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InTheLoop | 09.02.2014

September 2, 2014

NERSC Exascale Scientific Applications Program Chooses 20 Projects for Fall Launch

The National Energy Research Scientific Computing Center (NERSC) has accepted 20 projects into the NERSC Exascale Scientific Applications Program (NESAP), a new collaborative effort that partners NERSC, Intel and Cray resources with code teams across the U.S. to prepare for Cori, the center’s next-generation supercomputer.

Cori, a Cray XC system slated to be deployed at NERSC in 2016, is intended to meet the growing computational needs of the Department of Energy’s (DOE) science community and serve as a platform for transitioning users to energy-efficient, manycore architectures.

NESAP represents a unique opportunity for researchers to work with NERSC and vendor staff to optimize application codes for Cori's Knights Landing manycore architecture. The program will provide access to early hardware and special training and preparation sessions, plus an opportunity for a postdoctoral researcher to investigate computational science issues associated with energy-efficient manycore systems. »Read more.

Prabhat to Lead NERSC Data and Analytics Services Group

Prabhat has been named Group Lead of the Data and Analytics Services (DAS) Group at the Department of Energy’s National Energy Research Scientific Computing Center (NERSC). 

The DAS group is responsible for providing data and analytics services and support to NERSC users to address the challenges arising from the increasing size and complexity of data from simulations and experiments. As the DAS Group Lead, Prabhat will play a key role in developing and implementing NERSC’s data strategic initiative: to increase the productivity, usability and impact of data intensive science by providing comprehensive data systems and services to store, analyze, manage and share data. He was previously a member of the Computational Research Division's Scientific Visualization group and the NERSC Analytics team. »Read more.

Kiersten Fagnan Named NERSC/JGI Engagement Lead

Kjiersten Fagnan has been named the NERSC/JGI Engagement Lead for Joint Genome Institute (JGI) computational and data analysis efforts carried out at the Department of Energy’s (DOE) National Energy Research Scientific Computing Center (NERSC). In her new role, Fagnan will coordinate NERSC activities carried out in support of JGI’s mission and lead NERSC’s JGI user support team, which provides expert technical computational science support and advice to JGI staff and users.  »Read more.

Katie Antypas Addresses CSG Fellows at Krell Institute

NERSC Services Department Head Katie Antypas spoke at the DOE Computational Science Graduate Fellowship (CSGF) HPC Workshop held at the Krell Institute in late July. In her talk, Antypas explored the challenges scientists face in prepping their applications for advanced manycore architectures and explained how NERSC's next supercomputer, nick-named Cori, was designed and built to assist in this upcoming challenge. Her talk and slides are »now available online.

Computing Sciences Staff Lend Expertise at NSF Cybersecurity Summit

The National Science Foundation hosted a “Cybersecurity Summit for Large Facilities and Cyberinfrastructure” in Arlington, Va., last week and the program included contributions from Berkeley Lab Computing Sciences. Attendees, by invitation only, included cybersecurity practitioners, technical leaders and risk owners from within the NSF Large Facilities and CI community, as well as key stakeholders and thought leaders from the broader scientific and information security communities.

The meeting began with a full-day workshop on Bro, the intrusion detection system developed by Vern Paxson and others at Berkeley Lab. The workshop was co-led by Robin Sommer of the Advanced Computing for Science Department. Bro, a network analysis framework used for security monitoring and network traffic analysis, has been adopted by major universities, research labs, supercomputing centers and government and corporate organizations.

On Friday, Aug. 29, ESnet Director Greg Bell chaired a panel discussion on “The Role of Information Sharing in Large Facility Security.” Denise Sumikawa, ESnet’s Strategic Security Officer, also participated in the summit.

ESnet Student Assistant Henrique Rodrigues Wins Best Student Paper Award at Hot Interconnects

Henrique Rodrigues, a Ph.D. student in computer science at the University of California, San Diego, who is working with ESnet, won the best student paper award at the Hot Interconnects conference held Aug. 26-28 in Mountain View, Calif. Known formally as the 2014 IEEE 22nd Annual Symposium on High-Performance Interconnects, Hot Interconnects is the premier international forum for researchers and developers of state-of-the-art hardware and software architectures and implementations for interconnection networks of all scales.

Rodrigues’ paper, “Traffic Optimization in Multi-Layered WANs using SDN,” was co-authored by Inder Monga, Chin Guok and Eric Poulyou of ESnet, Abhinava Sadasivarao and Sharfuddin Syed of Infinera Corp. and Tajana Rosing of UC San Diego.

“Special thanks to ESnet that gave me the opportunity to work on such an important and interesting topic,” Rodrigues wrote to his ESnet colleagues. “Also to the reviewers of my endless drafts, making themselves available to provide feedback at all times. I hope to continue with the good collaboration moving forward!”

This Week's CS Seminars

»CS Seminars Calendar

UCB Seminar: From Harmonic Oscillators to Kardar-Parisi-Zhang Equation

Tuesday, Sept. 2, 3:30p.m. – 5p.m., 736 Evans Hall, UC Berkeley Campus
Fraydoun Rezakhanlou, UC Berkeley

As a classical problem in Statistical Mechanics, consider an infinite one-dimensional chain of harmonic oscillators that are interacting via a repulsive potential. Macroscopically, the density functions for mass, momentum and energy satisfy the Euler Equation. By adding noise to the system we may violate some of the conservation laws and simplify the corresponding macroscopic equations. I present a family of models for which only mass is conserved and the fluctuations of the mass density is expected to satisfy Kardar-Parisi-Zhang Equation. So far this has been established rigorously for a single example in this family.

Efficient implementation of time-dependent density-functional theory to treat non-linear dynamical processes in molecular nanostructures and solids

Angel Rubio, Universitdad de Pais Vasco, Spain
Wednesday, Sept. 3, 3:30p.m.-4:30p.m., 939 Evans Hall, UC Berkeley Campus

In the present talk I will review the recent advances in algorithm development and numerical implementation of a real-space scheme to solve the time-dependent Kohn-Sham equations of time-dependent density functional theory. I will illustrate the perfromance towards petaflop computing and discuss the open problems from both physical concepts as well as algorithm development. A review of the recent work to describe spectroscopic properties of different semiconducting nanostructures and biomolecules will be discussed including both the linear and non-linear response regimes.

I will describe a new method to address the electron-ion dynamics within the Ehrenfest scheme where no explicit orthogonalization is necessary and we can increase the time step while keeping the system close to the adiabatic dynamics. The method is easily implemented and scales very well with the system size. Applications to the excited state dynamics in some organic molecules will be used as test cases to illustrate the performance of the approach. In particular we will show the effect of electron-hole attraction in those systems. Pros and cons of present functionals will be highlighted and provide insight in how to overcome those limitations by using many-body perturbation theory.

The goal of the group activities in the long-run is to provide a detailed, efficient, and at the same time accurate microscopic approach for the ab-initio description and control of the dynamics of decoherence and dissipation in quantum many-body systems. With the help of quantum optimal control (QOC) theory and the mastery over spectroscopy we could direct the movement of electrons, selectively trigger chemical reactions and processes, and create new materials. The present developments constitute a basic ingredient for the development of the European Theoretical Spectroscopy Facility (ETSF, http://etsf.eu) as well as its Vice presidency for Scientific development in San Sebastian.