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INTEL® HPC DEVELOPER CONFERENCE
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Software-Defined Visualization: Getting the most out of ParaView w/ OSPRay
▶ Intel HPC Developer ConferenceNovember, 2016
Paul A. Navrátil, Ph.D.TACC
David E DeMarleKitware
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Software-Defined Visualization
Performant Visualization across Hardware Platforms
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Agenda
▶ Part I-A: Visualization Rendering – A Brief Overview
▶ Hardware configurations and considerations
▶ Rasterization summary
▶ Ray tracing summary
▶ Part I-B: Obtaining SDVis Components (sdvis.org)
▶ OpenSWR – openswr.org
▶ OSPRay – ospray.github.io
▶ ParaView– tacc.github.io/pvOSPRay
▶ Part II: Demonstrations – ParaView + OSPRay
▶ Wavelet data source
▶ Meningioma
▶ FIU ground core sample
▶ Remote Visualization to TACC
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Part II : Hands On
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❏ What you need❏ SSIS Intel_Connect pwd “saltlake16”
paraview (download 5.2 RC4)data:
www.paraview.org/Wiki/ Intel_HPC_Dev_Con_ParaView_and_OSPRay_Tutorial
USB’s (please return them)local SMB fileshare:
“afp://172.17.4.105” or “smb://172.17.4.105”.
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Workflow Overview – HPC vs. Vis
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Typical HPC Workflow
Initial Conditions01001101011001
11001010010101
00101010100110
11101101011011
00110010111010
αβγ
ParametersSimulation
Timestep 101001101011001
11001010010101
00101010100110
11101101011011
00110010111010
Timestep n01001101011001
11001010010101
00101010100110
11101101011011
00110010111010
Results
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Typical Visualization Workflow
Timestep 101001101011001
11001010010101
00101010100110
11101101011011
00110010111010
Timestep n01001101011001
11001010010101
00101010100110
11101101011011
00110010111010
Visualization Algorithms
Geometry
Rendering Images Display
Iterate! 8
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Original Community Solution: Move All Interaction to Client for Vis
File Size
100Gbps
10 Gbps 1 Gbps 300
Mbps 54
Mbps
1 GB < 1 sec 1 sec 10 sec 35 sec 2.5 min
1 TB ~100 sec ~17 min ~3
hours~10
hours~43
hours
1 PB ~1 day ~12 days
~121 days >1 year ~5
years
Files too large to move out of data center where they were generated 9
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Visualization Rendering Methods
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Vis Algorithm Renderer
Scientific Visualization Process
▶ the primary goal of visualization is insight
▶ a picture really is worth 1,000 words or (potentially) tera-/peta-/exa-bytes of data
▶ as dataset sizes increase so does the need for scientific visualization
0100110101100111001010010101001010101001101110110101101100110010111010
Raw Data Geometry Pixels
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Rasterization and Ray-Tracing
▶ Rasterization – project 3D data onto 2D image plane, step across image plane to determine color
▶ Often accelerated by purpose-built hardware
▶ Performance complexity a function of total geometry
▶ Shading typically not physically-based
▶ Ray Tracing – sample 3D data through 2D image plane, simulating light ray travel
▶ Efficient with modern many core, wide vector CPUs
▶ Performance complexity a function of visible data
(acceleration structure build a function of total data)
▶ Physically-based shading “easy” (performance varies)
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Rasterization Pipeline
Modeling Transformatio
ns
Rasterization Display
Trivial Rejection
IlluminationViewing
Transformations
Clipping Projection
Starts with data or models that are described in (x,y,z) coordinates. The data usually defines solids or boundaries in terms of their skins. Transform from data coordinates to something called world space.
Object Space
World Space
(tessellated)
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Rasterization Pipeline
Modeling Transformatio
ns
Rasterization Display
Trivial Rejection
IlluminationViewing
Transformations
Clipping Projection
Attempt to eliminate any objects that can not possibly be seen. Check endpoints of a triangle, line segment or point and store a flag for inside or outside. Perform a logical and of the endpoints to determine whether the entity is wholly in or out of the view.
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Rasterization Pipeline
Modeling Transformatio
ns
Rasterization Display
Trivial Rejection
IlluminationViewing
Transformations
Clipping Projection
Compute normals at the endpoints for lighting calculation:
Ambient Diffuse Specular
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Rasterization Pipeline
Modeling Transformatio
ns
Rasterization Display
Trivial Rejection
IlluminationViewing
Transformations
Clipping Projection
Change coordinate systems such that the eye sits at the origin and the viewing plane is defined. This is called eye space.
-X
Y
Z
Right Handed Viewing System
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Rasterization Pipeline
Modeling Transformatio
ns
Rasterization Display
Trivial Rejection
IlluminationViewing
Transformations
Clipping Projection
Eliminate any triangles or points that are not within the view frustum (outside the scene) so that we don’t have to draw them.
-X
Y
Right Handed Viewing System
Z
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Rasterization Pipeline
Modeling Transformatio
ns
Rasterization Display
Trivial Rejection
IlluminationViewing
Transformations
Clipping Projection
Project 3D objects to 2D Viewing plane. This is a projection from eye space to screen space.
-X
Y
Z
Right Handed Viewing System
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Rasterization Pipeline
Modeling Transformatio
ns
Rasterization Display
Trivial Rejection
IlluminationViewing
Transformations
Clipping Projection
Convert the object into pixels using some sort of interpolation (usually linear).
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Rasterization Pipeline
Modeling Transformatio
ns
Rasterization Display
Trivial Rejection
IlluminationViewing
Transformations
Clipping Projection
Starts with data or models that are described in (x,y,z) coordinates. The data usually defines solids or boundaries in terms of their skins. Transform from data coordinates to something called world space
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OpenGL Pipeline
Vertex operations such as lighting, clipping, projection and viewport mapping
Series of framebuffer addresses and values.
Series of conditional tests such and modifications such as blending and z-buffering
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Recursive Ray Tracing Example
A
C
B
DA
CB
D
ray tree
E
E
…
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Recursive Ray Tracing Example
A
C
B
DA
B C
D
ray tree
primary ray
secondary rays
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Acceleration Structures
▶ First ray tracers tested every object for intersectionCreated acceleration structures to reduce object tests
▶ Focus object tests on those that are likely to be hit
▶ Bound a complex object with a simpler one if simple test fails, no need for complex test
▶ Partition space to group objects, only test objects when a ray enters their partition
▶ Acceleration structure creates groups of scene data
▶ These groups determine which data are accessed together
▶ Nearby objects accessed together only if they occupy the same part of the acceleration structure
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Bounding Volume Hierarchy
A
CE
B
D
A
B C
D E
• Subdivides object space
• Bounded regions can overlap
• Must test all regions per level to find nearest intersection
boxes for B and C overlapC and E are nearby in the scene but occupy different parts of acceleration structure
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K-D Tree
▶ Subdivides scene space
▶ Objects may be duplicated or split to fit
▶ Structure can be unbalanced and deep
A
CE
B
D
A
C
ED
B,C
C overlaps C duplicated in tree
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Why Ray Tracing?
Jeffrey Howard, Intel Corporation
• Images compare “easy” rasterization with “easy” ray tracing
• Advanced rasterization can simulate some ray tracing effects, but ray tracing produces higher quality and is generally easier to implement
intereflection
caustic
soft shadows anti-aliasing
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Realistic Optic Effects
Motion Blur Depth of Field
R. Cook, T. Porter, L. Carpenter T. Kim
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Accurate Simulation of Light Travel
Copyright Audi AG
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Better Lighting for Visualization
C. Gribble and S. Parker
local shading ambient occlusion
shadows diffuse interreflections
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Better Lighting for Visualization
C. Gribble and S. Parker
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Richtmyer-Meshkov InstabilityCarson Brownlee, Aaron Knoll, Paul Navrátil, TACC
Ingo Wald, Carsten Benthin, Sven Woop, Intel
OpenGL version – flat lighting, constant shadows, limited depth perception 32
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Richtmyer-Meshkov InstabilityCarson Brownlee, Aaron Knoll, Paul Navrátil, TACC
Ingo Wald, Carsten Benthin, Sven Woop, Intel
Embree RT version – rich lighting, ambient occlusion, improved depth perception 33
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Richtmyer-Meshkov InstabilityCarson Brownlee, Aaron Knoll, Paul Navrátil, TACC
Ingo Wald, Carsten Benthin, Sven Woop, Intel
Embree RT version with ‘glass’ planes – integrated, realistic material behavior 34
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South Florida Ground Core SampleSade Garcia, Michael Sukop (Florida International University),
Kevin Cunningham (US Geological Survey), Carson Brownlee, Aaron Knoll (TACC)
OpenGL version – flat lighting, constant shadows, limited depth perception35
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South Florida Ground Core SampleSade Garcia, Michael Sukop (Florida International University),
Kevin Cunningham (US Geological Survey), Carson Brownlee, Aaron Knoll (TACC)
Embree RT version – rich lighting, ambient occlusion, improved depth perception36
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South Florida Ground Core SampleSade Garcia, Michael Sukop (Florida International University),
Kevin Cunningham (US Geological Survey), Carson Brownlee, Aaron Knoll (TACC)
Embree RT version – rich lighting, ambient occlusion, improved depth perception37
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Implicit Surface Intersection
▶ Ray tracing can intersect surfaces directly without explicit tessellation
▶ Example: molecular data from materials simulations
▶ “ball and stick” surfaces + potential field volumes
20× – 100× memory savingsand faster image generation! 38
A. KnollA. Knoll
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Simulation of N-Acetyl-L-tryptophanamide through a Cellular Membrane
Alfredo Cardenas, Ron Elber (ICES UT Austin)Aaron Knoll, Anne Bowen (TACC), Ingo Wald (Intel)
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tryptophan locations clearly expressed
Simulation of N-Acetyl-L-tryptophanamide through a Cellular Membrane
Alfredo Cardenas, Ron Elber (ICES UT Austin)Aaron Knoll, Anne Bowen (TACC), Ingo Wald (Intel)
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Software-Defined Visualization Libraries
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SDVis Rasterization
▶ Mesa 3D Graphics Library – mesa3d.org
▶ Open-source general OpenGL implementation
▶ Often included in Linux distros
▶ Convenient, if not always performant, default for CPU
▶ OpenSWR – openswr.org
▶ Open-source OpenGL implementation tuned for Intel CPUs
▶ Performant rendering using wide-vector instructions
▶ OpenGL coverage for visualization and more
(integrated into Mesa3D 12.0)
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SDVis Ray Tracing
▶ GLuRay – tacc.github.io/GLuRay/
▶ Provides basic ray tracing via OpenGL intercept
▶ Fallback to rasterized OpenGL (OpenSWR, Mesa, HW)
▶ Supported in part by NSF award ACI-1339863
▶ GraviT – tacc.github.io/GraviT/
▶ Provides efficient memory management and work scheduling for distributed-memory ray tracing
▶ Uses GLuRay for basic interface, advanced interface for improved performance and feature support
▶ Designed to generalize for use in simulation codes
▶ Supported in part by NSF award ACI-1339863
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SDVis Ray Tracing▶ Manta – mantawiki.sci.utah.edu
▶ Open-source, generally performant ray tracer
▶ ParaView plug-in available
▶ OSPRay – ospray.github.io
▶ Open-source ray tracer tuned for Intel hardware
▶ ParaView plug-in available (tacc.github.io/pvOSPRay/)
▶ OptiX – developer.nvidia.com/optix
▶ Closed-source ray tracer tuned for NVIDIA hardware
▶ Supports CPU execution (though less performant)
▶ IndeX – nvidia-arc.com/products/index.html
▶ Closed-source DVR tuned for NVIDIA hardware
▶ Requires license to operate
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❏ What you needparaview (download 5.2 RC4)data:
www.paraview.org/Wiki/ Intel_HPC_Dev_Con_ParaView_and_OSPRay_Tutorial
USB’s (please return them)local SMB fileshare:
“afp://172.17.4.105” or “smb://172.17.4.105”.
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Part II : Hands On
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▶ What is ParaView?An application and architecture for display and
analysis of massive* scientific datasets.Client/Server architecture lets it runs on variety of
platforms from netbooks to the largest machines in the world
Open Source, commercially friendly BSD licenseLarge user/developer baseCommercial support available through Kitware
▶ http://www.paraview.org/download/
▶ http://www.paraview.org/Wiki/The_ParaView_Tutorial Presented Monday @ SC
1.1 Trillion Cells on 1/19’th of DOE Trinity & OpenSWR
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ParaView
HistoryStarted in 2000 as collaborative effort between Los
Alamos National Laboratories and Kitware Inc. (lead by James Ahrens).
ParaView 0.6 released October 2002.September 2005: collaborative effort between
Sandia National Laboratories, Kitware Inc. and CSimSoft to rewrite user interface to be more user friendly and develop quantitative analysis framework.
3.0 May 2007, Qt, Python, 2d Plots5.0 October 2015 - SWR, TACC pvOSPRay plugin5.1 May 2016 - integrated OSPRay for surfaces5.2 November 2016 - add OSPRay volumes
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▶ Based on VTKVisualization Pipeline
OSPRay integrated into VTK, so any VTK app can usehttps://blog.kitware.com/ray-traced-rendering-revisited/
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User Interface
Menu Bar
Toolbars and Shortcuts
Pipeline Browser
Properties PanelApply ButtonSearch FieldShow Advanced
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▶ http://www.paraview.org/Wiki/The_ParaView_Tutorial Presented Monday @ SC
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File->Open “disk_out_ref.ex2”
Filters->Contour
Click on disk_out_ref.ex2 to make it active again
Filters->Extract Surface
Filters->Clip SHOW
HIDE
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OSPRay Rendering
Wavelet : procedurally generated volumetric data
Sources->Wavelet
Outline, Surface, Solid Color -> “RTData”, Volume
View Section at bottom of Properties -> Enable OSPRay
Volume->Wireframe, zoom in compare
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Not colormapped?
Too thin? Thick?
OSPRay OpenGL
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Filters->Contour isosurfaces
Turn on Shadows
Notes:* scene and self shadowing* speckle shadow bug with
line/cylinders and point/spheres
* “LightKit” 6 lights in scene, mostly above and from camera better controls soon
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Volumes Cast Shadows w/ OSPRay
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Level Of Detail - not at all helpful
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Unlike rasterization framerate doesn’t really depend on how many primitives in scene. Also switching back and forth is slower than with GL.
Glyph Mode : Uniform Spatial -> All PointsGlyph Type : 2D Vertex -> Sphere
Disable ParaView’s LODEdit->Settings (OSX: ParaView->Preferences) -> Render View -> LOD Threshold to max
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Implicit Spheres and Cylinders
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Filters->Glyph Traditional: Glyph Type = Sphere Ray traced implicit : 2D Glyph, Vertex
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▶ Scaled Implicits, finer control than “Point Size”
Filters-> Python Calculator : expression = RTData/max(RTData)uncheck “Interpolate Scalars before mapping”check “OSPRay Use Scale Array on”change from “OSPRay Scale Array = RTData” to “= result”Hit “OSPRay Scale, Edit” to change value->Radius transfer function “
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Part II : Hands On
Real Data: Meningioma
longitudinal study
Load MRBrainTumor1,2
isocontour
slice
extract VOI, volume render
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Part II : Hands On
Real Data:
FIU
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Part II : Hands On
▶ Demonstration : remote visualization
▶ https://portal.tacc.utexas.edu/user-guides/maverick#visapps-paraview
▶ possibly File->Connect (internal) or TACC startup with desktop forwarding
▶ Run parallel job
▶ Explain secondary rays problem, GraviT, Intel’s MPI DMP volumes
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TACC Remote Visualization
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Why Visualize Remotely?
- Avoid moving data (especially TB or PB!)
- Access many nodes for enhanced analysis powerHundreds to thousands of compute nodes available
- Visualize together with simulation computation- in situ / co-processing- computational steering
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TACC Remote Visualization
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Two Connection Models:
- TACC Visualization Portalhttps://vis.tacc.utexas.edu/
- SLURM Job on Login Nodessh stampede.tacc.utexas.edu ORssh login-knl1.stampede.tacc.utexas.edusbatch -A <acct> /share/doc/slurm/job.vnc <opts>
- Both use VNC remote desktop
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TACC Visualization Portal
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- Which machine- Project to be billed- Session Type
- VNC- Rstudio- iPython / Jupyter Notebook
- VNC desktop resolution- Number of compute nodes- Number of processes per node- Click < Start Job >
- Before first run, must set VNC Password(different from login, 6-8 char)
Need TACC or XSEDE login credentials
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Enter VNC password here
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TACC Visualization Portal
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- VNC job blocks on this xterm (black background)Close it to end job
- Closing the web browser DOES NOT end the VNC job
- Allows you to reconnect without losing work
- If not expressly ended, job will run until time limit reached
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Select Jobs tab for running jobs
Click Terminate Session to end job
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VNC SLURM Job
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After connecting to login node:vncpasswd # only needed before first executiontouch vncserver.out # only needed if file does not existsbatch -A <acct> /share/doc/slurm/job.vnc <opts>
for example:sbatch -A A-ccvis /share/doc/slurm/job.vnc -geometry 19020x1080
monitor job status by following output file:tail -f vncserver.out
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VNC SLURM Job
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When job runs, displays VNC port connection info:Created reverse ports on Stampede KNL loginsYour VNC server is now running!To connect via VNC client: SSH tunnel port 36602 to
login-knl1.stampede.tacc.utexas.edu:36602 Then connect to localhost::36602
To tunnel port from localhost (for secure connection):ssh -f -N -L 36602:login-knl1.stampede.tacc.utexas.edu:36602 \
login-knl1.stampede.tacc.utexas.edu
Then connect VNC viewer to localhost:<VNC port>vncviewer localhost:36602
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FIU Dataset Demo
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Groundwater flow through karst limestone core sampledata courtesy of Florida International University and U.S. Geological Survey
Data available at /work/00401/pnav/data/fiu_nhdr
We will visualize: the karst substrate (rho, ~0.9 GB)the fluid flow (u, ~1.4 GB)
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Load nhdr data
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Create stream tracer
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Enable ambient occlusion (AO)
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Create contour
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Create clip plane
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▶ What’s next?▶ In-situ optimizations▶ Progressive Refinement, Path Tracer, Lights, Materials▶ Secondary Rays in DMP
▶ Want to know more?▶ The ParaView Tutorial, Monday at SC16▶ Come see us at the TACC, Kitware and Intel booths▶ Sunday talk by Paul▶ Sunday talk by Dave
Thank you!
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INTEL® HPC DEVELOPER CONFERENCE