18 results on '"Nicholas A. Nystrom"'
Search Results
2. System Integration of Neocortex, a Unique, Scalable AI Platform.
- Author
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Paola A. Buitrago, Julian A. Uran, and Nicholas A. Nystrom
- Published
- 2021
- Full Text
- View/download PDF
3. Neocortex and Bridges-2: A High Performance AI+HPC Ecosystem for Science, Discovery, and Societal Good.
- Author
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Paola A. Buitrago and Nicholas A. Nystrom
- Published
- 2020
- Full Text
- View/download PDF
4. Delivering Scalable Deep Learning to Research with Bridges-AI.
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Paola A. Buitrago, Nicholas A. Nystrom, Rajarsi Gupta 0001, and Joel H. Saltz
- Published
- 2019
- Full Text
- View/download PDF
5. Open Compass: Accelerating the Adoption of AI in Open Research.
- Author
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Paola A. Buitrago and Nicholas A. Nystrom
- Published
- 2019
- Full Text
- View/download PDF
6. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.
- Author
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Michael P. Snyder, Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija, Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang 0020, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, Zorina S. Galis, Long Cai, Cole Trapnell, Dana Jackson, Garry P. Nolan, William James Greenleaf, Sylvia K. Plevritis, Sara Ahadi, Stephanie A. Nevins, Hayan Lee, Christian Martijn Schuerch, Sarah Black, Vishal Gautham Venkataraaman, Ed Esplin, Aaron Horning, Amir Bahmani, Xin Sun, Sanjay Jain 0006, James S. Hagood, Gloria Pryhuber, Peter V. Kharchenko, Bernd Bodenmiller, Todd Brusko, Michael Clare-Salzler, Harry Nick, Kevin Otto 0001, Clive Wasserfall, Marda Jorgensen, Maigan Brusko, Sergio Maffioletti, Richard M. Caprioli, Jeffrey M. Spraggins, Danielle Gutierrez, Nathan Heath Patterson, Elizabeth K. Neumann, Raymond Harris, Mark P. de Caestecker, Agnes B. Fogo, Raf Van de Plas, Ken Lau, Guo-Cheng Yuan, Qian Zhu, Ruben Dries, Peng Yin, Sinem K. Saka, Jocelyn Y. Kishi, Yu Wang, Isabel Goldaracena, Dong Hye Ye, Kristin E. Burnum-Johnson, Paul D. Piehowski, Charles Ansong, Ying Zhu, Tushar Desai, Jay Mulye, Peter Chou, Monica Nagendran, Sarah A. Teichmann, Benedict Paten, Robert F. Murphy, Jian Ma 0004, Vladimir Yu. Kiselev, Carl Kingsford, Allyson Ricarte, Maria Keays, Sushma Anand Akoju, Matthew Ruffalo, Margaret Vella, Chuck McCallum, Leonard E. Cross, Samuel H. Friedman, Randy W. Heiland, Bruce William Herr II, Paul Macklin, Ellen M. Quardokus, Lisel Record, James P. Sluka, Griffin M. Weber, Philip D. Blood, Alexander Ropelewski, William Shirey, Robin M. Scibek, Paula M. Mabee, W. Christopher Lenhardt, Kimberly Robasky, Stavros Michailidis, John C. Marioni, Andrew Butler, Tim Stuart, Eyal Fisher, Shila Ghazanfar, Gökcen Eraslan, Tommaso Biancalani, Eeshit D. Vaishnav, Pothur Srinivas, Aaron Pawlyk, Salvatore Sechi, Elizabeth L. Wilder, and James Anderson
- Published
- 2019
- Full Text
- View/download PDF
7. Bridges: a uniquely flexible HPC resource for new communities and data analytics.
- Author
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Nicholas A. Nystrom, Michael J. Levine, Ralph Z. Roskies, and J. Ray Scott
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- 2015
- Full Text
- View/download PDF
8. Bridges-2: A Platform for Rapidly-Evolving and Data Intensive Research
- Author
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Nicholas A. Nystrom, Sergiu Sanielevici, Robin Scibek, Shawn T. Brown, Edward Hanna, and Paola A. Buitrago
- Subjects
Interoperation ,Workflow ,Resource (project management) ,Computer science ,Emerging technologies ,business.industry ,Scalability ,Data analysis ,Usability ,Supercomputer ,business ,Data science - Abstract
Today’s landscape of computational science is evolving rapidly, with a need for new, flexible, and responsive supercomputing platforms for addressing the growing areas of artificial intelligence (AI), data analytics (DA) and convergent collaborative research. To support this community, we designed and deployed the Bridges-2 platform. Building on our highly successful Bridges supercomputer, which was a high-performance computing resource supporting new communities and complex workflows, Bridges-2 supports traditional and nontraditional research communities and applications; integrates new technologies for converged, scalable high-performance computing (HPC), AI, and data analytics; prioritizes researcher productivity and ease of use; and provides an extensible architecture for interoperation with complementary data intensive projects, campuses, and clouds. In this report, we describe Bridges-2’s hardware and configuration, user environments, and systems support and present the results of the successful Early User Program.
- Published
- 2021
9. System Integration of Neocortex, a Unique, Scalable AI Platform
- Author
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Nicholas A. Nystrom, Julian A. Uran, and Paola A. Buitrago
- Subjects
Workflow ,Software ,business.industry ,Computer science ,Process (engineering) ,Deep learning ,Scalability ,Hyperparameter optimization ,System integration ,Artificial intelligence ,Supercomputer ,business ,Software engineering - Abstract
To advance knowledge by enabling unprecedented AI speed and scalability, the Pittsburgh Supercomputing Center (PSC), a joint research center of Carnegie Mellon University and the University of Pittsburgh, in partnership with Cerebras Systems and Hewlett Packard Enterprise (HPE), has deployed Neocortex, an innovative computing platform that accelerates scientific discovery by vastly shortening the time required for deep learning training and inference, fosters greater integration of deep AI models with scientific workflows, and provides promising hardware for the development of more efficient algorithms for artificial intelligence and graph analytics. Neocortex advances knowledge by accelerating scientific research, enabling development of more accurate models and use of larger training data, scaling model parallelism to unprecedented levels, and focusing on human productivity by simplifying tuning and hyperparameter optimization to create a transformative hardware and software platform for the exploration of new frontiers. Neocortex has been integrated with PSC’s complementary infrastructure. This papers shares experiences, decisions, and findings made in that process. The system is serving science and engineering users via an early user access program. Valuable artifacts developed during the integration phase have been made available via a public repository and have been consulted by other AI system deployments that have seen Neocortex as an inspiration.
- Published
- 2021
10. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program
- Author
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William J. Greenleaf, Sarah A. Teichmann, Margaret Vella, Ajay Pillai, Aviv Regev, Ananda L. Roy, Kristin E. Burnum-Johnson, Cole Trapnell, Yiing Lin, Marda Jorgensen, Gloria S. Pryhuber, Leslie Gaffney, Ken S. Lau, Kimberly Robasky, Jeffrey M. Spraggins, Chuck McCallum, Stavros Michailidis, Randy Heiland, Orit Rozenblatt-Rosen, Allyson Ricarte, Xin bSun, Kevin J. Otto, Amir Bahmani, Zorina S. Galis, James S. Hagood, Monica Nagendran, Gökcen Eraslan, Robin M. Scibek, Jocelyn Y. Kishi, Jay Mulye, Maria Keays, Griffin M. Weber, Caltech-UW Tmc, Charles Ansong, Nicholas A. Nystrom, Vishal G. Venkataraaman, Vladimir Yu. Kiselev, Ucsd Tmc, Ellen M. Quardokus, Tushar bDesai, Bruce Herr, Engagement Component, James E. Anderson, Shin Lin, Lisel Record, Peter V. Kharchenko, Robert F. dMurphy, Stanford-WashU Tmc, Yu Wang, Jian Ma, Sergio Maffioletti, Sarah Black, Matthew Ruffalo, Salvatore Sechi, John C. Marioni, Ziv Bar-Joseph, Richard M. Caprioli, Stanford Ttd, Garry P. Nolan, Marishka Brown, Elizabeth L. Wilder, Maigan A. Brusko, Peter Chou, Tommaso Biancalani, Christian Martijn Schuerch, Julia Laskin, Richard Conroy, Jonathan C. Silverstein, Paula M. Mabee, Dena Procaccini, Pehr B. Harbury, Michael Snyder, Pothur Srinivas, Jennifer Rood, Dana Jackson, Sanjay Jain, Katy Börner, Visualization HuBMAP Integration, William E. Shirey, Sinem K. Saka, James P. Sluka, Agnes B. Fogo, Isabel Goldaracena, Sushma A. Akoju, Raymond C. Harris, Rahul Satija, Sylvia K. Plevritis, Tim Stuart, Shila Ghazanfar, Peng Yin, Harvard Ttd, Aaron M. Horning, Ed Esplin, Amanda Posgai, Michael J. Clare-Salzler, Raf Van de Plas, Aaron Pawlyk, Guo-Cheng Yuan, Benedict aten, DongHye Ye, Hayan Lee, Eyal Fisher, Jay Shendure, Long Cai, Danielle cGutierrez, Carl Kingsford, Ruben Dries, Sara Ahadi, Paul D. Piehowski, Bernd bBodenmiller, Purdue Ttd, Stephanie A. Nevins, Philip D. Blood, Andrew Butler, W. Christopher Lenhardt, Ying Zhu, Alexander J. Ropelewski, Harry S. Nick, Nathan Heath Patterson, Elizabeth K. Neumann, Anna Hupalowska, Samuel H. Friedman, Clive hWasserfall, Qian Zhu, Mark P. deCaestecker, Leonard E. Cross, Mark A. Atkinson, Paul Macklin, Todd M. Brusko, Eeshit Dhaval Vaishnav, Nils Gehlenborg, and Kun Zhang
- Subjects
Male ,Models, Anatomic ,Aging ,Biomedical Research ,media_common.quotation_subject ,International Cooperation ,Art history ,Technology development ,Molecular resolution ,03 medical and health sciences ,0302 clinical medicine ,Atlases as Topic ,Computational platforms and environments ,Research community ,Common fund ,Humans ,Molecular Biology ,030304 developmental biology ,media_common ,0303 health sciences ,Shared vision ,Multidisciplinary ,Spatial mapping ,Art ,Genomics ,United States ,3. Good health ,Cellular resolution ,National Institutes of Health (U.S.) ,Health ,Organ Specificity ,Perspective ,Female ,Single-Cell Analysis ,030217 neurology & neurosurgery - Abstract
Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions., HuBMAP supports technology development, data acquisition, and spatial analyses to generate comprehensive molecular and cellular three-dimensional tissue maps.
- Published
- 2019
11. Porting Third-Party Applications Packages to the Cray T3D: Programming Issues and Scalability Results.
- Author
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Frank C. Wimberly, Michael H. Lambert, Nicholas A. Nystrom, Alex Ropelewski, and William Young
- Published
- 1996
- Full Text
- View/download PDF
12. Neocortex and Bridges-2: A High Performance AI+HPC Ecosystem for Science, Discovery, and Societal Good
- Author
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Nicholas A. Nystrom and Paola A. Buitrago
- Subjects
Service (systems architecture) ,010308 nuclear & particles physics ,business.industry ,Computer science ,Process (engineering) ,Data management ,Big data ,010501 environmental sciences ,Supercomputer ,01 natural sciences ,Data science ,Workflow ,0103 physical sciences ,Scalability ,Sustainability ,business ,0105 earth and related environmental sciences - Abstract
Artificial intelligence (AI) is transforming research through analysis of massive datasets and accelerating simulations by factors of up to a billion. Such acceleration eclipses the speedups that were made possible though improvements in CPU process and design and other kinds of algorithmic advances. It sets the stage for a new era of discovery in which previously intractable challenges will become surmountable, with applications in fields such as discovering the causes of cancer and rare diseases, developing effective, affordable drugs, improving food sustainability, developing detailed understanding of environmental factors to support protection of biodiversity, and developing alternative energy sources as a step toward reversing climate change. To succeed, the research community requires a high-performance computational ecosystem that seamlessly and efficiently brings together scalable AI, general-purpose computing, and large-scale data management. The authors, at the Pittsburgh Supercomputing Center (PSC), launched a second-generation computational ecosystem to enable AI-enabled research, bringing together carefully designed systems and groundbreaking technologies to provide at no cost a uniquely capable platform to the research community. It consists of two major systems: Neocortex and Bridges-2. Neocortex embodies a revolutionary processor architecture to vastly shorten the time required for deep learning training, foster greater integration of artificial deep learning with scientific workflows, and accelerate graph analytics. Bridges-2 integrates additional scalable AI, high-performance computing (HPC), and high-performance parallel file systems for simulation, data pre- and post-processing, visualization, and Big Data as a Service. Neocortex and Bridges-2 are integrated to form a tightly coupled and highly flexible ecosystem for AI- and data-driven research.
- Published
- 2021
13. Delivering Scalable Deep Learning to Research with Bridges-AI
- Author
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Rajarsi Gupta, Nicholas A. Nystrom, Joel H. Saltz, and Paola A. Buitrago
- Subjects
business.industry ,Computer science ,Deep learning ,Big data ,010501 environmental sciences ,Supercomputer ,01 natural sciences ,Data science ,GeneralLiterature_MISCELLANEOUS ,03 medical and health sciences ,ComputingMethodologies_PATTERNRECOGNITION ,0302 clinical medicine ,Software deployment ,030220 oncology & carcinogenesis ,Server ,Container (abstract data type) ,Scalability ,Artificial intelligence ,Architecture ,business ,0105 earth and related environmental sciences - Abstract
Artificial intelligence (AI), particularly deep learning, is enabling tremendous advances and is itself of great research interest. To address these research requirements, the Pittsburgh Supercomputing Center (PSC) expanded its Bridges supercomputer with Bridges-AI, providing the world’s most powerful AI servers to the U.S. national research community and their international collaborators. We describe the motivation and architecture of Bridges-AI and its integration with Bridges, which adds to Bridges’ capabilities for scalable, converged high-performance computing (HPC), AI, and Big Data. We then describe the software environment of Bridges-AI, particularly the introduction of containers for deep learning frameworks, machine learning, and graph analytics, and PSC’s approach to container deployment. We close with a discussion of the range of research challenges that Bridges-AI is enabling breakthroughs, highlighting development of AI-driven methods to identify immune responses with automated tumor detection in breast cancer.
- Published
- 2020
14. Open Compass
- Author
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Nicholas A. Nystrom and Paola A. Buitrago
- Subjects
Computer science ,business.industry ,Deep learning ,Testbed ,Ontology (information science) ,computer.software_genre ,Data science ,GeneralLiterature_MISCELLANEOUS ,Software framework ,Identification (information) ,Open research ,Compass ,Applications of artificial intelligence ,Artificial intelligence ,business ,computer - Abstract
Artificial intelligence (AI) has immense potential spanning research and industry. AI applications abound and are expanding rapidly, yet the methods, performance, and understanding of AI are in their infancy. Researchers face vexing issues such as how to improve performance, transferability, reliability, comprehensibility, and how better to train AI models with only limited data. Future progress depends on advances in hardware accelerators, software frameworks, system and architectures, and creating cross-cutting expertise between scientific and AI domains. Open Compass is an exploratory research project to conduct academic pilot studies on an advanced engineering testbed for artificial intelligence, the Compass Lab, culminating in the development and publication of best practices for the benefit of the broad scientific community. Open Compass includes the development of an ontology to describe the complex range of existing and emerging AI hardware technologies and the identification of benchmark problems that represent different challenges in training deep learning models. These benchmarks are then used to execute experiments in alternative advanced hardware solution architectures. Here we present the methodology of Open Compass and some preliminary results on analyzing the effects of different GPU types, memory, and topologies for popular deep learning models applicable to image processing.
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- 2019
15. Bridges: Converging HPC, AI, and Big Data for Enabling Discovery
- Author
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Philip D. Blood, Nicholas A. Nystrom, and Paola A. Buitrago
- Subjects
Computer science ,business.industry ,Big data ,business ,Data science - Published
- 2019
16. Blacklight: Coherent Shared Memory for Enabling Science
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Phil Blood, Eng Lim Goh, Nicholas A. Nystrom, and Joel Welling
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Shared memory ,Human–computer interaction ,Computer science - Published
- 2017
17. Bridges
- Author
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Ralph Roskies, J. Ray Scott, Michael J. Levine, and Nicholas A. Nystrom
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Web server ,business.industry ,Computer science ,Data management ,Big data ,Virtualization ,computer.software_genre ,World Wide Web ,Workflow ,Cyberinfrastructure ,Shared memory ,Systems management ,business ,computer - Abstract
In this paper, we describe Bridges, a new HPC resource that will integrate advanced memory technologies with a uniquely flexible, user-focused, data-centric environment to empower new research communities, bring desktop convenience to HPC, connect to campuses, and drive complex workflows. Bridges will differ from traditional HPC systems and support new communities through extensive interactivity, gateways (convenient web interfaces that hide complex functionality and ease access to HPC resources) and tools for gateway building, persistent databases and web servers, high-productivity programming languages, and virtualization. Bridges will feature three tiers of processing nodes having 128GB, 3TB, and 12TB of hardware-enabled coherent shared memory per node to support memory-intensive applications and ease of use, together with persistent database and web nodes and nodes for logins, data transfer, and system management. State-of-the-art Intel® Xeon® CPUs and NVIDIA Tesla GPUs will power Bridges' compute nodes. Multiple filesystems will provide optimal handling for different data needs: a high-performance, parallel, shared filesystem, node-local filesystems, and memory filesystems. Bridges' nodes and parallel filesystem will be interconnected by the Intel Omni-Path Fabric, configured in a topology developed by PSC to be optimal for the anticipated data-centric workload. Bridges will be a resource on XSEDE, the NSF Extreme Science and Engineering Discovery Environment, and will interoperate with other advanced cyberinfrastructure resources. Through a pilot project with Temple University, Bridges will develop infrastructure and processes for campus bridging, consisting of offloading jobs at periods of unusually high load to the other site and facilitating cross-site data management. Education, training, and outreach activities will raise awareness of Bridges and data-intensive science across K-12 and university communities, industry, and the general public.
- Published
- 2015
18. Porting third-party applications packages to the Cray T3D: Programming issues and scalability results
- Author
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Michael H. Lambert, Alex Ropelewski, William Young, Frank C. Wimberly, and Nicholas A. Nystrom
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Cray XK7 ,ComputerSystemsOrganization_COMPUTERSYSTEMIMPLEMENTATION ,Workstation ,Computer Networks and Communications ,Computer science ,Parallel computing ,ComputerSystemsOrganization_PROCESSORARCHITECTURES ,Supercomputer ,computer.software_genre ,Cluster (spacecraft) ,Computer Graphics and Computer-Aided Design ,Porting ,Theoretical Computer Science ,law.invention ,Alpha (programming language) ,Artificial Intelligence ,Hardware and Architecture ,Red Storm ,law ,Scalability ,Operating system ,computer ,Software - Abstract
In the spring of 1993 a number of highly used third-party packages were selected for porting to the Cray MPP which was to be delivered to the Pittsburgh Supercomputing Center later in the year. Using the T3D Emulator and a cluster of Alpha workstations and eventually the MPP hardware in Eagan and Pittsburgh these packages were successfully reimplemented with varying degrees of difficulty. In this paper we will describe for three of those packages: the major difficulties, the novel solutions and current performance relative to the Cray C90.
- Published
- 1996
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