cyberinfrastructure support at penn state - internet2 · cyberinfrastructure support at penn state...

Cyberinfrastructure Supportat

Penn State

CRCC Workshop

April 2006

Vijay Agarwala, Kevin Morooney

Information Technology Services

vijay at psu.edu, kxm at psu.edu

Outline

• Service model description

• Some examples

• The Good, The Bad

Service Opportunities

• Computation

• Visualization

• Collaboration

• Networking

ITS Clusters

• Condominium model of usage and acquisition

– Started over 20 years ago, many lessons learned

– When you aren't using yours, others can

– When you are using yours, you can use more than yours

• We end up with a bigger single “image” to enable bigger science

• Each partner gets the perception and reality of computing more than they could if they went on their own

A typical cluster - ownership view

ITS

Research Group A

Research Group B

Research Group C

Research Group D

Research Group E

Research Group F

A typical cluster - “weekly” view

ITS

Research Group A

Research Group A

Research Group A

Research Group D

Research Group E

Research Group F

ITS

Research Group E

Research Group E

Research Group C

Research Group E

Research Group E

Research Group F

A typical cluster - another “weekly” view

One way to look at it...V

endors, solutions

Facu

lty

Facilities

ITS-research methodologies-funding trends-funding availability-skillsets-partner?

-direction-viability-performance-price-partner?

Typical Acquisition Timeline

0 1 2 3

Some Base Philosophies

• Take technology risks so faculty don't have to

• Achieve institutional efficiencies

• Stay “in-line” with federal/regional/technology trends and facilities

• Do what faculty don't want to do/can't do/won't do/shouldn’t do

Computation - our value proposition

• Reliability

• Serviceability

• Security

• Performance

• Staying on an technology edge

• Maintaining vendor relationships

• Applications availability

Computation - our value proposition

• Reliability

• Serviceability

• Security

• Performance

• Staying on an technology edge

• Maintaining vendor relationships

• Applications availability

Why wouldfaculty ever wantto go it alone?!?!?

Dr. James B. Anderson, Evan Pugh Professor of ChemistryDr. Craig S. Bishop, Associate Professor of MeteorologyDr. Ottar N. Bjornstad, Assistant Professor of Entomology and StatisticsDr. James G. Brasseur, Professor of Mechanical EngineeringDr. Lance R. Collins, Professor of Chemical EngineeringDr. William M. Frank, Professor of MeteorologyDr. Barbara J. Garrison, Shapiro Professor of ChemistryDr. Ross C. Hardison, Professor of Biochemistry and Molecular BiologyDr. Jainendra K. Jain, Erwin W. Mueller Professor of PhysicsDr. Izabela Makalowska, Director of the Computational Genomics CenterDr. Wojciech Makalowski, Associate Professor of BiologyDr. Webb C. Miller, Professor of Computer Science and EngineeringDr. Katriona Shea, Assistant Professor of Biology

LION-XE Participants

LION-XE Computational Cluster

128 Dell PowerEdge 1550s

• Dual 1 Ghz Intel Xeon Processors

• 1 GB of ECC RAM

• 36 GB of SCSI disk

BlueArc Fileserver

Dolphin SCI high-speed interconnect

http://gears.aset.psu.edu/hpc/systems/lionxe/

LION-XL Computational Cluster


• Dual 2.4 Ghz Intel Xeon Processors

• 4 GB of ECC RAM


BlueArc Fileserver

Quadrics high-speed interconnect

Dr. James B. Anderson, Evan Pugh Professor of Chemistry Dr. Long-Qing Chen, Professor Materials Science and Engineering Dr. Qiang Du, Professor of Mathematics Dr. Barbara J. Garrison, Shapiro Professor of Chemistry Dr. Daniel Haworth, Assistant Professor of Mechanical Engineering Dr. Zi-Kui Liu, Associate Professor of Materials Science and Engineering Dr. Anton Nekrutenko, Assistant Professor Biochemistry and Molecular Biology Dr. Padma Raghavan, Associate Professor Computer Science and Engineering Dr. Jorge Sofo, Director of the Materials Simulation Center Dr. Jinchao Xu, Director of the Center for Computational Mathematics and Applications

Dr. Ludmil Zikatanov, Assistant Professor of Mathematics

LION-XL Participants

http://gears.aset.psu.edu/hpc/systems/lionxl/

LION-XM Computational Cluster


• Dual 3.06 GHz Intel Xeon Processors

• 4 GB of ECC RAM


BlueArc Fileserver

Myrinet high-speed interconnect

Dr. Douglas Cowen, Associate Professor of Physics, Astronomy and Astrophysics Dr. Melik Demirel, Assistant Professor of Engineering Science and MechanicsDr. Dan Haworth, Associate Professor of Mechanical Engineering Dr. Costas Maranas, Associate Professor of Chemical Engineering Dr. Mike Modest, Professor of Mechanical Engineering Dr. Martin Moeck, Assistant Professor of Architectural EngineeringDr. Paul Plassman, Associate Professor of Computer Science and Engineering

Dr. Stephen Rathbun, Associate Professor of Statistics

LION-XM Computational Partners

http://gears.aset.psu.edu/hpc/systems/lionxm/

Pleiades Computational Cluster

The Pleiades Cluster, a partnership between Dr. Lee

Samuel Finn, Director of the Center for Gravitational

Wave Physics, and the GEaRS group, is dedicated to

the analysis of data from the Laser Interferometer

Gravitational-Wave Observatory (LIGO ), whose

goal is the detection of gravitational waves and their

use as a new tool of astronomical discovery.

128 Sun V60x servers

• Dual 2.8 GHz Intel Xeon Processors

• 2 GB memory

28 Dell 1750 servers

• Dual 3 GHz Intel Xeon Processors

• 2 GB memory

9 Dell PowerEdge 1750 file servers

18 Dell PowerVault 220S SCSI enclosures

• 35.1 TB aggregate storage

168-port Alcatel 7800 Gigabit Ethernet switch http://ligo.aset.psu.edu/

LION-XO Computational Cluster

80 Sun SunFire v20z Compute Servers

• Dual 2.4 GHz AMD Opteron Processors

• 8 GB of ECC RAM (Expandable to 16 GB)



• Quad 2.6 GHz AMD Opteron Processors

• 40 Servers with 16 GB of ECC RAM

• 12 Servers with 32 GB of ECC RAM


Silverstorm Infiniband high-speed interconnect

Dr. Antonios Armaou, Assistant Professor of Chemical Engineering

Dr. Susan Brantley, Director, Earth and Environmental Systems Institute

Dr. Barbara Garrison, Shapiro Professor of Chemistry

Dr. James Kubicki, Associate Professor of Geosciences

Dr. Janna Maranas, Assistant Professor of Chemical Engineering

Dr. Mark Maroncelli, Professor of Chemistry

Dr. Patrick Reed, Assistant Professor of Civil and Environmental Engineering

Dr. Mark Shriver, Associate Professor of Anthropology

Dr. Thorsten Wagener, Assistant Professor of Civil Engineering

LION-X0 Computational Partners

http://gears.aset.psu.edu/hpc/systems/lionxo/

LION-XA Computational Cluster

32 Dell PowerEdge 1850 Compute Servers

• Dual 3.6 GHz Intel Xeon EM64T Processors

• 8 GB of ECC RAM


Dr. Bryan Grenfell, Professor of Biology

Dr. Edward Holmes, Professor of Biology

Dr. David Lemmon, Center for Development and Health Research Methodology

Dr. Klaus Keller, Assistant Professor of Geosciences

Dr. Katernya Makova, Assistant Professor of Biology

Dr. Randen Patterson, Assistant Professor of Biology

LION-XA Computational Partners

http://gears.aset.psu.edu/hpc/systems/lionxa/

Hammer Computational Cluster


• Quad AMD Opteron 2.6 GHz Processors

• 32 GB of ECC RAM


Largely for interactive and code development work

http://gears.aset.psu.edu/hpc/systems/hammer/

Unisys ES7000 SMP Server

The Unisys ES7000 is targeted at serving research

needs that require either a large amount of

addressable memory or a large number of shared

memory processors.

2 ES7000 Domains

• 16 1.5 Ghz Itanium2 processors

• 6 MB of L3 Cache

• 32 GB of RAM

1 ES7000 Domain

• 32 1.6 Ghz Itanium2 processors

• 6 MB of L3 Cache

• 128 GB of RAM

What's next

• BlueGene, Cell processor, Galaxy servers (8-way dual core systems), GPUs

• HTX adapters (Pathscale/QLogic)

• Next gen Infiniband (Silverstorm)

Application Support

Finite Element Solvers: ABAQUS, ANSYS, FLUENT, LS-DYNA, MSC/Nastran

Mathematical and Statistical Libraries and Programs: ATLAS, BLAS, IMSL, LAPACK, Mathematica, Matlab, Intel MKL, PETSc, GNU R

Computational Chemistry and Materials Science: Gamess, Gaussian 03, NWChem, WIEN2K, Vasp

Computational Biology: BLAST, ClustalW, ClustalX, PHRED/PHRAP/Consed, RepeatMasker

Solid Modeling: I-DEAS, MSC/Patran

Compilers: Absoft ProFortran, GNU Pascal, IBM Java2, IBM XL Fortran Compiler, Intel C++ Compiler, Intel Fortran Compiler, Jikes, Lahey/Fujitsu Fortran 95 Pro, Portland PGI Compliers and Tools, SUN Java2

http://gears.aset.psu.edu/hpc/software/

Education/Training

• On demand teaching and learning

– where you want it– when you want it

– what you want

• Go where the research groups are and teach customized material

– location, location, location

– no excuses

What’s going well

• Build it together, not “build it and they will come”

• More frequent publication acknowledgement, authorship

• More frequent and prominent role in faculty recruitment

• Inroads to new departments

• Better platform diversity

• Graduate Minor alive and well

• Joint funding of staff, live in our eco-system

What needs help

• Institutionalization of the condo

• Space, power, cooling

• Solving the VO problem

• It’s a two front battle - grass roots and leadership

• Staff retention and recruitment

Visualization

• A bit harder to define – means different things to different faculty

• Different kinds of facilities on campus

• We try to fill the niches which aren't being met

• Guiding principle – lower the bar for adoption both in terms of cost and usability

System Description:• 12 projector tiled display

• High resolution (4096 x 2304 pixels)• Large format (7 x 11 ft.)

• 24 CPU/12 node Linux cluster• Allows display of significant detail throughout a larger spatial context• Provides a large format, high-resolution, multi- window workspace

Adaptable Software Development Environment:• Parallel clustered graphics applications• Hi-resolution tiling of OpenGL applications• Unified tiled Linux desktop• Linux, Chromium, DMX, VTK, OpenDX• Similar software environment now being applied in IEL clustered VR solution

Tiled Display WallScalable, Parallel, Open Source Graphics Development Environment

http://gears.aset.psu.edu/viz/facilities/displaywall/

System description:

• 1, 2 or 3-screen – Windows, Linux, Mac – flexible display • 2 + 1 screen Windows desktop VR and multimedia use• 3 screen panoramic VR using Linux clustered graphics• Unified Linux desktop for use of existing applications• Scalable, open source, development – Chromium, DMX, OpenSG, VRPN, Qt, JAVA3D, C++, VRML

Primary teaching and research facilitated:• Undergraduate design studio (Kalisperis)• Digital design media (Kalisperis, Muramoto) • NSF engineering education, new facility funded (Messner)• LARCH 3D perception/communication studies

Development items and extended impacts:• Pending proposals (AE/NSF/VaTech, Arch/Comm/AE)• IEL techniques applied in Sports Medical research• Investigating 3D telecollaboration and enhanced user interactions (e.g. in-room wireless, shared desktops among laptops & tablet PCs), touch screen, tracking)• Collaborative opportunities with private firms

ITS/SALA Immersive Environments Lab; A/E Engineering Education VR Lab Affordable, Accessible Projection Based VR for Research and Instruction.

http://gears.aset.psu.edu/viz/facilities/iel/

Stereo-enabled Multimedia Technology Classroom

System description:

• Stereo-enabled enhanced multimedia projection for

lecture use in a technology classroom

• Based on IEL two-screen Windows desktop design

• Collaboration among ITS units (GEaRS, CLC, MTSS)

Implementation status:

• Initial installation completed in 158 Willard (Fall 2003)

• Room is in the generally schedulable classroom pool

• Several demonstrative 3D applications installed

• Now in marketing and “friendly user” period to better

assess and accommodate faculty needs

http://gears.aset.psu.edu/viz/facilities/stereoclassroom/

Sports Medicine VR LabApplication description:

• Integration of VR display and graphics programming with motion tracking, force platform, EEG, fMRI and potentially other human performance measurement devices for kinesiology and psychology studies of perception, cognition and postural stability in normal and brain injured subjects• VR stimuli coding using open development tools, data analysis visualization using Matlab

Research tracks supported:

• Lasch building lab of adapted IEL design for working with concussed athletes (Slobounov, Sebastianelli, Ray) • Computer building Idesk lab for Parkinson’s patients (Newell, Haibach)• Adaptation of previous balance protocols for use during fMRI measurement at NIH (Slobounov)• Emotional image response posture studies (Ray)• NIH proposal (Slobounov) pending review

http://gears.aset.psu.edu/viz/facilities/sportsmed/

Visualization-Applications and Programming Consulting, Collaboration and Training

GEaRS staff provide local expertise for Penn State faculty on the application of visualization and VR systems, applications and programming toolkits within a range of research and teaching contexts. Current focus areas include:

• Graphics, modeling and data visualization applications (e.g. Tecplot, FormZ, VMD, Matlab)

• Open source data visualization toolkits and development environments (e.g. VTK, OpenDX)

• 3D graphics programming/VR development (e.g. OpenSG, VRPN, JAVA3D, OpenGL, VRML, X3D)

• Parallel graphics development (e.g. Chromium, DMX, Paraview)

• Languages (e.g. C++, Tcl/Tk, Qt, JAVA, Python)

Staff expertise is made available to faculty through individual consulting and/or collaboration, staff participation or assistance in credit course instruction, customized on-demand seminars for specialized disciplines or research groups, etc.

ACCESS Grid NodeThe ACCESS Grid (AG) node will support large-scale distributed meetings, collaborative work sessions, seminars, lectures, tutorials, etc. It enables group-to-group communications using multicast internet-working, voice and video teleconferencing, and desktop applications sharing among multiple remotely-located participants. The AG node enables rich multimedia exchanges among the participants, and is supported by a large number of organizations in academia and industry.

Recent conferences and meetings enabled:• 2nd and 3rd Virtual Conferences on Genomics and Bioinformatics, SC Global, HPC Seminars, SC2 Visualization Group, EMS WUN (Dr. DiBiase), AG Art (Dr. Thurman), National Internet2 Day

Adaptable solutions:• PIG setup/testing for individual access• Connectivity with TNS H.323 via VRVS• Currently adding Access Grid functionality to IEL for enhanced 3D telecollaboration

Http: //gears.aset.psu.edu/viz/facilities/gridnode/

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