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Amit Majumdar

Contact Information
 
E-address Postal Address
majumdar@sdsc.edu
Phone: (858) 534-8356 
Fax: (858) 534-5113
University of California San Diego
San Diego Supercomputer Center
9500 Gilman Drive 
La Jolla, CA 92093-0505 
Activities

Director of SDSC's Data Enabled Scientific Computing (DESC) divison. DESC is responsible for four major groups: High Performance Computing Systems, User Services, Scientific Computing Applications and Scientific Visualization. SDSC's XSEDE program is coordianted from the DESC divison by Nancy Wilkins-Diehr, Co-PI of the XSEDE program.

Previously I was director of the Scientific Computing Applications group at the San Diego Supercomputer Center. The computational scientists, in the group, have expertise and experience in High Performance Computing (HPC) and have degrees in various domain sciences such as mechanical engineering, hydrology, biochemistry, nuclear engineering, and physics. The group's main activities are HPC research and development work in collaboration with domain science users of NSF funded HPC resources. This collaborative R&D effort allows SDSC's experienced computational scientists to work with domain scientists regarding algorithm development, code optimization, code profiling/tuning, mathematical library implementation, new programming model implementation etc.

I am an Associate Professor in the Department of Radiation Medicine and Applied Sciences , UCSD . Our collaborative interdisciplinary research involves application of HPC for adaptive radiation therapy. We are specifically exploring use of GPUs for real-time re-planning where we need to solve three computationally intensive tasks: patient modeling based on deformable image registration, radiation transport simulation and dose calculation using Monte Carlo methods, and treatment optimization as a large scale optimization problem.

Education

I received B.S. degree in Electronics and Telecommunication from the Jadavpur University , Calcutta, India, M.S. degree in Nuclear Engineering from Idaho State University and Ph.D degree in the interdisciplinary program of Nuclear Engineering and Scientific Computing from the University of Michigan . My dissertation was done under the supervison of Prof. William R. Martin. Before joining the SDSC I worked for a year at the Engineering and Computer Center at the Ford Research Laboratory in Dearborn, Michigan.

Current Funded Projects

  1. PI of a NSF Division of Biological Infrastructure (DBI) funded grant (2015 - 2018) on implementing REST services utilizing the Neuroscience Gateway for computational neuroscientists. This is collaborative proposal between the San Diego Supercomputer Center (UCSD), Yale University and University College London. The NSG-R will allow ondemand, automated communication between neuroscience community projects such as Open Source Brain (OSB), ModelDB, and Neuroscience Information Framework (NIF) and HPC resources via NSG. It will also enable access to NSG via REST services from individual researcher's desktop or laptop. Subha Sivagnanam (SDSC) is the co-PI from SDSC, and Ted Carnevale from Yale is the PI of the Yale award. Prof. Angus Silver, from University College London, is the PI of the BBSRC, UK award and research scientist Padraig Gleeson (UCL) is a collaborator of this research project. SDSC NSF abstract , Yale NSF abstract , and BBSRC, UK abstract page.
  2. PI of NSF (IIS) funded BIGDATA project (2014 - 2017), between Ohio State (lead institution) and SDSC, on bringing HPC technologies (multi/many-core architectures, RDMA-enabled networking, NVRAMs and SSDs) and BigData middleware (Hadoop, Hbase and Spark) into a 'convergent trajectory'. DK Panda (Ohio State) is the lead PI and Mahidhar Tatineni (SDSC) is a Co-PI on this project. Link to NSF abstract page.
  3. Co-PI of a NSF ACI division funded SI2-SSI project (2013 -2018), between Indiana University (lead institution), SDSC, and Univ. Texas Health Science Center San Antonio, on science gateway as a platform (SciGaP). SciGaP will create a set of hosted services which can be easily adopted by other gateways from various domain sciences. Mark Miller is the SDSC PI. Other PI, Co-PIs are Marlone Pierce (IU, lead PI), Suresh Marru (IU, Co-PI), and Borries Demeler(PI from UTHSCSA). Link to NSF abstract page.
  4. Subcontract (consultant) on a NSF funded ACI grant (2014-2016) to U. North Carolina for developing mechanisms for mapping collaborations onto the new type of dynamically configurable, deeply networked institutional cloud infrastructure for data. PI is Ilya Baldin, RENCI, UNC. Link to NSF abstract page.

Past Funded Projects

  1. PI of NSF (CCF) funded SHF collaborative project (2012 - 2016), between Ohio State (lead institution), Texas Advanced Computing Center (TACC), and SDSC, on unified runtime for supporting hybrid programming models on heterogeneous architecture; Yifeng Cui (SDSC) is a Co-PI on this project. Other PIs and Co-PIs are DK Panda (Ohio State), Karl Schulz (TA CC), Bill Barth (TACC). Dmitry Pekurovsky, Robert Harkness, Mahidhar Tatineni (all from SDSC) are senior personnel in this project. Link to NSF abstract page
  2. PI of a NSF funded Division of Biological Infrastructure (DBI) grant (2012 - 2016) for creating a neuroscience gateway that will allow neuroscientists to access and utili ze High Performance Computing (HPC) resources for compuational modeling of cells and networks. This will enable computation al neuroscience research by eleminating the administrative and technical barrier for accessing HPC resources and thus democratize participation in science by all inclu ding historically underrepresented groups who find it difficult to access supercomputers. This is a collaborative project between SDSC (lead institution) and Yale; Ted Carnevale being the PI from Yale Univerisity. Maryann Martone (Neuros cience, UCSD) is a Co-PI from UCSD. Other UCSD and SDSC staff are Subha Sivagnanam (SDSC), Anita Bandrowski (Neuroscience, UCSD), Vadim Astakhov (Neuroscience, UCSD), Kenneth Yoshimoto (SDS C). Link to NSF grant abstract pag e .
  3. PI of a NSF (OCI) funded SI2 collaborative project (2012 - 2016), between Ohio State (lead institution), Texas Advance d Computnig Center (TACC), and SDSC, on comprehensive performance tuning framework for the MPI stack. Other PIs and Co-PIs are DK Panda (Ohio State), Bill Barth (TACC), Tommy Minyard (TACC). Dongju Choi, Mahidhar Tatineni (SDSC) ar e senior personnel in this project. Link to NSF abstract page.
  4. Co-PI of an Air Force (Air Force Office of Scientific Research - AFOSR) funded grant (2011 - 2015) for Dynamic Data Driven Application System (DDDAS) focusing on computational steering of large-scale structural systems through advanced simulation, optimization and structural health monitoring. PI is Yuri Bazilevs, Str uctural Engineering, UCSD and other Co-PIs are A. L. Marsden (Dept. of Mechanical and Aerospace Engr, UCSD), F. Lanza di Scalea (Structural Engr. Dept., UCSD), and Mahidhar Tatineni (SDSC).
  5. PI of a SDSC internal funded project (2012 - 2013) titled, "In-site Visualization, Data Mining and Computational Steering on t he Gordon Machine". Co-PI is Mahidhar Tatineni from SDSC. Non-SDSC collaborators are Homa Karimabadi (UCSD), Burlen Loring (LBNL), William Daughton (LANL), Patric O'Leary (Kitware Inc.), and Berk Gevici (Kitware, Inc.).
  6. Co-PI of a NSF (OCI) PRAC grant (2009-2013) for Petascale computations for complex turbulent flows. Lead PI i s P.K Yeung (Georgia Tech) and other co-PIs are Robert Moser (U. Texas), James J. Riley (U. Washington) and Dmitry Pekurovsky (SDSC). Link to NSF grant abstract page
  7. Co-PI of a NSF (OCI) funded PRAC grant (2010-2013) for petscale kinetic simulation of the magnetoshpere on the Blue Waters machine at NCSA. Lead PI of this project is Homa Karimabadi (UCSD, Sciber Quest), and another Co-PI is Keven Quest (UCSD). Link to NSF grant abstract page
  8. Co-PI of a NSF (OCI) funded collaborative PetaApps project (2009-2013) on petascale kinetic simulations of the magnetosphere. PI is Homa Karimabadi (UCSD) and the other co-PIs are Kevin Quest, Yuri Omelchenko (UCSD); other PI: Umit V. Catalyurek (Ohio State Unive rsity). Mahidhar Tatineni (SDSC) is a senior personnel this project and Amit Chourasia (SDSC) is involved in this project. Link to NSF grant abstract page
  9. Co-PI of a UCLab funded project (2009-2012) on developing optimized on-line adaptive therapy for radiation treatment of cancer using high performance computing. This is in collaboration with the PI of the project Steve Jiang (Director of Research, Dept of Radiation Oncology, UCSD) ; A.J. Mundt, MD, (Chairman, Dept of Radiation Oncology, UCSD); Todd Pawlicki (Director of Medical Physics and Clinical Operations, Dept of Radiation Oncology, UCSD), Dong Ju Choi (SDSC), and Mike Holst (Mathematics Dept, UCSD). Other collaborators are Marie-Anne Descalle (LLNL) and H. Edwin Romeijn (Department of Industr ial and Operations Engineering, University of Michigan).
  10. PI of a NSF (OCI) funded collaborative STCI project (2009 - 2012) on toplogy-aware MPI communication and scheduling for petascale systems. This is a collaborative project between Ohio State (lead institution), TACC and SDSC. Other PIs and co-PIs are D.K. Panda (Ohio State University), Karl Schulz and Bill Barth (Texas Advanced Computing Center, U. Texas). Yifeng Cui, Mahidhar Tatineni, and Dmitry Pekurovsky (all from SDSC) are senior personnel in this project. Link to NSF grant abstract page
  11. PI of a NSF (OCI) funded collaborative PetaApps project (2007 - 2012) on High Reynolds Number Turbulence Simulation. This is a collaborative project between Georgita Tech (lead institution), University of Texas, Austin and University of Washtington. Other PI and Co-PIs are P.K. Yeung (Georgia Tech), Dmitry Pekurovsky (SDSC), David Bader (Georgia Tech), Robert D. Moser (U. Texas) , James J. Riley (U. Washington), Stephen B. Pope (Cornell). Link to NSF grant abstract page
  12. PI of a Microsoft gift grant (2008 - 2011) project to port scientific applica tions on a Windows HPC Server 2008 cluster. Mahidhar Tatineni, Ross Walker, Larry Diegel, Don Thorp and Dong Ju Choi (all from SDSC) are involved in this project.
  13. Co-PI of a NSF (OCI) SGER grant ( 2009 - 2011) on parallel 3D FFT library enhancement developed by Dmitry Pekur ovksy, SDSC - PI of the award. Link to NSF grant abstract page
  14. PI of a SDSC internal funded project (2010 - 2011) on computational framework for cardiovascular surgical procedures. Other Co-PIs are Alison Marsden (Dept. of Mechanical and Aerospace Engr, UCSD), Yuri Bazilevs (Dept. of Structural Engr, UCSD), Mahidhar Tatineni (SDSC). Postdoc Sethuraman Sankaran and graduate student Kenneth Benner (Dept. of Structural Engr, UCSD) are involved in this project.
  15. Co-PI of a NSF (OCI) PRAC grant (2009-2011) for Petascale computations for complex turbulent flows. Lead PI is P.K Yeung (Georgia Tech) and other co-PIs are Robert Moser (U. Texas), James J. Riley (U. Washington). Link to NSF grant abstract page
  16. PI of a NSF (CISE) funded collaborative HECURA project (2008 - 2010) on improving one-sided MPI communication for ultra scale HPC machines. This is a collaborative project between Ohio State (lead institution), TACC and SDSC. Other PIs are D.K. Panda (Ohio State University) and Karl Schulz (Texas Advanced Computing Center, U. Texas). Yifeng Cui and Dmitry Pekurovksy (both from SDSC) are senior personnel in this project and Mahidhar Tat ineni (SDSC) is involved in this project. Link to NSF grant abstract page
  17. NSF (Engr) funded educational project through which we are providing Cyberinfrastructure experiences ( Cyberinfrastructure Experiences for Graduate Students (CIEG-2007) , CIEG-2008 ) for graduate students.
  18. Co-PI, of an NSF ITR funded project (2004-2007) on image guided neurosurgery (PI Kim Baldridge, SDSC/U.Zurich; Co-PI: Maryann Martone (UCSD), Simon K. Warfield, Brigham and Women's Hospital, Harvard Medical School; Collaborators: Dong Ju Choi, SDSC, and Petr Krysl, Structural Engineering, UCSD.). This project is in collaborations with the Computational Radiology Laboratory at the Brigham and Women's Hospital, Harvard Medical School. Link to NSF grant abstract page
  19. PI of an NSF (OCI) funded collaborative SGER project (2006 - 2007) on analyzing performance and scaling of SCEC AWM code (Other PI: Tom Jordan, USC (lead institution), Senior Personnel: Yifeng Cui, SDSC). Link to NSF grant abstract page

Publications

Professional Organization Membership

  • Society for Industrial and Applied Mathematics (SIAM)
  • Institute of Electrical and Electronics Engineers (IEEE)
  • Americal Physical Society (APS)
  • Organization for Computational Neuroscience (OCNS)