san diego supercomputer center academic associates program (aap) at san diego supercomputer center...

SAN DIEGO SUPERCOMPUTER CENTER

Academic Associates Program (AAP)at

San Diego Supercomputer Center (SDSC)

Subhashini Sivagnanam AAP Liaison, SDSC


SDSC: An international leader in high-end computing and data management

• Founded in 1985 • Affiliated with UCSD• NSF-funded supercomputer

center• Provides resources to national

academic and non-profit community above and beyond what an individual university can provide

• Free usage to academics/non-profits


• Employs nearly 400 researchers, staff and students

• Leading edge site for NSF’s National Partnership for Advanced Computational Infrastructure (NPACI)

• One of the sites of NSF’s TeraGrid/ETF project

• Home of many associated activities including

• Protein Data Bank• Alliance for Cell Signaling• Cooperative Association for Internet Data Analysis

(CAIDA)• High Performance Wireless Research and

Education Network (HPWREN)• Geosciences Network (GEON)• Joint Center for Structural Genomics etc.

SDSC


The Mission of SDSC

To extend the reach of scientific accomplishments by providing

• high-performance hardware technologies

• integrative software technologies

• deep inter-disciplinary expertise to the community


AAP: Pathway to collaborations since 1995

• Academic Associates Program, formerly known as the Block Grant program, was started in 1995.

• Goal is to provide University of California (UC) researchers access to supercomputing time and resources at the San Diego Supercomputer Center (SDSC).


Variety of benefits

• Early access candidates to new SDSC systems● Under the Academic Associates Program, SDSC hardware resources

may also be used for classes taught by UC faculty● An internship program (1-2 weeks) at SDSC for selected research

groups; one per campus per year● The Strategic Applications Collaborations (SAC) program pairs

academic researchers with SDSC staff to accelerate the researchers' efforts on relatively short time scales (3-12 months).


Few Campuses currently enrolled in AAP

• UC Berkeley

• UC Davis

• UC Irvine

• UC Los Angeles

• UC Riverside

• UC Santa Barbara

• UC Santa Cruz

• UC San Diego:➢ Campus➢ Scripps➢ School of Medicine

• UC San Francisco


Resources available through AAPComputing Resources

• DataStar : Our most powerful machine with major expansion plans

➢ 10 teraflops IBM Power4-based system with total memory of 4.2 terabytes

➢ 176 8-way IBM p655 nodes, 16 GB memory per node

➢ 4 32-way IBM Regatta p690 nodes, with 128 GB memory per node

➢ All nodes connected via IBM Federation high-performance interconnect

➢ Ability to write output to General Parallel File System (GPFS)


• 4 teraflops IA-64 system

• 256 IBM cluster nodes

• Each node has dual 1.5 GHz Intel® Itanium® 2 processors

• 4 gigabytes (GBs) of physical memory per node.

● TeraGrid : Unified user environment across heterogeneous resources


TeraGrid Resource Partners


● Blue Gene: The new kid on the block

• 4.6 teraflops IBM PowerPC system

• 1,024 compute nodes and 128 I/O nodes

• Each node consists of two PowerPC processors that run at 700 MHz

• Processors share 512 MB of memory

• First academic Blue Gene system

• Invite you to run on a novel platform

• Cheaper than DataStar


Software: variety of HPC software available on our compute resources

● Installed HPC software covers a range of disciplines in science and engineering.

● Large-scale data collections, such as the Protein Data Bank (PDB), National Virtual Observatory (NVO), and the 2-Micron All Sky Survey (2MASS) are available, together with user-friendly software for accessing large data collections.

● SDSC also offers a software toolkit, ROCKS, for building, monitoring, and using state-of-the-art computational clusters, now in use at more than 200 sites.

● A variety of data analysis, mining and visualization tools


• Production software➢ Applications in variety of research areas:

Biomolecular Structure Molecular Mechanics/Dynamics Quantum Chemistry Eng. Structural Analysis Finite Element Methods Fluid Dynamids Numerical Libraries Linear Algebra Differential Equations Graphics/Scientific Visualization Grid Computing

DataStar: http://www.sdsc.edu/user_services/applications/cgi-bin/applications.cgi

TeraGrid: http://www.sdsc.edu/teragrid/guide.html#sw


Storage Resources

• Tape Storage: ➢ High Performance Storage System

(HPSS) stores more than 1.4 PB of data in approximately 20 million files

➢ Capacity to store 6 PB of data

• Disk Storage:➢ 1.1 Petabytes online disk storage


Training

• Workshops, Training classes➢ Summer Institute each year

provide researchers with an introduction to the concepts and tools available in established and new technologies

➢ Coming soon: So.Cal & No.Cal AAP workshop

• Live web cast of CyberInfrastructure (CI) related training, talks and cross-site meetings


Support

• Technical support from SDSC UserServices through online/ phone consulting (9AM - 5PM PST)

• Help provided from logging in to optimizing/parallelizing code

Email us: [email protected]

Talk To A Consultant

1-866-336-2357 (Toll-Free)


How to apply• UC Researcher can request on-line computing time by visiting

http://www.sdsc.edu/user_services/aap/

REVIEW PROCESS• Apply online using the AAP Application Form.• AAP administrator/coordinator approves/denies request (varies by

campus).• You will receive a packet within a week containing your login and

information to get you started. • Each campus has access to limited amount of computing time (CPU

hours on SDSC machines) under AAP.


Web page: New Features

• A renewal form to make it easy for users to extend their access to resources.

• An improved FAQ to help users get started and resolve questions.

• A feedback form to encourage user suggestions to further improve the program.

• Help with selecting the right computing or storage resource, which many users requested.


Strategic Applications Collaborations• SDSC staff paired with domain scientists for 3-12 month projects

• Past successes include• Biomedical imaging (U Michigan)• Brain mapping/computational anatomy (Johns Hopkins)• Computational modeling of the cochlea (U Michigan)• Molecular dynamics in large biomolecular systems (UCSF, TSRI)• SEQUEST (U Washington)• SCWRL (Fox Chase Cancer Center)• Protein Structure prediction (UCSD)• Protein fold recognition and classification (UCSD)


Data Central : Data Collection and DataBase hosting• Hardware:

➢ Online disk➢ Database servers➢ Archival

• Software:➢ SRB: Client-server middleware that provides a uniform interface

for connecting to heterogeneous data resources over a network and accessing replicated data sets

➢ R: Opensource tool for statistical computing and graphics➢ DB2: Parallel Relational Database Management System ➢ MySQL: Open source Relational Database Management System

• Long-term storage (tape and disk)

• Data collection & Database hosting

http://datacentral.sdsc.edu


Take Advantage of CyberInfrastructure• Availability of globally accessible information and computational

infrastructure to drive research and education

• Organize aggregate of technologies that enable us to access and integrate today's

➢ information technology resources data➢ computation➢ communication➢ visualization➢ networking➢ scientific instruments➢ expertise to facilitate strategic objectives within science, engineering and business.

• SDSC supported by new Office of Cyberinfrastructure reporting directly to the director of NSF


Synthesis Center: Collaboration space for computational science and

visualization• Groups of collaborating scientists and engineers come together for face-to-

face sessions to directly address science questions using cyberinfrastructure tools

• Unique environment of wall-sized tiled and stereo display systems at SDSC

• Sessions may run for a day, a few days, or even a few weeks

http://www.syncenter.org/


Visualization Services : Not just beautiful, also educational

• Provides assistance, innovative tools and representative images that enable new insights and advances.

• Visualization Service Grid• Cancer Center Visualizations• Cosmological models of the early universe• Stereographic (3-D) image presentations for scientific visualization

• Customized visualization solutions• Gaming Grid for Research and Education• Tools

• VISTA—A volume renderer with camera and animation capabilities.• Maya—A three-dimensional animation tool

http://visservices.sdsc.edu/


UCSD Cancer Center Visualizations


TeraShake


Volume Visualization of the Orion NebulaThe San Diego Supercomputer Center and

The American Museum of Natural History Hayden Planetarium

Hubble Space Telescope images of the Orion Nebula and the HST-10 proplyd.


SDSC is much more...

• CHRONOS - Works with the Earth science community to develop a dynamic, interactive and time-calibrated network of databases and visualization and analytical methodologies for sedimentary geology and paleobiology.

• Cooperative Association for Internet Data Analysis (CAIDA) - Provides tools and analyses promoting the engineering and maintenance of a robust, scalable global Internet infrastructure.

• Protein Data Bank (PDB) - the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.


Major Projects Contd..

• NEES it - A service-focused organization that operates and supports the extensive IT infrastructure for the Network for Earthquake Engineering Simulation (NEES) Collaboratory.

• Science Environment for Ecological Knowledge (SEEK) - A five year initiative designed to create cyberinfrastructure for ecological, environmental, and biodiversity research and to educate the ecological community about ecoinformatics.

• Southern California Earthquake Center (SCEC) - Gathers and integrates new information about earthquakes in Southern California, into a comprehensive and predictive understanding of earthquake phenomena.


GEON

Finding Answers to Vital QuestionsEstimating flood and landslide potential, groundwater problems, volcanic activity, and soil quality—all with the best data available Accelerating scienceThrough the GEON Portal, researchers will be able to discover relationships of the type that led to plate tectonics in days instead of years Democratizing Grid Technologies

Building cyberinfrastructure for a wide range of users, from scientists and educators to policymakers and engineers

Building Reusable CyberinfrastuctureA model for the Earth Sciences and beyond

Enabling Integrated Views of the Earth System by


3D Earthquake Modeling in GEON


BIRN

NIH NCRR award to …• Enhance access to 4T – 8T MRI & other

imaging modalities for neuroscience studies• Enhance telecommunications & telemedicine

efforts for GCRC sites, co-located with NCRR imaging centers

• Develop bioinformatics tools & data fusion for PET, CAT, EEG, MRI

• Extend to all NCRR Resource sites & expand model to other areas

Partners• National Institutes of Health (NIH)• National Science Foundation (NSF)• UCSD• SDSC


We are interested in collaborating with you

• Questions and Suggestions• Email : [email protected]• AAP : http://www.sdsc.edu/user_services/aap


TeraGrid Resources

YesYesYesInstruments

10

CHI

30

LA

10

CHI

30

CHI

10

ATL

30

CHI

10

CHI

30

LA

30

CHINetwork

(Gb/s,Hub)

2 PB6 PB2.4 PB3 PB1.2 PBMass

Storage

YesYesYesYesYesVisualization

YesYesYesYesYesData Collections

50 TB540 TB150 TB1 TB600 TB32 TB155 TB20 TBOnline Storage

IA-32(6.3 TF)

Sun (Vis)

Itanium2(4.4 TF)

Power4+(1.1 TF)

Hetero (1.7 TF)

XT3(10 TF)TCS (6 TF)Marvel(0.3 TF)

IA-32(0.3 TF)

Itanium2 (10 TF)

SGI SMP(6.5 TF)

Itanium2(0.2 TF)

IA-32(2.0 TF)

Itanium2(0.8 TF)

Itanium2(0.5 TF)

IA-32(0.5 TF)

Compute

Resources

TACCSDSCPurduePSCORNLNCSAIUCaltechANL/UC

Partners will add resources and TeraGrid will add partners!


The TeraGrid Strategy

• Building a distributed system of unprecedented scale–40+ teraflops compute

–1+ petabyte storage

–10-40Gb/s networking

• Creating a unified user environment across heterogeneous resources–User software environment,

User support resources.

–Created an initial community of over 500 users, 80 PI’s.

• Integrating new partners to introduce new capabilities– Additional computing,

visualization capabilities

– New types of resources- data collections, instruments

Make it extensible!

san diego supercomputer center academic associates program (aap) at san diego supercomputer center...

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