The Linked Environments for Atmospheric Discovery [LEAD] project is
building cyberinfrastructure to enable scientists to predict
mesoscale weather events, like tornadoes. Kelvin Droegemeier, at
the University of Oklahoma, is overall director of the project, and
Dennis Gannon and Beth Plale at Indiana University are the PIs for
the LEAD Science Gateway.
To bring some state-of-the-art fun to aspiring meteorologists, and
encourage use of these tools, the WX Challenge contest invites
students, faculty, and staff at higher education institutions to
compete in forecasting maximum and minimum temperatures,
precipitation, and maximum wind speeds for select U.S. cities over
a ten-week period each semester. Brad Illston from the Oklahoma
Climatological Survey and University of Oklahoma is managing the
contest, which involves
* ~1600 participants (from Freshmen to Faculty/Staff)
* 56 schools participating in both US and Canada
* 45 classes using the contest as part of their curriculum
The WX Challenge student teams were invited to use the LEAD tools,
in the first public test of the LEAD gateway. Suresh Marru and
Marcus Christie of the TeraGrid Gateway Grid Infrastructure Group
staff monitored the students' progress. During the Challenge, the
students ran 220 weather simulations, and produced 2.5 Terabytes
of data. The simulations take up to eight hours to run on 160
processors on IU's Big Red supercomputer.
More information on the contest is available at
http://www.wxchallenge.com/
The LEAD Science Gateway is at
https://portal.leadproject.org/
Indiana University Cyberinfrastructure News
-
-
Terabytes of spatial data are available online for professionals and
the general public via the Indiana Spatial Data Portal [ISDP]. As
part of the 2005 Statewide Digital Orthophotography Program, the
ISDP archives more than 142,000 high resolution digital aerial
photographs, as well as other data including elevation models and
topographic maps. Local government agencies throughout the state use
these images to support homeland security, emergency management, and
other business and government services. The service is especially
popular among engineering firms statewide.
Staff from IU's Data Management Support Group worked closely with
data vendors, the Indiana Geographic Information Council, and IU's
Distributed Storage Systems Group to deliver these geospatial
datasets from the high performance storage system (HPSS).
Developers created the ISDP Multi-file Download Tool, a .NET
application which provides a graphical user interface allowing
end-users to select files from a geographic area of interest, see
metadata about file size and format, and download one or more files.
Users can easily transfer files ranging in size from megabytes to
gigabytes.
Nathan Eaton, Information Services Manager at the Indiana Geological
Survey, is a long-time GIS user, and regularly encourages others to
take advantage of the ISDP. According to Eaton, "Without question,
this is the best repository of aerial photos, elevation models, and
topographic maps in the state of Indiana. In fact, it's probably the
best of its kind among state repositories in the nation. Nowhere
else can you go to download multiple years of aerial photos in both
raw TIFF and compressed MrSID formats. The ISDP is truly unique, and
an invaluable resource to thousands of users who need access to
large images for use as GIS base maps."
More information on geographic information systems at IU is
available at
http://gis.iu.edu/ -
Indiana University faculty and staff can access the High Performance
Storage System [HPSS] via the Heirarchical Storage Interface [HSI].
Fast, robust, and user-friendly, this provides the best performance
interface between IU's supercomputers and HPSS. HSI also selects
the best class of service for a given upload, automatically. IU's
HSI installation accepts either Kerberos authentication (an IU
Network ID) or Globus authentication (TeraGrid allocations).
On Libra and the Research Database Cluster, HSI is installed in
/usr/local/bin (so it's in the default path). On Big Red, you may
need to add "+hpss" (without the quotes) to the beginning of your
.soft file and give the "resoft" command to make it available (you
need only do this once).
HSI commands will seem familiar to UNIX and FTP users. A session
might look like the following (here % is the UNIX shell prompt,
? is the HSI prompt):
%
% hsi
Principal: jdoe
[jdoe]Password:
Username: jdoe UID: 11021 CC: 11021 Copies: 1 [hsi.3.3.3 Fri
Jan 12 13:36:06 EST 2007]
?
? ls
/hpss/j/d/jdoe/:
NPB-ppcc.tar foobar/ movies/
?
? du -k
861309 /hpss/j/d/jdoe/
-----------------------
861309 total 1024-byte blocks, 6 Files (881,979,719 bytes)
?
? put myfile1.dat
put myfile1.dat : /hpss/j/d/jdoe/myfile.dat ( 10485760 bytes,
12283.4 KBS (cos=3))
? cd movies
? get myfile2.mov
Scheduler: retrieving file(s)
get myfile2.mov : /hpss/j/d/jdoe/movies/myfile2.dat
(2005/09/29 08:49:03 10485760 bytes, 16842.8 KBS )
?
? stage -w myfile3.dat
?
? exit
%
There may be a delay of seconds to minutes in retrieving a file that
has not been accessed recently. The "stage" command prepares a file
for fast download at a future time, by moving it from tape to disk.
More information on HSI is available at
http://kb.iu.edu/index.cgi?search=hsi -
The mission of Scientific Data Services (SDS) is to help researchers
gain access to the data they need and manage the data they already
have. SDS will help determine the right tools and processes to
manage your data, including workflow analysis, software choices and
database design.
SDS provides Oracle database hosting, facilitates access to life
sciences data, and helps researchers design and implement data
management systems. The staff is experienced with database design,
application development, data mining, and grid technologies. For
more information, see
http://scidata.iu.edu/ -
The planned retirement of the AVIDD system will begin on May 1 as
originally scheduled, but portions of the system will remain online
until mid-July. UITS will retire AVIDD-T, AVIDD-N, and AVIDD-I on
May 1, but delay the retirement of AVIDD-B and AVIDD-O pending
installation of a replacement system based on X86-64 technology.
If you use AVIDD-B or AVIDD-O, UITS encourages you to migrate to
Big Red and/or the TeraGrid. For help, contact
researchtechnologies@iu.edu.
For full information about computing systems available at Indiana
University, see
http://uits.iu.edu/scripts/ose.cgi?alul.ose.help
--------
Wednesday, May 30, 12:30-1:30 -- ICTC Room 497 & IMU Walnut Room
Research Technologies Brown Bag Talk
Staff from the UITS Advanced Visualization Lab will describe the
visualization technologies and consulting available to the IU
community. -
Indiana University is offering a TeraGrid-related tutorial, "Using
IU's Big Red PowerPC Cluster and IU Storage Resources via the
TeraGrid" at the following conferences:
Indy '07 Bioinformatics conference, Indianapolis, IN
Tutorial offered 31 May, 8:00 am - noon
http://compbio.iupui.edu/indy/
TeraGrid '07 conference, Madison, WI
Tutorial offered 4 June, 8:30 am- noon
http://www.union.wisc.edu/teragrid07/
BiBE 2007 (Bioinformatics and Biomedical Engineering), Boston, MA
Tutorial offered 14 October 2007
http://www.cs.gsu.edu/BIBE07/index.php
Indiana University's Big Red system, a 40 TFLOPS IBM e1350 cluster,
is presently the third largest supercomputer integrated with the
TeraGrid. Big Red supports the TotalView debugger and the Vampir
performance analysis system, and is capable of excellent performance
on applications scaling beyond 1000 processors.
The primary purpose of this tutorial is to enable TeraGrid users to
learn about the Big Red system so that they can easily use codes
already ported and optimized for that system (e.g. WRF, NAMD, MILC)
or rapidly migrate other applications to Big Red.
Within a TeraGrid environment dominated overall by Intel processors,
PowerPC processors may be perceived as a barrier. This tutorial
specifically introduces the compilers and optimizations that provide
the best performance with the Power instruction set and the PowerPC
processor.
In addition, as massive computations commonly depend on massive data
sets as input, and produce massive data sets as output, it may be
useful to obtain a working knowledge of IU's archival data storage
system, and how to store and access files via gridftp.
Plan to attend to gain hands-on experience with Big Red and IU's
High Performance Storage System, as resources on the TeraGrid. -
CALL FOR PAPERS:
Workshop on Progress Toward Petascale Applications in Bioinformatics
and Computational Biology, to be held in conjunction with the IEEE
7th International Symposium on Bioinformatics & Bioengineering
(BIBE 2007)Organizers:
* Craig Stewart, Indiana University
* Geoffrey Fox, Indiana University
* Malinda Lingwall, Indiana University
* Matthias Mueller, High Performance Computing Center Stuttgart
* David Bader, Georgia Institute of Technology
* Rick Stevens, Argonne National Laboratory
Over the past several years there have been repeated analyses of the
potential value of petascale bioinformatics and computational
biology applications, as well as analyses of the system engineering
steps required to implement applications and systems at such scale.
Most recently and notably, Snavely et al. published the ÒWorkshop
Report: Petascale applications in biological sciencesÓ
(http://www.sdsc.edu/PMaC/BioScience_Workshop/Publications/
PetascaleBIOworkshopreport.pdf).
By one measure the era of petascale computing in biology began in
2006 with the successful clocking of the Riken Institute Protein
Explorer system at 1.0 PetaFLOPS. Still, the state of the art of
current applications in bioinformatics and computational biology is
generally yet orders of magnitude away from petascale, especially
in terms of actual performance.
The purpose of this is workshop is to survey the current state of
the art in computational biology and bioinformatics at scale.
Suggested topics for papers and posters include, but are not
limited to, the following specific subjects:
* What is the current upper limit of scale of applications in
bioinformatics and computational biology? What are the factors
limiting scalability of these applications?
* Can we, as recommended by Snavely et al., identify candidate
petascale applications in any of the following areas: biomolecular
structure modeling, modeling complex biological systems, genomics,
customized patient care, ecological components of earth systems
modeling, infections disease modeling, or other areas?
* What are the best ways to measure performance scalability of
bioinformatics and computational biology applications? Can we
measure what really counts in terms of next generation
bioinformatics applications with FLOPS and bytes?
* The NSF workshop organized by Snavely, Jacobs, and Bader
identified several specific applications as candidates for
scaling. The resulting report called for attention to progress in
scaling applications by identifying problems, resolving those
problems, and trying to anticipate problems at larger scales and
making the step to larger scales. Presentations that discuss the
steps, challenges, and solutions to incremental scaling of
bioinformatics and computational biology applications are
particularly encouraged. Practice and experience papers related to
this topic will be of particular value to the scientific community
as we strive toward petascale applications.
For more information about this workshop, see:
http://www.cs.gsu.edu/BIBE07/workshops.php
Submission Guidelines:
Papers must be written in English in the IEEE two-column format
and should be limited to 8 pages. A detailed description of the
conference paper format (8.5" x 11", Two-Column Format) can be
found at IEEE Computer Society Conference Publishing Services (CPS):
http://www.computer.org/portal/site/cscps/. The paper to be uploaded
must be in Adobe's PDF format. The deadline for submitting an
abstract along with the original paper in PDF via an online paper
submission system is June 8, 2007.
Papers should be uploaded and identified as being contributions to
the Workshop on Petascale Applications in Bioinformatics and
Computational Biology. Details on the submission process are
available at http://www.cs.gsu.edu/BIBE07/submission.php
Because we are interested in new and developing research projects,
authors may at their option choose to submit a full paper or an
extended outline for work that is yet in progress.
Submission of a paper should be regarded as a commitment that,
should the paper be accepted, at least one of the authors will
register and attend the conference workshop to present the paper or
the poster.
Papers will be refereed and accepted on the basis of their
scientific merit and relevance to the workshop topics. -
Outages
-------
System Date Time Failure
libra02 04/04/07 12:00 NAS issues forced reboot
Planned maintenance
-------------------
System Date Time Action
AVIDD 05/01/07 08:00-17:00 OS Patches
Libra 05/01/07 08:00-17:00 OS Patches
Big Red 05/01/07 20:00-24:00 OS Patches
RDC 05/01/07 08:00-17:00 OS Patches
ArcIMS updates
ArcSDE updates
Steel 05/06/07 06:00-10:00 OS Patches
BigRed 05/07/07 08:00+7d BigRed expansion -
If you have questions pertaining to IU's cyberinfrastructure, or you
are encountering some difficulty, there are several ways to obtain
help.
An introduction and overview titled "Indiana University's
CyberInfrastructure: The least you need to know" has been updated
and is available at http://rc.uits.iu.edu/education_and_training/ .
The IU Knowledge Base (http://kb.iu.edu) is an excellent source of
help on how to do things.
If you have problems which the KB does not enable you to solve,
questions about system outages, or if you just have a problem and
you don't know who to contact, send email to
researchtechnologies@iu.edu.
