Annual Report Home | Executive Summary | New, Improved and Continued Services | Research Services | Project/Initiative Highlights | Professional/Personal Activities | By the Numbers

The Graduate Education and Research Services (GEaRS) Group in ASET strives to meet the computing technology needs of scholars in their education and research endeavors at Penn State. The group pursues cutting-edge advances in research computing technology in partnerships with faculty members and in strong technical collaborations with various technology companies and institutions. The GEaRS Group is comprised of three service groups, each with its own long history of service to the community of scholars at Penn State.

High Performance Computing
http://gears.aset.psu.edu/

In the area of High Performance Computing, the GEaRS group continued to expand its partnerships and collaborations with faculty members, assisting them to take advantage of computational resources primarily delivered on Intel CPU-based servers running the Linux operating system. GEaRS group staff members continue to maintain a strong commitment to teaching the use of application packages and libraries and supporting the same in research across many academic disciplines.

Lion-XE
http://gears.aset.psu.edu/hpc/systems/lionxe/

The Lion-XE computational cluster, a 128 node machine, was a partnership with 13 faculty members representing 10 academic disciplines. Built in January 2001, Lion-XE was decommissioned at the end of June 2004.

Lion-XE was built with a high-speed low-latency interconnect on 81 of its nodes dedicated to running high performance parallel jobs. Lion-XE consisted of 128 Dell PowerEdge 1550 servers, each with dual 1GHz processors and 1GB of RAM. Each node was one rack unit high so the entire cluster was built into a very compact footprint. For the period July 1, 2003 through June 30, 2004, Lion-XE ran 193,482 jobs and delivered in its lifetime 704,600 CPU hours.

For a listing of Lion-XE Partners, visit the Lion-XE PC Cluster page.

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Lion-XL
http://gears.aset.psu.edu/hpc/systems/lionxl/

Lion-XL, a 1.3 teraflop machine, consists of a total of 176 Dell PowerEdge 2650 servers, each configured with dual Intel processors, 4GB of memory and a 36GB Ultra320 15K revolutions per minute (rpm) SCSI drive. The first subset of Lion-XL, 128 dual 2.4GHz CPU nodes, are connected with a Quadrics QsNet Elan3 high performance network. All 176 nodes are connected with fast Ethernet. During the period from July 1, 2003 through June 30, 2004, Lion-XL ran 103,623 jobs and delivered 2,732,318 CPU hours.

For a listing of Lion-XL Partners, visit the Lion-XL PC Cluster page.

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Lion-XM
http://gears.aset.psu.edu/hpc/systems/lionxm/
In fall 2003, the GEaRS group deployed its most powerful cluster to date. Lion-XM consists of 128 Dell PowerEdge 1750s, each configured with dual 3.06 Intel Xeon processors, 4GB of memory and a 36GB Ultra320 15K rpm SCSI drive. Lion-XM is connected via a high-performance Myrinet network from Myricom.

During the period from October 1, 2003 through June 30, 2004, Lion-XM ran 169,199 jobs and delivered 873,405 CPU hours.

For a listing of Lion-XM Partners, visit the Lion-XM PC Cluster page.

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Lion-XD Angstrom
LION-XD is a new cluster aimed at simultaneously providing better support for the development needs of the High-Performance Computing community at Penn State and exploring cutting-edge computational technology. It consists of 16 dual 2.0GHz Opteron blades, each with 4GB of RAM, and is connected via a high-speed, low-latency InfiniBand interconnect from TopSpin Communications.

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Unisys
The Unisys ES7000 system's 32 Intel 64-bit Itanium2 processors provide access to large amounts of shared and high bandwidth memory. The centerpiece of the installation consists of a Unisys ES7000/430 with two domains of 16 Itanium2 processors at 1.5GHz each. The ES7000/430 will be particularly useful for researchers who need more than 4GB of memory per process and those working with large database applications. This clustered technology will provide an alternative approach to how GEaRS currently meets the high performance computing needs of the range of researchers it supports.

During the period from January 1, 2004 through June 30, 2004, the Unisys system ran 1,892 jobs and delivered 34,810 CPU hours.

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Grid Computing (iVDGL/LIGO)/Pleiades Cluster
http://ligo.aset.psu.edu/
Computational grids are persistent environments that are expected to enable software applications to integrate instruments, displays and computational and information resources that are managed by diverse organizations in widespread locations. At Penn State, Dr. Sam Finn, Director of the Center for Gravitational Wave Physics, is a lead participant in the NSF-funded LIGO project. The Laser Interferometer Gravitational-Wave Observatory (LIGO) is a facility dedicated to the detection of cosmic gravitational waves and the harnessing of these waves for scientific research. LIGO is a partner in iVDGL (International Virtual Data Grid Laboratory), which is tasked with establishing and utilizing an international laboratory of unprecedented scale and scope, and is comprised of heterogeneous computing and storage resources in the U.S., Europe and ultimately other regions linked by high-speed networks, and operated as a single system for the purposes of interdisciplinary experimentation in Grid-enabled, data-intensive scientific computing.

As a part of the LIGO project, the GEaRS group has worked with Dr. Finn to build a Tier 2 computing facility. Pleiades consists of 128 Sun V60x compute nodes with 2 2.8GHz Intel Xeon processor with 2GB of memory, 28 Dell 1750 compute nodes with 2 3GHz Intel Xeon processor with 2GB memory, and 9 Dell PowerEdge 1750 file servers. Pleiades also has 35.1TB of storage organized in 18 RAID-5 Dell PowerVault 220S enclosures with 14 146 GB 10K rpm Ultra 320 SCSI disks per enclosure; 160 of the nodes are connected with InfiniconŐs InfinIO high-speed network fabric (6 Gigabits/second). Pleiades currently has a theoretical peak computing capacity of 1.3 Teraflops.

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Lab-on-Wheels
The Lab-on-Wheels provides a mobile teaching facility capable of being deployed quickly and easily, and virtually anywhere so that the typical restrictions of site and time found in scheduling a fixed computer lab are removed. This allows the GEaRS group to present seminars or teach a hands-on workshop wherever the instruction is desired and most easily accessible to a larger group. In order to launch this initiative, GEaRS acquired nine Dell Inspiron 8200 laptops, each with 1.8GHz Pentium 4 processors, 1GB of RAM, and a 60GB drive. All laptops have both Windows and Linux operating systems installed to accommodate a wide range of software packages. The Lab-on-Wheels facility was designed to couple with GEaRS' Seminars-on-Demand initiative.

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Seminars-on-Demand
http://gears.aset.psu.edu/education/
Seminars-on-Demand is a GEaRS group initiative designed to provide high performance computing and visualization-related education to the University community. The goal is simple: to deliver seminars that are tailored to precisely fit researchersŐ needs and taught at a time and place to suit his/her convenience. These seminars are taught using the GEaRS Lab-on-Wheels facility, noted above.

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Major Partnerships
http://gears.aset.psu.edu/hpc/partners/

• Materials Simulation Center (MSC)
  This year, the Materials Simulation Center (MSC) at Penn State acquired 64 nodes in the new 176-node Lion-XL computational cluster, making MSC the largest partner in this state-of-the-art computing facility. The MSC is devoted to promoting the use of computer simulation of materials by facilitating better access to software and computing hardware. The GEaRS group worked with Drs. Vincent Crespi and Jorge Sofo on this alliance.
• MATCASE
  Throughout the year, the GEaRS group worked with Drs. Long-Qing Chen, Zi-Kui Liu, Padma Raghavan and Jorge Sofo on this materials science project. They have acquired 32 nodes in Lion-XL for computational work as well as development of Web-based tools.
• CCMA
  During 2003 - 2004, the GEaRS group worked with Drs. Jinchao Xu, Qiang Du, and Ludmil Zikatanov of the Center for Computational Mathematics and Applications (CCMA) at the Department of Mathematics. They have acquired 32 nodes in Lion-XL. The GEaRS group has also helped them acquired and did the initial systems work on five high-end desktop machines.

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Bioinformatics
Bioinformatics involved the research, development or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data. These approaches help organize and extract important information from this huge wealth of new data and make it accessible and understandable to people in the medical and biological fields. GEaRS is working with the Huck Institute for Life Sciences, and faculty members in many academic departments to provide several bioinformatics-focused services including Compugen, a bioinformatics portal, and BioWeb, a bioinformatics server. This year, the GEaRS group worked closely with Drs. Blair Hedges, Anton Nekrutenko, Arthur Lesk, Ross Hardison and Webb Miller.

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Visualization
http://gears.aset.psu.edu/viz/

The Visualization Group in GEaRS investigates emerging visual computing technologies and implements several leading-edge solutions in a cost-efficient manner to help faculty better integrate such tools in instructional and research programs at Penn State. The group provides facilities and consulting expertise in the areas of scientific and artistic visualization, digital animation, as well as digital media and hardcopy output.

3D Stereoscopic and Widescreen Multimedia Technology Classroom
http://gears.aset.psu.edu/viz/facilities/stereoclassroom/
Room 158 Willard Building was upgraded to enable 3D stereoscopic display of spatial data by faculty in their teaching. In addition to offering standard technology classroom capabilities, the new installation includes a dual-screen Windows XP graphics workstation and a multi-projector display to allow wide-screen projection of three-dimensional information in passive stereo using inexpensive Ňtheme parkÓ style polarized glasses. The Stereo and Enhanced Multimedia Classroom is the result of a combined effort of the University Committee for Instructional Facilities (UCIF), Classroom and Laboratory Computing (CLC), in Teaching and Learning with Technology (TLT), a unit of ITS, and the Visualization group, along with Media Technology Support Services (MTSS) of University Libraries. Stereo projection is provided under a research partnership with CyViz, AS of Norway.

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Immersive Environments Lab (IEL)
http://gears.aset.psu.edu/viz/facilities/iel/
The ITS/SALA Immersive Environments Lab (IEL) is a partnership project between ITS and the School of Architecture and Landscape Architecture (SALA). The motivation for the lab has been to bring affordable, robust, easy-to-use, surround-screen, projection-based virtual reality (VR) techniques into the mainstream of teaching and research in the design arts and other disciplines. Under the faculty leadership of Loukas Kalisperis, professor of architecture, the IEL has become an integral part of the undergraduate architecture design curriculum, allowing students to better visualize their respective designs at human scale, as well as to combine virtual reality, more traditional presentation and multimedia techniques for better communications and understanding of the various attributes of their proposed design solutions. In supporting this activity, the IEL also serves as a test bed for evaluating underlying Open Source VR software development toolkits, and various aspects of system integration and end-user computing support issues associated with such specialized implementations.

In 2004, the Visualization group began extensive work in the IEL with John Messner, assistant professor of architectural engineering, on the development and assessment of VR tools and techniques for use in construction planning. Dr. Messner has received funding from NSF for the construction of a new VR facility, of similar construction to the IEL, for continuing his work in the efficacy of VR tools for teaching, research and professional practice in construction planning and related areas. These new tools involve linking building information models, construction scheduling information, etc., to interactive CAD models in order to better understand and communicate construction planning processes. A test case is under development using the new SALA Building currently under construction at University Park. The new building project has afforded a unique opportunity for the involvement of construction management staff and representatives of key subcontractors in order to gain their professional insight into the opportunities and obstacles likely to be encountered in the development of the proposed tools.

In 2004, four masters theses significantly involved the use of the IEL:

Rajitha Gopinath, Architectural Engineering. "Immersive Virtual Facility Prototyping for Design and Construction Process Visualization."

Bimal Balakrishnan, Architecture. "Digital Meida and Virtual Reality: A Multimodal Approach for Architectural Representation."

Eric Mainzer, Landscape Architecture. "Develop and Validate the ITS/SALA Immersive Environments Lab as a Visualization Tool for Use in the Fields of Architecture and Landscape Architecture."

Jana Zelenski, Landscape Architecture. "Comprehending the Products of Design: Digital and Traditional."s Recipient of a Special Recognition Award from the American Society of Landscape Architects.

The IEL and new Architectural Engineering VR facility to be built in 2005, will continue to serve as test beds for the development of cost-effective, easy-to-use virtual reality and integrated digital media techniques within the context of architectural and engineering design communications and analyses.

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ACCESS Grid Node
http://gears.aset.psu.edu/viz/facilities/gridnode/
The Access Grid (AG) Node represents a global effort to deploy open solutions for high bandwidth group-to-group multi-modal telecollaboration over existing high-performance computing networks. The AG node supports large-scale distributed meetings collaborative work sessions, seminars, lectures, and tutorials, enabling group-to-group communications using multicast Internet-working, voice and video teleconferencing, and desktop applications sharing among multiple remotely-located participants. In room 140 Computing Building, the GEaRS group offers a local venue for members of the Penn State community to participate in Access Grid events from a University Park location. The room has helped enable members of the Penn State academic community to participate in scheduled Access Grid events or explore the technology for communications and collaboration with colleagues from other Access Grid-enabled institutions.

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Display Wall
http://gears.aset.psu.edu/viz/facilities/displaywall
The Display Wall, located in room 139 Computer Building, continued to gain interest and use this year. It uses scalable real-time rendering techniques on a cluster of 12 computers to display high-resolution images with nearly 10 million pixels on a 6-foot-by-11-foot large-format screen. The 12-tile display makes it possible to view fine detail in complex visualization problems, or to alternatively serve as a very high-resolution workspace for display and cross comparison of multiple related images, application windows or related data. The facility seeks to enable researchers in many disciplines gain better intuitive insights into complex data relationships and additionally serves as a test bed for open source and parallel graphics development within a clustered Linux environment.

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Sports Medical Research
http://gears.aset.psu.edu/viz/facilities/sportsmed/
The GEaRS group has participated in establishing a sports medicine VR lab in the Lasch Football Building. This work is in partnership with faculty from the Penn State Departments of Kinesiology and Psychology, and the College of Medicine at the Hershey Medical Center, under the faculty leadership of Semyon Slobounov, Associate Professor of Kineseology. The project has been funded by a College of Medicine DeanŐs Feasibility Grant with additional funding, equipment and in-kind support from GEaRS and the Departments of Kinesiology and Psychology.

The new lab combines VR display techniques with kinesiology and brain imaging measurements to understand better how kinesthetic responses to perceived motion and underlying neurological mechanisms may be affected by mild traumatic brain injury. Currently, subject data is being collected from Penn State football players to study the effects of concussions and other mild brain trauma. An additional study has begun that will be the basis of a doctoral dissertation for James Thompson, Ph.D. candidate in kinesiology. That study will focus on the assessment of Penn State Rugby players.

The Lasch lab builds upon pilot research conducted using GEaRS' Immersadesk VR facility and employs a VR display design that was developed for the ITS/SALA Immersive Environments Lab. Previous Immersadesk protocols also are being adapted for use by Pam Haibach, a Ph.D. candidate in kinesiology, in the study of perceptual/postural disturbances in stroke patients. Pilot data has been collected using student volunteers and the GEaRS Immersadesk. Subject trials with stroke patients is scheduled to begin during fall 2004.

In a related development during 2003 - 2004, programming and device integration assistance was provided in support of Dr. Semyon Slobounov's sabbatical research at NIH in Bethesda for assessing cognitive responses to postural imagery using MRI imaging techniques.

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