Using CINET presentation as part of the CINET Workshop on July 10th, 2015 in Blacksburg, VA. CINET applications include Granite, GDS Calculator, and EDISON.

1. Using
CINET
NSF
Software
Development
for
CyberInfrastructure
Grant
OCI-­‐1032677
Additional
support
by
grants
from
DTRA
V&V,
DTRA
CNIMS,
NSF
NetSE,
NSF
DIBBS
Team
Virginia
Tech,
Indiana
Uni.,
SUNY
Albany,
Jackson
State,
Argonne
Na>onal
Lab,
U.
Chicago,
NCAT,
U.
Houston
Downtown

2. CINET
2

3. CINET:
Applica2ons
• Granite
– Network
structural
analyses.
• GDS
Calculator
(GDSC)
– Complete
network
dynamics
on
networks.
• EDISON
– Forward
trajectory
(dynamics)
on
networks.
3

4. GRANITE
4

5. Granite:
Ini>al
Screen
• Go
to:
– hGp://cinet.vbi.vt.edu/granite/granite.html
– or
hGp://cinet.vbi.vt.edu
and
click
Granite
• Then
login
• To
create
a
new
account,
click
register

6. Features
Available
features:
§ Network
Analysis
§ Network
Generators
§ Network
List
§ Measure
List
§ Visualiza2on
§ NetScript
§ Others

7. Networks
and
Proper>es
Network
§ a
set
of
nodes,
represen2ng
some
en22es,
depicted
by
circles
§ a
set
of
edges,
represen2ng
rela2onships,
depicted
by
lines
A
network
with
6
nodes
and
7
edges

8. Networks
and
Proper>es
(cont.)
Density
Number
of
edges
/
max.
no.
of
possible
edges
Density
=
2*7
/
(5*6)
=
7
/
15
=
0.47
=
m
n
2
!
"
#
$
%
&
=
2m
n n −1( )

9. Networks
and
Proper>es
Connec>vity:
Connected
network
disconnected
network

10. Network
Analysis
§ In
the
menu
bar,
select
network
analysis
§ You
can
see
a
list
of
analyses
done
earlier
§ To
perform
a
new
analysis,
click
+New
Analysis
§ Type
a
name
for
the
analysis
§ Select
one
or
more
networks
§ You
can
browse
or
use
the
search
box
§ You
can
see
the
list
of
selected
networks
§ Click
Con>nue

11. Network
Analysis
(cont.)
§ Select
one
or
more
measures
§ You
can
browse
or
use
the
search
box
§ You
can
see
some
details
of
the
measures
§ If
necessary,
provide
parameter
values
§ You
can
see
the
list
of
selected
measures
§ Click
Analyze
§ The
new
analysis
is
now
in
the
list
§ Look
at
the
status
§ When
it
is
COMPLETED,
click
View
Report.
§ See
the
results
in
the
report
sec2on
§ To
download
the
results,
click
Download.

12. Random
Networks
Random
Networks
§ Edge
are
added
randomly
Erdős-­‐Rényi,
G(n,
p),
network
§ Each
poten2al
edge
is
added
with
probability
p
A
G(n,
p)
network
with
p
=
1/3
A
star
graph:
is
a
determinis2c
graph

13. Network
Generators
§ In
the
menu
bar,
select
Network
Generators
§ You
can
see
a
list
of
generators
created
earlier
§ Click
+New
Network
Generator
§ Type
a
name
for
the
generator
§ Select
one
or
more
generators
§ You
can
browse
or
use
the
search
box
§ You
can
see
the
list
of
selected
generators
§ Specify
parameters
if
required
and
click
submit
§ Click
Generate

14. Network
Generators
(cont.)
§ The
new
generator
is
now
in
the
list
of
generators
§ Look
at
the
status
§ When
it
is
COMPLETED,
click
View
Report.
§ See
the
results
in
the
report
sec2on
§ To
download
the
network,
click
Download.

15. Add
a
New
Network
§ In
the
menu
bar,
select
Networks
§ Click
+New
Network
§ Select
Directly
upload
a
file
§ Click
Done
§ Click
Choose
File
§ Provide
a
name
of
the
network
and
other
info
§
Click
Save
§ Now
you
can
see
the
added
network
in
the
list

16. Network
Visualiza>on
§ In
the
menu
bar,
select
Networks
§ You
can
see
the
list
of
networks
§ Click
on
a
network
name
to
visualize
§ Click
visualiza>on
(on
the
right
hand
side)
§ Click
+Add
Visualiza>on
§ Select
visualiza2on
parameters
§ leave
them
as
they
are
to
use
the
default
values
§ Click
Generate

17. GDS
CALCULATOR
(GDSC)
17

18. GDS: Phase Space Results—nor Vertex Function
• Inputs
– Graph:
Circle4
– Vertex
state
space:
K={0,1}
– Vertex
func>ons:
nor3
– Update
scheme:
• synchronous
Phase Space: Synchronous update
System state x = (x1,x2, x3, x4)
nor3 function
xi-1 xi xi+1 nor3
0 0 0 1
0 0 1 0
0 1 0 0
0 1 1 0
1 0 0 0
1 0 1 0
1 1 0 0
1 1 1 0
What does this do for us?
-Understanding of all
system state dynamics.
-Which onerous states are
attained once, or
frequently.
-Different equivalences.

19. GDS: Phase Space Results—nor Vertex Function
• Inputs
– Graph:
Circle4
– Vertex
state
space:
K={0,1}
– Vertex
func>ons:
nor3
– Update
scheme:
• synchronous
Phase Space: Synchronous update
System state x = (x1,x2, x3, x4)
nor3 function
xi-1 xi xi+1 nor3
0 0 0 1
0 0 1 0
0 1 0 0
0 1 1 0
1 0 0 0
1 0 1 0
1 1 0 0
1 1 1 0
What does this do for us?
-Understanding of all
system state dynamics.
-Which onerous states are
attained once, or
frequently.
-Different equivalences.
Number
of
state
transi>ons
is
(n!
|K|n).
Only
analyze
small
graphs.

20. GDS: Phase Space Results—nor Vertex Function
• Inputs
– Graph:
Circle4
– Vertex
state
space
– Vertex
func>ons:
nor3
– Update
scheme:
• sequen2al
with
order
π=(1,2,3,4)
• synchronous
Phase Space: Sequential update π=(1,2,3,4)
Phase Space: Synchronous update
System state x = (x1,x2, x3, x4)
Update scheme (sequential or synchronous) makes
a difference.
Figures at right are different.

21. GDS
Calculator:
Web
App
Specify
Graph
Specify Vertex
Functions
Specify
Update
Scheme
Specify
System
States
Post-
Process
Results
Submit Job
Activity sequence to run an analysis in GDSC
13 graph
templates can
be composed to
quickly generate
networks.
Directed and
undirected
networks.
15 types of
vertex functions.
Each vertex can
have a different
function. Arbitrary update
schemes:
-synchronous
-sequential
-block sequential
-fair and unfair word
orders.
Typically use all
system states, but can
specify any subset.
-Phase spaces for
each update
sequence.
-Which GDS are the
same (i.e., functionally
equivalent).
-Which GDS have the
same long-term
dynamics (i.e., cycle
equivalence).
-Largest limit cycles.

22. GDSC:
How
to
Log
In
• Op2on
1:
CINET
home
page
– Go
to
the
CINET
landing
page
hGp://www.vbi.vt.edu/
ndssl/cinet
– From
there,
click
on
“GDScalc”
then
click
on
“Start
GDSCalc.”
•
Op2on
2:
From
GDSCalc
landing
page
– Go
to
hGp://taos.vbi.vt.edu/gdscalc/welcome.html
– Then
click
on
“Start
GDSCalc.”
• Op2on
3:
Go
to
GDSC
login
page
– hGp://taos.vbi.vt.edu/gdscalc/
22

23. Specify
Graph
Specify
Vertex
Functions
Specify
Update
Scheme
Specify
System
States
Post-
Process
Results
Submit
Job
Activity sequence to run an analysis
GDSC:
Demo

24. Specify
Graph
Specify
Vertex
Functions
Specify
Update
Scheme
Specify
System
States
Post-
Process
Results
Submit
Job
Activity sequence to run an analysis
GDSC:
Demo

25. Specify
Graph
Specify
Vertex
Functions
Specify
Update
Scheme
Specify
System
States
Post-
Process
Results
Submit
Job
Activity sequence to run an analysis
GDSC:
Demo

26. Specify
Graph
Specify
Vertex
Functions
Specify
Update
Scheme
Specify
System
States
Post-
Process
Results
Submit
Job
Activity sequence to run an analysis
GDSC:
Demo

27. Specify
Graph
Specify
Vertex
Functions
Specify
Update
Scheme
Specify
System
States
Post-
Process
Results
Submit
Job
Activity sequence to run an analysis
GDSC:
Demo

28. Specify
Graph
Specify
Vertex
Functions
Specify
Update
Scheme
Specify
System
States
Post-
Process
Results
Submit
Job
Activity sequence to run an analysis
GDSC:
Demo
Each
of
the
four
update
schemes:
-­‐generates
only
fixed
points
as
limit
sets
-­‐the
only
limit
set
states
are
(0,0,0,0,0)
and
(1,1,1,1,1).

29. How
is
GDS
Calculator
Useful?
• Educa2on:
understanding
dynamics.
• Research:
– Running
web
app
enables
us
to
build
intui2on
about
problems.
– Convert
concrete
results
into
abstract
theorems
(that
are
applicable
to
much
large
[finite]
systems).
– Crucial
element
of
experimental
mathema.cs,
or
computa.onal
mathema.cs.

30. Take
Aways
• Dynamics
on
graphs.
• Evalua2on
of
all
system
state
transi2ons.
• Small
graphs
because
number
of
state
transi2ons
exponen2al
in
number
of
ver2ces;
problem
size
explodes.
• Understand
complete
dynamics.
• Elements
– Graph.
– Vertex
state
set.
– Vertex
func2ons.
– Update
schemes
for
vertex
func2ons.
• Three
published
works
using
this
system:
Automata
2011,
Theore2cal
Computer
Science
2014,
J.
Cellular
Automata
2015.
30

31. EDISON
31

32. GDS: Phase Space Results—nor Vertex Function
• Inputs
– Graph:
Circle4
– Vertex
state
space
– Vertex
func>ons:
nor3
– Update
scheme:
• sequen2al
with
order
π=(1,2,3,4)
• synchronous
Phase Space: Sequential update π=(1,2,3,4)
Phase Space: Synchronous update
System state x = (x1,x2, x3, x4)
Update scheme (sequential or synchronous) makes
a difference.
Figures at right are different.

33. GDS: Forward Trajectory—nor Vertex Function
• Inputs
– Graph:
Circle4
– Vertex
state
space
– Vertex
func>ons:
nor3
– Update
scheme:
• sequen2al
with
order
π=(1,2,3,4)
• synchronous
Phase Space: Sequential update π=(1,2,3,4)
Phase Space: Synchronous update
System state x = (x1,x2, x3, x4)
Update scheme (sequential or synchronous) makes
a difference.
Figures at right are different.

34. EDISON
Sample
Applica2ons
34
0"
0.001"
0.002"
0.003"
Base"
0+10"
11+20"
21+30"
31+40"
41+50"
51+60"
61+70"
71+80"
81+90"
Frac%of%Popula,on%
Age%Range%for%Vaccina,on%
Time
histories
of
Ebola
outbreaks.
Effects
of
Interven2ons
on
outbreak
size.
0"
0.05"
0.1"
0.15"
1" 2" 5" 10"
Frac.&of&Popula-on& Gov.&Interven-on&Factor,&eta&
C1"
C2"
C1C2"
Contagion
C1
is
awareness
of
harmful
behavior.
Contagion
C2
is
engaging
in
harmful
behavior.
Contagion
C1C2
is
both
being
aware
and
engaging
anyway.
Effect
of
government
interven2ons.

35. EDISON
• We
demonstrate
some
of
the
features
of
the
UI.
• The
backend
compute
engine
(hybrid
mul2-­‐
thread,
MPI)
has
been
used
in
several
works.
35

36. 36
END