A Generalization of Algebraic Surface Drawing
ACM Transactions on Graphics (TOG)
OptiX: a general purpose ray tracing engine
ACM SIGGRAPH 2010 papers
In Situ Visualization for Large-Scale Combustion Simulations
IEEE Computer Graphics and Applications
Quantifying the impact of GPUs on performance and energy efficiency in HPC clusters
GREENCOMP '10 Proceedings of the International Conference on Green Computing
Immersive molecular visualization and interactive modeling with commodity hardware
ISVC'10 Proceedings of the 6th international conference on Advances in visual computing - Volume Part II
Journal of Computational Physics
Parallel Contour-Buildup algorithm for the molecular surface
BIOVIS '11 Proceedings of the 2011 IEEE Symposium on Biological Data Visualization
Accelerated visualization of dynamic molecular surfaces
EuroVis'10 Proceedings of the 12th Eurographics / IEEE - VGTC conference on Visualization
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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.