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Amit Majumdar

 

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

1. Director of SDSC's Data Enabled Scientific Computing (DESC) divison.

   DESC division is responsible for the following:

   High Performance Computing Systems group led by Christopher Irving
   User Services group led by Mahidhar Tatineni
   Scientific Computing Applications group led by Andrea Zonca
   Cloud Software Development group led by Shava Smallen
   Cyberinfrastructure Services and Solutions-HPC group led by Subha Sivagnanam
   SDSC's ACCESS program is coordinated from the DESC division by Shava Smallen, ACCESS Site PI of Track 3 and Track 4.
   HPC Network management and architecture is led by Tom Hutton
   HPC Education, Outreach and Training led by Mary Thomas and Bob Sinkovits
   Andreas Goetz leads a group in data-driven and high-performance computational chemistry
   Wayne Pfeiffer is a distinguished scientist focusing on bioinformatics and high-performance computing

2. Associate Professor in the Applied Sciences Division, Department of Radiation Medicine and Applied Sciences , UCSD . Collaborative interdisciplinary research involves application of HPC and computational methods for various aspects of radiation therapy such as adaptive radiation therapy, machine learning based treatment planning etc.

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, M.S. degree in Mathematics from the University of Michigan, 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.

Publications

Long CV

Current Funded Projects

1. Co-PI of the NSF CSSI Frameworks collaborative award (2022 - 2027) called the Cybershuttle project that creates highly usable scientific research environment that integrates all of a scientist's research tools and data, which may be on the scientist's laptop, a computing cloud, or a university supercomputer. Lead institution is Indiana University with Suresh Marru as the PI. Other UCSD PI, Co-PIs, and research staff are Giri Krishnan, Maksim Bazhenov, Shava Smallen, Kenneth Yoshimoto and Paul Hoover. Other institutions involved are UIUC and Allen Institute. Link to NSF abstract page.
2. SDSC site-PI of NSF AI Institute award (2021 - 2026) on the theme of AI and Advanced Cyberinfrastructure. Project title "Intelligent CyberInfrastructure with Computational Learning in the Environment (ICICLE)". Lead PI is DK Panda from Ohio State; other Co-PIs are Vipin Chaudhary (CWRU), Raghu Machiraju (OSU), Beth Plale (IU), and Eric Fosler-Lussier(OSU). This project brings together multidisciplinary team of scientists and engineers to develop intelligent CI for plug-and-play AI. Application areas include precision agriculture, animal ecology and smart foodsheds. It builds a diverse workforce through education, outreach and broadening participation in computing. Link to NSF abstract page.
3. PI of NSF OAC award (2020 - 2026) for the Voyager machine to enable AI science and engineering applications for the user community. Co-PIs are Rommie Amaro, Javier Duarte, Mai Nguyen and Robert Sinkovits. Link to NSF abstract page .
4. DOE grant (2023 - 2026); UCSD Site Co-PI, UCSD Site PI Frank Wuerthwein, with Lead PI Brian Sammuli and Co-Lead PI Raffi Nazikian (both from General Atomics); other UCSD Co-PIs Rose Yu and Sicun Gao; Hewlett Packard Enterprise Site PI Martin Foltin, SapientAI LLC Site PI Craig Michoski; The project will develop and deploy a Fusion Data Platform (FDP) and then demonstrate the platform's capabilities by developing reactor relevant AI/ML workflows. Link to DOE abstract page .
5. PI of a collaborative NSF Division of Biological Infrastructure (DBI) funded grant (2020 - 2024) that adds to the capacity of the Neuroscience Gateway to make it more suitable for data-driven neuroscience research. Subhashini Sivagnanam (SDSC) is the Co-PI and Kenneth Yoshimoto (SDSC) is a senior personnel. Ted Carnevale from Yale University is the PI of the Yale University award. Abstracts of the collaborative grant are available here (SDSC) and here (Yale) .
6. PI of a NIH, National Institute of Biomedical Imaging and Bioengineering funded (2019-2024) project; Co-Investigators are Subhashini Sivagnanam (SDSC) and Ted Carnevale (Yale University). Kenneth Yoshimoto, Marty Kandes, Steven Yeu and Trevor Peterson (ex-perticipant)from SDSC are involved in this project. This project focuses on expanding the capabilities of the Neuroscience Gateway (NSG) such that it becomes a platform for neuroscience tool dissemination, in addition the high performance computing capability it provides for neuroscience simulations. Link to NIH abstract page .
   1. PI of a NIH Office of Data Science Strategy Supplement grant (2022-2023) to improve the AI/ML-Readiness of NIH-Supported Data, with collaborator Dr. Satya Sahoo from the Case Western University and SDSC researchers Co-I Subhashini Sivagnanam and Kenneth Yoshimoto. This allows to integrate within NSG (i) Sahoo's group developed NeuroIntegrative Connectivity (NIC) tool that has meta-data, provenance etc. built in, and (ii) Sivagnanam's Open Science Chain (OSC) project and securely store research artifacts such as metadata, data and workflows into the OSC blockchain.
7. PI of a NIH, National Institute of Mental Health funded (2019-2024) project; multiple PIs are Scott Makeig (contact PI), Arnaud Delorme (both from UCSD) and Russ Poldrack (Stanford). Choonhan Yooon, Subha Sivagnanam, Kenneth Yoshimoto, and Dave Nadeau (ex-participants in the project), from SDSC are researchers involved in this project in addition to researchers Ramon Martinez, Dung Truong, Makato Miyakoshi, Zeynep Akalin Acar, Robert Buffington and others from the Swartz Center for Computational Neuroscience, UCSD. The project involves development of a BRAIN INITIATIVE funded human neuroeletromagnetic data archive and tools resources (NEMAR) that utilize the openneuro.org (Stanford) and nsgportal.org (SDSC) gateways. Link to NIH abstract page .
8. Co-PI of NSF OAC award (2019 - 2025) for the ~6 Petaflop Expanse supercomputer at SDSC which went into production for users starting December, 2020 and will operate for five years. PI of the grant is Mike Norman; other Co-PIs are Ilkay Altintas, Shawn Strande (former Co-PI), Robert Sinkovits, and Mahidhar Tatineni. NSF abstract page.

Completed Funded Projects

1. PI of a NSF OAC funded CSSI Frameworks collaborative project (2019-2023) with DK Panda (Ohio State)as the lead PI, and Bill Barth, the PI from TACC. Co-PIs of this project are Mahidhar Tatineni (SDSC), Karen Tomko (Ohio Supercomputer Center), Hari Subramoni (Ohio State), Samuel Khuvis (OSC) and Zhao Zhang (TACC). Research involves enhancing MPI middleware to take advantage of technologies to deliver the best possible scale-up and scale-out for HPC and Deep Learning (DL) applications on emerging dense GPU systems. Link to SDSC's NSF abstract page .
2. Co-PI of a NSF Division of Computer and Network Systems (CNS) funded grant (2018 - 2022) on developing a platform for large-scale neuromorphic computing. The project provides openly to the community a general-purpose neuromorphic cognitive computing platform. It is available via the Neuroscience Gateway (NSG). The reconfigurable platform allows both emulation and simulation of up to 128 million neurons with flesible connectivity and plasticity of up to 32 billion synapses. PI: Gert Cauwenberghs (UCDS); Co-PI: Emre Neftci (UC Irvine); senior personnel: Subha Sivagnanam (SDSC, UCSD). NSF abstract page .
3. PI of a NIH, National Institute of Biomedical Imaging and Bioengineering, funded project (2017 - 2022); this has multiple PIs - Scott Makeig (contact PI), Arnaud Delorme, Schwartz Center for Computational Science. Proposal title "The Open EEGLAB Portal Project" is a joint proposal between EEGLAB project and the Neuroscience Gateway (NSG) project; it involves processing of multimodal imaging data and integration of EEGLAB with NSG. Subha Sivagnanam, Kenneth Yoshimoto from SDSC, researchers Ramon Martinez, Zeynep Akalin Acar, Dung Truong and Robert Buffington, and others from the Swartz Center for Computational Science (SCCN) are involved in this project. Link to NIH abstract page.
4. PI of a NSF OAC funded grant (2018 - 2021) that provides travel fund to ten US students to attend the second workshop on "Software Challenges to Exascale Computing (SCEC)" in Delhi, India, Dec 13-14, 2018. This will contribute towards HPC workforce development by allowing students to learn about HPC software devlopment and will also provide opportunities for networking and establishing international collaboration. NSF abstract page .
5. Co-PI of a NSF OAC grant (2013 - 2021) for the Comet supercomputer at the San Diego Supercomputer Center and enabling long tail of science, science gateway users, high throughput users and data processing for the XSEDE user community. PI is Mike Norman; other Co-PIs are Shawn Strande, Robert Sinkovits and Mahidhar Tatineni; former Co-PIs: Nancy Wilkins-Diehr, Richard Moore, Phil Papadopoulus, Chaitanya Baru. NSF abstract page .
6. Co-PI of a NSF (OAC) funded project (2017 - 2021) with Satish Nair, PI, Prasad Calyam, Co-PI, David Bergin Co-PI from University of Missouri-Columbia. This proposal will result in development of cyberinfrastructure-based training modules for data-intensive neuroscience learning and research. Link to NSF abstract page.
7. PI of a NSF (CCF) funded collaborative project (2016 - 2020) with DK Panda (Ohio State)as the lead PI, and Bill Barth, the PI from TACC. Co-PIs of this project are Mahidhar Tatineni (SDSC), Karen Tomko (Ohio State), Hari Subramoni (Ohio State), Carlos Rosales-Fernandez (TACC), Jerome Vienne (TACC). This research involves high-performance and scalable communication mechanicsms for next generation Dense Many-Core architectures and how applications that use the MPI+X programming models are impacted in terms of performance. Link to NSF abstract page.
8. PI of a NSF Division of Biological Infrastructure (DBI) funded grant (2015 - 2020) 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.
9. Co-PI of a NSF ACI division funded SI2-SSI project (2013 -2019), 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; SDSC staff Subhashini Sivagnanam. 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.
10. PI of a subcontract (2017 - 2019) from DOD HPCMP's User Productivity Enhancement, Technology Transfer and Training (PETTT) Program. Co-PI on this project are Pietro Cicotti, Manu Shantharam, and Mahidhar Tatineni. As a part of this project we will develop and implement parallel I/O technologies which will be available as a part of the Naval Computational Science Library.
11. 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.
12. PI of a subcontract (2016 - 2017) from DOD HPCMP's User Productivity Enhancement, Technology Transfer and Training (PETTT) Program. Co-PI on this project are Pietro Cicotti, Mahidhar Tatineni, Dongju Choi and senior personnels is Manu Shantharam. As a part of this project we are looking into new I/O technologies and softare for scientific applications of interest to DOD.
13. 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.
14. PI of an Engility Corporation grant for student project (Summer, 2016). The project involved application of data analytics methods on I/O performance data of users' jobs to various file systems such as NFS, node local SSDs, Lustre parallel file system.
15. 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
16. 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 .
17. 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.
18. 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).
19. PI of an Intel Parallel Computing Center (IPCC) at SDSC. Other PIs are RossWalker and Andrea Goetz. As a part of this project we are looking into optimizing molecular dynamics and neuroscience applications on many- and multi-core processors. Link to IPCC page for this project.
20. 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.).
21. Co-PI of a NSF (OCI) PRAC grant (2011-2016) 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
22. 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
23. 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
24. 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).
25. PI of a NSF (OCI) funded collaborative project (2009 - 2013) 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
26. PI of a NSF (OCI) funded collaborative PetaApps project (2007 - 2013) 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
27. 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.
28. Co-PI of a NSF (OCI) SGER grant ( 2009 - 2011) on parallel 3D FFT library enhancement developed by Dmitry Pekurovsky , SDSC - PI of the award. Link to NSF grant abstract page
29. 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.
30. Co-PI of a NSF (OCI) PRAC grant (2009-2012) 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
31. 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
32. NSF (Engr) funded educational project through which we are providing Cyberinfrastructure experiences ( Cyberinfrastructure Experiences for Graduate Students (CIEG-2007) , CIEG-2008 ) for graduate students.
33. 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
34. 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

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