This document discusses the Virtus software for cardiovascular flow simulation and analysis. It begins with an overview of heart diagnosis techniques such as imaging and fractional flow reserve measurement. It then describes the computational fluid dynamics framework used by Virtus to simulate blood flow. The rest of the document outlines Virtus' workflow and key components: segmentation from medical images, meshing, simulation, and visualization. It emphasizes Virtus' ease of use, with automated functions and an intuitive graphic user interface.

1. VITRTUS
CFD
OF
THE
BLOOD
FLOW
IN
THE
CLOUD
JAKUB
POLA
SOFTWARE
DEVELOPER,
VRATIS
LTD.

2. HEART
DIAGNOSIS
! Non-­‐invasive:
‒ X-­‐Ray
Computer
Tomography.
‒ MagneMc
Resonance
Imaging.
‒ Electrocardiography.
! Invasive:
‒ Angiography.
‒ FracMonal
Flow
Reserve.
2
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

3. HEART
DIAGNOSIS
FRACTIONAL
FLOW
RESERVE
EXAMPLE
! COURAGE,
FAME2:
FFR
VALUE
Stent
implantaMon
Drug
therapy
! DeFACTO
(2012):
FFR
3
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL
FFR
CT

4. COMPUTATIONAL
FLUID
DYNAMICS
FRAMEWORK
! Solve
Navier
–
Stokes
equaMons
! Procedure:
‒ Preprocessing:
‒ DefiniMon
of
the
geometry.
‒ GeneraMon
of
volumetric
mesh.
‒ DefiniMon
of
physical
model.
‒ DefiniMon
of
boundary
condiMons.
‒ SimulaMon:
iteraMve
solvers.
‒ Post-­‐processing:
‒ Analysis
‒ VisualisaMon
! How
to
obtain
geometry
and
create
a
mesh?
!
How
to
solve
the
problem
fast
and
efficiently?
4
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

5. CFD
IN
MEDICINE
! Stent
grac
design:
‒ DeterminaMon
of
proper
shape
of
the
stent
grac
! Design
of
heart
valves:
‒ DeterminaMon
of
shape
and
biological
and
mechanical
properMes
! Drug
delivery:
‒ DeterminaMon
of
the
delivery
device
‒ DeterminaMon
of
the
drug
state
5
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

6. VIRTUS:
OVERVIEW
Mesh
storage
format
User
Interface
Database
PACS
SoQware
as
a
Service
AcHve
Mesh
6
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL
CalculaHons

7. VIRTUS:
WORKFLOW
CT
/
MRI
Scanning
SegmentaMon
CFD
SimulaMon
7
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL
Meshing
Post-­‐processing
/
VisualisaMon

8. VIRTUS:
ARCHITECTURE
STL
SegmentaMon
CT/MRI
V
Mesh
Surface
representaMon
of
volumetric
mesh
SimulaMon
4
txt
config
files
Set
boundary
condiMons
VisualizaMon
8
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL
GeneraMon
of
Volumetric
Mesh
(NETGEN)
surface
&
U,
p,
WSS
SimulaMon

9. VIRTUS:
GRAPHIC
USER
INTERFACE
9
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

10. VIRTUS:
ARCHITECTURE
STL
SegmentaMon
CT/MRI
V
Mesh
Surface
representaMon
of
volumetric
mesh
SimulaMon
4
txt
config
files
Set
boundary
condiMons
VisualizaMon
10
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL
GeneraMon
of
Volumetric
Mesh
(NETGEN)
surface
&
U,
p,
WSS
SimulaMon

11. VIRTUS:
SEGMENTATION
! Create
3D
model
from
series
of
images.
! Very
Mme
consuming
task.
! Require
mesh
modeling
to:
‒ fix
the
errors
in
the
mesh
‒ prepare
mesh
to
generate
volumetric
mesh
11
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

12. VIRTUS:
SEGMENTATION
ACTIVE
MESH
! Input:
‒ CT
or
MRI
scans
in
DICOM
format.
! Outputs:
‒ Surface
mesh
in
STL
format.
‒ Volumetric
mesh
in
OpenFOAM
format.
! Real-­‐Mme
procedure.
! Fasat
algorithm.
! Many
mesh
ediMng
tools:
‒ Global/local
mesh
smoothing.
‒ Cut
Mesh.
‒ Freeze
Mesh.
‒ Push
Mesh.
‒ Define
Flow
Inlets
and
Outlets
‒ Automated
determinaMon
of
artery
centerline(s)
12
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

13. VIRTUS:
MESHING
MODULE
13
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

14. VIRTUS:
ARCHITECTURE
STL
SegmentaMon
CT/MRI
V
Mesh
Surface
representaMon
of
volumetric
mesh
SimulaMon
4
txt
config
files
Set
boundary
condiMons
VisualizaMon
14
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL
GeneraMon
of
Volumetric
Mesh
(NETGEN)
surface
&
U,
p,
WSS
SimulaMon

15. VIRTUS:
SIMULATION
MODULE
USER
SIDE
! Just
two
steps:
‒ Type
of
simulaMon:
‒ Transient
flows.
‒ Steady-­‐state
flows.
‒ Inlet
boundary
condiMon:
‒ Inlet
velocity.
‒ Inlet
pressure.
‒ Point
and
click
procedure
! ConfiguraMon
‒ Just
four
txt
files
15
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

16. VIRTUS:
SIMULATION
MODULE
USER
SIDE
16
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

17. VIRTUS:
SIMULATION
MODULE
SERVER
SIDE
! Three
ways
to
execute
simulaMon:
‒ Using
CPU
in
parallel
mode.
‒ Using
CPU
+
GPU
in
parallel
mode.
‒ Using
GPU
only.
17
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

18. VIRTUS:
SIMULATION
MODULE
SERVER
SIDE:
CPU
CPU
Read
mesh
No
Assembly
matrices
Ax=b
~33%
Conv
erged
?
Yes
Finalize
18
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL
Solve
Ax=b
~66%

19. VIRTUS:
SIMULATION
MODULE
SERVER
SIDE:
CPU
+
GPU
CPU
PCI
GPU
Ax=b
Solve
Ax=b
Read
mesh
Assembly
matrices
Ax=b
No
Conv
erged
?
Yes
Finalize
19
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL
x

20. VIRTUS:
SPEEDIT
TOOLKIT
! Solvers:
‒ Conjugate
Gradient.
‒ Bi-­‐Conjugate
Gradient.
! PrecondiMoners:
‒ Diagonal.
‒ Approximate
Inverse.
‒ Algebraic
MulMgrid
with
Smoothed
AggregaMon
(CUSP).
! Support
for
MulM-­‐GPU.
! Plaqorms:
‒ OpenCL.
‒ CUDA.
20
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

21. VIRTUS:
SIMULATION
MODULE
SERVER
SIDE:
CPU
+
GPU
CPU
PCI
GPU
Ax=b
Solve
Ax=b
Read
mesh
Assembly
matrices
Ax=b
No
Conv
erged
?
Yes
Finalize
21
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL
x

22. VIRTUS:
SIMULATION
MODULE
SERVER
SIDE:
GPU
CPU
Read
mesh
PCI
GPU
Mesh
Assembly
matrices
Ax=b
No
Finalize
22
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL
x
Solve
Ax=b
Conv
erged
?
Yes

23. VIRTUS:
SPEEDIT
FLOW
! Full
GPU
implementaMon
of:
‒ PISO
(Pressure
Implicit
with
Split
Operator)
–
transient
solver
for
incompressible
flows.
‒ SIMPLE
(Semi-­‐implicit
Method
for
Pressure
Linked
EquaMons):
Steady-­‐state
solver
for
incompressible
flows.
! Boundary
CondiMons:
‒ Zero
Gradient
‒ Time
dependent
and
Fixed
value.
! Adjustable
Mme
step.
! Roadmap:
‒ Support
for
OpenCL
‒ Turbulence
(RANS,
kOmegaSST
model)
‒ Support
for
MulM-­‐GPU
23
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

24. SPEEDIT
FLOW
TEST
CASES
! U-­‐shaped
pipe
‒ Radius
–
1in
‒ 4M
hex
cells
‒ Transient
flow
simulaMon:
‒ U(t)
=
Asin(ωt)
+
B
‒ Steady-­‐state
simulaMon
‒ Re
=
100
‒ Re
=
1000
! Basilar
artery*:
‒ 2M
hex
cells
‒ Transient
flow.
‒ Two
heart
cycles.
*
Geometry
obtained
from
AneuriskWeb
project.
Emory
University,
Department
of
Math&CS,
2012
24
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

25. SPEEDIT
FLOW:
U-­‐SHAPED
PIPE
SIMULATION
EXECUTION
TIME
25
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

26. SPEEDIT
FLOW:
U-­‐SHAPED
PIPE
ACCELERATION
RATIO
26
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

27. SPEEDIT
FLOW:
BASILAR
ARTERY
SIMULATION
EXECUTION
TIME
27
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

28. SPEEDIT
FLOW:
BASILAR
ARTERY
ACCELERATION
RATIO
28
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

29. VIRTUS:
ARCHITECTURE
STL
SegmentaMon
CT/MRI
V
Mesh
Surface
representaMon
of
volumetric
mesh
SimulaMon
4
txt
config
files
Set
boundary
condiMons
VisualizaMon
29
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL
GeneraMon
of
Volumetric
Mesh
(NETGEN)
surface
&
U,
p,
WSS
SimulaMon

30. VRATIS:
VISUALIZATION
MODULE
30
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

31. SUMMARY
! VIRTUS
is
a
pla]orm
for
personalized
medicine
and
CFD
based
diagnosis.
! Cloud-­‐based
approach
simplifies
the
usage.
! GPU
reduces
Mme-­‐to-­‐soluMon.
31
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

32. ! QuesMons?
! Comments?
Jakub
Pola
jakub.pola@vraMs.com
virtus.vraMs.com
Acknowledemnents:
VraHs:
Wojciech
Tarnawski,
Lukasz
Miroslaw,
Pawel
Czubinski
Wroclaw
Uni.:
Zbigniew
Koza,
Piotr
Olkiewicz
Wroclaw
Uni.
of
Technology:
Tadeusz
Tomczak,
Andrzej
Kosior
32
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL

33. DISCLAIMER
&
ATTRIBUTION
The
informaMon
presented
in
this
document
is
for
informaMonal
purposes
only
and
may
contain
technical
inaccuracies,
omissions
and
typographical
errors.
The
informaMon
contained
herein
is
subject
to
change
and
may
be
rendered
inaccurate
for
many
reasons,
including
but
not
limited
to
product
and
roadmap
changes,
component
and
motherboard
version
changes,
new
model
and/or
product
releases,
product
differences
between
differing
manufacturers,
socware
changes,
BIOS
flashes,
firmware
upgrades,
or
the
like.
AMD
assumes
no
obligaMon
to
update
or
otherwise
correct
or
revise
this
informaMon.
However,
AMD
reserves
the
right
to
revise
this
informaMon
and
to
make
changes
from
Mme
to
Mme
to
the
content
hereof
without
obligaMon
of
AMD
to
noMfy
any
person
of
such
revisions
or
changes.
AMD
MAKES
NO
REPRESENTATIONS
OR
WARRANTIES
WITH
RESPECT
TO
THE
CONTENTS
HEREOF
AND
ASSUMES
NO
RESPONSIBILITY
FOR
ANY
INACCURACIES,
ERRORS
OR
OMISSIONS
THAT
MAY
APPEAR
IN
THIS
INFORMATION.
AMD
SPECIFICALLY
DISCLAIMS
ANY
IMPLIED
WARRANTIES
OF
MERCHANTABILITY
OR
FITNESS
FOR
ANY
PARTICULAR
PURPOSE.
IN
NO
EVENT
WILL
AMD
BE
LIABLE
TO
ANY
PERSON
FOR
ANY
DIRECT,
INDIRECT,
SPECIAL
OR
OTHER
CONSEQUENTIAL
DAMAGES
ARISING
FROM
THE
USE
OF
ANY
INFORMATION
CONTAINED
HEREIN,
EVEN
IF
AMD
IS
EXPRESSLY
ADVISED
OF
THE
POSSIBILITY
OF
SUCH
DAMAGES.
ATTRIBUTION
©
2013
Advanced
Micro
Devices,
Inc.
All
rights
reserved.
AMD,
the
AMD
Arrow
logo
and
combinaMons
thereof
are
trademarks
of
Advanced
Micro
Devices,
Inc.
in
the
United
States
and/or
other
jurisdicMons.
SPEC
is
a
registered
trademark
of
the
Standard
Performance
EvaluaMon
CorporaMon
(SPEC).
Other
names
are
for
informaMonal
purposes
only
and
may
be
trademarks
of
their
respecMve
owners.
33
|
PRESENTATION
TITLE
|
NOVEMBER
19,
2013
|
CONFIDENTIAL