Visualization of Energy Conversion Processes in a Light Harvesting Organelle at Atomic Detail

February 11th, 2015


The cellular process responsible for providing energy for most life on Earth, namely, photosynthetic light-harvesting, requires the cooperation of hundreds of proteins across an organelle, involving length and time scales spanning several orders of magnitude over quantum and classical regimes. Simulation and visualization of this fundamental energy conversion process pose many unique methodological and computational challenges. We present, in an accompanying movie, light-harvesting in the photosynthetic apparatus found in purple bacteria, the so-called chromatophore. The movie is the culmination of three decades of modeling efforts, featuring the collaboration of theoretical, experimental, and computational scientists. We describe the techniques that were used to build, simulate, analyze, and visualize the structures shown in the movie, and we highlight cases where scientific needs spurred the development of new parallel algorithms that efficiently harness GPU accelerators and petascale computers.

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, 2014. Paper PDF

Webinar on April 8th: Geospatial 3D Visualization in the Cloud with GPUs

April 2nd, 2014

This webinar covers how Geoweb3d uses the GPU for real-time geospatial 3D visualization, modeling, and analytics. Geoweb3D will demonstrate how native, high resolution datasets including GIS, CAD, 3D Models, LIDAR, and FMV are fused together in real-time with game quality graphics and pixel accurate analysis. The 3D engine uses a GPU resident mesh that adapts to any resolution data on the fly eliminating the need to preprocess any data prior to real-time use. Demonstration will include Geoweb3d Mobile which now uses HTML5 for use on any device in the cloud including phones and tablets.

To register follow this link:

GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting

March 26th, 2014


Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures of large biomolecular complexes. Evaluating the quality-of-fit obtained from hybrid fitting is computationally demanding, particularly in the context of a multiplicity of structural conformations that must be evaluated. Existing tools for quality-of-fit analysis and visualization have previously targeted small structures and are too slow to be used interactively for large biomolecular complexes of particular interest today such as viruses or for long molecular dynamics trajectories as they arise in protein folding. We present new data-parallel and GPU-accelerated algorithms for rapid interactive computation of quality-of-fit metrics linking all-atom structures and molecular dynamics trajectories to experimentally-determined density maps obtained from cryo-electron microscopy or X-ray crystallography. We evaluate the performance and accuracy of the new quality-of-fit analysis algorithms vis-a-vis existing tools, examine algorithm performance on GPU-accelerated desktop workstations and supercomputers, and describe new visualization techniques for results of hybrid structure fitting methods.

(John E. Stone, Ryan McGreevy, Barry Isralewitz, and Klaus Schulten: “GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting”. Faraday Discussion 169, 2014. [DOI])

GPU-Accelerated Molecular Visualization on Petascale Supercomputing Platforms

March 5th, 2014


Petascale supercomputers create new opportunities for the study of the structure and function of large biomolecular complexes such as viruses and photosynthetic organelles, permitting all-atom molecular dynamics simulations of tens to hundreds of millions of atoms. Together with simulation and analysis, visualization provides researchers with a powerful “computational microscope”. Petascale molecular dynamics simulations produce tens to hundreds of terabytes of data that can be impractical to transfer to remote facilities, making it necessary to perform visualization and analysis tasks in-place on the supercomputer where the data are generated. We describe the adaptation of key visualization features of VMD, a widely used molecular visualization and analysis tool, for GPU-accelerated petascale computers. We discuss early experiences adapting ray tracing algorithms for GPUs, and compare rendering performance for recent petascale molecular simulation test cases on Cray XE6 (CPU-only) and XK7 (GPU-accelerated) compute nodes. Finally, we highlight opportunities for further algorithmic improvements and optimizations.

(John E. Stone, Kirby L. Vandivort, and Klaus Schulten: “GPU-Accelerated Molecular Visualization on Petascale Supercomputing Platforms”. UltraVis’13: Proceedings of the 8th International Workshop on Ultrascale Visualization, pp. 6:1-6:8, 2013. [DOI])

Fast Visualization of Gaussian Density Surfaces for Molecular Dynamics and Particle System Trajectories

August 1st, 2012


We present an efficient algorithm for computation of surface representations enabling interactive visualization of large dynamic particle data sets. Our method is based on a GPU-accelerated data-parallel algorithm for computing a volumetric density map from Gaussian weighted particles. The algorithm extracts an isovalue surface from the computed density map, using fast GPU-accelerated Marching Cubes. This approach enables interactive frame rates for molecular dynamics simulations consisting of millions of atoms. The user can interactively adjust the display of structural detail on a continuous scale, ranging from atomic detail for in-depth analysis, to reduced detail visual representations suitable for viewing the overall architecture of molecular complexes. The extracted surface is useful for interactive visualization, and provides a basis for structure analysis methods.

(Michael Krone, John E. Stone, Thomas Ertl, and Klaus Schulten, “Fast visualization of Gaussian density surfaces for molecular dynamics and particle system trajectories”, In EuroVis – Short Papers 2012, pp. 67-71, 2012. [WWW])

VMD 1.9.1 released

February 9th, 2012

VMD is a popular molecular visualization and analysis program used by thousands of researchers worldwide. VMD accelerates many of the most computationally demanding visualization and analysis features using GPU computing techqniques, resulting in improved performance and new capabilities beyond what is possible using only conventional multi-core CPUs. VMD 1.9.1 advances these capabilities further with a CUDA implementation of the new QuickSurf molecular surface representation, enabling smooth interactive animation of moderate sized biomolecular complexes consisting of a few hundred thousand to one million atoms, and allowing interactive display of molecular surfaces for static structures of very large complexes containing tens of millions of atoms, e.g. large virus capsids.

More information:

Efficient High-Quality Volume Rendering of SPH Data

September 27th, 2010

Efficient High-Quality Volume Rendering of SPH DataAbstract:

High quality volume rendering of SPH data requires a complex order-dependent resampling of particle quantities along the view rays. In this paper we present an efficient approach to perform this task using a novel view-space discretization of the simulation domain. Our method draws upon recent work on GPU-based particle voxelization for the efficient resampling of particles into uniform grids. We propose a new technique that leverages a perspective grid to adaptively discretize the view-volume, giving rise to a continuous level-of-detail sampling structure and reducing memory requirements compared to a uniform grid. In combination with a level-of-detail representation of the particle set, the perspective grid allows effectively reducing the amount of primitives to be processed at run-time. We demonstrate the quality and performance of our method for the rendering of fluid and gas dynamics SPH simulations consisting of many millions of particles.

(Roland Fraedrich, Stefan Auer, and Rüdiger Westermann: “Efficient High-Quality Volume Rendering of SPH Data”, IEEE Transactions on Visualization and Computer Graphics (Proceedings of IEEE Visualization 2010), vol. 16, no. 6, Nov.-Dec. 2010, Link to project webpage including paper, pictures and video)

VMD 1.8.7 release supports CUDA on MacOS X, Linux, Windows

August 31st, 2009

VMD is a molecular visualization program for building, displaying, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. One of the key advancements included in VMD 1.8.7 is support for GPU-accelerated visualization and analysis, based on CUDA. VMD uses CUDA to accelerate several of its most computationally demanding algorithms, with additional modules planned for GPU acceleration in upcoming releases. Typical GPU acceleration factors for the algorithms in VMD are: electrostatics 22x to 44x, implicit ligand sampling 20x to 30x, molecular orbital calculation 100x to 120x.

Real-Time Particle Level Sets with Application to Flow Visualization

May 24th, 2007

This technical report by N. Cuntz, R. Strzodka and A. Kolb describes a particle level set (PLS) system for fast and accurate surface tracking on the GPU. The technique demonstrates the coupling of grid and particle information by using vertex/fragment buffer objects, shaders and blending functionality in an innovative way. Improvements over the original PLS technique include a sub-voxel interface representation and a more accurate level set correction using more precise particle radii. As a concrete application the authors demonstrate that their fast and accurate PLS is well suited to the visualization of dynamic flows. An accurate evolution of time surfaces and representation of path volumes offer a more reliable basis for data interpretation. (Real-Time Particle Level Sets with Application to Flow Visualization. Technical report, 2007)

GPGPU Application wins 1st prize in IEEE Visualization Contest

October 31st, 2005

Jens Schneider, Polina Kondratieva, Jens Krüger, and Rüdiger Westermann from TU Munich have won the 2005 IEEE Visualization Contest with their work “All you need is particles!” Check out the video of their results; it’s very interesting.