VMD: Immersive Molecular Visualization and Interactive Ray Tracing for Domes, Panoramic Theaters, and Head Mounted Displays
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1 VMD: Immersive Molecular Visualization and Interactive Ray Tracing for Domes, Panoramic Theaters, and Head Mounted Displays John E. Stone Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign 9:00am, Monday August 10, 2015 BOF: Immersive Visualization for Science and Research Siggraph 2015, Los Angeles, CA NIH BTRC for Macromolecular Modeling and Bioinformatics
2 VMD Visual Molecular Dynamics Visualization and analysis of: molecular dynamics simulations particle systems and whole cells cryoem densities, volumetric data quantum chemistry calculations sequence information User extensible w/ scripting and plugins Research/vmd/ Whole Cell Simulation MD Simulations Sequence Data Quantum Chemistry NIH BTRC for Macromolecular Modeling and Bioinformatics CryoEM, Cellular Tomography
3 Goal: A Computational Microscope Study the molecular machines in living cells Ribosome: target for antibiotics Poliovirus
4 VMD GPU-Accelerated Ray Tracing Engine Complementary to VMD OpenGL GLSL renderer Key ray tracing benefits: Ambient occlusion lighting and shadows High quality transparent surfaces Depth of field focal blur and similar optical effects Mirror reflection Single-pass stereoscopic rendering Special panoramic and 360 cameras: Planetarium dome master format Equirectangular spheremap projections Cubemap projections
5 Two lights, no shadows Lighting Comparison Two lights, hard shadows, 1 shadow ray per light Ambient occlusion + two lights, 144 AO rays/hit NIH BTRC for Macromolecular Modeling and Bioinformatics
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8 VMD Molecular Structure Data and Global State Scene Graph Graphical Representations DrawMolecule Non-Molecular Geometry User Interface Subsystem Tcl/Python Scripting Mouse + Windows VR Input Tools VMDDisplayList DisplayDevice Display Subsystem OpenGLDisplayDevice FileRenderer NIH BTRC for Macromolecular Modeling and Bioinformatics Windowed OpenGL GPU OpenGL Pbuffer GPU Tachyon CPU RT TachyonL-OptiX GPU RT Batch + Interactive
9 VMD Interactive GPU Ray Tracing High quality lighting, shadows, transparency, depth-of-field focal blur, etc. VMD now provides interactive ray tracing on laptops, desktops, and remote visual supercomputers Movie was recorded live while using remote visualization NIH BTRC for Macromolecular Modeling and Bioinformatics
10 VMD TachyonL-OptiX Interactive RT w/ Progressive Rendering Scene Graph RT Rendering Pass Seed RNGs Accumulate RT samples Accum. Buf TrBvh RT Acceleration Structure Normalize+copy accum. buf Compute ave. FPS, adjust RT samples per pass Output Framebuffer
11 VMD TachyonL-OptiX: Multi-GPU on NVIDIA VCA Cluster VMD Scene Scene Data Replicated, Image Space / Sample Space Parallel Decomposition onto GPUs VCA 0: 8 K6000 GPUs VCA N: 8 K6000 GPUs
12 VMD Planetarium Dome Master Camera Fully interactive RT with ambient occlusion, shadows, depth of field, reflections, and so on Both mono and stereoscopic No further post-processing required
13 Stereoscopic Panorama Ray Tracing w/ OptiX Render 360 images and movies for VR headsets such as Oculus Rift, Google Cardboard Ray trace panoramic stereo spheremaps, cubemaps that are displayed on to VR headset via OpenGL texturing Stereo requires spherical camera projection not well suited to rasterization Benefits from OptiX multi-gpu rendering, and load balancing NIH BTRC for Macromolecular Modeling and Bioinformatics
14 Future Work Further integration of interactive ray tracing into VMD o Seamless interactive RT in main VMD display o Support trajectory playback in interactive RT o Multi-node interactive RT on HPC systems Improved performance / quality trade-offs in interactive RT stochastic sampling strategies Optimize GPU scene DMA and BVH regen speed for time-varying geometry, e.g. MD trajectories Optimization of GPU-specific RT intersection routines, memory layout GPU-accelerated movie encoder back-end Interactive RT combined with remote viz on HPC systems, much larger data sizes NIH BTRC for Macromolecular Modeling and Bioinformatics GPU Ray Tracing of HIV-1 Capsid Detail
15 Acknowledgements Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign NVIDIA CUDA Center of Excellence, University of Illinois at Urbana- Champaign NVIDIA CUDA team NVIDIA OptiX team NCSA Blue Waters Team Funding: DOE INCITE, ORNL Titan: DE-AC05-00OR22725 NSF Blue Waters: NSF OCI , PRAC The Computational Microscope, ACI , ACI NIH support: 9P41GM104601, 5R01GM NIH BTRC for Macromolecular Modeling and Bioinformatics
16 Research Publications Research/vmd/ Visualization of Energy Conversion Processes in a Light Harvesting Organelle at Atomic Detail. M. Sener, J. E. Stone, A. Barragan, A. Singharoy, I. Teo, K. L. Vandivort, B. Isralewitz, B. Liu, B. Goh, J. C. Phillips, L. F. Kourkoutis, C. N. Hunter, and K. Schulten. SC'14 Visualization and Data Analytics Showcase, Unlocking the Full Potential of the Cray XK7 Accelerator. M. D. Klein and J. E. Stone. Cray Users Group, Lugano Switzerland, May GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting. J. E. Stone, R. McGreevy, B. Isralewitz, and K. Schulten. Faraday Discussions, 169: , GPU-Accelerated Molecular Visualization on Petascale Supercomputing Platforms. J. Stone, K. L. Vandivort, and K. Schulten. UltraVis'13: Proceedings of the 8th International Workshop on Ultrascale Visualization, pp. 6:1-6:8, Early Experiences Scaling VMD Molecular Visualization and Analysis Jobs on Blue Waters. J. Stone, B. Isralewitz, and K. Schulten. In proceedings, Extreme Scaling Workshop, Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories. M. Krone, J. Stone, T. Ertl, and K. Schulten. EuroVis Short Papers, pp , Immersive Out-of-Core Visualization of Large-Size and Long-Timescale Molecular Dynamics Trajectories. J. Stone, K. L. Vandivort, and K. Schulten. G. Bebis et al. (Eds.): 7th International Symposium on Visual Computing (ISVC 2011), LNCS 6939, pp. 1-12, 2011.
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