October 2013 - Core-sysadmins - mailman3.cels.anl.gov

Seminar Announcement: Statistical Learning Machines for Protein Structure Prediction in the Era of High-Throughput Sequencing
by Ninfa Mayorga 23 Apr '14

23 Apr '14

Computation Institute Presentation Speaker: Jinbo Xu, Toyota Technological Institute at Chicago Host: Ian Foster Date: October 17, 2013 Time: 1:00 PM - 2:00 PM Location: University of Chicago, Searle 240A, 5735 S. Ellis Ave. This talk will be broadcast via Adobe Connect (see below) Statistical Learning Machines for Protein Structure Prediction in the Era of High-Throughput Sequencing Abstract: If we know the primary sequence of a protein, can we predict its 3D structure by computational methods? This is one of the most important and challenging problems in computational molecular biology and has tremendous implications for the understanding of life process, diseases and drug discovery. Depending on whether or not there is one solved structure similar to the protein sequence under consideration, computational methods for protein folding can be classified into two categories: template-based and template-free modeling. The former uses similar solved structures as templates to predict the structure of a protein while the latter does not. This talk will demonstrate how statistical learning methods especially probabilistic graphical models can be applied to address some fundamental challenges facing template-based and template-free protein folding by taking advantage of high-throughput sequencing and protein structure initiatives. Information: Lunch will be provided This talk will be broadcast to Argonne National Laboratory, TCS Building 240, Room 5172. You may join the broadcast from your location by joining Adobe Connect Meeting. To join the meeting: http://anl.adobeconnect.com/tcs-ci -Enter as a guest If you have never attended an Adobe Connect meeting before: Test your connection: http://anl.adobeconnect.com/common/help/en/support/meeting_test.htm Get a quick overview: http://www.adobe.com/go/connectpro_overview

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Fwd: Apple visit
by Craig Stacey 02 Dec '13

02 Dec '13

It's not clear if we're invited to the "cyber security meeting" part of the below. But I've been asked to share this with my area. I'll be on vacation. -- Craig Begin forwarded message: >>> Russ/Shawn, >>> >>> See the draft agenda below. We have a large population of computational scientists in the building, so I though it might be nice to do a seminar and hit both OS, developer and IT folks all at once. We can then do a deep dive with the cyber team after lunch. Let me know what you think. >>> >>> Also - for the cyber discussion, we could link FNAL or just about anyone else for that matter, by video conference. Do you think there would be interest? >>> >>> >>> Paul >>> >>> >>> Tuesday, December 3, 2013 >>> 10:30 - 11:30 Joint CELS/CIS Seminar: Inside Apple's iOS data security model, Shawn Geddis (Apple) >>> 11:45 - 12:45 Lunch >>> 1:00 - 2:00 Apple / cyber security meeting >>> >

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Seminar Announcement: Nonlinear Optimization and X-Ray Microscopy
by Ja-Quel Bullock 19 Nov '13

19 Nov '13

Mathematics and Computer Science Division Speaker: Ashish Tripathi, Postdoc Interviewee Host: Stefan Wild Date: Tuesday, October 29, 2013 Time: 10:30 AM - 11:30 AM Location: Argonne National Laboratory, Building 240, Seminar Room 4301 Title: Nonlinear Optimization and X-Ray Microscopy Abstract: Coherent x-ray diffractive imaging is a form of microscopy that does not require optics to image a sample. Instead, it measures diffraction intensity generated by placing a sample in the path of a coherent x-ray beam, and numerically inverts this diffraction using nonlinear optimization techniques. This algorithmic approach solves the "phase problem", which arises due to the inability of x-ray detectors to measure complex valued wave fields. Knowledge of the experimental arrangement is used to enforce constraints in the optimization algorithms to ensure effective numerical recovery. We discuss various schemes of using nonlinear optimization to image samples from their diffraction intensities.

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Reminder: Seminar Announcement - On Determining a Viable Path to Resilience at Exascale
by Kristina M. Conrad 15 Nov '13

15 Nov '13

REMINDER: Today Mathematics and Computer Science Division Speaker: Prof. Frank Mueller, North Carolina State University Host: Pavan Balaji (balaji(a)mcs.anl.gov) Date: August 14, 2013 Time: 1:00 PM - 2:00 PM Location: Argonne National Laboratory, Building 240, Conference Room 4301 On Determining a Viable Path to Resilience at Exascale Exascale computing is projected to feature billion core parallelism. At such large processor counts, faults will become more common place. Current techniques to tolerate faults focus on reactive schemes for recovery and generally rely on a simple checkpoint/restart mechanism. Yet, they have a number of shortcomings. (1) They do not scale and require complete job restarts. (2) Projections indicate that the mean-time-between-failures is approaching the overhead required for checkpointing. (3) Existing approaches are application-centric, which increases the burden on application programmers and reduces portability. To address these problems, we discuss a number of techniques and their level of maturity (or lack thereof) to address these problems. These include (a) scalable network overlays, (b) on-the-fly process recovery, (c) proactive process-level fault tolerance, (d) redundant execution, (e) the effort of SDCs on IEEE floating point arithmetic and (f) resilience modeling. In combination, these methods are aimed to pave the path to exascale computing. BIO : Frank Mueller is a Professor in Computer Science and a member of multiple research centers at North Carolina State University. Previously, he held positions at Lawrence Livermore National Laboratory and Humboldt University Berlin, Germany. He received his Ph.D. from Florida State University in 1994. He has published papers in the areas of parallel and distributed systems, embedded and real-time systems and compilers. He is a member of ACM SIGPLAN, ACM SIGBED and a senior member of the ACM and IEEE Computer Societies as well as an ACM Distinguished Scientist. He is a recipient of an NSF Career Award, an IBM Faculty Award, a Google Research Award and a Fellowship from the Humboldt Foundation.

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Seminar Announcement: Distributed Multi-agent Optimization in a Stochastic Derivative-free Setting
by Ja-Quel Bullock 04 Nov '13

04 Nov '13

Mathematics and Computer Science Division Speaker: Jeffrey Larson, Postdoc Interviewee Host: Stefan Wild Date: Thursday, October 24, 2013 Time: 10:30 AM - 11:30 AM Location: Argonne National Laboratory, Building 240, Seminar Room 4301 Title: Distributed Multi-agent Optimization in a Stochastic Derivative-free Setting This talk presents a distributed algorithm for the cooperative optimization of multiple agents connected by a network. We attempt to optimize a global objective which is a sum of the agents' objectives, while assuming each agent can only query his objective under stochastic noise. While convergence results for the complete algorithm have yet to be established, we present two intermediate results that are of interest on their own. We first show that a common technique for distributed optimization, the alternative direction method of multipliers (ADMM), converges when agents' models are inexact. Such an inexact minimization is show to improve the performance of ADMM on problem classes where it is already successful. We then propose and prove almost-sure convergence of a method for stochastic optimization which constructs models that are used in a trust region framework. When optimizing stochastic functions without derivatives, many existing algorithms either 1) evaluate the function in a fixed pattern, 2) require the user to define a decaying sequence of step sizes, or 3) repeatedly sample points of interest. Our method avoids such requirements and is shown to out perform existing algorithms on a benchmark suite of problems. We lastly outline how these two results will be combined to prove convergence in the stochastic multi-agent setting.

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Undelivered Mail Returned to Sender
by MAILER-DAEMON＠mcs.anl.gov 31 Oct '13

31 Oct '13

This is the Postfix program at host breeze.mcs.anl.gov. I'm sorry to have to inform you that your message could not be delivered to one or more recipients. It's attached below. For further assistance, please send mail to <postmaster> If you do so, please include this problem report. You can delete your own text from the attached returned message. The Postfix program <saithal(a)alcf.anl.gov>: host 140.221.7.6[140.221.7.6] said: 550 5.1.1 <saithal(a)alcf.anl.gov>: Recipient address rejected: User unknown in relay recipient table (in reply to RCPT TO command)

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Group holiday lunch
by Craig Stacey 31 Oct '13

31 Oct '13

Anyone interested in doing our semi-traditional-yet-always-fun holiday lunch this year? Where will be dependent on who's going and what's available, but locking in a date now will help me get a place lined up. Any day from December 13th through the 20th work for me. Here's a doodle poll so y'all can vote on it. Put your name in and a +1 if you're bringing someone. Thanks! http://doodle.com/3xp54nwp67ysdktc Also, Nick from TekSystems is planning to come out here on December 12th and provide us with yummy Jimmy John's sandwiches for lunch. So, you know, we got that going for us, too. -- Craig

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Where's JohnV?
by John Valdes 31 Oct '13

31 Oct '13

My dad's being discharged from the rehab center today; I should be in as usual this afternoon, but if it takes longer getting him back home and settled, I'll work from home instead. John

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REMINDER - "Revised" Seminar Announcement: Portable, MPI-Interoperable Coarray Fortran
by Mary Dzielski 31 Oct '13

31 Oct '13

SEMINAR IS STARTING IN FEW MINUTES! Mathematics and Computer Science Division Speaker: Chaoran Yang, PhD Student from Rice University Host: Wesley Bland <wbland(a)mcs.anl.gov> Time: 1:00 PM - 2:00 PM Date: October 31, 2013 Location: Argonne National Laboratory, Building 240, Conference Room 4301 Portable, MPI-Interoperable Coarray Fortran The past decade has seen the advent of a number of parallel programming models such as Coarray Fortran (CAF), Unified Parallel C, X10, and Chapel. Despite the productivity gains promised by such programming models, most parallel scientific applications are slow to adopt these models and continue to rely on MPI as their data movement model of choice. One of the reasons for this trend is that it is not easy for users to incrementally adopt these newer programming models within their existing MPI applications. Because most of these new programming models have their own runtime systems, using multiple programming models within a single application duplicates runtime resources and is potentially error-prone. Such independent runtime systems for each programming model were deemed necessary because MPI was considered insufficient to play this role for these languages. With the recently released MPI-3, however, several new capabilities have been added to MPI, including a much more comprehensive one-sided communication framework. In this paper, we investigate whether MPI-3 can form a runtime system for one example programming model, CAF, with a broader goal of enabling a single application to use both MPI and CAF simultaneously without duplicating runtime resources. Bio: Chaoran Yang is a fifth-year Ph.D. student from the Department of Computer Science at Rice University, Houston, Texas, advised by Dr. John Mellor-Crummey. His research interests focus on parallel models, runtime systems, compilers for HPC applications. Since May, Chaoran has been working with Dr. Pavan Balaji at Argonne National Laboratory on building a MPI-interoperable Coarray Fortran runtime system. _______________________________________________ Subscription to this list is automatic based on your appointment in the MCS division.

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Where's max?
by Max Trefonides 31 Oct '13

31 Oct '13

I'm feeling pretty crappy. Not getting sleep Please put me down for 1/2 sick day,, I'll be online from home in the afternoon. -- Max

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