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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.
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 delivered on AMD and 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.
In the past year, ITS' Graduate Education and Research Services group made available over 1,300 processors to the University's research community, making it possible for more than 350 researchers across 15 colleges and campuses to run a total of 1.3 million computational simulations using more than 6 million hours of CPU time.
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 2.4 GHZ 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, 2004 through June 30, 2005, Lion-XL ran 146,275 jobs and delivered 2,682,358 CPU hours to over 165 users. Since its inception, Lion-XL has run 313,571 jobs delivering 6,899,011 CPU hours.
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.
This year, Lion-XM ran 478,990 jobs and delivered 2,026,381 CPU hours to over 190 users. Since its inception during fall 2003, Lion-XM has run 668,540 jobs delivering 2,913,764 CPU hours.
For a listing of Lion-XM Partners, visit the Lion-XM PC Cluster page.
Lion-XO was deployed in October 2004 with 80 dual processor 2.4 GHz Sun SunFire V20z compute servers, each configured with 8GB of ECC RAM and 73GB of SCSI disk. Lion-XO is connected via a high-speed Infinicon Infiniband network.
This year, Lion-XO ran 130,167 jobs and delivered 724,536 CPU hours to over 160 users.
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 processor at 1.5 GHz each. The ES7000/430 has been particularly useful for researchers who have needed more than 4GB of memory per process and those working with large database applications. This cluster technology provides an alternative approach to how GEaRS currently meets the high performance computing needs of the range of researchers it supports.
Since the Unisys machine came online, it has run 6,397 jobs and delivered 92,786 CPU hours.
Computational grids are persistent environments that are expected to enable software applications to integrate instruments, displays, and computational and information resources being managed by diverse organizations in widespread locations. At Penn State, Dr. Lee Samuel Finn, director of the Center for Gravitational Wave Physics, is a lead participant in the National Science Foundation (NSF)-funded Laser Interferometer Gravitational-Wave Observatory (LIGO) project. The 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 International Virtual Data Grid Laboratory (iVDGL), 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 worked with Dr. Finn to build a Tier 2 computing facility based around the computational cluster, Pleiades. Pleiades consists of 128 Sun V60x compute nodes with 2 2.8Ghz Intel Xeon processors with 2GB of memory each, as well as 28 Dell 1750 compute nodes with 2 3Ghz Intel Xeon processors with 2GB of memory each, 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 146GB of 10K rpm Ultra 320 SCSI disks per enclosure. Pleiades currently has a theoretical peak computing capacity of 1.3 Teraflops.
Bioinformatics involves 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, which include Compugen, a bioinformatics portal, and BioWeb, a bioinformatics server. This year, the GEaRS group worked closely with Drs. Anton Nekrutenko, Arthur Lesk, and several others. The GEaRS group also has visited the Hershey Medical Center several times this year to forge new partnerships.
The GEaRS group continues to forge major new partnerships with academic departments and research groups. The major new initiatives for 2004 - 2005 are:
Staff in GEaRS worked with Dr. Nick Salamon in the College of Engineering by providing instructor information on various Fortran compilers, graphics options for his classes, and pointers to Fortran manual information.
GEaRS' staff also worked with Ramatsemela Mphahlele and Kostadin N. Ivanov, graduate students in the Department of Nuclear Engineering of the College of Engineering, to examine why their very large Fortran application would not run on a PC. GEaRs' staff, along with Ramatsemela and Kostadin, several individuals from the Nuclear Energy Agency within the Organization for Economic Co-operation and Development (OECD), and Oak Ridge National Laboratory (ORNL), the team finally made a breakthrough. They were able to get the large volume of code to run under any version of the Windows operating system. The exact code changes were then made available to OECD and ORNL.
Staff in GEaRS also worked with Dr. Stan Pennypacker, Professor Emeritus of Plant Pathology, to help him develop deed interpretation and map making software.
GeaRS' staff also worked with Sam Peppernick of the Departments of Materials Science and Physics respectively to assist him with the implementation of his computations for wave point correlations and subsets.
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 and digital animation as well as digital media and hardcopy output.
Architectural Design, Construction Planning, and Building Systems Engineering
During 2004 - 2005, the GEaRS Visualization group continued its partnerships and support for the use of projection-based visually immersive systems for research and teaching. The ITS/SALA Immersive Environments Lab (IEL), a three-screen surround-screen facility, which is used in the Departments of Architecture and Landscape Architecture for developing spatial understanding among undergraduate design students, is now in the process of moving to a new space specifically designed for this use. Its new home will be in the Stuckeman Building, the newly constructed home to the School of Architecture and Landscape Architecture (SALA). Construction of the new lab provides an opportunity for incremental improvements to the design, which is based on three years of experience in the IEL's previous location. Loukas Kalisperis, Professor of Architecture, is the lead faculty member on the IEL initiative.
The former IEL space in Engineering Unit C is being remodeled simultaneously by Architectural Engineering in order to house the new Immersive Construction (iCon) Lab. The iCon lab, which also provides a three-screen design similar to the IEL, will be used for developing and assessing the use of immersive techniques for construction planning and building systems engineering tasks. Preliminary work for iCon projects has been conducted using the former IEL. John Messner, Assistant Professor of Architectural Engineering, is the faculty lead for the iCon lab.
Both the IEL and iCon labs are Access Grid-enabled (see below), providing a means for immersive and tele-collaborative work sessions among remotely located participants. Both labs also can be made available for free scheduled use by any faculty interested in exploring the potential of immersive applications within their respective fields of study.
This single-screen immersive lab, located in the Lasch Football Building and developed in partnership with Visualization staff, continues to be utilized for research to assess disturbances in the processing of visually perceived motion as part of maintaining posture and balance in concussed athletes. Sam Slobounov, Associate Professor of Kinesiology, and Wayne Sebastianelli, Orthopaedic Surgeon and Director of Athletic Medicine, are lead faculty partners on the Lasch Lab. Related studies of motion perception and postural issues in the elderly also were conducted this year using GEaRS' Immersadesk facility, located in the Computer Building. Pamela Haibach, Ph.D. candidate, conducted this research under the direction of Karl Newell, Professor of Kinesiology.
Visualization staff have been working with faculty of the newly formed Center for Environmental Kinetics Analysis, directed by Susan Brantley, Professor of Geosciences, regarding proposed visualization and related outreach activities to be led by Chuck Anderson, visualization specialist for CEKA. Under the proposal, multiple single-screen 3-D stereo, projection-based Geowalls will be deployed for analyses and outreach communications of CEKA-sponsored research. Visualization staff look forward to continued opportunities to work with the CEKA group to facilitate the successful integration of data visualization techniques into the range of science and engineering activities supported through this center.
In conjunction with Jorge Sofo, Associate Professor of Physics, the Visualization group has begun an equipment upgrade and reactivation for an existing RAVE display (single-screen, projection-based, user-tracked, virtual reality display) located in Osmond Lab. The revitalized facility will focus on applications for Eberly College of Science faculty located at University Park.
The Tiled Display Wall serves as a test bed for evaluating scalable, parallel graphics rendering techniques. Techniques deployed on the Display Wall have been adapted for use in the Linux cluster host systems for the Immersive Environments Lab (IEL) and Immersive Construction Lab (iCon), in addition to pointing to possibilities for tele-collaborative use of data renderings over the Access Grid. GEaRS continues to seek new faculty partners who would be interested in using this large-format, high-resolution display and associated parallel rendering techniques to better visualize high-density data.
The Access Grid provides a scalable and extensible environment for voice and video tele-collaboration including voice, video, desktop applications, and data sharing among multiple remotely located participants using multicast internetworking. GEaRS' Access Grid node provides a local, University Park-based, access point for the Penn State community to participate in multi-group to multi-group meetings, tele-conferences, workshops, etc., within the burgeoning Access Grid community (see http://www.accessgrid.org/community/nodes/nodes.html for a representative global listing of nodes that have registered with Access Grid organizers). The Room 140 Computer Building node has been used regularly for World University Network (WUN) planning meetings, to support local participation in international conferences (e.g., Virtual Conference on Genomics and Bioinformatics, SC Global, etc.), as well as more individual or ad hoc use by Penn State faculty for meetings with collaborators at other institutions. Access Grid capabilities have been added to both the IEL and to the iCon, providing two classroom size (30+ seats) venues for using immersive and tele-collaborative techniques in teaching and research. GEaRS also facilitates the development of Access Grid meeting spaces at other campus locations, as part of evaluating the functionality of Access Grid for faculty and researchers with unique tele-collaborative needs as compared to more established videoconferencing approaches or technologies. Faculty from any Penn State location who are interested in exploring this emerging venue for rich media tele-collaboration should contact access-grid@psu.edu.
In addition to the GEaRS facility-related projects listed above, Visualization staff consult with faculty on the application of advanced visualization techniques in support of research, teaching, and outreach for any academic department. Projects for the 2004 - 2005 year include:
Lab-on-Wheels
The Lab-on-Wheels provides a mobile teaching facility capable of being deployed quickly, 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. The Lab currently consists of 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.
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 tailored to precisely fit a researcher's 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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Last revised: Monday, August 15, 2005.