Advanced scientific visualization laboratory
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Advanced Scientific Visualization Laboratory. Paul Navrátil 28 May 2009. Topics. Remote and Collaborative Visualization Remote Visualization on Spur Scripted Visualization with VisIt. Old Model (No Remote Capability). Local Visualization Resource. HPC System. Pixels. Mouse. Data

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Advanced scientific visualization laboratory

AdvancedScientific VisualizationLaboratory

Paul Navrátil

28 May 2009


Topics

Topics

  • Remote and Collaborative Visualization

  • Remote Visualization on Spur

  • Scripted Visualization with VisIt


Old model no remote capability

Old Model (No Remote Capability)

Local

Visualization

Resource

HPC

System

Pixels

Mouse

Data

Archive

Display

Wide-Area

Network

Remote Site

Local Site


New model remote capability

New ModelRemote Capability

Pixels

Large-Scale

Visualization

Resource

HPC

System

Display

Mouse

Data

Archive

Wide-Area

Network

Remote Site

Local Site


New model multi user and collaborative capability

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

Remote Site

Local Site B


Spur visualization system

Spur - Visualization System

128 cores, 1 TB distributed memory, 32 GPUs

spur.tacc.utexas.edulogin node, no GPUsdon’t run apps here!

ivisbig.rangerSun Fire X4600 server

8 AMD Opteron dual-core CPUs @ 3 GHz

256 GB memory

4 NVIDIA FX5600 GPUs

ivis[1-7].rangerSun Fire X4440 server

4 AMD Opteron quad-core CPUs @ 2.3 GHz

128 GB memory

4 NVIDIA FX5600 GPUs


Spur ranger topology

Spur / Ranger topology

visqueue

$SCRATCH

spur

$WORK

$HOME

Vis nodesivis[1-7|big]

login3.ranger

normaldevelopment<etc>queues

HPC nodesixxx-xxx

login4.ranger

Login Nodes

Compute Nodes

File System


Topics1

Topics

  • Remote and Collaborative Visualization

  • Remote Visualization on Spur

  • Scripted Visualization with VisIt


Starting a remote vis job on spur lab exercise

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


Starting a remote vis job on spur lab exercise1

Starting a Remote Vis Job on Spur(Lab Exercise)

Step 2: ssh <username>@spur.tacc.utexas.edu


Starting a remote vis job on spur lab exercise2

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


Starting a remote vis job on spur lab exercise3

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.outonce job launches

Use visq to monitor job status


Starting a remote vis job on spur lab exercise4

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 <port>:spur.tacc.utexas.edu:<port> <user>@spur.tacc.utexas.edu

vnc communication is unencryptedso create ssh tunnel between your laptop and spur login

<port> : port assigned by vnc job

<user> : 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 <port> to remote machine:<port>


Starting a remote vis job on spur lab exercise5

Starting a Remote Vis Job on Spur(Lab Exercise)

Step 6: Connect to that display by using a vnc client

(3)

(1)

(2)


Starting a remote visualization job on maverick lab exercise

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


Starting a remote visualization job on maverick lab exercise1

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 <app>

vglrun –d :0.1 <app>

vglrun –d :0.2 <app>

vglrun –d :0.3 <app>


Starting a remote vis job on spur lab exercise6

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


Topics2

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


One slide intro to python

One-Slide Intro to Python

def count_fingers(n):

if (n < 0):

print “How do you count negative fingers?!”

elif (n > 10):

print “I only have ten fingers!”

else:

for i in range(0,n):

print “%d little piggy” % (i + 1)


Inspecting visit python classes

Inspecting VisIt Python Classes

>>> s = SaveWindowAttributes()

>>> 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

>>> s.format = s.PNG

>>> s.width, s.height = (1600, 1200)

>>> SetSaveWindowAttributes(s)


Basic visit classes and functions

Basic VisIt Classes and Functions

  • OpenDatabase( “<Full Path to DB>” )

  • AddPlot( “<Plot Name>” )

    pa = <Plot Name>Attributes()SetPlotOptions( pa )

  • AddOperator( “<Operator Name>” )

    oa = <Operator Name>Attributes()SetOperatorOptions( 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 at:https://wci.llnl.gov/codes/visit/1.4.1/PythonInterface1.4.1.pdf


Function to change view axis

Function to Change View Axis

def change_view(normal, up, nsteps=10, start=0):

c0 = GetView3D()

c1 = GetView3D()

c1.viewNormal = normal

c1.viewUp = up

cpts = (c0, c1)

x = (0., 1.)

for i in range(start, nsteps+1):

t = float(i) / float(nsteps)

c = EvalCubicSpline(t, x, cpts)

SetView3D(c)

# SaveWindow() # uncomment to save image of each step


Lab 1 create isosurface plot

Lab #1 – Create Isosurface Plot

  • Open RectGrid2.vtk

  • Create Pseudocolor plot on scalars variable

  • Apply Isosurface operator


Lab 2 clip isosurface plot on y

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


Lab 3 save image stack

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


Lab 4 fly around plot

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)


Obrigado pnav@tacc utexas edu

[email protected]


Helpful hints for labs 1 and 2

Helpful Hints for Labs #1 and #2


Visit

VisIt

Open the file RectGrid2.vtk

  • Click File -> Open

  • Select RectGrid2.vtk

  • Click OK

  • Active dataset highlighted


Visit1

VisIt

Open the file RectGrid2.vtk

  • Click File -> Open

  • Select RectGrid2.vtk

  • Click OK

  • Active dataset highlighted


Visit2

VisIt

Create isosurfaces

  • Click Plots -> Pseudocolor -> scalars

  • Click Operators -> Isosurface

  • Click OpAtts -> Isosurface…

  • Keep defaults, click Dismiss

  • Click Draw


Visit3

VisIt

Create isosurfaces

  • Click Plots -> Pseudocolor -> scalars

  • Click Operators -> Isosurface

  • Click OpAtts -> Isosurface…

  • Keep defaults, click Dismiss

  • Click Draw


Visit4

VisIt

Create isosurfaces

  • Click Plots -> Pseudocolor -> scalars

  • Click Operators -> Isosurface

  • Click OpAtts -> Isosurface…

  • Keep defaults, click Dismiss

  • Click Draw


Visit5

VisIt

Create isosurfaces

  • Click Plots -> Pseudocolor -> scalars

  • Click Operators -> Isosurface

  • Click OpAtts -> Isosurface…

  • Keep defaults, click Dismiss

  • Click Draw


Visit6

VisIt

Create isosurfaces

  • Click Plots -> Pseudocolor -> scalars

  • Click Operators -> Isosurface

  • Click OpAtts -> Isosurface…

  • Keep defaults, click Dismiss

  • Click Draw


Visit7

VisIt

Create isosurfaces

  • Click Plots -> Pseudocolor -> scalars

  • Click Operators -> Isosurface

  • Click OpAtts -> Isosurface…

  • Keep defaults, click Dismiss

  • Click Draw


Visit8

VisIt

Clip isosurfaces

  • Rotate view to +Y axis

  • Click Operators -> Clip

  • Click OpAtts -> Clip…

  • Change Normal to 0 -1 0

  • Click Apply

  • Click Dismiss


Visit9

VisIt

Clip isosurfaces

  • Rotate view to +Y axis

  • Click Operators -> Clip

  • Click OpAtts -> Clip…

  • Change Normal to 0 -1 0

  • Click Apply

  • Click Dismiss


Visit10

VisIt

Clip isosurfaces

  • Rotate view to +Y axis

  • Click Operators -> Clip

  • Click OpAtts -> Clip…

  • Change Normal to 0 -1 0

  • Click Apply

  • Click Dismiss


Visit11

VisIt

Clip isosurfaces

  • Rotate view to +Y axis

  • Click Operators -> Clip

  • Click OpAtts -> Clip…

  • Change Normal to 0 -1 0

  • Click Apply

  • Click Dismiss


Visit12

VisIt

Clip isosurfaces

  • Rotate view to +Y axis

  • Click Operators -> Clip

  • Click OpAtts -> Clip…

  • Change Normal to 0 -1 0

  • Click Apply

  • Click Dismiss


Visit13

VisIt

Clip isosurfaces

  • Rotate view to +Y axis

  • Click Operators -> Clip

  • Click OpAtts -> Clip…

  • Change Normal to 0 -1 0

  • Click Apply

  • Click Dismiss


  • Login