ITCWeb: ITC Research Computing Support Newsletter - October 2006

ITC Research Computing Support Newsletter - October 2006

This is the October 2006 newsletter for ITC Research Computing Support. If you have any questions or concerns regarding the information presented here, please contact ITC Research Computing Support by emailing Res-Consult@virginia.edu, or phoning either the Research Computing Lab in Brown Library at 243-8799 or the Scholars Lab in Alderman Library at 243-8800.

Contents

Go to the index of previous Research Computing Support Newsletters

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Please Join Us for the Grand Opening of the Scholars' Lab on Oct. 20!

Mark your calendar to attend the grand opening of the new Scholars' Lab on Friday, October 20, from 3 to 5 p.m. Speakers will be Karin Wittenborg, University Librarian, and James Hilton, Vice President and Chief Information Officer.

You are invited to explore the University's newest venture in digital scholarship for the Humanities, Arts, and Social Sciences:

The Scholars' Lab provides space for research, collaboration, and technical support, integrating the services formerly offered by the GeoStat, E-Text, and ITC Research Computing Support centers.

The Scholars' Lab is located on the fourth floor of Alderman Library.

Refreshments will be served.

Contact ITC Research Computing Support by email to Res-Consult@Virginia.edu or at the Scholars Lab in Alderman Library (243-8800) if you have questions.

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Software and Hardware..........

Important Linux Cluster Updates; Aspen Retirement on Oct. 16

The ITC Birch Linux cluster (birch.itc.virginia.edu) will be unavailable on October 17, October 18, and October 19 in order to upgrade it to the same operating system and library versions as the new Dogwood cluster. The ITC Cedar Linux cluster (cedar.itc.virginia.edu) was down October 10 through October 12 for a similar upgrade.

As part of these changes, we want to emphasis that our new 200-node Linux cluster, Dogwood, is now available (dogwood.itc.virginia.edu) and users of the other clusters are strongly urged to try their codes on it in order to detect any problems that may arise with new versions of the compilers and system libraries. Users should plan to use Dogwood while Birch is down. For details about the new Dogwood Linux cluster, please see more below.

Aspen.itc.virginia.edu will no longer be available after October 16, 2006. Aspen users should begin immediate migration to the newer clusters. Aspen users should test their codes on Dogwood as soon as possible. The Aspen cluster is over four years old, long out of warranty and experiencing ever-increasing failures. With the addition of 200 nodes in the new Dogwood cluster, we anticipate migration from, and shutdown of, Aspen to be a relatively smooth transition.

We apologize for any inconvenience or difficulties these downtimes and transitions may cause. We urge you to contact Research Computing Support if you have any questions, concerns, or difficulties related to these upgrades and transitions or need help migrating your codes and programs.

Contact ITC Research Computing Support by email to Res-Consult@Virginia.edu or at either the Research Computing Lab in the Brown Science and Engineering Library (243-8799) or the Scholars' Lab in Alderman Library (243-8800).

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Dogwood Cluster Available

ITC announces the availability of Dogwood (dogwood.itc.virginia.edu), our newest cluster. Dogwood consists of 200 nodes with dual single-core Intel EMT cpus. Each node offers 3 GB of RAM memory and an 80-GB disk. Like Cedar, Dogwood has a 4-node test queue for short (under one hour) jobs.

Dogwood has considerably more nodes than Cedar (nearly twice as many) so we will permit larger parallel jobs; up to 48 cpus may be used. At the same time, up to 8 simultaneous jobs will be allowed per user. This limit is smaller than is the case for Cedar and is intended to try to improve overall throughput and turnaround.

view of Dogwood cluster view of Dogwood cluster view of Dogwood cluster

Dogwood runs ROCKS 4.2, which is based on Red Hat Enterprise Linux 4. This operating system features a new kernel that handles high loads better than the older kernel, as well as newer versions of all utilities. The compilers have also been upgraded; the Intel compiler is version 9.1 while the PGI compiler is version 6.2. The same application libraries and commercial software as are present on Cedar are also provided on Dogwood.

After Dogwood has passed its "shakedown" period, the operating systems and compilers of Birch and Cedar will be upgraded to match it, while Aspen will be retired from service.

Our initial testing has suggested that MPICH users should begin to migrate to mpich2 on this system. To use mpich2, load your usual module but with mpich2 rather than mpich; for example:


     module load mpich2-eth-intel

It will be necessary to recompile your program to use mpich2. To run an mpich2 program, use


     mpiexec -comm mpich2-pmi yourexec

Mpich2 offers many advantages and new features, but existing MPI-1 codes should compile without modifications. Mpich2 is also available on Aspen, Birch, and Cedar. We have not tested it under Myrinet on Birch but it should work. The same comm option to mpiexec is used for both Ethernet and Myrinet.

Please report any problems you encounter on Dogwood to ITC Research Computing Support by emailing Res-Consult@Virginia.edu or phoning either the Research Computing Lab in the Brown Science and Engineering Library (243-8799) or the Scholars' Lab in Alderman Library (243-8800).

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Secure Access Only to Dogwood Cluster

In the interest of security, ITC has disabled off-Grounds direct ssh access to the new Dogwood Linux cluster. In order to access this system from off Grounds, you must use either the UVa Anywhere VPN client (http://www.itc.virginia.edu/desktop/pki/vpn/) or your normal ssh client, such as SecureCRT, to log in to blue.unix.virginia.edu initially.

If you log in to blue.unix and you have had an ITC profile for a while, you may be confronted with the text menu system known as "umenu" and it is archaic. One of the options is to turn it off, and we suggest you do so. Once umenu is turned off, when you log in to blue.unix you will be at a normal shell prompt.

If you need to log on to Dogwood before disabling umenu, choose "9" for "go to Unix" and this will drop you to a shell prompt.

From the shell prompt, type
     ssh dogwood.itc.virginia.edu
or
     slogin dogwood.itc.virginia.edu
(these two commands have the identical result) and you will be on Dogwood. If you have X11 forwarding enabled in your desktop ssh client, blue.unix will pass this through.

When the Birch and Cedar clusters are upgraded, access to these machines will, like Dogwood's, be from U.Va. network addresses only, in an effort to make them more secure and less vulnerable to attack. The Birch upgrade is scheduled for October 17-19, 2006 and the Cedar upgrade is scheduled for October 10-12, 2006.

Direct access will continue to be available from on-Grounds locations as usual. Only off-Grounds access is affected by this policy.

Please contact ITC Research Computing Support if you have questions by emailing Res-Consult@Virginia.edu or by telephoning or visiting either the Research Computing Lab in the Brown Science and Engineering Library (243-8799) or the Scholars' Lab in Alderman Library (243-8800).

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Matlab SimBiology 2.0 Toolbox Trial Use Extended

ITC has obtained a trial 10-user network license for the Matlab SimBiology Toolbox version 2.0 that has been extended through November 1, 2006. The SimBiology toolbox extends MATLAB with tools for modeling, simulating, and analyzing biochemical pathways. SimBiology lets you simulate a model using stochastic or deterministic solvers and analyze your pathway with tools such as parameter estimation and sensitivity analysis. For more information, see the Web page at
    http://www.mathworks.com/products/simbiology/

and note the "Demos and Webinars" link. This toolbox complements MathWork's other offering in computational biology, the Bioinformatics Toolbox, which ITC currently licenses.

Users can add version 2.0 of the SimBiology Toolbox to their existing (and required) Matlab 7.2 installation (for Windows, Mac OS X, or Linux) by licensing and downloading it from the ITC licensing database at
     http://www.web.virginia.edu/rescomp/

It will also be available for Linux machines that mount the Matlab installation from the UNIX server jeeves.itc.

General information about the availability of Matlab at U.Va. can be found on the Web page at
    http://www.itc.virginia.edu/research/matlab/

People who are interested in having the SimBiology Toolbox become part of U.Va.'s Matlab site license should contact ITC Research Computing Support by emailing Res-Consult@Virginia.edu or by telephoning or visiting the Research Computing Lab in the Brown Science and Engineering Library (243-8799).

 

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Wolfram Workbench: A Mathematica Integrated Development Environment

Wolfram Research has released Wolfram Workbench, an integrated development environment that makes it easier to build and maintain software solutions written with Mathematica technologies.

Wolfram Workbench is currently available as a prerelease exclusively to Premier Service customers, which includes Mathematica users at the University of Virginia. You can download a free copy now for any U.Va.-owned computing on-grounds on which you've installed Mathematica through the site license.

Key features in Workbench enable users to:

  • Group files, code, and other Mathematica resources into a single project
  • Perform source-code editing with syntax highlighting, error reporting, local variable coloring, and many more options
  • Study code as it runs to easily detect and fix any problems
  • Profile code's execution and develop and run tests, with an array of insightful reporting methods
  • Manage multiple versions of files and access their version histories
  • Build and deploy Mathematica packages

For more information about Workbench, visit our website at
    http://www.wolfram.com/workbench

To download Wolfram Workbench, go to:
     http://www.wolfram.com/services/premiersupport/workbench.cgi?License=26266593

Further information on how to access and use Mathematica can be found on the Research Computing Services Web page at
     http://www.itc.virginia.edu/research/mathematica/

General questions concerning the use of Mathematica should be directed to ITC Research Computing Support; email us at Res-Consult@virginia.edu or telephone or visit either the Research Computing Lab in the Brown Science and Engineering Library (243-8799) or the Scholars' Lab in Alderman Library (243-8800).

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Events and Announcements..........

Linux Cluster Hands-On Tutorial to be Held October 24 and 26

All new users, as well as any longer-term users who would like to firm up their skills and understanding of using the ITC Linux clusters, are invited to attend a Hands-On Tutorial to be held on October 24 and 26 from 3:30-5 p.m. in the Electronic Classroom of the Brown Science and Engineering Library in Clark Hall. We will go through logging on to the cluster, compiling a program, using the make utility, and submitting the job to the cluster. The second session on October 26 will cover compiling and submitting parallel jobs using MPI.

Users are encouraged to bring their own laptops; however, if you do so, be sure that you have Cavalier wireless networking working before you attend. You should also have SecureCRT and SecureFX installed on your machine. An X server such as Exceed is optional. We will have CDs of a free X server for Windows available. We also recommend that users have some familiarity with some Unix text-based editor such as pico (the simplest), vi, or emacs.

Users without a laptop must have an Eservices account before attending the workshop. Eservices accounts can be obtained from http://www.itc.virginia.edu/accounts/createacct.html. Access to one of the library machines (and to power plugs for laptops) will be on a first-come, first-served basis.

Please contact ITC Research Computing Support if you have questions by emailing Res-Consult@Virginia.edu or by telephoning or visiting the Research Computing Lab in the Brown Science and Engineering Library (243-8799).

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Vacation Email Change Effective Oct. 17

As part of an ongoing initiative to ensure that email to and from members of the U.Va. community is delivered in a timely manner, ITC is changing its method for handling vacation email messages (Out-of-Office auto-responses). Some anti-spam services outside the University have recently begun blocklisting ITC's central email servers, because of automatically-generated replies sent by our servers in response to spam messages. The blocklisting has resulted in delays or, in some cases, outright rejection of U.Va. email by outside sites that use the anti-spam services.

Beginning October 17, 2006, vacation messages that are sent in response to email from non-University addresses will no longer be delivered, if the incoming messages are most likely spam. "Most likely spam," in this case, means that the incoming message has been tagged with a potential spam rating of 5 or higher. (All vacation responses to email from within the University will continue to be delivered, regardless of spam rating.)

The impact of these measures is that, while a small number of vacation auto-responses may fail to be delivered to legitimate email correspondents, the overall timeliness and reliability of U.Va. email delivery should improve.

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Immediate Opening for Research Computing Student Consultants

Information Technology and Communication's (ITC) Research Computing Support (RCS) is now accepting applications for student research computing consultant. The positions can start as soon as suitable candidates are found. It is expected that the students hired will start this summer and work at least through this academic year (2006-2007). ITC-RCS provides support for a wide variety of statistical, mathematical, scientific, and visualization software programs across a wide spectrum of computer platforms. Please see our website at
     http://www.itc.virginia.edu/researchers/service.html

for a listing of the software package and breadth of support and services offered by ITC research computing support.

To qualify for the position you must have a good working knowledge of at least one of the primary statistical, scientific, or mathematical packages we support and familiarity with at least one other software package.

The primary software packages are: SPSS, Matlab, SAS, Mathematica, Maple, S-Plus, and Stata. The most competitive candidates should have some working knowledge with more than one software package. In addition, you should be experienced using at least one of the computer systems below:

  1. Microsoft Windows
  2. Apple Macintosh
  3. UNIX (blue.unix, Linux, or other flavors)

An applicant must be a student who possesses the maturity and social skills needed to work closely with a variety of computer users, ranging from undergraduates to senior faculty and from novice to experienced users and the computer skills to work on a variety of computers and software programs.

The research computing consultant is responsible for helping users successfully run their research software programs and understand the output generated.

The position offers a research or quantitatively oriented graduate student exposure to a wide variety of scientific computing and statistical analysis projects and a broad assortment of research projects from many departments in the University and extensive experience using computers for data analysis and computational science.

Students interested in applying for a position should complete the application online at:

     http://web.virginia.edu/labcon/applications/labconapp.asp

Please make sure you check the box "Research/Statistical Computing Support" to indicate you are applying for this consultant position.

If you have questions or concerns about this position, please feel free to contact the ITC Research Computing Support Coordinator, Nancy Kechner, by sending electronic mail to nek8n@Virginia.EDU or by telephone at 243-8800.

Applications will be accepted until the positions are filled. Apply as soon as possible. (AA/EOE)

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Mathematica Free Online Seminars

The Wolfram Education Group has begun offering free online seminars to Mathematica customers worldwide. Taught by experienced Wolfram Research staff, presentations are given twice weekly. The seminar series began with S10: A Technical Overview of Mathematica located at
     http://www.wolfram.com/weg/seminars

For a list of dates and to enroll, visit:
     http://www.wolfram.com/weg/calendar

Further information on how to access and use Mathematica can be found on the Research Computing Services Web page at
     http://www.itc.virginia.edu/research/mathematica/

Please contact ITC Research Computing Support if you have questions by emailing Res-Consult@Virginia.edu or by telephoning or visiting either the Research Computing Lab in the Brown Science and Engineering Library (243-8799) or the Scholars' Lab in Alderman Library (243-8800).

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Stay Informed About SAS Users Group Activities!

SAS Institute has many exciting SAS users group events planned for 2006 and beyond - and they want to keep you up-to-date on the activities that will interest you most. To help them do that, please visit and log in with your existing SAS profile or create a new one at
     http://sems.sas.com/bess/get?id=559.1:-n81zun:ey2&RZNVY=gswg@ivetvavn.rqh&nccvq=5344

Stay informed and enjoy the unique opportunities for networking, learning and professional development that only SAS users group events can offer. Mark your calendar for the SAS Global Forum (formerly SUGI) that will be held April 16-19, 2007, in Orlando. They look forward to seeing you at one of these upcoming events! (Posted by:Michael H. Smith, SAS Users Group Support, Manager, SAS Institute).

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SESUG Website Updated with Presentation Lineup and FAQ

The SESUG website has been recently updated with some new details about the conference.

But if your question is not answered here, feel free to contact the conference chairs, Marje Fecht at AcademicChair2006 at sesug.org or Deborah Skinner at OperationChair2006 at sesug.org.

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9th Annual Conference on Computational Genomics: October 28-31, 2006, Baltimore, MD

The Virginia Bioinformatics Institute at Virginia Tech (VBI) and The Jackson Laboratory are hosting the 9th Annual Conference on Computational Genomics to discuss the latest advances in bioinformatics and computational biology. The goal of this meeting is to provide a forum comprised of invited speakers, speakers selected from submitted abstracts, and poster presenters to discuss their work and exchange ideas.

Themes for this year:

  • High-throughput automated genome annotation
  • Bioinformatics for biological networks
  • Bioinformatics for infectious diseases

For more information visit
     http://www.cpe.vt.edu/genomics/index.html

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Hands-on Workshop Using COMSOL Multiphysics Software on November 8

COMSOL Multiphysics (formerly FEMLAB) is a modeling package for the simulation of any physical process you can describe with partial differential equations (PDEs). It features state-of-the-art solvers that address complex problems quickly and accurately, while its intuitive structure is designed to provide ease of use and flexibility. See the website
     http://www.comsol.com/products/multiphysics/
for more information.

COMSOL will hold a free hands-on Workshop on November 8th at the University of Virginia. This event offers a live demonstration of the newly released COMSOL Multiphysics 3.3, as well as the opportunity for you to try the tool for yourself in a hands-on computer session.

Event Info
Date: November 8, 2006
Location: University of Virginia, Brown Science and Engineering Library, Room 133, Clark Hall
Program:
10:00am - 11:00am Intro and Live Demo
11:00am - 1:00pm Hands-on Session

For event details and registration, visit
     http://www.comsol.com/events/charlottesville_va/1325

Seating is limited, so advance registration is advised. Feel free to contact Mia Johansson with any questions at 781-273-3322 or email miaj at comsol.com.

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Technical Session: Using MATLAB & Simulink in Life Sciences on November 16

The MathWorks invites you to a free technical session to help university professors, researchers, and students learn how to use MATLAB and Simulink in Life Sciences.

This technical session will show how MATLAB and Simulink products are used as a flexible platform for technical computing and application development in life science and biomedical research. We will also demonstrate the use of several toolboxes including the Statistics, Image Processing, Bioinformatics, Signal Processing Toolboxes and SimBiology to analyze and visualize biosignal data, perform microarray analysis, and customize statistical algorithms in bioinformatics.

Event Details
When: Thursday, November 16, 2006 from 1:00 to 4:00 p.m.
Where: University of Virginia, Old Medical School Building (Health System), First Floor, Classroom C1 Charlottesville, VA
For directions to the Old Medical School Building (#24 on webmap), please visit
     http://www.virginia.edu/webmap/BHealthSciences.html
How: Register now at
     http://www.mathworks.com/seminars/uva
or call 978-659-6104.
Who Should Attend: Professors, researchers and students.
Topics Covered:

  • Data Acquisition and Import
    • Pulse Oximetry - Streaming data from hardware
    • Gene expression - Importing data from Excel
    • Filtering Tumor data - Pulling data from databases, building SQL statements
    • Gene Ontology - Importing data from Web databases
  • Analysis, Automation, and Visualization
    • Mass spectrometry (SELDI-TOF) - Developing user-interfaces for advanced analysis
    • Quantification of metastatic lesions - Automating image processing
    • Estimating retinal blood flow - Advanced image processing
    • Pharmacokinetics - Modeling and estimating parameters in Simulink
  • Sharing and Communicating your Research
    • Flow cytometry - Publishing HTML reports
    • Gene expression - Creating Excel plug-ins and stand-alone executables
  • Leveraging Distributed and Parallel Computing
For more information contact:
Scott Benway
sbenway at mathworks.com
Account Manager, Education Department
508-647-7741
www.mathworks.com

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Now is the time to encourage your colleagues and students to join us and learn about research computing support at U.Va. We only send out an e-mail once or twice a month to this mail list. Anyone can subscribe to this "itc-research" mail list via the Web page at:
http://list.mail.virginia.edu/mailman/listinfo/itc-research

Please encourage your colleagues to subscribe to our Research Computing mail list today!

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