High Performance
Computing at
University of Hawaii
Susan T. Brown, Ph.D.
Director, HPC Outreach
Office of the CIO, ITS
Overview
What IS HPC?
 The HPC Community
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 Across
the Islands
 Relationship with MHPCC
Programs
 Stay in touch
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High Performance Computing
(HPC)
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What currently
constitutes HPC?
Clusters?
Parallel?
How many CPUs?
Grid computing?
Vector computing?
The UH HPC Community
Maui High Performance Computing
Center (MHPCC)
History in Brief
MHPCC is an Air Force Distributed Center
for HPC
 Hires out for administrative management
from University of Hawai’i through RCUH
 Faculty, staff, and students access and
use facility through and Educational
Partnership Agreement (EPA).
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MHPCC Equipment
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Squall
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Hurricane
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No DoD related data or codes
No DoD work to be performed on Squall
32-processor cluster
SSH to use
National Agency Check (NAC) not required
Phasing out within a month
10 P4 nodes, 320 processors
SSH to use
National Agency Check (NAC) not required
Came online March 2007
Jaws
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5,120 processor Dell PowerEdge
NAC required for account
Accessed via Kerberos and SecureID
Number 11 on the Top 500 List
Details on equipment can be found at
http://www.mhpcc.hpc.mil/doc/Doc.html
Note: Other machines are
located at MHPCC and
are used only by the Air
Force, i.e., not available
for UH use.
UH MHPCC users
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Dr. Duane Stevens, Heleakala Weather Center, WRF Modeling
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Dr. Maqs Alam, Biochemistry, Advanced Studies in Genomics, Proteomics
and Bioinformatics
Dr. Neil Frazer, Oceanography
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Grad Student, Yuewei Liu
Dr. Chitteranjan Ray, Civil and Environmental Engineering
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Eva-Marie Nosal, Grad Student, The Kohola Project
Dr. Albert Kim, Civil and Environmental Engineering, The PAM Group
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Guangxia Cao, Grad Student
Dr. Kevin Roe, MHPCC staff collaborator
Kim Kido, Undergrad Student, FEMWATER model
Dr. Patricia Fryer, Geology & Geophysics
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Grad Student, Tom Fedenczuk, Analysis of Data from Mud Volcanoes!
The UH HPC Community
Maui Community College
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Offers ECET (Electronic and Computer
Engineering Technology) Program
 High
Performance Computing Speciality
 Trains systems operators and center support staff
 Currently about 50 enrolled
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18-node Dell cluster for teaching purposes
(cluster sysadmin and parallel programming)
The UH HPC Community
Dr. Sevki Erdogan, University of Hawaii, Hilo
(UHH)
 System Architecture
classes
 Processing of Satellite Data
 Huinalu
 Linux
Supercluster
 128 nodes, 254 processors
 Migrated from MHPCC
 Used by Manoa researchers and Hilo
students
The UH HPC Community
UH Manoa
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Department of Meteorology
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Dr. Yi-Leng Chen
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Weather modeling specializing in terrain effects on islands, especially Hawaiian islands
and Taiwan
Has a 20-node Dell cluster, uses NCAR, local Dell cluster, is in acquisition phase for
larger machine.
Daily Weather Data
 Dr. Vaughan Philips
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Dr. Tim Li
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Weather modeling
Has 64-node Dell cluster on campus
Cyclone modeling
Environmental studies with IPRC
IPRC – International Pacific Research Center
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Has Several Clusters: Cray SV1 32 processors, Altix 32 node cluster, Linux 64 nodes
4 main themes; many researchers
Effects of Global Warming on Cyclones in the Pacific
Electrical Engineering
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Dr. David Y.Y. Yun
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LIPS 240-node computer
Assimilates data from MRI scans to get a total picture of the brain
for analysis
Mechanical Engineering
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Dr. Marcelo Kobayashi
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Uses Genetic Algorithm for wing design
Design of Micro UAVs
Long-Range Lightning Detection for TPARC
N Pac Storm.mov
S Businger, A Pessi, K Squires – University of Hawaii
K Cummins, N Demetriades – Vaisala
N Pac Storm.mov
Dr. Kwok Fai Cheung, ENDEAVOR Project
Ocean and Resources Engineering
3rd Generation Spectral Wave Models
ENDEAVOR Website
Normal Tradewinds
Global (WW3)
Regional (WW3)
Extreme Swell
Ship Motions Models
Local (SWAN)
Location Specific
Wave Spectra
Computational Chemistry
John Head, Department of Chemistry, UHM
Goal: use first principle quantum mechanical methods to predict the
electronic structure properties of new materials
Example project: design of optoelectronic devices using OH and CH3 passivated silicon
clusters.
Global optimization methods were developed to identify the lowest energy (most stable) structures
for passivated silicon nanoclusters.
Si10(OH)16
Si10(CH3)16
Theoretical Investigation of Low Energy SixLy Clusters L=H, CH3, OH and F
Yukihide Shiraishi1, David Robinson2, Yingbin Ge3 and John D. Head4
1.Department of Material Science and Environmental Engineering,
Tokyo University of Science, Yamaguchi, SanyoOnoda-shi, Yamaguchi, 756-0884, Japan
2. Department of Chemistry, University of Tulsa, OK.
3. Ames Laboratory, Iowa State University, IA.
4. Department of Chemistry, University of Hawaii, 2545 The Mall, Honolulu, HI 96822
Si10(CH3)16 U structure
Si10(OH)16 A structure
L2Si=SiL2 versus LSi-SiL3
Low energy Si10L16 clusters
MOTIVATION
•Unlike bulk Si, which is an indirect gap semiconductor,
porous Si and Si nanoparticles exhibit a bright
photoluminescence which may eventually find use in a
Si based optoelectronic device [1,2].
•This poster investigates the preferred geometric
arrangement for Si atoms for a Si cluster passivated by
different ligands L.
•Previous calculations often assume the atoms in the
Six core form a bulk Si lattice like structure [3,4].
•Our previous global optimizations calculation have
found the Six core to be bulk Si like in SixHy clusters
with enough H atoms to fully passivate the cluster [5,6].
•However, we recently found the lowest energy SixFy
clusters to be very different to the structure found for
SixHy [7]
•In this poster we discuss preliminary low energy
structures we have found for Si2L4 and Si10L16 with
L=H,CH3,OH and F. H and CH3 have similar
electronegativities and were expected to have similar
low energy structures. The OH electronegativity is
intermediate between H and F and it is not obvious
which structure would be preferred.
COMPUTATIONAL METHOD
• Geometry optimizations were performed using B3LYP/631G(d) calculations using PC GAMESS [8,9].
• Low energy Si10(CH3)16 and Si10(OH)16 clusters were
generated by replacing the L atoms in the 3 lowest energy
Si10H16 (U,V,W) and Si10F16 (A,B,C) structures.
• Several low energy Si10H16 [6] and Si10F16 [7] structures
were determined using a genetic algorithm (GA) based
global optimization strategy [5].
• Calculation consistency checks were by performed using
L2Si=SiL2 and LSi-SiL3 where L is only treated as a nonbridging ligand.
Table of L2Si=SiL2 and LSi-SiL3 relative energies
(kcal/mol)
B3LYP/
B3LYP/
MP2/
6-31G(d)
LAN2DZ
LAN2DZ
H2Si=SiH2
0
0
0
HSi-SiH3
5.2
12.1
10.5
(CH3)2Si=Si(CH3)2
0
0
0
CH3Si-Si(CH3)3
5.3
2.5
8.6
(HO)2Si=Si(OH)2
8.7
7.9
13.1
HOSi-Si(OH)3
0
0
0
F2Si=SiF2
7.3
12.7
8.1
FSi-SiF3
0
0
0
•Hydrogen and methyl favour a L2Si=SiL2 structure
•Fluorine and hydroxide favour a LSi-SiL3 structure.
.
REFERENCES
1. L. T. Canham, Appl. Phys. Lett., 57, 1046 (1990).
2. W. L. Wilson, P. F. Szajowski, L. E. Brus, Science, 262,
1242 (1993).
3. Z. Zhou, R. A. Friesner, L. E. Brus, J. Am. Chem. Soc.,
125, 15599 (2003).
4. E. Degoli et al., Phys. Rev. B, 69, 155411 (2004).
5. Y. Ge, J. D. Head, J. Phys. Chem. B, 108, 6025 (2004).
6. Y. Ge, J. D. Head, Chem. Phys. Lett., 398, 107 (2004).
7. Y. Ge, J. D. Head, Mol. Phys., 103, 1035 (2005).
8. M. W. Schmidt et al., J. Comput. Chem., 14, 1347
(1993).
9. A. A. Granovsky, PC GAMESS version 7.0,
http://classic.chem.msu.su/gran/gamess/index.html
A
B
U
V
C
W
Figure showing different Si10L16 cluster types where L=F.
Structure U has a Si10 core like bulk Si and corresponds to
the global minimum structure previously found for Si10H16 [5].
Structure A is the global minimum structure previously
found for Si10F16 [7].
Table of Si10L16 ranking and relative energies
(kcal/mol)
Si10H16
A
6 13.6
Si10(CH3)16
Si10(OH)16
2 0.9
1 0.0
CONCLUSION
Si10F16
1
0.0
• H and CH3 give U as the lowest energy cluster to presumably
favor forming more readily Six cores with bulk Si like structures.
• F and OH have A as the lowest energy structure
preferring to form SiL3 groups over low strain Si rings.
B
ACKNOWLEDGEMENTS
5 1.4
3 5.5
3
5 13.5
1.7
D.R. acknowledges summer support from the UH REU
program funding by NSF grant CHE03-53251.
We are gratefully for the generous supply of computer
tiime on the University of Hawaii Dell Cluster.
Geology and Geophysics
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Dr. Eric Gaidos
 Jillian
Ward, Grad
Student
 Understanding gene
evolution through the
study of placozoans
 UH/MHPCC
Engagement Grant
Recipient
Molecular Biosciences and
Bioengineering
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Dr. Gernot Presting
 Protein
folding, Gene annotation
 Uses Dell cluster and MHPCC
 Aren Ewing, Engagement Grant Awardee
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Phylogenetic Profiling of the Arabidopsis Genome
Information & Computer Science
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Dr. Henri Casanova
 Virtual
Compute systems
 Networking
 Dell 96 node cluster open for general use
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Dr. Guylaine Poisson
 Bioinformatics
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Dr. Philip Johnson
 Parallel
Programming Optimization
 Hackystat
How Many Clusters on Manoa Campus?
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I don’t honestly know, but those I have found to date:
Department/Person
Make/size
ICS/Henri Cassanova
Dell/96 compute nodes w/dual processors
Meteorology/Vaughan Phillips
Dell/64 nodes w/dual processors
CEE/Albert Kim
Dell/16 nodes/32 processors
IPRC/Ron Merrill
32 dual node Linux cluster, 4 Linux quads, 16 dual
node linux cluster, 48 processor linux cluster, 32
processor IRIX cluster
EE/ David Y.Y. Yun
LIPS 240 Intel Celeron Processors
Meteorlogy/Yi-Ling Chen
20 nodes, Bidding for larger machine
ORE/Kwok Fai Cheung
Will have Dell 10 nodes/8 processors each – as soon
as the ink dries!
INBRE/Steven Siegfried
Dell 20 node cluster
Meteorology/ Steven Businger
8 node Dell cluster, 10 Mac quadras
Current Programs for
Faculty/Students
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Engagement Grants
UH/MHPCC Summer internships
DoD Mod Office Joint Opportunities for
Minorities (JEOM) summer internships
Find out about these by signing up for the email list
uh-hpc today or going to www.hawaii.edu/hpc or
emailing me at stbrown@hawaii.edu
UH/MHPCC Engagement Grants
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Started in 2004
Start-up; for student support only
Must use MHPCC computational resources
Must have UH faculty sponsor
9-month or 12-month
Subject matter not restrictive
Applications open this month for Sept 2007!
Current Programs for
Faculty/Students
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
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Engagement Grants
UH/MHPCC Summer internships
DoD Mod Office Joint Opportunities for
Minorities (JEOM) summer internships
Find out about these by signing up for the email list
uh-hpc today or going to www.hawaii.edu/hpc or
emailing me at stbrown@hawaii.edu
UH/MHPCC Summer Internships
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Started in 2004
About 5 students each year
Live in Maui; Work at MHPCC
Systems, SciVis, Data Base, Security Systems
Students from any UH Campus eligible
Term from June 1 - July 31
Applications open in February 08 for Summer 08
Current Programs for
Faculty/Students
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
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Engagement Grants
UH/MHPCC Summer internships
DoD Mod Office Joint Opportunities for
Minorities (JEOM) summer internships
Find out about these by signing up for the email list
uh-hpc today or going to www.hawaii.edu/hpc or
emailing me at stbrown@hawaii.edu
DoD Mod Office Joint Opportunities for Minorities
(JEOM) summer internships
New this year!
 Located at MHPCC or on a UH campus
 Graduate or Undergraduate students
 Must be minority
 Applications not open yet for Summer 07!
 Watch for the small window of
opportunity….
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Current Programs for
Faculty/Students



Engagement Grants
UH/MHPCC Summer internships
DoD Mod Office Joint Opportunities for
Minorities (JEOM) summer internships
Find out about these by signing up for the email list
uh-hpc today or going to www.hawaii.edu/hpc or
emailing me at stbrown@hawaii.edu