Visualizing Biomolecular Complexes on x86 and KNL Platforms: Integrating VMD and OSPRay
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1 Visualizing Biomolecular Complexes on x86 and KNL Platforms: Integrating VMD and OSPRay John E. Stone Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign Research/vmd/ Intel HPC Developer Conference, 4:15pm to 5:05pm, Omni Downtown Austin Saturday Nov 14 th, 2015, Austin, TX
2 VMD Visual Molecular Dynamics Visualization and analysis of: molecular dynamics simulations quantum chemistry calculations particle systems and whole cells sequence data User extensible w/ scripting and plugins Research/vmd/ Poliovirus Ribosome Sequences Electrons in Vibrating Buckyball Cellular Tomography Cryo-electron Microscopy Whole Cell Simulations
3 Goal: A Computational Microscope Study the molecular machines in living cells Ribosome: target for antibiotics Poliovirus
4 Ray Tracing in VMD Support for ray tracing of VMD molecular scenes began in1995 Tachyon parallel RT engine interfaced with VMD (1999) Tachyon embedded as an internal VMD rendering engine (2002) Built-in support for large scale parallel rendering (2012) Refactoring of VMD to allow fully interactive ray tracing as an alternative to OpenGL (2014)
5 Tachyon Ray Tracing Engine Originally developed on Intel ipsc/860 hypercube (1994) First support for MPI (1995) Multithreading for Intel Paragon XP/S, large SGI and Sun shared memory machines (1995) In-situ CFD visualization (1996) Support for OpenMP w/ Kuck and Associates KCC (1998) Co-developed w/ VMD, 1998-present Rendering of Numerical Flow Simulations Using MPI. John Stone and Mark Underwood. Second MPI Developers Conference, pages , An Efficient Library for Parallel Ray Tracing and Animation. John E. Stone Master's Thesis, University of Missouri-Rolla, Department of Computer Science, April Early Experiences Scaling VMD Molecular Visualization and Analysis Jobs on Blue Waters. John E. Stone, Barry Isralewitz, and Klaus Schulten.. Extreme Scaling Workshop (XSW), pp , 2013.
6 Biomolecular Visualization Challenges Geometrically complex scenes Spatial relationships important to see clearly: fog, shadows, AO helpful Often show a mix of structural and spatial properties Time varying!
7 Geometrically Complex Scenes Ray tracing techniques well matched to molecular viz. needs: Curved geometry, e.g. spheres, cylinders, toroidal patches, easily supported Greatly reduced memory footprint vs. polygonalization Runtime scales only moderately with increasing geometric complexity Occlusion culling is free, RT acceleration algorithms do this and much more
8 Ray Tracing for Stereoscopic Planetarium Dome Masters, Panoramic Displays RT aptly suited to 360 panoramic rendering Single-pass rendering of stereo pairs, spheremaps, cubemaps, planetarium dome masters Stereo panoramas require spherical camera projection scheme that is (very) poorly suited to rasterization Easy to correct for VR headset lens distortions, e.g. Oculus Rift, Google Cardboard
9 Ray Tracing Naturally Supports Advanced Lighting and Shading Techniques Two lights, no shadows: typical of OpenGL Two lights, hard shadows, 1 shadow ray per light Two lights, shadows, ambient occlusion w/ 144 AO rays/hit
10 Benefits of Advanced Lighting and Exploit visual intuition Shading Techniques Spend computer time in exchange for scientists time, make images that are more easily interpreted
11 Ray Tracing Large Biomolecular Complexes: Large Physical Memory Required (128GB)
12 Ray Tracing Performance Well suited to massively parallel hardware Peak performance requires full exploitation of SIMD/vectorization, multithreading, efficient use of memory bandwidth Traditional languages and compilers not currently up to the task: Efficacy of compiler autovectorization for Tachyon and other classical RT codes is very low Core ray tracing kernels have to be explicitly designed for the target hardware, SIMD, etc.
13 Fast Ray Tracing Frameworks Applications focus on higher level RT ops SPMD-oriented languages and compilers address the shortcomings of traditional tools Intel RT frameworks provide performancecritical algorithms on IA hardware: Embree: triangles only OSPRay: general RT framework, includes not only basic kernels but also complete renderer implementations
14 Initial OSPRay support in VMD Support researchers with allocations at supercomputer centers with machines based on Knights Landing or Intel Xeon processors OSPRay functionality general enough for rendering requirements of the majority of VMD scenes Initial VMD-OSPRay development uses general purpose OSPRay renderers not specific to VMD Built-in OSPRay renderers could be used by any visualization tool VMD compensates for currently-unimplemented geometry types and mesh formats through automatic internal conversion
15 Molecular Structure Data and Global VMD State Scene Graph Graphical Representations User Interface Subsystem DrawMolecule Non-Molecular Geometry Tcl/Python Scripting Mouse + Windows VR Input Tools VMDDisplayList Display Subsystem Windowed OpenGL OpenGLDisplayDevice OpenGL Pbuffer DisplayDevice FileRenderer Tachyon OSPRay
16 VMD Scene Graph in OSPRay VMD currently flattens internal scene graph, transforms geom. to eye space, maps to native OSPRay geom. and materials Many opportunities for reduction of memory footprint, avoidance of reformatting Ongoing work: streamlining implementation, achieving close or identical shading where possible
17 VMD-OSPRay Offline/Batch Mode Ray Tracing Loop Scene Graph and RT accel. data structures Batch RT Rendering ospframebufferclear(osp_fb_accum) osprenderframe( OSP_FB_ACCUM) Loop until required antialiasing and ambient occlusion lighting samples have been accumulated ospmapframebuffer() Write Image to Disk ospunmapframebuffer() Write Output Framebuffer
18 VMD-OSPRay Interactive Ray Tracing with Progressive Refinement Scene Graph and RT accel. data structures RT Progressive Refinement Loop ospframebufferclear(osp_fb_accum) osprenderframe( OSP_FB_ACCUM) Check for User Interface Inputs, Update OSPRay Renderer State ospmapframebuffer() Draw ospunmapframebuffer() Draw Output Framebuffer
19 Early VMD+OSPRay Renderings
20 DNA and Silicon Nanopore
21 Polio Virus
22 Ribosome
23 Planar Photosynthetic Membrane Patch
24 Future Work Continue optimization of OSPRay renderer class Stereosopic, panoramic rendering in OSPRay Support upcoming ANL Aurora machine Interactive ray tracing of time-varying molecular geometry
25 Acknowledgements Theoretical and Computational Biophysics Group, University of Illinois at Urbana-Champaign Funding: NSF OCI NSF PRAC The Computational Microscope NIH support: 9P41GM104601, 5R01GM
26
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