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PERFORMANCE COMPUTING FOR RESEARCH
Frank J. Wessel, Tony Soeller, Evan Klinger, and Afshin Mahini
Research Computing Support
Network and Academic Computing Services
University of California, Irvine
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NETWORK AND ACADEMIC COMPUTING SERVICES
(http://www.nacs.uci.edu)
• NETWORK & TELEPHONE– Network, wireless, remote user access– Telephone, cell sites, life-line modem– Campus directory services
• CAMPUS WIDE SUPPORT– Response center, training,– Instructional computing,– Software licensing, – Web development,– Calendaring, mailing lists,– Department support,– Research computing support
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RESEARCH COMPUTING SUPPORT http://www.nacs.uci.edu/rcs
• MISSION:– To facilitate the efficient use of information
technologies and campus resources in the UCI research community
• OBJECTIVES– Extend NACS support to research, – Promote awareness of campus resources,– Provide custom assistance as needed– Large and small “consumers”
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MOTIVATION
• Increasing demands placed on researchers– Discipline specific needs– Technology/hardware/software trends– Expertise available within NACS/elsewhere
• Centralized vs. distributed support – More efficient use of resources– Machine room, networking, etc– Campus collaborations help win grants
• Shared expertise – Awareness of projects and implementations– Disseminate information to campus– Promote researcher liaisons
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RESEARCH “DEMOGRAPHICS” AT UCI
• Few examples of centralized support
• Mostly at the department/IRU/ORU level
• School support largely for Beowulf clusters
• SMP installations are few
• SDSC (UCSD) is a notable exception
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Education
ICSGSM Arts
SocEco
Engineering
Bio Sci SocSciPhysSci
Humanities
CoM
0
20
40
60
80
100
120
140
160
180
200
# FTE Faculty Vs. Research Funds-by Academic Unit '01-'02
Res. Funds $M
# FTE Reg. Faculty
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UCI PERFORMANCE COMPUTING RESOURCES
• NACS– ESMF supercomputer, 7x8cpu, 32cpu– Krein 32cpu, SGI Origin 2000– MPC - 200+cpu Beowulf– GRADEA - 16cpu Beowulf
• SDSC/NPACI– Academic Associates Program– “Access grants” for HPC resources
• Other – NCAR, NCSA, DoE Labs, etc
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NACS MACHINE ROOM
4500 sq. ft. floor spaceClimate controlled24/7 operator attended100 kVA UPS
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krein.math32p
SGI Origin 2500
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MPC Beowulf Clustermpc.uci.edu
16p Athlons150p “night nodes”52p dual Opterons
GigE
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mpc.uci.edu
• Campus collaboration with researchers– 25% “donation” to mpc– 75% dedicated queue– Free sys. admin., – Free “co-location” – Software– Racks/switches
• Installed software– OPBS, MPICH, PGI CDK, Gaussian, SAS,– Mathematica, Fluent, MATLAB, IDL,– CFDACE+,IMSL, etc.
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Computational Environmental Sciences LaboratoryDepartment of Mechanical and Aerospace Engineering
Air Quality Modeling of the South Coast Air Basin of California Tyler August Reid, Marc Carreras, Prof. Donald Dabdub
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The CIT Airshed Model
( ) ( )chemistry
km
aerosol
km
kssources
kmk
mkm
km
t
Q
t
Q
t
QQKuQ
t
Q⎟⎟⎠
⎞⎜⎜⎝
⎛+⎟⎟
⎠
⎞⎜⎜⎝
⎛+⎟⎟
⎠
⎞⎜⎜⎝
⎛+∇⋅∇=⋅∇+
∂
∂
∂
∂
∂
∂
∂
∂
sin/
1100 m
40 m150 m
0 m
310 m
670 m
80 Cells
30Cells
47 Gas Species152 Aerosols: 19 species, 8 sizes121 Reactions
47 Gas Species152 Aerosols: 19 species, 8 sizes121 Reactions
Each Cell: 5 x 5 km2
General Dynamics Equation:
Aero
sol P
hase
O3NO3
NO
O3
hv
HO2
H2ONH3
HNO3
SO2
H2SO4
OH
CO, RH, RCHO
SOA
N2O5
NO3 NO2
Aerosol Phase
H2O
RO2
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One Time Purchase vs. 4 Sequential Quarterly Purchases
Throughput
1218
2436
phased purchase
one-time purchase
1200
1800
2400
3600
672
1447
2222
3772
0
500
1000
1500
2000
2500
3000
3500
4000
Months
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EARTH SYSTEM MODELING FACILITY (
ESMF)•7 each, p655 8-CPU MCMs, 1.5 GHz, 16 GB (32GB)
•1 each, p690 32-CPU SMP cluster, 1.5 GHz, 64 GB
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32 TB Disk:RAID 5 +LUSTRE
SINTINAGFS
GNBD
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ESMF MISSION
To simulate climate change and answer questions how global warming, man-made pollutants, polar-ice movements, chemical cycles, etc. impact the Earth and its inhabitants over future decades and centuries.
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ESMF
7EACH, 8-CPU, P655s, 1 EACH P690, 32 TB RAID STORAGE
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Power4 Architecture
Shared L2
Chip to chip
8-way SMP on a Multichip Module
(MCM):The basic processor building block of the
pSeries 690
40+GFLOPS /MCM
World's fastest 64-bit processor
First SMP server system-on-a-chip
Reliability, Availability, Serviceability on the processor
IBM copper and SOI technology delivers more performance at lower power levels, saving on licensing fees and operating costs
POWER 4: The Heart of pSeries' Performance Advantage
2000 Technology Award "Advanced Chip Projects"From: Micro Design Resources/Microprocessor Report
POWER464-bit 1.1 or 1.3GHz
Microprocessor
LPAR
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ESMF ACQUISITION
• Earth System Modeling Facility (ESMF)• High Performance (Super) Computer
– Benchmarked on CCSM and CAM codes
• High Performance Disk System- 32 TB disk, single name-space
• Network Interconnect– As fast as possible
• Purchase Price $1,000,000.00– Including tax, maintenance, and shipping
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ESMF HARDWAREACQUISITION (contd.)
• 12/20/02 - MRI Pre-proposal to RGS• 1/23/03 - Proposal submitted to NSF• 5/29/03 - NSF award to UCI• 7/16/03 - RPF issued to vendors• 8/5/03 - Bidders conference• 9/17/03 - Bids received
– HP - 96 CPU, dual I2 Beowulf cluster, w/ Myrinet– SGI - 96 CPU Altix, I2 SMP cluster– IBM - 88 CPU, Power 4+, SMP cluster– SUN - requested private negotiations
• 10/1/03 - IBM selected• 12/1/03 - ESMF delivered
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Who
Prof. Charles Zender
Atmospheric Physicist
Microphysical and general circulation models
Trace gases, aerosols,dust, clouds
Satellite remote sensing
Open Source Initiative
"The ESMF IBM Supercomputer will provide sustained
compute capability, speed and storage capacity necessary to best meet the challenges involved in understanding the atmosphere and its interactions with the Earth system, as well as developing methods for predicting its behavior. The ESMF will also allow researchers to pursue data-
intensive research utilizing the large geophysical datasets from current and next generation
numerical models and satellite observations.
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Who
Prof. J. Keith Moore
Oceanographer
Biogeochemical cycles
Marine biota influence
Marine ecosystem dynamics
Satellite remote sensing
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HIPERWALL
32 TB RAID
PRO-MICRO
7 IBM P655
CLUSTERS
1 IBM P690
CLUSTER
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Who
• Prof. Falko Kuester• Scientific visualization• Real-time computer graphics• Virtual reality• Collaborative virtual environments• Distributed/remote visualization• Biomedical imaging• Computer aided design
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Who
• Prof. Steven Jenks• Parallel and distributed
computing• Large-scale distributed
memory systems• Thread migration to exploit
locality• Real-time distributed systems
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Consortium of Universities for the Advancement of Hydrologic Science,
Inc.(CUASHI)
• Proposal to CUASHI to support the national community of hydro-geologists
• UCI is one of four finalists
• Faculty in Civil and Environmental Engineering and Earth System Science
• Develop a National Center for Hydro-Geologic Synthesis (NCHS)
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NATIONAL CENTER FOR HYDRO-GEOLOGIC SYNTHESIS
• Real-time integration of process models and visualizations
• Capable of rapidly deploying evolving data models
• Provide and online collaborative environment for complex modeling.
• http://hydis8.eng.uci.edu/hydis-unesco/
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Who
• Prof. Saroosh Saroosian• Hydrology• Hydrometeorology• Hydroclimate modeling• Remote sensing• Water sources management
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Who
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• Prof. Bisher Imam• Hydro-logic data and
information systems• Watershed processes• GIS modeling and analysis
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RCS CONSULTING
• Software specific requests• Grant-writing activities
– Hardware, software
• New technologies– Videoconferencing– Visualization– Benchmarking
• Training• Access to research forums
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TRAINING
• NACS RCS summer workshops
• Workshop1 - Supercomputing resources and HPC programming
• Workshop2 - Data analysis and visualization
• Workshop3 - Computational software in biological and medical research
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NACS RESEARCH SOFTWARE
• NACS “licensed software”
• Coordinate “critical-mass usage”
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• Mathematical– Mathematica– Matlab– Maple– IMSL (on GradEA)
• Statistical– SAS– SPSS– SigmaPlot/SigmaStat– S-Plus
• GIS & Image Processing– ArcGIS / ArcIMS / ArcPad– IDL (on GradEA)– Matlab
• Laboratory– LabVIEW– Matlab
• Bioinformatics– Lasergene
NACS RESEARCH SOFTWARE
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MATLAB: Import DataMATLAB: Import DataImporting from Excel:
1) Goto File2) Click on Import3) Select the desired file4) Click “ok”5) And Import Wizard will pop up6) Preview to see if data are
imported correctly7) Click “Finish”
Data are loaded in workspace
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MATLAB Plotting BasicsMATLAB Plotting Basics
x = 0:0.05:6 plot(x, cos(x),'k',x,1./cosh(x),'k',[4.73 4.73],[-1 1],'k')
xlabel('x')
ylabel('Value of functions')
title('Visualization of two intersecting curves')
text(4.8,-0.1,'x=4.73')
text(2.1,0.3,'1/cosh(x)')
text(1.2,-0.4,'cos(x)')
legend('cos(x)', '1/cosh(x)',3)
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Octave
Open source mathematical package
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OpenDXOpen source visualization package
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Most earth and space science data sets contain multiple parameters. Along with the temperature data there are horizontal winds. To add this data to the picture, place an Import module on the canvas
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CONCLUSIONS
Be involved, understand research needs
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Remain flexible, be willing to compromise
Think big, take risks
Expand your horizons, but be patient
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?????