) Program. Aided numerous NASA supported investigators in achieving greater than 100 gigaflops on the Cray T3E. Scientific domains included weather/climate (UCLA), numerical relativity (UI), data assimilation (GSFC), synthetic aperture radar (JPL), and magnetohydrodynamics (NRL, LANL. CU, U. of Chicago).


Postdoctoral Researcher

University of Colorado - Boulder, Colorado

1993 - 1997

  • Investigated turbulent transport and magnetic dynamos within stellar onvection zones via direct simulation.
  • Parallelized multiple pseudospectral models and was primary developer of the ASH model which is still actively used for research.

Education


1993 - Ph. D., Physics, University of California at Berkeley

1990 - M.A., Physics, University of California at Berkeley

1988 - B.S., Physics, Massachusetts Institute of Technology

Other Professional Information


H-index: 13

Publications


Refereed

Way, M. J., N. Georgakarakos, and T. L. Clune. 2023. Exploring Climate with Obliquity in a Variable-eccentricity Earth-like World The Astronomical Journal 166 (6): 227 [10.3847/1538-3881/ad0373]

Martin, R. V., S. D. Eastham, L. Bindle, et al. E. W. Lundgren, T. L. Clune, C. A. Keller, W. Downs, D. Zhang, R. A. Lucchesi, M. P. Sulprizio, R. M. Yantosca, Y. Li, L. Estrada, W. M. Putman, B. M. Auer, A. L. Trayanov, S. Pawson, and D. J. Jacob. 2022. Improved advection, resolution, performance, and community access in the new generation (version 13) of the high-performance GEOS-Chem global atmospheric chemistry model (GCHP) Geoscientific Model Development 15 (23): 8731-8748 [10.5194/gmd-15-8731-2022]

Nazarenko, L. S., N. Tausnev, G. L. Russell, et al. D. Rind, R. L. Miller, G. A. Schmidt, S. E. Bauer, M. Kelley, R. Ruedy, A. S. Ackerman, I. Aleinov, M. Bauer, R. Bleck, V. Canuto, G. Cesana, Y. Cheng, T. L. Clune, B. I. Cook, C. A. Cruz, A. D. Genio, G. S. Elsaesser, G. Faluvegi, N. Y. Kiang, D. Kim, A. A. Lacis, A. Leboissetier, A. N. LeGrande, K. K. Lo, J. Marshall, E. E. Matthews, S. McDermid, K. Mezuman, L. T. Murray, V. Oinas, C. Orbe, C. P. García‐Pando, J. P. Perlwitz, M. J. Puma, A. Romanou, D. T. Shindell, S. Sun, K. Tsigaridis, G. Tselioudis, E. Weng, J. Wu, and M. Yao. 2022. Future Climate Change under SSP Emission Scenarios with GISS‐E2.1 Journal of Advances in Modeling Earth Systems [10.1029/2021ms002871]

Bindle, L., R. V. Martin, M. J. Cooper, et al. E. W. Lundgren, S. D. Eastham, B. M. Auer, T. L. Clune, H. Weng, J. Lin, L. T. Murray, J. Meng, C. A. Keller, W. M. Putman, S. Pawson, and D. J. Jacob. 2021. Grid-stretching capability for the GEOS-Chem 13.0.0 atmospheric chemistry model Geoscientific Model Development 14 (10): 5977-5997 [10.5194/gmd-14-5977-2021]

Miller, R. L., G. A. Schmidt, L. Nazarenko, et al. S. E. Bauer, M. Kelley, R. Ruedy, G. L. Russell, A. Ackerman, I. Aleinov, M. Bauer, R. Bleck, V. Canuto, G. Cesana, Y. Cheng, T. L. Clune, B. Cook, C. A. Cruz, A. D. Del Genio, G. S. Elsaesser, G. Faluvegi, N. Y. Kiang, D. Kim, A. A. Lacis, A. Leboissetier, A. N. LeGrande, K. K. Lo, J. Marshall, E. E. Matthews, S. McDermid, K. Mezuman, L. T. Murray, V. Oinas, C. Orbe, C. P. García‐Pando, J. P. Perlwitz, M. J. Puma, D. Rind, A. Romanou, D. T. Shindell, S. Sun, N. Tausnev, K. Tsigaridis, G. Tselioudis, E. Weng, J. Wu, and M. Yao. 2021. CMIP6 Historical Simulations (1850‐2014) with GISS‐E2.1 Journal of Advances in Modeling Earth Systems 13 e2019MS002034 [10.1029/2019ms002034]

Kelley, M., G. A. Schmidt, L. S. Nazarenko, et al. S. E. Bauer, R. Ruedy, G. L. Russell, A. S. Ackerman, I. Aleinov, M. Bauer, R. Bleck, V. Canuto, G. Cesana, Y. Cheng, T. L. Clune, B. I. Cook, C. A. Cruz, A. D. Del Genio, G. S. Elsaesser, G. Faluvegi, N. Y. Kiang, D. Kim, A. A. Lacis, A. Leboissetier, A. N. LeGrande, K. K. Lo, J. Marshall, E. E. Matthews, S. McDermid, K. Mezuman, R. L. Miller, L. T. Murray, V. Oinas, C. Orbe, C. P. García‐Pando, J. P. Perlwitz, M. J. Puma, D. Rind, A. Romanou, D. T. Shindell, S. Sun, N. Tausnev, K. Tsigaridis, G. Tselioudis, E. Weng, J. Wu, and M. Yao. 2020. GISS‐E2.1: Configurations and Climatology Journal of Advances in Modeling Earth Systems 12 (8): [10.1029/2019ms002025]

Del Genio, A. D., M. J. Way, D. S. Amundsen, et al. I. Aleinov, M. Kelley, N. Y. Kiang, and T. L. Clune. 2019. Habitable Climate Scenarios for Proxima Centauri b with a Dynamic Ocean Astrobiology 19 (1): 99-125 [10.1089/ast.2017.1760]

Way, M. J., A. D. Del Genio, I. Aleinov, et al. T. L. Clune, M. Kelley, and N. Y. Kiang. 2018. Climates of Warm Earth-like Planets. I. 3D Model Simulations The Astrophysical Journal Supplement Series 239 (2): 24 [10.3847/1538-4365/aae9e1]

Eastham, S. D., M. S. Long, C. A. Keller, et al. E. Lundgren, R. M. Yantosca, J. Zhuang, C. Li, C. J. Lee, M. Yannetti, B. M. Auer, T. L. Clune, J. Kouatchou, W. M. Putman, M. A. Thompson, A. L. Trayanov, A. M. Molod, R. V. Martin, and D. J. Jacob. 2018. GEOS-Chem High Performance (GCHP v11-02c): a next-generation implementation of the GEOS-Chem chemical transport model for massively parallel applications Geoscientific Model Development 11 (7): 2941-2953 [10.5194/gmd-11-2941-2018]

Way, M. J., I. Aleinov, D. S. Amundsen, et al. M. A. Chandler, T. L. Clune, A. Del Genio, Y. Fujii, M. Kelley, N. Y. Kiang, L. Sohl, and K. Tsigaridis. 2017. Resolving Orbital and Climate Keys of Earth and Extraterrestrial Environments with Dynamics (ROCKE-3D) 1.0: A General Circulation Model for Simulating the Climates of Rocky Planets The Astrophysical Journal Supplement Series 231 (1): 12 [10.3847/1538-4365/aa7a06]

Kouatchou, J., T. L. Clune, B. M. Auer, J. E. Nielsen, and A. M. Molod. 2017. Parallel Performance Analysis of Two Infrastructure Frameworks for GMI Chemistry American Meteorological Society’s Third Symposium on High Performance Computing for Weather, Water, and Climate

Rilee, M. L., K.-S. Kuo, T. Clune, et al. A. Oloso, P. G. Brown, and H. Yu. 2016. Addressing the big-earth-data variety challenge with the hierarchical triangular mesh 2016 IEEE International Conference on Big Data (Big Data) [10.1109/bigdata.2016.7840700]

Doan, K., A. O. Oloso, K.-S. Kuo, et al. T. L. Clune, H. Yu, B. Nelson, and J. Zhang. 2016. Evaluating the impact of data placement to spark and SciDB with an Earth Science use case 2016 IEEE International Conference on Big Data (Big Data) [10.1109/bigdata.2016.7840621]

Way, M. J., A. D. Del Genio, N. Y. Kiang, et al. L. E. Sohl, D. H. Grinspoon, I. Aleinov, M. Kelley, and T. Clune. 2016. Was Venus the first habitable world of our solar system? Geophysical Research Letters 43 (16): 8376-8383 [10.1002/2016gl069790]

Kuo, K.-S., A. Oloso, K. Doan, T. L. Clune, and H. Yu. 2016. Implications of data placement strategy to Big Data technologies based on shared-nothing architecture for geosciences 2016 IEEE International Geoscience and Remote Sensing Symposium (IGARSS) [10.1109/igarss.2016.7730983]

Theurich, G., C. DeLuca, T. Campbell, et al. F. Liu, K. Saint, M. Vertenstein, J. Chen, R. Oehmke, J. Doyle, T. Whitcomb, A. Wallcraft, M. Iredell, T. Black, A. M. Da Silva, T. Clune, R. Ferraro, P. Li, M. Kelley, I. Aleinov, V. Balaji, N. Zadeh, R. Jacob, B. Kirtman, F. Giraldo, D. McCarren, S. Sandgathe, S. Peckham, and R. Dunlap. 2016. The Earth System Prediction Suite: Toward a Coordinated U.S. Modeling Capability Bulletin of the American Meteorological Society 97 (7): 1229-1247 [10.1175/bams-d-14-00164.1]

Way, M., A. Del Genio, M. Kelley, I. Aleinov, and T. Clune. 2015. Exploring the Inner Edge of the Habitable Zone with Fully Coupled Oceans ArXiv e-prints

Peters-Lidard, C. D., E. M. Kemp, T. Matsui, et al. J. A. Santanello, S. V. Kumar, J. P. Jacob, T. L. Clune, W.-K. Tao, M. Chin, A. Hou, J. L. Case, D. Kim, K.-M. Kim, W. K. Lau, Y. Liu, J. J. Shi, D. O. Starr, Q. Tan, Z. Tao, B. F. Zaitchik, B. Zavodsky, Q. Zhang, and M. Zupanski. 2015. Integrated modeling of aerosol, cloud, precipitation and land processes at satellite-resolved scales Environmental Modelling and Software 67 149-159 [doi:10.1016/j.envsoft.2015.01.007]

Nazarenko, L., G. A. Schmidt, R. L. Miller, et al. N. L. Tausnev, M. Kelley, R. A. Ruedy, G. L. Russell, I. Aleinov, M. P. Bauer, S. E. Bauer, R. Bleck, V. M. Canuto, Y. Cheng, T. L. Clune, A. D. Del Genio, G. S. Faluvegi, J. E. Hansen, R. J. Healy, N. Y. Kiang, D. Koch, A. A. Lacis, A. N. LeGrande, J. Lerner, K.-W. Lo, S. Menon, V. Oinas, J. P. Perlwitz, M. J. Puma, D. H. Rind, A. Romanou, M. Sato, D. T. Shindell, S. Sun, K. Tsigaridis, N. Unger, A. Voulgarakis, M.-S. Yao, and J. Zhang. 2015. Future climate change under RCP emission scenarios with GISS ModelE2 J. Adv. Model. Earth Syst. 7 (1): 244-267 [doi:10.1002/2014MS000403]

Miller, R. L., G. A. Schmidt, L. Nazarenko, et al. N. L. Tausnev, S. E. Bauer, A. Del Genio, M. Kelley, K.-W. Lo, R. A. Ruedy, D. T. Shindell, I. Aleinov, M. P. Bauer, R. Bleck, V. M. Canuto, Y. Chen, Y. Cheng, T. L. Clune, G. S. Faluvegi, J. E. Hansen, R. J. Healy, N. Y. Kiang, D. Koch, A. A. Lacis, A. N. Legrande, J. Lerner, S. Menon, V. Oinas, C. Perez Garcia Pando, J. P. Perlwitz, M. J. Puma, D. Rind, A. Romanou, G. L. Russell, M. Sato, S. Sun, K. Tsigaridis, N. Unger, A. Voulgarakis, M.-S. Yao, and J. Zhang. 2014. CMIP5 historical simulations (1850-2012) with GISS ModelE2 J. Adv. Model. Earth Syst. 6 (2): 441-477 [10.1002/2013MS000266]

Schmidt, G. A., M. Kelley, L. Nazarenko, et al. R. A. Ruedy, G. L. Russell, I. Aleinov, M. P. Bauer, S. E. Bauer, M. K. Bhat, R. Bleck, V. M. Canuto, Y. Chen, Y. Cheng, T. L. Clune, A. D. Del Genio, R. de Fainchtein, G. S. Faluvegi, J. E. Hansen, R. J. Healy, N. Y. Kiang, D. Koch, A. A. Lacis, A. N. LeGrande, J. Lerner, K.-W. Lo, E. E. Matthews, S. Menon, R. L. Miller, V. Oinas, A. O. Oloso, J. P. Perlwitz, M. J. Puma, W. M. Putman, D. H. Rind, A. Romanou, M. Sato, D. T. Shindell, S. Sun, R. A. Syed, N. L. Tausnev, K. Tsigaridis, N. Unger, A. Voulgarakis, M.-S. Yao, and J. Zhang. 2014. Configuration and assessment of the GISS ModelE2 contributions to the CMIP5 archive J. Adv. Model. Earth Syst. 6 (1): 141-184 [10.1002/2013MS000265]

Clune, T. L., K.-S. Kuo, S. Freeman, et al. R. Burns, C. A. Cruz, and J. Kouatchou. 2013. Tool for Automated Retrieval of Generic Event Tracks (TARGET) NASA Tech Brief GSC-16665-1

Clune, T. L., R. Numrich, and K.-S. Kuo. 2013. A New Parallel Version of the DDSCAT Code for Electromagnetic Scattering from Big Targets PIERS Proceedings 722-726

Clune, T. L., and R. B. Rood. 2011. Software Testing and Verification in Climate Model Development IEEE Software 28 (6): 49-55 [10.1109/MS.2011.117]

Roberts, P. H., G. A. Glatzmaier, and T. L. Clune. 2010. Numerical simulation of a spherical dynamo excited by a flow of von Karman type Geophysical and Astrophysical Fluid Dynamics 104 207-220

Zhou, S., D. Q. Duffy, T. L. Clune, et al. M. J. Suarez, S. Williams, and M. Halem. 2009. The impact of IBM Cell technology on the programming paradigm in the context of computer systems for climate and weather models Concurrency and Computation: Practice and Experience 21 (17): 2176-2186 [10.1002/cpe.1482]

Non-Refereed

Kouatchou, J., A. Molod, J. E. Nielsen, and T. Clune. 2015. GEOS-5 Chemistry Transport Model User's Guide GMAO Office Note 8

Clune, T. L., S. Freeman, and K.-S. Kuo. 2012. Leveraging Data Intensive Computing To Support Automated Event Services 2012 IEEE International Geoscience and Remote Sensing Symposium (IGARSS) 5352 - 5355 [10.1109/IGARSS.2012.6352398]

Freeman, S. F., T. L. Clune, and R. Burns. 2010. Latent risks and dangers in the state of climate model software development FoSER `10 Proceedings of the FSE/SDP workshop on Future of software engineering research 111-114 [10.1145/1882362.1882386]

Zhou, S., D. Q. Duffy, T. L. Clune, et al. M. J. Suarez, S. W. Williams, and M. Halem. 2008. Impacts of the IBM Cell Processor on Supporting Climate Models International Supercomputing Conference (ISC) 2008

Zhou, S., A. O. Oloso, M. R. Damon, and T. L. Clune. 2006. Application Controlled Parallel Asynchronous Input/Output (Asynch I/O) SC 2006 Poster Reception

Talks, Presentations and Posters


Other

T. Clune, K. Kuo. "Test-Driven Development: Lessons from Simple Scientific Models"

2010