Summary of the ExaViz project in English
New challenges in life and material sciences rely on the precise knowledge of structures and functions from nanometric down to the atomic length-scales. High performance computing is currently reaching the exascale and has the potential to face this major technical challenge.
There is need for new tools to cope with the growing size of the underlying simulations and datasets. In Life Science, molecular dynamics simulations are central to the study of complex biological assemblies. The size of such simulations has grown exponentially, but post-processing, analysis, visualization and exploration of the generated data have stalled. Exascale simulations require new, scalable software tools to mine this data and extract the relevant biological information. In materials science, nuclear magnetic resonance (NMR) spectroscopy, combined with numerical simulations, has the potential to play a major role in the molecular-level understanding of solid-state compositions and architectures, to ultimately aid the design of innovative advanced materials. Making this major step forward will necessitate an interface for the visualization of (potentially periodic) molecular structures and NMR spectra, in order to build currently missing bridges between experiments, numerical models and structural information.
The ExaViz project aims at developing a framework for the interactive visual analysis of experimental and simulation data, and capable of handling the complex datasets generated by exascale simulations and the difficulties inherent to the integration of heterogeneous codes. By coupling virtual reality, scientific visualization and parallel simulation, we target two grand challenge applications: modeling a complete influenza virus and analyzing simulations of the GLIC receptor that we recently published in the journals Nature and PNAS.
We propose to gather interdisciplinary skills to design from component-based approaches a specific programming environment for scalable scientific visualization and visual analytics integrating new and efficient ways of building and deploying the applications on PC clusters. This framework, dedicated to experimentalists as well as theoreticians, will enable an interactive visual interpretation of phenomena to encourage cooperation and exchange between chemists, physicists and biologists. While the classical desktop is the first target for controlling the analysis process, we will also support and experiment immersive environments such as CAVEs as well as web and mobile devices.
These objectives will be achieved though the unique combination of highly complementary expertise from five partners. The LBT has a long experience in molecular simulation of biological macromolecules and in virtual reality approaches. The CEMHTI partner provides know-how in the combination of experimental and numerical approaches to solid-state NMR spectroscopy for materials science. The LIFO and Moais partners have developed FlowVR, a component oriented middleware for running parallel interactive applications on PC clusters. They both have a long-standing experience in parallel algorithms, code coupling and interactive visualization. The LIMSI partner is at the forefront of state-of-the-art virtual reality platforms in Europe. Further support will finally be provided by external collaborations with Prof. M.S.P. Sansom (Oxford Univ.) for simulations of viral capsids running on thousands of processors, and Prof. T. Ertl (Univ. of Stuttgart), an international leader on rendering and visual analytics, for the integration of codes (eg Megamol) developed in his group.
Through the development of a framework for the analysis and visualization of large molecular simulations, ExaViz will open the way to exascale in silico experiments. Scenarios resulting from a close collaboration between domain experts and computer scientists will validate ExaViz. The distribution of our open code base may gather a community of users and contributors well beyond the patterns of the project.
