Katie Antypas
Biographical Sketch
Katie is the group leader for User Services at NERSC, a team of consultants who work directly with scientists to help them use the NERSC resources effectively. We provide expert advice in the following areas.
- Help user debug, run, and optimize applications
- Provide high quality system and software documentation
- Hold frequent training sessions to teach users best practices for running applications on large systems
- Lead user science requirements workshops
- Participate in large system procurements
- Provide expert advice on data management, software, compilers and tools
- Report system bugs and configure systems for maximum usability
- Provide a large suite of third party applications and libraries
Prior to becoming the Group Leader of USG, Katie was a consultant in the group from 2006-2010. She was the co-implementation team lead on the Hopper project. Hopper is NERSC's first petaflop system, a Cray XE6 with over 150,000 compute cores which delivers more than 3 million computing hours to scientists each day.
Before coming to NERSC, Katie worked at the ASC Flash Center at the University of Chicago supporting the FLASH code, a parallel adaptive mesh refinement astrophysics application. She also spent 2 years as a management consultant at Cambridge Strategic Management Group. She has an M.S. in Computer Science from the University of Chicago and a B.A. in Physics from Wellesley College.
Journal Articles
A. Dubey, K. B. Antypas, C. Daley, “Parallel Algorithms for Moving Lagrangian Data on Block Structured Eulerian Meshes”, Parallel Computing, 2011, 37 (2):101 - 113,
A. Dubey, K. Antypas, M.K. Ganapathy, L.B. Reid, K.M. Riley, D. Sheeler, A. Siegel, K. Weide, “Extensible Component Based Architecture for FLASH: A Massively Parallel, Multiphysics Simulation Code”, Parallel Computing, July 1, 2009, 35 (10-1:512-522,
R. Fisher, S. Abarzhi, K. Antypas, S. M. Asida, A. C. Calder, F. Cattaneo, P. Constantin, A. Dubey, I. Foster, J. B. Gallagher, M. K. Ganapathy, C.C. Glendenin, L. Kadano, D.Q. Lamb, S. Needham, M. Papka, T. Plewa, L.B. Reid, P. Rich, K. Riley, and D. Sheeler., “Tera-scale Turbulence Computation on BG/L Using the FLASH3 Code”, IBM Journal of Research and Development., March 1, 2008, Vol 52 (:127-136,
K.B. Antypas, A. C. Calder, A. Dubey, J. B. Gallagher, J. Joshi, D. Q. Lamb, T. Linde, E. Lusk, O. E. B. Messer, A. Mignone, H. Pan, M. Papka, F. Peng, T. Plewa, P. M. Ricker, K. Riley, D. Sheeler, A. Siegel, N. Taylor, J. W. Truran, N. Vladimirova, G. Weirs, D. Yu, Z. Zhang., “FLASH: Applications and Future.”, Parallel Computational Fluid Dynamics 2005: Theory and Applications, edited by A. Deane, G. Brenner, A. Ecer, D. R. Emerson, j. McDonough, J. Periaux, N. Satofuka, D. Tromeur-Dervout., January 1, 2006, 325,
Conference Papers
Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, “Shared Library Performance on Hopper”, A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,
Zhengji Zhao, Yun (Helen) He and Katie Antypas, “Cray Cluster Compatibility Mode on Hopper”, A paper presented in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 1, 2012,
Yun (Helen) He and Katie Antypas, “Running Large Jobs on a Cray XE6 System”, Cray User Group 2012 Meeting, Stuttgart, Germany, April 30, 2012,
A.C. Uselton, K.B. Antypas, D. Ushizima, J. Sukharev, “File System Monitoring as a Window into User I/O Requirements”, CUG Proceedings, Edinburgh, Scotland, March 1, 2012,
K. Antypas, Y. He, “Transitioning Users from the Franklin XT4 System to the Hopper XE6 System”, CUG Procceedings, Fairbanks, Alaska, May 23, 2011,
- Download File: CUG2011Hopperpaper.pdf (pdf: 1.5 MB)
The Hopper XE6 system, NERSC’s first peta-flop system with over 153,000 cores has increased the computing hours available to the Department of Energy’s Office of Science users by more than a factor of 4. As NERSC users transition from the Franklin XT4 system with 4 cores per node to the Hopper XE6 system with 24 cores per node, they have had to adapt to a lower amount of memory per core and on- node I/O performance which does not scale up linearly with the number of cores per node. This paper will discuss Hopper’s usage during the “early user period” and examine the practical implications of running on a system with 24 cores per node, exploring advanced aprun and memory affinity options for typical NERSC applications as well as strategies to improve I/O performance.
A. Uselton, K. Antypas, D. M. Ushizima, J. Sukharev, “File System Monitoring as a Window into User I/O Requirements”, Proceedings of the 2010 Cray User Group Meeting, Edinburgh, Scotland, Edinburgh, Scotland, May 24, 2010,
K. Antypas and A. Uselton, “MPI-I/O on Franklin XT4 System at NERSC”, CUG Proceedings, Atlanta, CA, May 28, 2009,
H. Shan, K. Antypas, J.Shalf., “Characterizing and Predicting the I/O Performance of HPC Applications Using a Parameterized Synthetic Benchmark.”, Supercomputing, Reno, NV, November 17, 2008,
A. C. Calder, N. T. Taylor, K. Antypas, and D. Sheeler, “A Case Study of Verifying and Validating an Astrophysical Simulation Code”, Astronomical Society of the Pacific, March 26, 2006, 119,
Presentation/Talks
Zhengji Zhao, Mike Davis, Katie Antypas, Yushu Yao, Rei Lee and Tina Butler, Shared Library Performance on Hopper, A talk in the Cray User Group meeting, Apri 29-May-3, 2012, Stuttgart, German., May 3, 2012,
Zhengji Zhao, Yun (Helen) He and Katie Antypas, Cray Cluster Compatibility Mode on Hopper, A talk in the Cray User Group meeting, April 29-May-3, 2012, Stuttgart, German., May 1, 2012,
K. Antypas, Best Practices for Reading and Writing Data on HPC Systems, February 1, 2012,
- Download File: Readingand-WritingDataNUGFeb2012.ppt (ppt: 5.1 MB)
K. Antypas, Parallel I/O From a User's Perspective, HPC Advisory Council, December 6, 2011,
- Download File: HPCAdvisoryCouncilIOTalkDec2011.pptx (pptx: 10 MB)
Zhengji Zhao, Mike Davis, Katie Antypas, Rei Lee and Tina Butler, Shared Library Performance on Hopper, Oct. 26, 2011, Cray Quarterly Meeting at St Paul, MN, October 26, 2011,
K. Antypas, NERSC: National Energy Research Scientific Computing Center, July 18, 2011,
K. Antypas, The Hopper XE6 System: Delivering High End Computing to the Nation’s Science and Research Community, Cray Quarterly Review, April 1, 2011,
K. Antypas, Introduction to Parallel I/O, ASTROSIM 2010 Workshop, July 19, 2010,
- Download File: ASTROSIMParallelIO2010.pdf (pdf: 45 MB)
K. Antypas, NERSC: Delivering High End Scientific Computing to the Nation's Research Community, November 5, 2009,
- Download File: EducauseNov2009antypas.pdf (pdf: 17 MB)
