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: http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/

Abstract:

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 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.

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)

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.
(http://wwwcg.in.tum.de/Research/Projects/VisContest05)

This IEEE Visualization 2005 paper (accepted for publication) describes a new algorithm for the illustrative rendering of iso-surfaces and polygonal models. Using a combination of multi-pass rendering and image-space processing passes, hidden structures and optional additional inner geometry are displayed in real-time. No pre-processing of the geometric models is necessary. This work is part of Jan Fischer’s PhD thesis. (Illustrative Display of Hidden Iso-Surface Structures, Jan Fischer et al., IEEE Visualization 2005)

Sudipto Guha, Shankar Krishnan and Suresh Venkatasubramanian are presenting a tutorial on the use of the GPU for data visualization and mining at the ACM International Conference on Knowledge Discovery and Data Mining (KDD 2005). (Data Visualization and Mining on the GPU)

This paper presents a particle system for interactive visualization of steady 3D flow fields on uniform grids. For large particle systems, particle integration needs to be accelerated and the transfer of particle data to the GPU must be avoided. To fulfill these requirements, this paper exploits features of recent graphics accelerators to advect particles in the graphics processing unit (GPU), saving particle positions in graphics memory, and then sending these positions through the GPU again to obtain images in the frame buffer. (http://wwwcg.in.tum.de/Research/data/Publications/tvcg05.pdf)

This paper by Valerio Pascucci describes a simple technique to compute isosurfaces on programmable GPUs. Given the vertices of a tetrahedron a simple vertex program computes the position of the vertices, normal and connectivity of the potential portion of an isosurface contained in the tetrahedron (a marching tet approach). One main advantage of this technique is to offload the CPU of the task of computing the isosurface and more importantly to avoid storing the surface in main memory. Interestingly, one could compile a display list for a tetrahedral mesh and display different isosurfaces by changing an OpenGL parameter and always rendering the same list. The paper presents and comments in detail all the source code of the vertex program. (Isosurface Computation Made Simple: Hardware Acceleration, Adaptive Refinement and Tetrahedral Stripping. V. Pascucci, Proceedings of VisSym 2004)