August 14, 2012
A new partnership is underway as the University of California San Diego (UCSD) and Yale University have been awarded a grant to build a neuroscience gateway. The three-year, $805,000, NSF-funded endeavor goes by the unwieldy name: "Advanced Biological Informatics Development: Building a Community Resource for Neuroscientists." While the moniker is quite a mouthful, the project aims to make neuroscience-based resources easily available to students and researchers.
The partners have been tasked with delivering HPC storage and compute resources as a service for neurological researchers. The details of the grant call for the San Diego Supercomputing Center (SDSC) to build a software infrastructure, taking advantage of the existing Neuroscience Information Framework (NIF) project.
Part of the new service involves developing a Web portal, the Neuroscience Gateway (NSG), which allows researchers to upload models, manipulate HPC job parameters, store and retrieve data and view HPC job statuses.
SDSC researcher Amit Majumdar, principal investigator for the project, was quoted in an official statement saying:
This gateway will allow neuroscientists to use HPC resources without having to have detailed knowledge about the implementation of the codes on HPC resources, or know all the complexities of how supercomputers work.
One task envisioned for the portal includes computational modeling of cells and neural networks. The research is extremely compute intensive, requiring capacity typically found only in elite supercomputing centers. Students and scientists without local access to machines of this ilk will be able to reach them remotely through the service. According to Majumdar, the Neuroscience Gateway is slated to use the SDSC Cloud to store simulation results, "where they will be secure and easily accessed and shared."
Compute capacity for the program will be provided by a collection of NSF supercomputing centers. These systems make up the Extreme Science and Engineering Discovery Environment (XSEDE) infrastructure and include some of the world's fastest systems. The list is an unofficial who's who of research facilities in the United States:
Blacklight – Pittsburgh Supercomputing Center
Forge – National Center for Supercomputing Applications
Gordon – San Diego Supercomputing Center
Kraken – National Institute for Computational Sciences
Lonestar – Texas Advanced Computing Center
Ranger – Texas Advanced Computing Center
Steele – Purdue University
Trestles – San Diego Supercomputing Center
Majumdar believes the specialized science portal will positively impact all researchers, but is especially significant for underserved groups that lack access to large HPC resources.
"Many of these investigators and students would otherwise find it very difficult, if not impossible, to implement and study models that press or exceed the storage and computing speed capabilities that are under their direct control," he said.
The new service will most likely interface with the Neuroscience Information Network, a project that touts itself as the largest source of neuroscience tools and data on the Web. Maryann Martone, NIF principle investigator as well as co-principal investigator for the UC San Diego Neuroscience Gateway award, says the gateway will also act as a collaborative space where researchers can share their ideas and data.
The ever-growing complexity of scientific and engineering problems continues to pose new computational challenges. Thus, we present a novel federation model that enables end-users with the ability to aggregate heterogeneous resource scale problems. The feasibility of this federation model has been proven, in the context of the UberCloud HPC Experiment, by gathering the most comprehensive information to date on the effects of pillars on microfluid channel flow.
Large-scale, worldwide scientific initiatives rely on some cloud-based system to both coordinate efforts and manage computational efforts at peak times that cannot be contained within the combined in-house HPC resources. Last week at Google I/O, Brookhaven National Lab’s Sergey Panitkin discussed the role of the Google Compute Engine in providing computational support to ATLAS, a detector of high-energy particles at the Large Hadron Collider (LHC).
Frank Ding, engineering analysis & technical computing manager at Simpson Strong-Tie, discussed the advantages of utilizing the cloud for occasional scientific computing, identified the obstacles to doing so, and proposed workarounds to some of those obstacles.
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04/02/2012 | AMD | Developers today are just beginning to explore the potential of heterogeneous computing, but the potential for this new paradigm is huge. This brief article reviews how the technology might impact a range of application development areas, including client experiences and cloud-based data management. As platforms like OpenCL continue to evolve, the benefits of heterogeneous computing will become even more accessible. Use this quick article to jump-start your own thinking on heterogeneous computing.