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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
  • Open the file RectGrid2.vtk
  • Click File -gt Open
  • Select RectGrid2.vtk
  • Click OK
  • Active dataset highlighted

30
VisIt
  • Open the file RectGrid2.vtk
  • Click File -gt Open
  • Select RectGrid2.vtk
  • Click OK
  • Active dataset highlighted

31
VisIt
  • Create isosurfaces
  • Click Plots -gt Pseudocolor -gt scalars
  • Click Operators -gt Isosurface
  • Click OpAtts -gt Isosurface
  • Keep defaults, click Dismiss
  • Click Draw

32
VisIt
  • Create isosurfaces
  • Click Plots -gt Pseudocolor -gt scalars
  • Click Operators -gt Isosurface
  • Click OpAtts -gt Isosurface
  • Keep defaults, click Dismiss
  • Click Draw

33
VisIt
  • Create isosurfaces
  • Click Plots -gt Pseudocolor -gt scalars
  • Click Operators -gt Isosurface
  • Click OpAtts -gt Isosurface
  • Keep defaults, click Dismiss
  • Click Draw

34
VisIt
  • Create isosurfaces
  • Click Plots -gt Pseudocolor -gt scalars
  • Click Operators -gt Isosurface
  • Click OpAtts -gt Isosurface
  • Keep defaults, click Dismiss
  • Click Draw

35
VisIt
  • Create isosurfaces
  • Click Plots -gt Pseudocolor -gt scalars
  • Click Operators -gt Isosurface
  • Click OpAtts -gt Isosurface
  • Keep defaults, click Dismiss
  • Click Draw

36
VisIt
  • Create isosurfaces
  • Click Plots -gt Pseudocolor -gt scalars
  • Click Operators -gt Isosurface
  • Click OpAtts -gt Isosurface
  • Keep defaults, click Dismiss
  • Click Draw

37
VisIt
  • Clip isosurfaces
  • Rotate view to Y axis
  • Click Operators -gt Clip
  • Click OpAtts -gt Clip
  • Change Normal to 0 -1 0
  • Click Apply
  • Click Dismiss

38
VisIt
  • Clip isosurfaces
  • Rotate view to Y axis
  • Click Operators -gt Clip
  • Click OpAtts -gt Clip
  • Change Normal to 0 -1 0
  • Click Apply
  • Click Dismiss

39
VisIt
  • Clip isosurfaces
  • Rotate view to Y axis
  • Click Operators -gt Clip
  • Click OpAtts -gt Clip
  • Change Normal to 0 -1 0
  • Click Apply
  • Click Dismiss

40
VisIt
  • Clip isosurfaces
  • Rotate view to Y axis
  • Click Operators -gt Clip
  • Click OpAtts -gt Clip
  • Change Normal to 0 -1 0
  • Click Apply
  • Click Dismiss

41
VisIt
  • Clip isosurfaces
  • Rotate view to Y axis
  • Click Operators -gt Clip
  • Click OpAtts -gt Clip
  • Change Normal to 0 -1 0
  • Click Apply
  • Click Dismiss

42
VisIt
  • Clip isosurfaces
  • Rotate view to Y axis
  • Click Operators -gt Clip
  • Click OpAtts -gt Clip
  • Change Normal to 0 -1 0
  • Click Apply
  • Click Dismiss
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