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Advanced Scientific Visualization Laboratory

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Title: Advanced Scientific Visualization Laboratory

1
AdvancedScientific VisualizationLaboratory

Paul Navrátil
28 May 2009

2
Topics

Remote and Collaborative Visualization
Remote Visualization on Spur
Scripted Visualization with VisIt

3
Old Model (No Remote Capability)
Local Visualization Resource
HPC System
Pixels
Mouse
Data Archive
Display
Wide-Area Network
Remote Site
Local Site
4
New ModelRemote Capability
Pixels
Large-Scale Visualization Resource
HPC System
Display
Mouse
Data Archive
Wide-Area Network
Remote Site
Local Site
5
New ModelMulti-User and Collaborative Capability
Local Site A
Large-Scale Visualization Resource
Pixels
HPC System
Display A
Mouse
Data Archive
Pixels
Display B
Mouse
Wide-Area Network
Local Site B
Remote Site
6
Spur - Visualization System

128 cores, 1 TB distributed memory, 32 GPUs
spur.tacc.utexas.edulogin node, no GPUsdont
run apps here!
ivisbig.ranger Sun Fire X4600 server
8 AMD Opteron dual-core CPUs _at_ 3 GHz
256 GB memory
4 NVIDIA FX5600 GPUs
ivis1-7.rangerSun Fire X4440 server
4 AMD Opteron quad-core CPUs _at_ 2.3 GHz
128 GB memory
4 NVIDIA FX5600 GPUs

7
Spur / Ranger topology
visqueue
normaldevelopmentltetcgtqueues
Login Nodes
Compute Nodes
File System
8
Topics

Remote and Collaborative Visualization
Remote Visualization on Spur
Scripted Visualization with VisIt

9
Starting a Remote Vis Job on Spur(Lab Exercise)

Step 1 Download a vnc client, preferably with
integrated compression
Recommended options
TightVNC
http//www.tightvnc.com/download.html
TurboVNC
http//www.virtualgl.org/Downloads/TurboVNC

10
Starting a Remote Vis Job on Spur(Lab Exercise)

Step 2 ssh ltusernamegt_at_spur.tacc.utexas.edu

11
Starting a Remote Vis Job on Spur(Lab Exercise)

Step 3 On Spur, set up your vnc password. This
only needs to be done oncevnc password shared
across Spur and Ranger
In your ssh, enter vncpasswd
Select and verify password.
NOTE vnc passwords are NOT secure!8 char limit
(rest ignored)
should NOT be your TACC password
stored in /.vnc/passwd

12
Starting a Remote Vis Job on Spur(Lab Exercise)

Step 4 Launch a vncserver job using SGE
qsub /share/sge/default/pe_scripts/job.vnc
touch /vncserver.out
tail f /vncserver.out

qsub sge submit command must
specify account job.vnc job script make
local copy to modify acct, runtime,
proc Connection instructions written to
/vncserver.out once job launches Use visq to
monitor job status
13
Starting a Remote Vis Job on Spur(Lab Exercise)

Step 5 Create ssh tunnel from your laptop to the
vnc session
ssh f N L ltportgtspur.tacc.utexas.edultportgt
ltusergt_at_spur.tacc.utexas.edu

vnc communication is unencryptedso create ssh
tunnel between your laptop and spur login ltportgt
port assigned by vnc job ltusergt your
username on spur Your vncviewer will connect to
port on your laptop (localhost) ssh tunnel
forwards connection to port on spur (login
node) spur automatically forwards to port on vis
node -f port forward only, no command -N
background after connect -L forward local
ltportgt to remote machineltportgt
14
Starting a Remote Vis Job on Spur(Lab Exercise)

Step 6 Connect to that display by using a vnc
client

(3)
(1)
(2)
15
Starting a Remote Visualization Job on Maverick
(Lab Exercise)

Step 7 Type glxgearsA common error extension
GLX missing!

By default, your vnc session cannot access OpenGL
or GPUs Any OpenGL-based application will
encounter this issue
16
Starting a Remote Visualization Job on Maverick
(Lab Exercise)

Step 8 Type vglrun glxgearsAccesses GPUs and
OpenGL libs via VirtualGL

VirtualGL captures framebuffer from GPU, forwards
it to vnc session Use vglrun d to specify which
GPU to use (d 0.0 is default) vglrun d
0.0 ltappgt vglrun d 0.1 ltappgt vglrun d
0.2 ltappgt vglrun d 0.3 ltappgt
17
Starting a Remote Vis Job on Spur(Lab Exercise)

Step 9 Type module avail in the xterm.

This will tell you which programs are available
to load and run. Some programs have module
dependencies (e.g. many vis programs) Some
programs are compiler and/or MPI-stack dependent
18
Topics

Remote and Collaborative Visualization
Remote Visualization on Spur
Scripted Visualization with VisIt
Python Primer
Create Image using Python Script
Change View and Apply Operators
Fly Around Dataset

19
One-Slide Intro to Python

def count_fingers(n)
if (n lt 0)
print How do you count negative fingers?!
elif (n gt 10)
print I only have ten fingers!
else
for i in range(0,n)
print d little piggy (i 1)

20
Inspecting VisIt Python Classes

gtgtgt s SaveWindowAttributes()
gtgtgt s
outputToCurrentDirectory 0
outputDirectory "C\Documents and
Settings\pnav\My Documents\VisIt 1.11.2\My
images"
fileName "visit"
family 1
format TIFF BMP, CURVE, JPEG, OBJ, PNG,
POSTSCRIPT, POVRAY, PPM, RGB, STL, TIFF, ULTRA,
VTK
width 1024
height 1024
screenCapture 0
saveTiled 0
quality 80
progressive 0
binary 0
stereo 0
compression PackBits None, PackBits, Jpeg,
Deflate
forceMerge 0
resConstraint ScreenProportions
NoConstraint, EqualWidthHeight, ScreenProportions

21
Basic VisIt Classes and Functions

OpenDatabase( ltFull Path to DBgt )
AddPlot( ltPlot Namegt )
pa ltPlot NamegtAttributes()SetPlotOptions( pa
)
AddOperator( ltOperator Namegt )
oa ltOperator NamegtAttributes()SetOperatorOptio
ns( oa )
DrawPlots()
once invoked, all commands that change plot will
update plot automatically
s SaveWindowAttributes()SetSaveWindowAttributes
( s )
SaveWindow()
view GetView3D()SetView3D( view )
DeleteAllPlots()
Full Interface description athttps//wci.llnl.go
v/codes/visit/1.4.1/PythonInterface1.4.1.pdf

22
Function to Change View Axis

def change_view(normal, up, nsteps10, start0)
c0 GetView3D()
c1 GetView3D()
c1.viewNormal normal
c1.viewUp up
cpts (c0, c1)
x (0., 1.)
for i in range(start, nsteps1)
t float(i) / float(nsteps)
c EvalCubicSpline(t, x, cpts)
SetView3D(c)
SaveWindow() uncomment to save image of
each step

23
Lab 1 Create Isosurface Plot

Open RectGrid2.vtk
Create Pseudocolor plot on scalars variable
Apply Isosurface operator

24
Lab 2 Clip Isosurface Plot on -Y

Rotate view from Z axis to Y axis
Create Clip operator
Change Clip attributes to change clip plane from
X axis to Y axis
Apply new clip attributes

25
Lab 3 Save Image Stack

Using change_view as a model, save an image stack
of the view changing
Bonus points change filename and image file type

26
Lab 4 Fly Around Plot

Using change_view as a model, create multiple
viewpoints to fly around dataset
Bonus points modulate viewpoints along wave
(will need to calculate orthogonal view and up)

27
Obrigado!pnav_at_tacc.utexas.edu
28
Helpful Hints for Labs 1 and 2
29
VisIt