Allen Hemberger, CG Supervisor for Avatar, will give a talk on Tuesday 4/27, at 7 pm, in 102 DBRT.  A showing of Avatar will follow the talk.

Allen is an ND 2001 graduate in CSE. He has worked the past five years for WETA Digital in New Zealand, and has recently accepted an offer to work for Pixar.

More information on his talk is available at:
  http://www.cse.nd.edu/abstracts/2010/allen-hemberger.html

CI Days at the University of Notre Dame Explores Solutions for Advancing Education and Research through Cyberinfrastructure

Notre Dame, Ind. – April 14, 2010. National and international leaders in computational technology advancements will participate in CI Days at the University of Notre Dame April 29 – 30, 2010.

The two-day conference, organized by Notre Dame’s Center for Research Computing and its peers, will address how Cyberinfrastructure continues to transform research in all disciplines, including science and engineering, as well as the humanities, arts and social sciences.

CI Days at the University of Notre Dame is open to all local communities, businesses, non-profit organizations and local administrations. The conference is free of charge for participants, but registration is required. Online registration is available at: CI.ND.edu/registration.

Activities will be held in the Mendoza College of Business Auditorium on the Notre Dame campus.

“We want to help educators, researchers, IT and library experts, business professionals and community leaders understand the potential benefits that CI can provide to their scholarship, teaching, research and outreach,” said Jarek Nabrzyski, CI Days conference chair and director of the Center for Research Computing at the University of Notre Dame. “CI Days will provide opportunities for collaboration and leverage of existing activities, as well as an opportunity to identify gaps in our current capabilities and services.”

In December 2009, the University of Notre Dame received funding from a National Science Foundation (NSF) grant awarded to a consortium of higher education associations led by Internet2 to develop and host a workshop on Cyberinfrastructure. As articulated in the 2003 report of the NSF Blue Ribbon Panel on Cyberinfrastructure, such formidable problems as understanding global climate change, mastering nanotechnology, and probing the fundamental character of matter will require CI at institutional, regional, national, and international scales. CI Days agendas, while focused on institutional capabilities and requirements, will also address the role of research universities in the global CI environment.

CI Days at the University of Notre Dame is supported by Notre Dame's Vice President for Research, all Notre Dame Colleges, the Office of Information Technology and Center for Research Computing. In addition, Dell, Inc., Panasas, Inc., Hewlett-Packard Company and Matrix Integration are sponsoring this event.

For more information about CI Days at the University of Notre Dame, go to CI.ND.edu. Or send an e-mail to: CI.Days@ND.edu.

World Vision Cites Analysis Released By Roll Back Malaria Partnership

malaria to a drop in deaths from the disease also shows that resources from donor governments still fall short of those needed for maximum impact against the world's fourth-biggest killer of children,...

Read Full Story

Mapping malaria incidence distribution that accounts for environmental factors in Maputo Province - Mozambique

...malaria system in Mozambique, climate forecasts become important...degree of predictability of climate fluctuations at a seasonal...malaria data cases arose under climate conditions that occurred...in years 2001 and 2002. The change in any of the

Read Full Story

CNN
'Super mosquitoes' could fight malaria

They are normally transmitters of the disease, but mosquitoes could one day be used to tackle malaria after scientists developed a genetically engineered version of the species that can deliver a vaccine.

Read Full Story

The last visitor as part of the Distinguished Lecture Series on Social Networks that iCeNSA is sponsoring is Douglas R. White, Professor of Anthropology and Mathematical Behavioral Science at the University of California, Irvine. As a social anthropologist Doug's work includes mathematical modeling and network analysis and simulation. His fields of study include political, economic and social networks, ethno-historical sociology, comparative and long-term ethnographic studies, global political history, and the role of cohesive marriage and kinship networks in larger socio-political systems. He teaches at the University of California, Irvine, in Anthropology and the Institute for Mathematical Behavioral Sciences, where he chairs the faculty in Social Dynamics and Complexity. Doug is also a complexity sciences external faculty of the Santa Fe Institute, Editor-in-Chief of the UC Structure and Dynamics eJournal and Editor and Sysop of the InterSciWiki in complexity and network sciences.

This is a do not miss visit! Doug is one of the most important social network scholars and his work is both very broad and deep.

Doug will be giving two talks, a general audience talk and a colloquium co-sponsored by iCeNSA and anthropology. If you would like to visit more with Doug while he is here please contact David Hachen who is putting together his schedule.


Afternoon Talk
"Networks: History Behind Our Backs (Evolutionary Learning and Globalization Policies as Competitive Network-Building 1300-2010)"
Thursday, March 25, 2010
4 p.m.
McKenna Hall, Room 100-114.
Abstract: This paper aims at sharpening the network analyses of historical processes in Eurasia and Africa in the last millennium. I examine the regular increments of policy-driven “evolutionary learning” of states in developing the technologies for attempts at economic and political domination and the effects that competition and warfare have on the growth and network structure of trade routes. Models of network properties are used to show effects of and/or consequences for: (1) mercantile betweenness versus financial flow centralities, (2) national government control of trade versus periods of malfeasance and corruption, (3) policies protecting domestic manufacture versus elitewealth, (4) periods of price equilibrium versus collapse in the global economy, (5) the the emergence of Kondratieff and shorter business cycles, (6) the mobility of nations in the postwar global economy and (7) issues of war and peace, private and government armies.


Noon Colloquium
"Beyond small world and scale-free to generalized entropic networks (the social circles model)"

Thursday, March 25, 2010
12 p.m.
Coffee Shop, Geddes Hall
Lunch provided

For more information on the Lecture Series and Doug’s visit to Notre Dame go to
http://icensa.nd.edu or http://icensa.nd.edu/henkel.html

David S. Hachen Jr.
Associate Professor, Department of Sociology, 810 Flanner Hall (Office: 747 Flanner)
Co-Director, iCeNSA (Inter-Disciplinary Center for Network Science and Applications), 384 Nieuwland Hall
University of Notre Dame, Notre Dame, IN 46556

CALL FOR POSTERS

ND Cyberinfrastructure Days Conference (http://ci.nd.edu) will hold a Poster Session and is now accepting poster submissions. The Poster Session is an opportunity for presenting late-breaking results, ongoing research projects, and speculative or innovative work in progress in the areas of cyberinfrastructure for the arts, humanities, social sciences, science and engineering. Technical posters, descriptions of completed work, and work in progress are all welcome.

Important Dates
March 24, 2010: Deadline for submissions
March 26, 2010: Notification of acceptance
April 19, 2010: Digital version of poster due

Submission
Authors must submit an abstract of no more than one page for review. Decisions about acceptance will be based on relevance to the conference, originality, potential significance, topicality and clarity.
At least one of the Poster/Demo authors must be a registered participant at the conference, and attend the Poster Session to present the work. The CRC will handle poster printing at no cost to participants. The abstracts for all accepted posters and the posters themselves will be published on the conference web site.
Please submit poster abstracts to: ci.days@nd.edu.


Further information

For further information and for any questions regarding the event or submissions, please contact the Poster Session chair Kristina Davis, kristina.davis@nd.edu.

2010 Summer Computer Simulation Conference (SCSC'10)

11-14 July 2010 - Ottawa, ON, Canada

CALL FOR PAPERS
(DEADLINE EXTENDED - MARCH 22,2010)

http://www.dacya.ucm.es/jlrisco/SCSC10/


Organized by the Society for Modeling and Simulation International
Co-Sponsored by ACM SIGSIM and ICST (pending)


Come to Ottawa, Canada for SCSC 2010 to witness the 42nd edition of this
leading conference in the field of Modeling and Simulation. SCSC’10 is
focused on basic and applied research in modeling and simulation.

SCSC 2010 features varied tutorials, tracks and workshops. The conference
focuses on modeling and simulation, tools, theory, methodologies and
applications, providing a forum the latest R&D results in academia and
industry.

All submissions will be reviewed based on the draft full paper and/or
extended abstract. The best contributed paper will be given an award. A
selected group of full papers will be selected for possible publication in a
special issue of the Simulation Journal (SCS). All papers will be published
in the ACM and the EU Digital Libraries (pending).


Important Dates:

Submission of full papers (and tutorials proposals): March 22nd, 2010
Notification of acceptance: April 30th, 2010
Final manuscript and Early Registration: May 28th, 2010


General Chair:
Gabriel Wainer, SCE, Carleton University, Canada

Program Chairs:
Mhamed Itmi, INSA Rouen, France
Peter Kropf, Université de Neuchâtel, Switzerland
Andreas Tolk, VMASC, USA


Current List Tracks & Workshops
Agent-Directed Simulation
Applications in Business, Management, Planning & Logistics
C3 - Complexity, Chaos and Combinatorics
Computer Graphics for Simulation
Emergency Simulation
Engineering and Management in the M&S Discipline
Executable Architecture (EA)
M&S for Defense & Security
Microarchitecture and circuits simulation (MCS)
Model-based Design and Simulation
Modeling and Simulation of Dynamic Structure Systems
Modeling and simulation languages
Modeling and Simulation of Ultra-Large-Scale Systems (MSULSS)
Simulation in Healthcare and Bioinformatics
Simulation for Transportation
Simulation of Complex Social Systems (SiCoSSys)
Simulation Education
Simulation for Transportation
Vivid representing, artificial to human


International Program Committee
M.A. Aziz-Alaoui, University of Le Havre, France.
Isaac Barjis, New York City College of Technology, USA
Joseph Barjis, TU Delft, The Netherlands
Fernando Barros, Universidade da Coimbra, Portugal
Mokhtar Beldjehem, Sainte-Anne's University, Canada
David W. Bauer, The MITRE Corporation, USA
Cyrille Bertelle, University of Le Havre, France.
Azzedine Boukerche, University of Ottawa, Canada
Amedeo D'Angiulli, Carleton University, Canada
Gérard H.E. Duchamp, University of Paris XIII, France.
Abdulmotaleb El Saddik, University of Ottawa, Canada
Gianfranco Fancello, University of Cagliari, Italy
Thomas Feng, Oracle, USA
Rubén Fuentes-Fernández, Complutense University of Madrid, Spain
Joseph Giampapa, Carnegie-Mellon University, USA
Steve Hall, Lockheed Martin Advanced Technology Center, USA
Drew Hamilton, Auburn University, USA
Phillip Hammonds, BAE Systems, USA
Franziska Klügl, University of Würzburg, Germany
Juan Lanchares, Computense University of Madrid, Spain
Francesco Longo, MSC-LES University of Calabria, Italy
Adolfo Lopez-Paredes, Universidad de Valladolid, Spain
Gregory Madey, University of Notre Dame, USA
Saurabh Mittal, Dunip Technologies, USA
John C. Nash, University of Ottawa, Canada
Fawzi Nashashibi, Mines, ParisTech, France
Gabriela Nicolescu, Ecole Polytechnique de Montréal, Canada
Tuncer I. Ören, University of Ottawa, Canada
Hiren D. Patel, University of Waterloo, Canada
Juan Pavón, Complutense University of Madrid, Madrid, Spain
Emil Petriu, University of Ottawa, Canada
Miquel Angel Piera, MISS - Spanish Center. Univ. Autónoma de Barcelona, Spain
John F. Richardson, SPAWAR System Center, PACIFIC, USA
José L. Risco-Martín, Computense University of Madrid, Madrid, Spain
Joseph M. Rosen, Dartmouth College, USA
Craig Rosenberg, UI Designer, USA
Stuart Rubin, SSC San Diego CA, USA
Helena Szczerbicka, Leibniz Universität Hannover, Germany
Shervin Shirmohammadi, University of Ottawa, Canada
Maarten Sierhuis, NASA Ames Research Center
Andreas Tolk, Old Dominion University, USA
Resit Unal, Old Dominion University, USA
Levent Yilmaz, Auburn University, USA
Bernard P. Zeigler, University of Arizona, USA
Yu Zhang, Trinity University, USA


Further information:
http://www.dacya.ucm.es/jlrisco/SCSC10/

http://simulation.ning.com

University of Notre Dame
Department of Computer Science & Engineering

SEMINAR

Dr. Douglas Densmore
Synthetic Biology Engineering Research Center Postdoctoral Fellow

"Platform-Based Design: From Cruise Control to Cancer Killer"

Abstract:
Platform-Based Design (PBD) is a design methodology within Computer Aided Design which at its core promotes the separation of functionality from implementation. Rigorous and formal applications of PBD have been shown to be very useful in the design of embedded electronic systems. This philosophy has manifested itself in the development of the Polis, Metropolis, and Metro II design environments at UC Berkeley. The emerging field of synthetic biology has the ability to leverage many of the concepts in PBD while at the same time presenting a unique set of challenges and obstacles. If applied correctly, PBD has the potential to intelligently increase the design space of synthetic biological systems and create an entire "Bio-Design Automation" field which will help to create more robust, re-usable, and reliable designs.

This talk will discuss the evolution of PBD from embedded electronics to synthetic biology. Specifically the creation of biological devices from standard, modular parts will be outlined along with the challenges of applying traditional design automation techniques.
Abstract functional biological specification, design constraint enforcement, data exchange and retrieval, and automated assembly together form the core of a bio-design automation framework. These concepts will be illustrated via several design examples using the Clotho design platform and the Eugene domain specific language. These tools lay the foundation for a fully automatic path from synthetic biological device specification to physical assembly which in many ways parallels the ASIC design flow developed by the electronics community and opens a tremendous interdisciplinary opportunity for biological and computer engineers.

Bio:
Douglas Densmore received his Bachelors of Science in Engineering (Computer Engineering) from the University of Michigan in 2001. He received his Masters of Science and his PhD both in Electrical Engineering in 2004 and 2007 from UC Berkeley. He was a UC Chancellor's postdoctoral fellow at UC Berkeley with Prof. Alberto Sangiovanni-Vincentelli from 2007 to 2009 and now is a postdoctoral research fellow in the Synthetic Biology Engineering Research Center.

His current research centers on extracting design techniques from electronic design automation (EDA) and applying them to the design of synthetic biological systems. Specifically he examines how to raise the level of abstraction in synthetic biology by employing standardized biological part based designs which leverage domain specific languages, constraint based device composition, visual editing environments, and automated assembly. These research agendas find a home in the "Clotho" unified toolset. Clotho is a two time winner of the "best software tool" at MIT's International Genetically Engineered Machine Competition and the first tool of its kind to employ EDA approaches to synthetic biology. He is also the co-founder of the International Workshop on Bio-Design Automation (IWBDA) which is co-located at the Design Automation Conference. His other research interests include system level design, computer architecture, embedded systems, and logic synthesis.

Thursday, February 25, 2010
3:30 p.m.
356 Fitzpatrick

In death if not in life, a bond unites King Tut, Egypt’s boy pharaoh, with the multitudes high and especially low through human history. Palace walls could not shield him from the enemy without: the anopheles mosquitoes infesting the Nile Valley with malaria parasites. A post-mortem on Tutankhamen’s mummy, scientists reported last week, shows that malaria was one of the most probable agents of his death at age 19, in the 14th century B.C.

(more)

http://www.nytimes.com/2010/02/21/weekinreview/21wilford.html

King Tutankhamen, the boy pharaoh, was frail and lame and suffered “multiple disorders” when he died at age 19 about 1324 B.C., but scientists have now determined the most likely agents of death: a severe bout of malaria combined with a degenerative bone condition.

(more)

http://www.nytimes.com/2010/02/17/science/17tut.html

2010 Summer Computer Simulation Conference (SCSC'10)

11-14 July 2010 - Ottawa, ON, Canada

CALL FOR PAPERS


http://www.dacya.ucm.es/jlrisco/SCSC10/
http://simulation.ning.com/

Organized by the Society for Modeling and Simulation International
Co-Sponsored by ACM SIGSIM (pending)


Come to Ottawa, Canada for SCSC 2010 to the 42nd edition of this leading conference in the field of Modeling and Simulation. SCSC’10 is focused on basic and applied research in Modeling and Simulation, a critical area for supporting Research and Development as well as competitiveness worldwide.

SCSC provides an International Forum for presenting the State of the Art to the International Simulation Community as well as the Effectiveness of Simulation Experiences in World Businesses. The purpose of the conference is to provide a forum for academic researchers, governmental and industrial investigators and practitioners to exchange ideas and discuss developments in this growing field.

SCSC 2010 features varied tutorials, tracks and workshops. The conference focuses on modeling and simulation, tools, theory, methodologies and applications, providing a forum the latest R&D results in academia and industry.

In parallel with technical presentations, companies and research groups will be exhibiting their most advanced products.

All submissions will be reviewed based on the draft full paper and/or extended abstract. The best contributed paper will be given a Best Paper Award. A selected group of full papers will be invited for a Special Issue Proposal of the Simulation Journal (SCS). All papers will be published in the ACM Digital Library.


Organizing Committee:
Gabriel Wainer, Carleton University, Canada (General Chair)
Mhamed Itmi, INSA Rouen, France
Peter Kropf, Université de Neuchâtel, Switzerland
Andreas Tolk, VMASC, USA

Further information:

http://www.dacya.ucm.es/jlrisco/SCSC10/


Or on the new Network on Modeling and Simulation Studies:

http://simulation.ning.com/

University of Notre Dame
Department of Computer Science & Engineering
Presents: Michael Schatz: University of Maryland

Thursday, February 18, 2010 2:30 p.m. 115-B Galvin

Scalable Solutions for DNA Sequence Analysis

We are at the dawn of a new era in computational biology. DNA sequencing projects that required years of effort and hundreds of millions of dollars of equipment just a few years ago can now be performed quickly and cheaply by individual labs This dramatic shift is ago, can now be performed quickly and cheaply by individual labs. This dramatic shift is expanding the scale and scope of sequencing to previously unimaginable limits, and will ultimately lead to new discoveries about our basic biology, the diversity of life, and personalized medicine. However, these ambitious goals can only be realized if we can develop new computational methods that can effectively analyze the overwhelming volumes of data generated.

In my presentation, I’ll describe my research developing efficient methods for analyzing large biological datasets including by using highly parallel commodity graphics large biological datasets, including by using highly parallel commodity graphics processing units produced by nVidia, and the parallel computing framework MapReduce developed by Google. My programs MUMmerGPU, CloudBurst, Crossbow, and Contrail demonstrate how these technologies can be applied to the critical tasks of large-scale alignment and assembly, enabling genotyping and de novo assembly of whole genome genomes from billions of short reads. Coupled with inexpensive cloud computing, these programs can quickly, cheaply, and accurately analyze tremendous biological datasets and have the potential to make otherwise infeasible studies practical.

Bio: Michael Schatz is a Ph.D. candidate in the Computer Science department at the University of Maryland, and holds positions at both the UMD Center for Bioinformatics and Computational Biology, and the UMD School of Medicine Institute for Genome Sciences.

Prior to starting his Ph.D., he worked for three years at the Institute for Genomic Research (TIGR) contributing to the assembly and analysis of the genomes of several significant organisms. His research interests include high performance computing and parallel organisms. His research interests include high performance computing and parallel algorithms design towards problems in computational biology and genomics. He received his M.S. in Computer Science from the University of Maryland in 2008, and his B.S. in Computer Science from Carnegie Mellon University in 2000.

More information about Michael’s research and publications is available at
http://www.cbcb.umd.edu/~mschatz.

Global Health Colloquium
Wednesday, February 17
4:00 – 5:00 PM
Galvin Life Science, Room 283


Three students will present their research this week

Dongyoung Shin - from Korea, got her Bachelor’s and Master’s degrees in the Department Agricultural Biology, Korea University. She studied about genetic differences in Trialeurodes varporariorum population occurred in vegetable greenhouses in her Master’s program. She entered the Department of Biological science in University of Notre Dame 2005 spring semester, in Dr. David Severson’s infectious disease laboratory.

Title: Pathway Analysis of the Meiotic Drive System in Aedes aegypti

Abstract

Meiotic drive in Aedes aegypti has potential as a mechanism for driving trangenes for pathogen resistance into natural Ae. aegypti populations. The endogenous meiotic drive system, found in some Ae. aegypti populations, causes the female determining chromosome to fragment during spermatogenesis. Mating between a drive male and a drive sensitive female results in highly male biased sex ratios. The molecular basis for the drive mechanism is presently unknown.
We conducted a whole transcripts analysis of testes from a meiotic drive carrying strain in comparison with a drive sensitive strain using microarrays based on the complete annotated Ae. aegypti gene set. We hypothesized that genes putatively involved in the meiotic drive system would show up-regulation in T37. Transcripts statistically significant for the meiotic drive system were mapped to pathways by gene functions and constructed gene networks. Immune response pathways were highly ranked in this study.
The network in this study showed a relation with Ras super-family signaling pathway in immune response. This study would also be useful for investigating the mechanism of the meiotic drive system. The candidate genes for the meiotic drive genes will be map to the chromosome and verify the gene function by RNAi.
____________________________________________________________

Kyanne Reidenbach received a B.S. in Entomology from Purdue University in December of 2006. She did undergraduate research under the direction of Dr. Catherine Hill where she assisted in the characterization of Aedes aegypti GPCRs. She joined the Besansky lab in March of 2007 and is an Arthur J. Schmitt Fellow. Her research covers many aspects of mosquito evolution, from broad scale phylogenetic relationships at the family level to incipient speciation within Anopheles gambiae.

Title: Behavioral responses of Anopheles gambiae M and S larvae to chemical stimuli

Abstract
Characterization of the M and S molecular forms of Anopheles gambiae has primarily been at the molecular level. Unfortunately, few quantitative investigations at the phenotypic level have been carried out, hindering our ability to link genotypic variation to phenotype. Previously, colony reared larvae were shown to elicit attractive or repulsive behavioral responses to several chemical stimuli. We investigated two of these chemicals for behavioral differences in M and S larvae captured from around Yaoundé, Cameroon. We found an unexpected difference in the strength of the phototactic responses between the forms. However, more investigation is needed before these differences can be confirmed.

____________________________________________________________

Nathan Konopinski - began working as a web developer for VectorBase in 2007 and since has taken over administration responsibilities of the web site. He was accepted into Notre Dame's Graduate School in 2009 where he continues to develop the VectorBase project and pursue a Master of Science in Biology under the direction of Dr. Frank Collins. Nathan is from South Bend, Indiana and received his Bachelor of Science in Electrical Engineering with a Minor in Music from Purdue University in 2006.


Title: BLAST@VectorBase.org: advancing the user experience

Abstract
VectorBase's most popular section went five years without any changes. During that time advances in web technologies were made to allow for a more enjoyable and efficient user experience on the internet. Specifically, the tools of JavaScript, AJAX, and CSS were used to streamline the user interface. Additionally, the distributed computing program XGrid was added for increased stability of BLAST job processing.

Global Health Colloquium

The Eck Institute for Global Health is proud to present:

Sean O'Brien, Associate Director
Center for Civil and Human Rights
University of Notre Dame

"Water and Human Rights"

Wednesday, February 3, 2010 from 4:00-5:00 PM in Galvin Room 283.

GLOBAL Health Colloquium

The Eck Institute for Global Health is proud to present:

Joseph Bock, Ph.D., Director of External Relations
Kroc Institute for International Peace Studies, University of Notre Dame

“Global Health in War Zones: Experiences from Cambodia and Afghanistan”

Wednesday, January 27, 2010 from 4:00 - 5:00 PM in Galvin Room 283

Center for Rare & Neglected Diseases Clinical-Translational Seminar
Lecture for Friday, January 22, 2010


Speaker: Patrick J. Lammie, Ph.D.
Dr. Lammie is a Senior Scientist with the Division of Parasitic Diseases, CDC
and Technical Director, Global Network for Neglected Tropical Diseases


Title: Elimination of Lymphatic Filariasis in Haiti: Where do we go from here?

Location: Lecture in 118 DeBartolo (new room)
Time: Friday, January 22, 2010; Lecture 3-4 pm.; Reception 4-5 pm.

Please find below informations about the MAPS2 Conference, dealing
with the "Teaching of-with Models in the Social Sciences" which will
take place in Paris, France on 8-9th May 2010.

Website of the event :
http://maps.csregistry.org/tiki-index.php?page=MAPS-2

Don't be hesitant to submitt a contribution,

Best regards,

Ion Tillier
--
Ion Tillier
ATER - Université de Nantes IGARUN
LETG (Littoral Environnement Télédétection Géomatique)
UMR 6554 CNRS - Laboratoire Géolittomer Nantes
http://letg.univ-nantes.fr/
ion.tillier@univ-nantes.fr
02 40 14 11 62

The CRC will be offering 4 sessions of our 1hr CRC Basics/Introductory course this semester. All new users are expected to attend this course once. All sessions will be held in the CRC Conference Room (111 ITC). If you have a laptop from which plan to access CRC resources please bring it with you.

Also please note that CRC engineers are available to provide CRC resource overview/training segments at your regular research group meetings upon request. Simply send the request to crcsupport@nd.edu and we will work to coordinate suitable schedules.

The CRC Basics sessions for Jan 2010

Tuesday Jan 19 10- 11:00am
Thursday Jan 21 10- 11:00am

Wed Jan 27 1-2:00pm
Friday Jan 29 1-2:00pm

--

With the December arrival of over 3600 additional cores via the new HP AMD Istanbul based servers, the SGE queueing configuration required substantial reconfiguring to reduce fragmentation.

The first and most pressing change has come with the Parallel Environments (PE):

- The ompi PE will become ompi-4, ompi-8, and ompi-12
likewise
- The mpich1 PE will become mpich1-4, mpich1-8, and mpich1-12

The new PEs are already in place and users should begin to use them immediately. The ompi and mpich1 PEs will be removed on Feb 1st.

The numeric designation indicates the number of cores per server. ompi-4 will only map to servers with a total of 4 cores (ddcopts for example), ompi-8 will only map to servers with a total of 8 cores (dqcneh for example), ompi-12 will only map to servers with a total of 12 cores (d6copt for example). This ensures that jobs submitted to a PE will not overlap one another on the same server. It is important to note that the number of cores requested MUST be a multiple of the total number of cores per server.

This is the first of multiple changes. Additional near term changes will focus on the queues to include a 30min debug queue and a 4hr short queue in addition to the default 'long' queue which supports up to 30days run time.

We have added a new wiki page to document the SGE environment.

http://crcmedia.hpcc.nd.edu/wiki/index.php/CRC_SGE_Environment

Also please note that CRC engineers are available to provide CRC resource overview/training segments at your regular research group meetings upon request. Simply send the request to crcsupport@nd.edu and we will work to coordinate suitable schedules.
Regards,
The CRC Staff

“A Network Theory of Life, the Universe, and Everything”

Stephen P. Borgatti
Chellgren Endowed Chair and Professor in the Dept. of Management at the Gatton College of Business and Economics, University of Kentucky

Thursday, January 28, 2010
4 p.m.
McKenna Hall, Room 210-214.
Open to the public

Abstract: A recent request-for-proposal by the Defense Threat Reduction Agency (DTRA) invited researchers to develop a broad, generic, adaptable, flexible and modular theory of social networks that spans all relevant disciplines. Having received a grant to do this, my co-workers and I are now faced with actually delivering the "integrated theory". When we began, we assumed the goal was unattainable, but that the journey would be useful in itself. Two years into it, we feel the journey has indeed allowed us to elucidate some fundamental issues in social network analysis. But in addition, we have surprised ourselves in becoming more positive about the possibility of integrating large portions of network theory.

For more information on the Lecture Series and Steve Borgatti’s visit to Notre Dame go to
http://icensa.nd.edu or http://icensa.nd.edu/henkel.html