SC11 workshop, travel funding for PASI fellows

We are very pleased to announce that— thanks to new funding secured by the PI, Prof. Lorena Barba— 16 PASI fellows will have travel support to attend the top event of the HPC world: the Supercomputing Conference 2011, being held in Seattle, WA.

This funding is made available via NSF award OISE 1143988, to hold a workshop as a follow-up to tha Pan-American Advanced Studies Institute (PASI) held in Valparaiso, Chile in January 2011. The primary goal of this workshop is to reinforce the network created during the PASI, reconnecting young scientists with senior researchers (PASI lecturers) and their peers, and, ultimately, to stimulate new collaborations.

In addition, being co-located with the top event in the field of high-performance computing, this PASI follow-up will be invaluable for these participants to enhance their careers and feed their enthusiasm for continuing their work in this field.

Special social occasion

Prof Ridgway Scott, one of the PASI lecturers, will open the doors of his house in Seattle to receive the PASI fellows and attending lecturers for a lovely party of nice food and conversation. The party will be held on Friday, Nov. 18, 6pm. We are grateful to Prof Scott for his hospitality. We also thank the students who formed a committee to help with the logistics of this party: Anshu Arya, Ben Payne, Andrew Reiter, and Jeff Stuart.

The students who receive travel funding through this initiative are:

Name, position, degree	Supervisor and institution	Background
Arya, Anshu PhD student (2009–) BE ChemE BS Comp Sc UDelaware	Laxmikant Kale Dept. Computer Science University of Illinois at Urbana-Champaign	Improving the massively parallel quantum chemistry package, OpenAtom, to operate efficiently on petaFLOP machines, in collaboration with IBM Watson. Research goals: improving the efficiency and utilization of heterogeneous (accelerated) clusters, e.g., using an an adaptive run-time system capable of load- balancing during program execution, although currently has limited first-hand experience with GPUs.
Cooper, Christopher PhD student (2010–) BSc / PEng Mech. Engrg. UTFSM (Chile)	Lorena Barba Mechanical Engineering, Boston University	Working on GPU computing for fluid dynamics, meshless vortex methods, and boundary element methods. He was a research visitor to University of Bristol, UK in 2008 with EC funding, and is a recipient of “Becas Chile” of CONICYT. Has CUDA expertise for applications in partial differential equations and sparse linear algebra using Cusp. Recently was the instructor for a one-month long intensive course on CUDA held at Universidad Técnica Federico Santa María, organized by the PI, Prof. Barba.
Gokey, Trevor MSc student (2008–) B.A. Psychology	Anton Guliaev Computing for Life Sciences Center, San Francisco State University	Trevor has a background in psychology and chemistry, combined with experience in system administration of small Linux clusters. He is currently a graduate student in computer science with a concentration in computing for the life sciences, with an advisor in the Chemistry and Biochemistry Department. He works in concert with a wet lab that makes point mutations of a very conserved digestive protein in mammals. His work involves using molecular simulation to elucidate changes due to the mutations under study.
Karpenko, Oleksiy PhD student (2008–) MSc Comp. Sci. 2001 (Ukraine)	Yang Dai Bioinformatics, University of Illinois at Chicago	His interest is massively parallel approaches to processing epigenomic data. Worked as software engineer before starting PhD; extensive programming experience in C++ and OOP and many languages and environments. Publications in Bioinformatics, Immunogentics, Methods in Molecular Biology.
Krishnan, Anush PhD student (2009–) B.Tech/M.Tech. Aerospace Engineering, IIT Madras	Lorena Barba Mechanical Engineering Boston University	He is currently working on implementing the immersed boundary method to simulate flows over moving bodies. The work could have potential applications for the study of insect flight and micro-air vehicles. He has experience with vortex methods and a solid background in computational fluid dynamics. His programming skills include various languages and libraries: C/C++, Python, bash, PETSc, CUDA, Boost.
Layton, Simon PhD student (2008–) BSc Math/CS Bristol MSc Mech. Eng. BU 2011	Lorena Barba Mechanical Engr. Dept., Boston University	His research has concentrated on the use of CUDA to accelerate various scientific problems including the Immersed Boundary Method and Fast Gauss Transform. Two conference presentations (USNCCM ’08, ParCFD ’11) and one journal paper (CPC ’11). Extensive programming experience in Python, C/C++ and CUDA. NVIDIA intern during Summer ’11 working on CUDA accelerated Algebraic Multigrid (AMG).
Li, Ying-Wai PhD student (2007–) BSc / MSc Physics Univ. Hong Kong	David P. Landau, Dept. Physics & Astronomy, University of Georgia	Her research focuses on Monte Carlo simulations of simplified lattice protein models, with focus on interaction of proteins with attractive substrates. She has four papers in high impact-factor journals, and additional conference papers. Has attended two summer schools on GPU, has experience with CUDA, as well as Python and C++
McKenzie, Amber PhD student (2008-) MSc linguistics	Manton Matthews Computer Science, University of South Carolina	She is currently working on implementing MapReduce natural language processing (NLP) algorithms on a cluster of GPUs, as the result of a grant of GPUs from Nvidia. Has experience programming in CUDA and the Hadoop MapReduce framework, as well as Python and NLTK.
Olson, Britton PhD student (2008-_ B.S. Mech. Engrg. Brigham Young University	Sanjiva Lele Aero/Astro, Stanford University	A DOE Computational Science Graduate Fellow, he is currently working on large eddy simulation of rocket nozzles. He has published in Physics of Fluids and Journal of Computational Physics and done internship twice at Lawrence Berkeley National Laboratory. Britton lived for two years in Mexico during his undergraduate career, mastering the Spanish language and providing humanitarian service.
Payne, Benjamin PhD student (2009–) MSc Physics MST BSc UWi	Alexey Yamilov Dept. Physics, Missouri University of Science and Technology	Ben previously worked as system administrator (100 users) at UWi-Madison and is in the Air Force National Guard. He has XSEDE experience with more than 16,000 processors, and four journal publications. His PhD research is focused on light propagation through media with randomly-placed scatterers.
Perilla, Juan PhD student (2005–) BSc Physics (Colombia)	Thomas Woolf Dept. of Biophysics and Physical Chemistry, Johns Hopkins University	Has developed and published new methods that tackle the problem of transition states for large biological systems reducing the computational cost compared to other alternatives. Has mainly focused on large parallel architectures (Kraken, Steele). Researcher at the Epilepsy Center, doing volumetric reconstructions from MRI and CT scans for accurately locating electrodes in patients with epilepsy that have to undergo brain surgery.
Reiter, Andrew MSc student (2010–) BSc Mathematics, UMass Amherst	Bruce Turkington Dept. of Applied Mathematics, UMass Amherst	Previously a computer security engineer, Andrew has broad experience as a developer of open-source software, network security consultant and operating system design. After several years in the computer industry, he decided to return to university to study mathematics. His current focus is in optimization and computational mathematics, with interests in the fields of mulecular biology and fluid mechanics.
Sidelnik, Albert PhD student BSc in computer science	David Padua Computer Science, UIUC	His main interests are developing programming models and optimization techniques for large-scale and many-core parallel systems. He is currently developing compiler optimizations and analytical models for high-level GPU programming. His focus is in language extensions and compiler techniques for the translation of programs from array languages (e.g. Chapel) to efficient CPU/GPU code. Albert has done internships at Nvidia Research, IBM Watson, and Cray. He has also worked at IBM on the bring up and development of the BlueGene/L and /P supercomputers. He has 8 published US patents on parallel computer architectures, and is a 2010-2011 and 2011-2012 Nvidia Fellowship recipient.
Stuart, Jeffery PhD student BB/MS Univ NV both in CS	John Owens Computer Science, University of California, Davis	Internships in Nvidia and Google; multiple computing conference presentations. Focusing almost exclusively on GPUs in his PhD research. Part of the SciDAC UltraViz institute. MapReduce implementation on a GPU cluster.
Waggy, Scott PhD student (2009-) B.Sc Mech. Engrg. Colorado School of Mines	S. Biringen Aero. Engrg. Sciences, Univ. Colorado Boulder	His current area of research is computational modelling of the atmospheric boundary layer, and he has developed a fully parallel Navier-Stokes solver for that purpose. The goal is to analyze the flow in the wake of a wind turbine to determine the effect the structure has on the surrounding environment.
Yang, Lun PhD student (2008-) B.Sc. Civil Engrg. Zhejiang University (China)	Kaushik Dayal Comput. Science and Engrg. Carnegie Mellon University	Lun’s research interests include mechanics of microstructure in solids and real-space phase field modeling of ferroelectrics-based materials. Current work involves modeling ferroelectrics with boundary element methods.

Name, position, degree

Supervisor and institution

Background

Arya, Anshu
PhD student (2009–)

BE ChemE BS Comp Sc UDelaware

Laxmikant Kale

Dept. Computer Science
University of Illinois at Urbana-Champaign

Improving the massively parallel quantum chemistry package, OpenAtom, to operate efficiently on petaFLOP machines, in collaboration with IBM Watson. Research goals: improving the efficiency and utilization of heterogeneous (accelerated) clusters, e.g., using an an adaptive run-time system capable of load- balancing during program execution, although currently has limited first-hand experience with GPUs.

Cooper, Christopher
PhD student (2010–)

BSc / PEng Mech. Engrg. UTFSM (Chile)

Lorena Barba

Mechanical Engineering, Boston University

Working on GPU computing for fluid dynamics, meshless vortex methods, and boundary element methods. He was a research visitor to University of Bristol, UK in 2008 with EC funding, and is a recipient of “Becas Chile” of CONICYT. Has CUDA expertise for applications in partial differential equations and sparse linear algebra using Cusp. Recently was the instructor for a one-month long intensive course on CUDA held at Universidad Técnica Federico Santa María, organized by the PI, Prof. Barba.

Gokey, Trevor
MSc student (2008–)

B.A. Psychology

Anton Guliaev

Computing for Life Sciences Center,
San Francisco State University

Trevor has a background in psychology and chemistry, combined with experience in system administration of small Linux clusters. He is currently a graduate student in computer science with a concentration in computing for the life sciences, with an advisor in the Chemistry and Biochemistry Department. He works in concert with a wet lab that makes point mutations of a very conserved digestive protein in mammals. His work involves using molecular simulation to elucidate changes due to the mutations under study.

Karpenko, Oleksiy
PhD student (2008–)

MSc Comp. Sci. 2001 (Ukraine)

Yang Dai

Bioinformatics, University of Illinois at Chicago

His interest is massively parallel approaches to processing epigenomic data. Worked as software engineer before starting PhD; extensive programming experience in C++ and OOP and many languages and environments. Publications in Bioinformatics, Immunogentics, Methods in Molecular Biology.

Krishnan, Anush
PhD student (2009–)

B.Tech/M.Tech. Aerospace Engineering, IIT Madras

Lorena Barba

Mechanical Engineering
Boston University

He is currently working on implementing the immersed boundary method to simulate flows over moving bodies. The work could have potential applications for the study of insect flight and micro-air vehicles. He has experience with vortex methods and a solid background in computational fluid dynamics. His programming skills include various languages and libraries: C/C++, Python, bash, PETSc, CUDA, Boost.

Layton, Simon
PhD student (2008–)

BSc Math/CS Bristol MSc Mech. Eng. BU 2011

Lorena Barba

Mechanical Engr. Dept., Boston University

His research has concentrated on the use of CUDA to accelerate various scientific problems including the Immersed Boundary Method and Fast Gauss Transform. Two conference presentations (USNCCM ’08, ParCFD ’11) and one journal paper (CPC ’11). Extensive programming experience in Python, C/C++ and CUDA. NVIDIA intern during Summer ’11 working on CUDA accelerated Algebraic Multigrid (AMG).

Li, Ying-Wai
PhD student (2007–)

BSc / MSc Physics Univ. Hong Kong

David P. Landau,

Dept. Physics & Astronomy, University of Georgia

Her research focuses on Monte Carlo simulations of simplified lattice protein models, with focus on interaction of proteins with attractive substrates. She has four papers in high impact-factor journals, and additional conference papers. Has attended two summer schools on GPU, has experience with CUDA, as well as Python and C++

McKenzie, Amber
PhD student (2008-)

MSc linguistics

Manton Matthews

Computer Science, University of South Carolina

She is currently working on implementing MapReduce natural language processing (NLP) algorithms on a cluster of GPUs, as the result of a grant of GPUs from Nvidia. Has experience programming in CUDA and the Hadoop MapReduce framework, as well as Python and NLTK.

Olson, Britton
PhD student (2008-_

B.S. Mech. Engrg. Brigham Young University

Sanjiva Lele

Aero/Astro, Stanford University

A DOE Computational Science Graduate Fellow, he is currently working on large eddy simulation of rocket nozzles. He has published in Physics of Fluids and Journal of Computational Physics and done internship twice at Lawrence Berkeley National Laboratory. Britton lived for two years in Mexico during his undergraduate career, mastering the Spanish language and providing humanitarian service.

Payne, Benjamin
PhD student (2009–)

MSc Physics MST
BSc UWi

Alexey Yamilov

Dept. Physics, Missouri University of Science and Technology

Ben previously worked as system administrator (100 users) at UWi-Madison and is in the Air Force National Guard. He has XSEDE experience with more than 16,000 processors, and four journal publications. His PhD research is focused on light propagation through media with randomly-placed scatterers.

Perilla, Juan
PhD student (2005–)

BSc Physics (Colombia)

Thomas Woolf

Dept. of Biophysics and Physical Chemistry, Johns Hopkins University

Has developed and published new methods that tackle the problem of transition states for large biological systems reducing the computational cost compared to other alternatives. Has mainly focused on large parallel architectures (Kraken, Steele). Researcher at the Epilepsy Center, doing volumetric reconstructions from MRI and CT scans for accurately locating electrodes in patients with epilepsy that have to undergo brain surgery.

Reiter, Andrew
MSc student (2010–)

BSc Mathematics, UMass Amherst

Bruce Turkington

Dept. of Applied Mathematics, UMass Amherst

Previously a computer security engineer, Andrew has broad experience as a developer of open-source software, network security consultant and operating system design. After several years in the computer industry, he decided to return to university to study mathematics. His current focus is in optimization and computational mathematics, with interests in the fields of mulecular biology and fluid mechanics.

Sidelnik, Albert
PhD student

BSc in computer science

David Padua

Computer Science, UIUC

His main interests are developing programming models and optimization techniques for large-scale and many-core parallel systems. He is currently developing compiler optimizations and analytical models for high-level GPU programming. His focus is in language extensions and compiler techniques for the translation of programs from array languages (e.g. Chapel) to efficient CPU/GPU code. Albert has done internships at Nvidia Research, IBM Watson, and Cray. He has also worked at IBM on the bring up and development of the BlueGene/L and /P supercomputers. He has 8 published US patents on parallel computer architectures, and is a 2010-2011 and 2011-2012 Nvidia Fellowship recipient.

Stuart, Jeffery
PhD student

BB/MS Univ NV both in CS

John Owens

Computer Science, University of California, Davis

Internships in Nvidia and Google; multiple computing conference presentations. Focusing almost exclusively on GPUs in his PhD research. Part of the SciDAC UltraViz institute. MapReduce implementation on a GPU cluster.

Waggy, Scott
PhD student (2009-)

B.Sc Mech. Engrg. Colorado School of Mines

S. Biringen

Aero. Engrg. Sciences, Univ. Colorado Boulder

His current area of research is computational modelling of the atmospheric boundary layer, and he has developed a fully parallel Navier-Stokes solver for that purpose. The goal is to analyze the flow in the wake of a wind turbine to determine the effect the structure has on the surrounding environment.

Yang, Lun
PhD student (2008-)

B.Sc. Civil Engrg. Zhejiang University (China)

Kaushik Dayal

Comput. Science and Engrg. Carnegie Mellon University

Lun’s research interests include mechanics of microstructure in solids and real-space phase field modeling of ferroelectrics-based materials. Current work involves modeling ferroelectrics with boundary element methods.

Other PASI fellows attending SC11 with own funding who will also join our PASI get-together are:

Name, position, degree	Supervisor and institution	Background
Cook, Henry PhD student (2009–) BSc Univ. Virginia	David Patterson, Krste Asanovic Computer Science, UC Berkeley	His main research interests are manycore chip architectures, software-managed memory hierarchies, composable abstractions of data locality, design space search and optimization. Currently, Henry is focusing on creating “programmable” software-managed memory hierarchies, including mechanisms that allow for software control of data placement, movement, coherence and partition-able capacity. He’s also studying auto-tuning libraries and frameworks that can take a high-level description of the computation and emit software control instructions (e.g. Sequoia). Henry did an internship at Nvidia Research this summer and is a 2010 recipient of the Nvidia Fellowship. He is co-author of four CS conference papers, including the 2010 International Symposium on Computer Architecture, and the ACM/IEEE Conference on Design Automation.
Peters, Amanda PhD student (2008–) BA Physics/CS 2005 Duke U	Efthimios Kaxiras Applied Physics, Harvard University	She has extensive programming experience, mainly MPI. Was software engineer for Blue Gene, 4 years working for IBM before starting PhD, in various roles. Multiple conference (CS) publications. Now working on large-scale simulation of cardiovascular hemodynamics. Has worked scaling CFD application to 294k procs. and is a finalist for Gordon Bell prize 2010. Starting to get involved with CUDA.

Name, position, degree

Supervisor and institution

Background

Cook, Henry
PhD student (2009–)

BSc Univ. Virginia

David Patterson, Krste Asanovic

Computer Science, UC Berkeley

His main research interests are manycore chip architectures, software-managed memory hierarchies, composable abstractions of data locality, design space search and optimization. Currently, Henry is focusing on creating “programmable” software-managed memory hierarchies, including mechanisms that allow for software control of data placement, movement, coherence and partition-able capacity. He’s also studying auto-tuning libraries and frameworks that can take a high-level description of the computation and emit software control instructions (e.g. Sequoia). Henry did an internship at Nvidia Research this summer and is a 2010 recipient of the Nvidia Fellowship. He is co-author of four CS conference papers, including the 2010 International Symposium on Computer Architecture, and the ACM/IEEE Conference on Design Automation.

Peters, Amanda
PhD student (2008–)

BA Physics/CS 2005 Duke U

Efthimios Kaxiras

Applied Physics, Harvard University

She has extensive programming experience, mainly MPI. Was software engineer for Blue Gene, 4 years working for IBM before starting PhD, in various roles. Multiple conference (CS) publications. Now working on large-scale simulation of cardiovascular hemodynamics. Has worked scaling CFD application to 294k procs. and is a finalist for Gordon Bell prize 2010. Starting to get involved with CUDA.

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