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InTheLoop | 04.23.2012

April 23, 2012

Kathy Yelick to Give Keynote at DOD Systems and Software Technology Conference

Kathy Yelick, Associate Laboratory Director for Computing Sciences, will deliver a keynote address Tuesday, April 23, on “Magellan: A Study in Cloud Computing for Science” at the 24thSystems and Software Technology Conference. An estimated 400 attendees, primarily from Department of Defense organizations, are expected for the April 23–26 meeting in Salt Lake City.

“The pioneering efforts of the Magellan project in exploring the applicability of cloud computing for scientific research is a natural fit for SSTC,” wrote Kevin Richens, the SSTC Conference Technical Manager of Yelick’s talk. “The lessons learned and scientific computing perspective gained from Magellan can be extremely valuable as other government organizations, including the DoD, struggle with deciding to what extent they migrate to the cloud.”

Originally organized by the Air Force, the conference is now managed by Utah State University with support from the Software Technology Support Center (STSC) at Hill AFB in Utah. The conference is held in cooperation with the Department of Homeland Security, IEEE and the IEEE Computer Society, the Technical Council on Software Engineering, and the International Council on Software Engineering. For more information, visit the conference website.


Larry Pezzaglia to Speak at HEPiX Spring Workshop

Larry Pezzaglia of NERSC’s Computational Systems Group is giving two presentations at the HEPiX Spring 2012 Workshop, which is being held this week, April 23–27, in Prague, Czech Republic. HEPiX meetings bring together IT system support engineers from high energy physics (HEP) laboratories, institutes, and universities worldwide. Larry will present “PDSF at NERSC: Site Report” and “CHOS in Production: Supporting Multiple Linux Environments on PDSF at NERSC.”


Andrew Uselton Is Panelist at Lustre User Group Conference

Andrew Uselton of NERSC’s Outreach, Software, and Programming Group will be a panelist on the Lustre Benchmarking Panel at the Lustre User Group Conference (LUG 2012), which is being held this week, April 23–25, in Austin, TX. Andrew has also been asked to be a member of the OpenSFS Benchmarking Work Group, which will focus on identifying and defining I/O workloads for the various Lustre markets.


LabTech Computing and Technology Conference Tomorrow

LabTech is a free event created by and for Berkeley Lab staff that focuses on computing and technology for science and operations. The inaugural event will take place on Tuesday, April 24, from 11:00 am to 6:00 pm in the Building 50 complex.

LabTech will feature technical tutorials, discussion sessions, networking opportunities, demonstrations, and more. LabTech will be a multi-track conference, with tracks aimed at scientists, technologists, and support staff. Whether you’re interested in the latest tools for data management for scientists, or the newest features in LBNL business systems, LabTech will have something for everyone.

Registration, including lunch and happy hour networking, is free for Berkeley Lab staff and affiliates. Go here to register.

Deadline Extended for SC12 Tech Program Submissions

The SC12 Technical Program committee has extended by one week the deadlines for submitting technical papers, entries for the ACM Gordon Bell Prize, proposals for tutorials, panels and workshops, and abstracts for the SCinet Research Sandbox.

The deadline for abstracts for technical papers and ACM Gordon Bell Prize has been extended to Friday, April 27. Full submissions for technical papers and ACM Gordon Bell Prize are now due Friday, May 4. The deadline for abstracts for the SCinet Research Sandbox has also been extended to Friday, May 4, with full proposals due June 1.

All submissions are now being accepted at https://submissions.supercomputing.org/.

SC12, the premier international conference on high performance computing, networking, storage and analysis, will take place Nov. 10–16, 2012, and is expected to bring as many as 11,000 attendees from academia, industry and government to the Salt Palace Convention Center in Salt Lake City. An overview of the SC12 Technical Program can be found at http://sc12.supercomputing.org/content/overview. For a complete list of SC12 program deadlines, see http://sc12.supercomputing.org/content/important-dates. Questions about the technical program should be directed to techprogram@info.supercomputing.org.

Safety Note: Contagious Strain of Hand, Foot and Mouth Disease Is Spreading

A Computational Research Division employee and her husband have both come down with hand, foot, and mouth disease, and both were originally misdiagnosed by doctors (he with “allergic reaction,” she with “strep throat”). Hand, foot, and mouth disease is a viral infection common in toddlers, but a new strain of the virus is infecting some adults and seems to be highly contagious. A recent San Francisco Chronicle article discusses the outbreak in detail.

The key preventive measure is frequent hand washing or use of sanitizers. Here are some important facts from the Chronicle article:

  • A larger, more widespread rash: In traditional hand, foot and mouth disease, the rash is made up of tiny, pimple-like spots on the hands and feet and in the mouth. With the new strain, the rash can spread up the arms and legs, across the torso and buttocks and onto the face. The pimple-like spots are also larger and can be connected, forming larger, fleshier lesions.
  • Loss of fingernails and toenails: Patients with the traditional disease occasionally lose nails, but nail loss appears to be more common in the new strain. Patients start to lose their nails about four to eight weeks after the infection has passed.
  • Adult infections: People over age 18 rarely get hand, foot and mouth disease, but some adults seem to be vulnerable to the new one.
  • Possible hospitalizations: Public health officials in the United States and abroad have reported a handful of hospitalizations from the new strain of hand, foot and mouth disease, but doctors say the illness seems to be minor for most people.
  • How it’s spread: In both strains of the disease, the virus can be spread the same way as the common cold - through sneezing, coughing and touching surfaces with infected hands, and by contact with fluids that may be discharged from the rash.
  • Preventive measures: Parents and other adults who work with children should wash their hands regularly and thoroughly, and disinfect toys and other surfaces children have touched.

This Week’s Computing Sciences Seminars

Molecular Simulation Studies of Nanoscale Hydrodynamics in Confined Complex Fluids
Monday, April 23, 10:00–11:00 am, 50F-1647
Swapnil Kohale, Texas Tech University

Developments in the field of micro- and nanofluidics have led to an increased interest in the nanoscale hydrodynamics in confined geometries. Nanofluidic devices, used for various applications such as single molecule analysis, and biomolecule separation and concentration, consist of fluids confined in nanoscale geometries. The conception and design of these devices requires a good understanding of confinement effects on the transport behavior of fluids. In these systems, where the size of the channel is on the order of the molecular scale, a large proportion of fluid is in contact with the channel surface, and the assumptions made in continuum methodologies for the calculation of transport properties may not remain valid. Accurate prediction of transport properties in these systems would require explicit treatment of fluid for a detailed understanding of hydrodynamic effects. In this work, we have used molecular dynamics simulations to study hydrodynamics in various complex fluid systems in nanoconfinement and we have made quantitative connections of our findings with continuum predictions.

We have developed a coarse-grained molecular dynamics simulation code, using the commonly used potential functions, to study these hydrodynamic interactions in confined complex fluids, by explicitly treating the particulate solvent. This talk is focused on two specific systems we have studied. In the first system, shear induced cross-stream chain migration in a dilute polymeric solution is studied in detail. The role of hydrodynamic interactions between the polymer chain and channel surface, and the effects of polymer conformational properties, interactions, confinement and chain concentration on the polymer migration phenomenon were studied. In the second system, molecular hydrodynamic effects in a dilute suspension of nanoparticles were studied to quantify the effect of confinement, boundary conditions at the nanoparticle surface, and cooperative hydrodynamic interactions between the nanoparticles on translational and rotational motion of nanoparticles. Our results show an existence of long range hydrodynamic effects that should be accounted for while studying similar systems. We make quantitative connections of our results with continuum simulations and suggest effective simulation strategies for studying hydrodynamics in nanoconfined fluids. Making use of the capabilities of our simulation code, we have also developed a novel “active nanorheology” simulation technique, to calculate the local viscoelastic properties of complex fluids. This technique is especially useful to explore the rheological properties of materials with structural inhomogeneities, such as polymer nanocomposites, and of polymer thin films.

Programmable IP-over-Optical Management Orchestration: Architecture and Use Cases
Monday, April 23, 11:00 am–12:00 pm, 50F-1647
Mohit Chamania, Technische Universität Carolo-Wilhelmina zu Braunschweig, Germany

The convergence of Internet data services and optical transport network services has been at the heart of carriers’ investments and business strategies. However, the difference in the evolution of the IP and optical transport networks has led to a significant disconnect in the management of these networks, which in turn dictates the operational separation observed between them in most commercial network carriers. This talk presents a framework for programmable cross-layer orchestration of management operations using a novel Service Oriented Architecture currently being developed in the European Project ONE (www.ict-one.eu). The talk outlines the challenges in programmable orchestration, and presents three use cases to demonstrate the capability of the proposed architecture. The first use cases demonstrate the capability of the architecture to facilitate basic cross-layer orchestration to setup a new IP link in the network. The second use case presents the integration of a planning tool within the framework to facilitate IP offloading, and the final use cases demonstrates the capability of the architecture to integrate specialized third-party systems, such as the PCE in a multilayer network.

LabTech 2012 — The Computing and Technology Conference
Tuesday, April 24, 11:00 am–6:30 pm, in and around Building 50

Go here for details.

About Computing Sciences at Berkeley Lab

The Lawrence Berkeley National Laboratory (Berkeley Lab) Computing Sciences organization provides the computing and networking resources and expertise critical to advancing the Department of Energy's research missions: developing new energy sources, improving energy efficiency, developing new materials and increasing our understanding of ourselves, our world and our universe.

ESnet, the Energy Sciences Network, provides the high-bandwidth, reliable connections that link scientists at 40 DOE research sites to each other and to experimental facilities and supercomputing centers around the country. The National Energy Research Scientific Computing Center (NERSC) powers the discoveries of 6,000 scientists at national laboratories and universities, including those at Berkeley Lab's Computational Research Division (CRD). CRD conducts research and development in mathematical modeling and simulation, algorithm design, data storage, management and analysis, computer system architecture and high-performance software implementation. NERSC and ESnet are DOE Office of Science User Facilities.

Lawrence Berkeley National Laboratory addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the DOE’s Office of Science.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.