ELF – α ELF – β
C1
C2
O2
O1
OH
O
C
OH
OH
C
P
Intermediate(Figure 5, Step-1)
glycosidic bond
isosurface of unpaired electron of carbon
toroidal isosurfaceof unpaired
electron of carbon
University of Delaware
The CLUSTER
The VENDORS
Animal & Food Sciences: Behnam
Abasht
Center for Applied Demography &
Survey Research: Ed Ratledge
Center for Bioinformatics and
Computational Biology: Cathy Wu
Chemistry & Biochemistry: Douglas
Doren
Chemical Engineering: Stanley Sandler,
Dion Vlachos
Civil & Environmental Engineering:
Rachel Davidson, Dominic Di Toro, Tian-
Jian Hsu, Paul Imhoff, James Kirby,
Jennifer McConnell, Christopher Meehan
Delaware Biotechnology Institute: Kelvin
Lee
Electrical & Computer Engineering:
Stephan Bohacek, Abhyudai Singh, Daniel
Weile, Ryan Zurakowski
Finance: Jayesh Khanapure
Geography: Luc Claessens, Tracy
DeLiberty
Geological Sciences: Holly Michael
Materials Science & Engineering:
Juejun Hu
Mathematical Sciences: Richard Braun,
Peter Monk, Yvonne Ou, Petr Plechac, Lou
Rossi, Peter Schwenk
Mechanical Engineering: Suresh Advani,
Kausik Sarkar, Lian-Ping Wang
Oceanography: Matthew Oliver,
Xaoi-Hai Yan
Physical Ocean Science & Engineering:
Cristina Archer, Tobias Kulkulka, Dana
Veron, Fabrice Veron
Physics & Astronomy: Daniel De Marco,
Paul Evenson, Edward Lynam, William
Matthaeus, Branislav Nikolic, Stanley
Owocki, Marianna Safrono, Qaisar Shafi,
Michael Shay
Plant & Soil Sciences: Randall Wisser, Psychology: Gregory Miller
RESEARCH SAMPLER
The STAKEHOLDERS
Study Morphodynamics in Fluvial, Estuarine and Costal Environments
3D Simulation of fine sediment transport in the bottom boundary layer
driven by a oscillatory motion (top panel) for a medium sediment
concentration case (middle panels, near bed concentration <C> 10
g/l) and a high concentration case (bottom panels, <C> 50 g/l).
Study Environmental Fluid Mechanics of Cloud Physics and Warm Rain
Reference: H. Gao, H. Li, L.-P. Wang (2011) Lattice Boltzmann simulation of
turbulent flow laden with finite-size particles. Computers & Mathematics with
Applications. doi:10.1016/j.camwa.2011.06.028
Building a multiscale simulation framework linking cloud microphysics
and cloud dynamics to larger scale weather and climate modeling.
Snapshot of particle-resolved
simulation of decaying particle-laden turbulent flow - 3D view and 2D
slice of vorticity contours and particle distribution.
Reference: C.E. Ozdemir, T.-J. Hsu, and S. Balachandar, (2011) A numerical
investigation of lutocline dynamics and saturation of fine sediment in the oscillatory
boundary layer. Journal of Geophysics Research, 116, C09012.
Electron Localization Function Analysis
Mapping the electronic
structure during biomass
pyrolysis reaction
Reference: A. Steffen, B. Rockstroh, C. Wienbruch, G.A. Miller (2011). Distinct
cognitive mechanisms in a gambling task share neural mechanisms.
Psychophysiology, 48, 1037-1046.
Developing a computational multi-scale engine to screen all explicit
solvents to elucidate the pathways of sugar conversion.
Analysis of Human Magnetoencephalographic (MEG) Data
Reference: M. Mettler et al. (2011) Energy and Environmental Science. (In Press)
Analysis of time course of brain activity while subjects make a decision
(a) and the brain surface distribution of neuromagnetic activity around
300 ms into the decision process (b).
Penguin Computing Inc.
AMD (Processors) Qlogic (Infiniband)
Arista (Switch) WhamCloud (Lustre)
APC (Racks) DotHill (Lustre Enclosures)
The MISSION
Based on priorities expressed in the
faculty's Research Computing Task
Force report (Apr. 2011), UD's
Information Technologies responded by
rapidly developing and implementing its
first HPC Community Cluster plan,
targeting production status by Jan. 2012.
Faculty interest quickly grew, resulting in
a 5,136-core, 49.3 Tflops (peak),
Infiniband- and Lustre-based system.
Faculty purchased the compute nodes
(24-48 core, 64-256 GB RAM) and IT
funded the storage, switch, maintenance,
and physical and staff infrastructure.
IT plans to solicit interest for additional
clusters every 12 months over the next
five years to respond to increasing
research needs at UD and emerging
HPC technologies.
The UD Community Cluster Program: A technical & financial collaboration between
faculty and Information Technologies
The TECHNICAL SPECS
Predict Protein-Protein Interaction Based on Domain Profiles
Study High Resolution Simulation of Vortex Lattice Dynamics
Ongoing projects that will be accelerated by the Community Cluster
Prediction using feature selection and support vector machines
provide highly accurate interaction domain identification in genome
prediction.
Reference: A.J. Gonzalez and L. Liao (2010) Predicting domain-domain interaction
based on domain profiles with feature selection and support vector machines, BMC
Bioinformatics 11, 537.
• Number of nodes: 200 dual & quad-socket nodes (12
cores/socket)
• Number of cores: 5,136 processor cores
• Processor: Dual Opteron 6234 12C, 2.4GHz
• Memory: 64-256 GB/node (total 14.5 TB)
• Total local disk space on the nodes: 208 TB
• Fabric: QDR Infiniband network interconnect
• File system: Lustre RAID-6 with 200 TB usable space
• Operating system: CentOS
• Cluster peak performance: 49.3 Tflops
Compute node: Altus 1804
Two weak vortices strip a
stronger central vortex in a
naturally adaptive, high
resolution simulation of
vortex lattice
dynamics. Adaptive,
scalable, high precision
methods like these are
essential tools for
investigators exploring
geophysical, aerodynamic
and industrial flows. Reference: L.A. Barba and L.F. Rossi (2010) Global field interpolation for particle
methods. Journal of Computational Physics, 229, pp. 1292-1310.
QDR Infiniband network
interconnect (Qlogic)
Powered by
Top Related