CI Days, Clemson University, May 20, 2008
Adventures
in
Cyberinfrastructure:
observations of an accidental tourist
Mark Lundstrom
Network for Computational Nanotechnology
Discovery Park, Purdue University
West Lafayette, IN
NCN
1
www.nanoHUB.org
some special people
Gerhard Klimeck, Michael McLennan, George Adams,
and Gerry McCartney (Purdue University)
Jim Bottum, Sebastien Goasguen, Krishna Madhavan,
(Clemson University)
José A.B. Fortes (Univ. of Florida)
Nirav Kapadia (Unisys)
+ the Purdue University leadership and NSF program
managers
NCN
2
www.nanoHUB.org
nanoelectronic devices and materials
molecular electronics
Al
Gate
HfO2
D
S
10 nm SiO2
p++ Si
NW/NT composites
carbon nanotube
D electronics
G S
SWNT
CoFeB (3)
MgO (0.85)
Insulator CoFeB (3)
Ru (0.85)
CoFe (2.5)
NCN
www.nanoHUB.org
nanowire PV
spin torque devices
nanowire
bio-sensors
3
why I compute
“The purpose of computing is insight - not numbers.”
-Richard Hamming
• to develop understanding
• to interpret experiments
• to explore new devices
• to set the stage for more serious simulations
NCN
4
www.nanoHUB.org
computational science and engineering
experimentalists
designers
CSE
algorithms
HPC
‘closer to the solution’
NCN
students
simulation/
CAD
theorists
modelers
‘closer to the problem’
educators
5
www.nanoHUB.org
the nanoHUB story
NCN
Nirav Kapadia, Purdue University
1991 - 2001
6
www.nanoHUB.org
PUNCH (1994-2005)
2000
PUNCH v.4
middleware
gridware
Software applications
NCN
-Unix
-text-based / forms-based
-graphical interface
www.nanoHUB.org
Compute servers
-Unix workstations
-parallel computers
-global condor pool
7
running applications with PUNCH
>7M hits (1994 - 2002)
2002
1994
NCN
AT&T
www.nanoHUB.org
grant
8
NCN
Network for Computational Nanotechnology
Norfolk
State
NCN
UTEP
Berkeley
NU
N
CN has a vision to pioneer the
development of nanotechnology
from science to manufacturing through
innovative theory, exploratory
simulation, and novel
cyberinfrastructure.
UIUC
Purdue
www.ncn.purdue.edu
‘an infrastructure and research network’
NCN
9
www.nanoHUB.org
NCN Mission
1) to connect computational
experts with experimentalist,
educators, and students
Norfolk
NCN
UTEP
Berkeley
2) to bridge disciplines and
promote collaboration
3) to support CSE
NU
UIUC
Purdue
4) to disseminate knowledge and
services
“cyberinfrastructure”
NCN
www.nanoHUB.org
5) to enable research and
education
10
NCN Outcomes
1) Advances in nanoscience and its
transition to nanotechnology
Norfolk
NCN
UTEP
Berkeley
2) Pervasive, critical, and effective use
simulation in nanotechnology
research and education
3) Advances in CSE
NU
UIUC
Purdue
4) Creation of a major, electronic
resource for nanotechnology
5) Dissemination of technology and best
practices to other communities.
NCN
11
www.nanoHUB.org
Rappture = Rapid Application Infrastructure
Rappture
=
Simulation
Code
Scientist
• Created by NCN in Nov 2004
• Works with your favorite
programming language
• Open source
• Online at http://rappture.org
NCN
12
www.nanoHUB.org
The Rappture approach
• standardizes interfaces
• improves usability and speeds program debugging
• complete record of each simulation
• a strategy to develop high quality software quickly
• and longer term, to assemble ambitious workflows
NCN
13
www.nanoHUB.org
middleware system architecture
Physical Machine
Content
Database
Maxwell’s
Daemon
Virtual Machine
0101
1011
1001
nanowire job
nanoHUB cluster
NCN
Violin
Rendering Farm
nanoVIS
14
www.nanoHUB.org
online simulation
more than 80 tools online
NCN
more that 100 in development
15
www.nanoHUB.org
nanoHUB tool page
user statistics
launch!
getting started
reviews and
citations
how to cite
NCN
16
www.nanoHUB.org
NCN’s software strategy
1) facilitate the sharing of SW tools emerging from research
2) disseminate high-quality simulation codes
3) develop specialized tools for experimentalists and educators
4) promote the intelligent, critical use of simulation
NCN
17
www.nanoHUB.org
more than simulation
tutorials and seminars
research seminars
learning modules
online courses
+ online meetings, Q and A,
NCN
reviews, SW development
tools, statistics, etc.…
18
www.nanoHUB.org
MIT OpenCourseWare
NCN
“A free and open educational resource - for educators, students, and
self-learners around the world.” All 1800 MIT courses are now online.
19
www.nanoHUB.org
nanoHUB usage
>65,000 users/year
www.nanoHUB.org
NCN
20
www.nanoHUB.org
usage
NCN
21
www.nanoHUB.org
users
use nanoHUB for
position
graduate student:
undergrad student:
pre-college student:
scientist / engineer:
faculty:
(April 2006)
55%
18%
1%
13%
13%
NCN
(March 2006)
33%
38%
28%
1%
(November 2006)
technical interests
age
18-25:
26-35:
36-45:
46-55:
56 or older:
research:
education:
both equally
other:
61%
29%
7%
2%
1%
nanoelectronics:
NEMS/nanofluidics:
nanomedicine
nanomaterials:
nanophotonics:
46%
9%
11%
16%
8%
(April 2006)
22
www.nanoHUB.org
HUBzero.org
• Linux/Apache/MySQL/PHP
• LDAP authentication
• Joomla Content Mgmt
• Hub website components
-tool development framework
-web publishing systems
-statistics collection / analysis
-online meetings
-topic pages
-recommendation engine
-Questions and Answers
-incentive system
-citations and DOO
• Maxwell’s Daemon
NCN
• Rappture Toolkit
23
www.nanoHUB.org
New Hubs Online
GlobalHUB.org – Dan Hirleman, ME at Purdue
global engineering education
online since 12/17/2007
pharmaHUB.org – Rex Reklaitis, CE at Purdue
pharmaceutical product development and manufacturing
online since 12/11/2007
thermalHUB.org – Tim Fisher, ME at Purdue
heat transfer
online since 12/6/2007
IndianaCTSI.org – Anantha Shekhar, IU
School of Medicine, Connie Weaver at Purdue
accelerating clinical and translational research in healthcare
online since 10/1/2007
nanohub.org – Mark Lundstrom, ECE at Purdue
the granddaddy of all hubs focused on nanotechnology
online since 2002
NCN
24
www.nanoHUB.org
impact
NCN
25
www.nanoHUB.org
Supriyo Datta
Concepts in Quantum Transport
From Atom to Transistor
Fundamentals of Nanoelectronics
Electronics from the Bottom Up
Supriyo Datta
9,999 nanoHUB users last year
NCN
‘datta’ is the most popular search term
on the nanoHUB
26
www.nanoHUB.org
M. Ashraf Alam
Problem:
For medium scale integration of carbon
Nanonet transistors for flexible electronics,
the contamination of metallic tubes makes
making large circuits difficult.
photo of you
Approach:
Develop fundamental understanding of
percolative transport so that the
threshold of percolation can be tuned for
specific circuits.
Results:
NCN
Theory of asymmetric percolation in
heterogenous system that allows development
of ~100 transistors integrated circuits on flexible
substrates.
www.nanoHUB.org
Muhammad A. Alam
27
Effect of metallic CNTs
NCN
28
www.nanoHUB.org
Striping: cutting the tubes for on-off ratio
expt
Theory
WS
NCN
Qing Cao, et al., “Medium Scale Carbon Nanotube Thin Film Integrated
Circuits on Flexible Plastic Substrates,” to appear in Nature, 2008
29
www.nanoHUB.org
Connection to NCN / nanoHUB
“The finite-size percolation model was
used to calculate the ID-VG
characteristics for NanoNET transistor
with channel length of 2 um …”
IEEE EDL Feb. 2007
NCN
www.nanoHUB.org
• promotes diffusion of knowledge
• encourages collaboration
• increases the impact of the
work
30
Network for Computational Nanotechnology
Problem:
Atomic level structure of semiconductor
heterostructures controls their
electronic properties.
Approach:
Molecular dynamics with interatomic
potentials derived from first principles
Tight binding for electronic structure
Alejandro Strachan
Results:
Size can be used to control strain in nanoscale heterostructures
NCN
31
www.nanoHUB.org
Strain relaxation in Si/Ge/Si nanobars
Simulations show that increasing
the bar height or decreasing its
width reduces transverse strain in
Ge section
Si
height
Ge
Si
Bar width (W)
• Atomistic prediction in good agreement
with experiments
• NCN
Theory can be used to optimize
material in silico before fabrication
www.nanoHUB.org
32
NCN / nanoHUB.org
nanoMATERIALS simulation toolkit: general purpose MD simulations
Input parameters
Interactive output:
molecular structure and graphs
nanoMATERIALS tutorial: https://www.nanohub.org/resources/2322
Lecture series on MD: https://www.nanohub.org/resources/3675
NCN
Materials Modeling and Simulation class (Fall 2008)
www.nanoHUB.org
33
Arvind Raman
Problem:
To mathematically simulate the motion of nanoscale
Atomic Force Microscope probe tips scanning over
organic and inorganic samples
Approach:
photo of you
Couple vibrating cantilever eigenmodes to realistic tipsample interaction force models that include van der
Waals, electrostatic, repulsive interactions. Use special
integration routines to improve simulation speed and
accurately integrate across high force gradients.
Arvind Raman
Results: Resonance enhancement in liquids for improved material contrast
NCN
34
www.nanoHUB.org
Mica substrate
(a)
Just before tapping
Tapping on PM, SP=94%
Tapping on mica, SP=94%
Slow Timescale
20
Amplitude (nm)
Resonance enhancement of harmonics in liquids
0
AFM Cantilever
Higher harmonics of tip motions in buffer solutions for
-20
Fast
Timescale
Tip
the imaging of soft biological samples have been
2
simulated. Some harmonics are enhanced due to the Purple membrane (PM) 0
second eigenmode resonance. This is a generic
(b) Mica substrate 10nm
-2
0
2T
T
2T 0
T
phenomenon in liquids for soft cantilevers used for
(a)
Time
Time
AFM imaging of biological samples.
Slow Timescale
Just
before
tapping
Just
before
tapping
DFT (dB)
Amplitude (nm)
Simulations predcted that if the images of these
resonance enhanced harmonics were mapped
across a sample, then significant improvement in
contrast of material properties is obtained
(proportional to local elasticity). Experiments
validated the predictions.
20
Tapping
on PM,
SP=94%
Tapping
on PM,
SP=94%
Tapping
on
mica,
SP=94%
Tapping on mica, SP=94%
0
-20
2
Fast Timescale
0
(c)(b)
0 0
T
10nm -2
10fd 2T 0
TimeFrequency
Just before tapping
Tapping on PM, SP=94%
Tapping on mica, SP=94%
T
Time
2Td
20f
50dB
DFT (dB)
X. Xu, J. Melcher, R. Reifenberger, A. Raman,
“Resonance enhancement of cantilever higher
harmonics in liquids: enhancing compositional
contrast with gentle forces”, In preparation
50dB
NCN
(c)
www.nanoHUB.org
0
10fd
35
Harmonic Frequency
number
20fd
NCN/nanoHUB.org
Review of Scientific
Instrumentation
• Increasing interest in CI to deliver virtual
instruments
• Collaboration with DOE Molecular
Foundry to include realistic noise sources
into the current (deterministic) models in
VEDA
A monthly journal devoted to scientific
instruments, apparatus, and techniques
June, 2008
NCN
www.nanoHUB.org
• In addition to scientists and students
worldwide, VEDA is being used by major
US AFM/nano-instrumentation companies
such as Veeco, Agilent, and Asylum for
both training and research.
* J. Melcher, S. Hu, A. Raman, “VEDA – a web based virtual environment for
dynamic Atomic Force Microscopy”, Invited article – Review of Scientific
Instruments, June 2008..
36
cyberinfrastructure
“The conduct of science and engineering is changing and
evolving. This is due, in large part, to the expansion of
networked cyberinfrastructure.”
NSF Strategic Plan 2006-2011
NCN
37
www.nanoHUB.org
shared research facilities
Birck Nanotechnology Center, Purdue University
NCN
Courtesy HDR Architecture, Inc./Steve Hall  Hedrich Blessing
38
www.nanoHUB.org
“service-oriented science”
Distributed Computing
VIEWPOINT
Service-Oriented Science
Ian Foster
New information architectures enable new approaches to publishing and
Accessing valuable data and programs… as services….. Thus, tools
formerly accessible only to the specialist can be made available to
all;…Such service-oriented approaches to science are already being
applied successfully, in some cases at substantial scales….
6 MAY 2005 VOL 308 SCIENCE www.sciencemag.org
NCN
39
www.nanoHUB.org
lessons learned
• it takes a dedicated core team with a
vision and something special to
share
NCN
• need people who are ‘close to the
problem’ and ‘close to the solution’
• people need to be doing the right
things
• must be willing to adapt and evolve
NCN
• IT and SW development is expensive
(so is assessment)
40
www.nanoHUB.org
NCN is a work in progress
network leadership
• refine and expand the SW collection
technology development
and support
• move from a ‘resource’ to a ‘community’
NCN
• continue to enhance the infrastructure
• expand coverage of nanotechnology
science
drivers
• grow the user base
• strengthen CSE engagement
• develop a sustainability model
NCN
41
www.nanoHUB.org
NCN in the future
centers,
groups,
PI’s
NCN
HUBzero.org
other
networks
other orgs
universities
NCN
42
www.nanoHUB.org
cyberinfrastructure
“The conduct of science and engineering is changing and
evolving. This is due, in large part, to the expansion of
networked cyberinfrastructure.”
NSF Strategic Plan 2006-2011
NCN
43
www.nanoHUB.org