s an d iego s upercomputer c enter cse190 honors seminar in high performance computing, spring 2000...
TRANSCRIPT
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
CSE 190
Honors Seminar in High Performance Computing, Spring 2000
Prof. Sid Karin
x45075
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
• Definitions• History• SDSC/NPACI• Applications
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Definitions of Supercomputers
• The most powerful machines available.• Machines that cost about 25M$ in year 2000 $.• Machines sufficiently powerful to model physical
processes including accurate laws of nature and realistic geometry, and including large quantities of observational/experimental data.
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Supercomputer Performance Metrics
• Benchmarks• Applications• Kernels• Selected Algorithms
• Theoretical Peak Speed• (Guaranteed not to exceed speed)
• TOP 500 List
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Misleading Performance Specifications in the Supercomputer Field
David H.BaileyRNR Technical Report RNR-92-005December 1,1992
http://www.nas.nasa.gov/Pubs/TechReports/RNRreports/dbailey/RNR-92-005/RNR-92-005.html
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
• Definitions• History• SDSC/NPACI• Applications
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Applications
• Cryptography• Nuclear Weapons Design• Weather / Climate• Scientific Simulation• Petroleum Exploration• Aerospace Design• Automotive Design• Pharmaceutical Design• Data Mining• Data Assimilation
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Applications cont’d.
• Processes too complex to instrument• Automotive crash testing• Air flow
• Processes too fast to observe• Molecular interactions
• Processes too small to observe• Molecular interactions
• Processes too slow to observe• Astrophysics
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Applications cont’d.
• Performance
• Price
• Performance / Price
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Theory Theory ExperimentExperiment
SimulationSimulation
Data-intensive
computing
(mining)
Data-intensive
computing (assimilation)
Numericallyintensive computing
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Supercomputer Architectures
• Vector• Parallel Vector, Shared Memory• Parallel
• Hypercubes• Meshes• Clusters
• SIMD vs. MIMD• Shared vs. Distributed Memory• Cache Coherent Memory vs. Message Passing• Clusters of Shared Memory Parallel Systems
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
The Cray - 1
• A vector computer that worked
• A balanced computing system• CPU• Memory• I/O
• A photogenic computer
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
1976: The Supercomputing “Island”
Today:A Continuum
Nu
mb
er o
f m
ach
ines
Performance
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
The Cray X-MP
• Shared Memory
• Parallel Vector
• Followed by Cray Y-MP, C-90, J-90, T90…..
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
The Cray -2
• Parallel Vector Shared Memory
• Very Large Memory (256 MW)
• Actually 256K MW = 262 MW
• One word = 8 Bytes
• Liquid Immersion cooling
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Cray Companies
• Control Data
• Cray Research Inc.
• Cray Computer Company Inc.
• SRC Inc.
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Thinking Machines
• SIMD vs. MIMD
• Evolution from CM-1 to CM-2
• ARPA Involvement
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
1st Teraflops System for US Academia“Blue Horizon”
• 1 TFLOPs IBM SP• 144 8-processor compute nodes• 12 2-processor service nodes• 1,176 Power3 processors at 222 MHz• > 640 GB memory (4 GB/node),
10.6GB/s bandwidth, upgrade to > 1 TB later
• 6.8 TB switch-attached disk storage
• Largest SP with 8-way nodes
• High-performance access to HPSS
• Trailblazer switch (current ~115MB/s bandwidth) interconnect with subsequent upgrade
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
UCSD Currently #10 on Dongarra’sTop 500 List
• Actual Linpack benchmark sustained 558 Gflops on 120 nodes
• Projected Linpack benchmark is 650 Gflops on 144 nodes
• Theoretical peak 1.023 Tflops
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
First Tera MTA is at SDSC
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Tera MTA• Architectural Characteristics
• Multithreaded architecture• Randomized, flat, shared memory• 8 CPUs, 8 GB RAM now going to 16 (later this year)• High bandwidth to memory (word per cycle per CPU)
• Benefits• Reduced programming effort: single parallel model for one
or many processors• Good scalability
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
SDSC’s road to terascale computing
108
109
1010
1011
1012
1013
1014
1980 1985 1990 1995 2000 2005
Peak s
peed
(fl
op
s)
Year installed
World's fastestsupers
SDSC'svectorsupers
SDSC'sscalablesupers
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
ASCI Blue Mountain Site Prep
12,000 sq ft
120 ft
100 ft
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
ASCI Blue Mountain Site Prep
12,000 sq ft
120 ft
100 ft
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
ASCI Blue Mountain Facilities Accomplishments
• 12,000 sq. ft. of floor space• 1.6 MWatts of power• 530 tons of cooling capability• 384 cabinets to house the 6144 CPU’s• 48 cabinets for metarouters• 96 cabinets for disks• 9 cabinets for 36 HIPPI switches• about 348 miles of fiber cable
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
ASCI Blue MountainSST System Final Configuration
Cray Origin 2000 - 3.072 TeraFLOPS peak 48X128 CPU Origin 2000 (250MHz R10K) 6144 CPUs: 48 X 128 CPU SMPs 1536 GB memory total:
• 32 GB memory per 128 CPU SMP
76 TB Fibre Channel RAID disks 36 x HIPPI-800 switch Cluster Interconnect To be deployed later this year: 9 x HIPPI-6400 32-way switch Cluster Interconnect
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
ASCI Blue MountainAccomplishments
• On-site integration of 48X128 system completed (including upgrades)
• HiPPI-800 Interconnect completed
• 18GB Fiber Channel Disk completed
• Integrated Visualization (16 IR Pipes)
• Most Site Prep completed
• System integrated into LANL secure computing environment
• Web based tool for tracking status
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
ASCI Blue MountainAccomplishments-cont
• Linpack - achieved 1.608TeraFLOPs• accelerated schedule-2 weeks after install• system validation• run on 40x126 configuration• f90/MPI version run of over 6 hours
• sPPM - turbulence modeling code
• validated full system integration• used all 12 HiPPI boards/SMP and 36 switches• used special “MPI” HiPPI bypass library
• ASCI codes scaling
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ASCI Codes Parallel Scaling
0
512
1024
1536
2048
2560
3072
3584
4096
4608
5120
5632
6144
6656
Time
CrestoneShavanoBlancaTellurideEolusAnteroEng. Apps
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Summary
• Installed ASCI Blue Mountain computer ahead of schedule and achieved Linpack record two weeks after install. ASCI application codes are being developed and used.
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Half
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Rack
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Trench
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
• Connect any pair of the DSM computers through the crossbar switches
• Connect directly only computers to switches, optimizing latency and bandwidth (there are no direct links DSM<==>DSM or switch<===>switch)
• Support a 3-D toroidal 4x4x3 DSM configuration by establishing non-blocking simultaneous links across all sets of 6 faces of the computer grid
• Maintain full interconnect bandwidth for subsets of DSM computers (48 DSM computers divided into 2, 3, 4, 6, 8,12, 24, or 48 separate, non-interacting groups)
Network Design Principles
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
1 2 3 4 5 6
6 Groups of 8 Computers each
18 16x16 Crossbar Switches
18 Separate Networks
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
sPPM Hydro on 6144 CPUs
Problem Subdomain:8x4x4 process layout128 CPUs/1 DSM)12 HiPPI-800 NICs
Router CPU on Neighbor SMP
1-HiPPI-800 NICRouter CPU
Problem Domain:(4x4x3 DSM layout48 DSMs/6144 CPUs)
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
sPPM Scaling on Blue Mountain
0
1000
2000
3000
4000
5000
6000
7000
0 1000 2000 3000 4000 5000 6000 7000
Number of Processors
Spe
edup
0%
20%
40%
60%
80%
100%
Linear Speedup %Efficiency
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
• Definitions• History• SDSC/NPACI• Applications
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
SDSCSDSCA National Laboratory for Computational
Science and EngineeringA National Laboratory for Computational
Science and Engineering
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
A Distributed National Laboratory for Computational Science and
Engineering
A Distributed National Laboratory for Computational Science and
Engineering
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Continuing Evolution
Individuals
SDSC NPACINPACIResources
EducationOutreach & Training
Resources
Partners
1985 2000
Technology & applications
thrusts
Enabling technologies
Applications
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
NPACI is a Highly Leveraged National Partnership of Partnerships
46 institutions
20 states
4 countries
5 national labs
Many projects
Vendors and industry
Government agencies
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Accelerate Scientific Discovery Through the development
and implementationof computationaland computerscience techniques
Mission
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
• Collect data from digital libraries, laboratories, and observation
• Analyze the data with models run on the grid
• Visualize and share data over the Web
• Publish results in a digital library
Changing How Science is Done
Vision
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Embracing the Scientific Community
• Capability Computing• Provide compute and information resources of exceptional
capability
• Discovery Environments• Develop and deploy novel, integrated, easy-to-use
computational environments
• Computational Literacy• Extend the excitement, benefits, and opportunities of
computational science
Goals: Fulfilling the Mission
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
NPACI Objectives
• Deploy teraflops-scale computers• Create a national metacomputing
infrastructure• Enable data-intensive computing• Create persistent intellectual infrastructure• Conduct outreach to new communities• Advance computing technology in support
of science
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Partnership Organizing Principle: “Thrusts”
Molecular ScienceNeuroscience
Earth Systems ScienceEngineering
Metasystems Programming Tools &
EnvironmentsData-intensive ComputingInteraction Environments
Computational LiteracyEOT
Discovery Environments
APPLICATIONSDiscovery Environments
TECHNOLOGIES
Capability Computing
RESOURCES
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Technology Thrusts
MetasystemsMetasystems Programming Tools and
Environments
Programming Tools and
Environments
Data-Intensive
Computing
Data-Intensive
Computing
Interaction Environments
Interaction Environments
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Applications ThrustsNeuroscienceNeuroscience
EngineeringEngineering
Molecular Science
Molecular Science
Earth Systems Science
Earth Systems Science
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Projects Meld Applications and Technology
Data-IntensiveComputing
+Neuroscience
Brain databasesBrain databases
Metasystems andParallel Tools
+Engineering
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
• Definitions• History• SDSC/NPACI• Applications
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Modeling Galaxy Dynamics and Evolution
• Project Leaders• Lars Hernquist, Harvard and
John Dubinski, U Toronto
• Stuart Johnson and Bob Leary, SDSC SAC Program
• First images from Blue Horizon Simulation• 24M particles = 10M stars + 2M
dark matter halo in each galaxy• Working on 120M particle run
• Run on all 1,152 processors during acceptance
Animation - Collision between Milky Way and Andromeda
“Due to SAC efforts, our simulations run two to three times faster,we can ask more precise questions and get better answers” ...Hernquist
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Bioinformatics Infrastructure for Large-Scale Analyses
• Next-generation tools for accessing, manipulating, and analyzing biological data• Russ Altman, Stanford University• Reagan Moore, SDSC
• Analysis of Protein Data Bank, GenBank and other databases
• Accelerate key discoveries for health and medicine
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Protein Folding in a Distributed Computing Environment
• Simulating protein movement governing reactions within cells
• Andrew Grimshaw, U Virginia• Charles Brooks, The Scripps
Research Institute
• Bernard Pailthorpe, UCSD/SDSC
• Computationally intensive• Distributed computing
power from Legion
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Telescience for Advanced Tomography Applications
• Integrates remote instrumentation, distributed computing, federated databases, image archives, and visualization tools.• Mark Ellisman, UCSD• Fran Berman, UCSD• Carl Kesselman, USC
• 3-D tomographic reconstruction of biological specimens
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
MICE: Transparent Supercomputing• Molecular Interactive
Collaborative Environment
• Gallery allows researchers, students to search for, visualize, and manipulate molecular structures
• Integrates key SDSC
technological strengths • Biological databases• Transparent
supercomputing• Web-based Virtual Reality
Modeling Language
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
The Protein Data Bank• World’s single scientific resource for
depositing and searching protein structures
• Protein structure data growing exponentially• 10,500 structures in PDB today• 20,000 by the year 2001
• Vital to the advancement of biological sciences
• Working towards a digital continuum from primary data to final scientific publication
• Capture of primary data from high-energy synchrotrons (e.g. Stanford Linear Accelerator Center) requires 50Mbps network bandwidth
1CD3: The PDB’s 10,000th structure.
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
• Biodiversity Species Workshop• Web interface to modeling tools
• Provides geographic, climate, and other base data
• Species Analyst• Compiles data from on-line
museum collections
• Scientists can focus on the scientific questions
• NPACI partners U Kansas, U New Mexico, and SDSC
Biological-scale Modeling
Predicted distribution of the mountain trogon. Data points (pins) are from 14 museum collections.
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Digital Galaxy• Collaboration with Hayden
Planetarium• American Museum of
Natural History
• Support from NASA
• Linking SDSC’s mass storage to Hayden Planetarium requires 155 Mbps
• MPIRE Galaxy Renderer • Scalable volume visualization
• Linked to database of astronomical objects
• Produces translucent, filament-like objects
An artificial nebula, modeled after a planetary nebula
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
Looking out for San Diego’s Regional Ecology• Unique partnership
• 31 federal, state, regional,and local agencies
• John Helly, et al., SDSC
• Combines technologies and multi-agency data• Sensing, analysis, VRML• Physical, chemical, and
biological data
• Web-based tool for science and public policy
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SAN DIEGO SUPERCOMPUTER CENTER
CSE190
AMICO: The Art of Managing Art• Art Museum Image Consortium
(AMICO) • 28 art museums working toward
educational use of digital multimedia
• Launch of the AMICO Library includes more than 50,000 works of art• AMICO, CDL, SDSC
• XML information mediation
• SDSC SRB data management
• Links between images, scholarly research, educational material
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CT Image(512x512x250)
MacNCTPlanTreatment Planning
Software
BeamCharacteristics
VoxelEnergy
Deposition
MCNP ParticleTransport Simulation(Typically 21x21x25)
MIT Nuclear Engineering Department
Beth Israel Deaconess Medical Center, Boston
Boron Neutron Capture Therapy
Beam Port
Borated Tumor
EpithermalNeutrons(1013/s)
BNCT & The Treatment Planning Process
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Typical MCNP BNCT simulation:• 1 cm resolution (21x21x25)• 1 million particles• 1 hour on 200 MHz PC
ASCI Blue Mountain MCNP simulation:• 4 mm resolution (64x64x62)• 100 million particles• 1/2 hour on 6048 CPUs
ASCI Blue Mountain MCNP simulation:• 1 mm resolution (256x256x250)• 100 million particles• 1-2 hours on 3072 CPUs
MCNP BNCT Simulation Results