Post-processing and visualisation of large-scale DEM simulation data with the open-source VELaSSCo platform

Regardless of its origin, in the near future the challenge will not be how to generate data, but rather how to manage big and highly distributed data to make it more easily handled and more accessible by users on their personal devices. VELaSSCo (Visualization for Extremely Large-Scale Scientific Computing) is a platform developed to provide new visual analysis methods for large-scale simulations serving the petabyte era. The platform adopts Big Data tools/architectures to enable in-situ processing for analytics of engineering and scientific data and hardware-accelerated interactive visualization. In large-scale simulations, the domain is partitioned across several thousand nodes, and the data (mesh and results) are stored on those nodes in a distributed manner. The VELaSSCo platform accesses this distributed information, processes the raw data, and returns the results to the users for local visualization by their specific visualization clients and tools. The global goal of VELaSSCo is to provide Big Data tools for the engineering and scientific community, in order to better manipulate simulations with billions of distributed records. The ability to easily handle large amounts of data will also enable larger, higher resolution simulations, which will allow the scientific and engineering communities to garner new knowledge from simulations previously considered too large to handle. This paper shows, by means of selected Discrete Element Method (DEM) simulation use cases, that the VELaSSCo platform facilitates distributed post-processing and visualization of large engineering datasets

Techniques and algorithms for immersive and interactive visualization of large datasets

Advances in computing power have made it possible for scientists to perform atomistic simulations of material systems that range in size, from a few hundred thousand atoms to one billion atoms. An immersive and interactive walkthrough of such datasets is an ideal method for exploring and understanding the complex material processes in these simulations. However rendering such large datasets at interactive frame rates is a major challenge. A scalable visualization platform is developed that is scalable and allows interactive exploration in an immersive, virtual environment. The system uses an octree based data management system that forms the core of the application. This reduces the amount of data sent to the pipeline without a per-atom analysis. Secondary algorithms and techniques such as modified occlusion culling, multiresolution rendering and distributed computing are employed to further speed up the rendering process. The resulting system is highly scalable and is capable of visualizing large molecular systems at interactive frame rates on dual processor SGI Onyx2 with an InfinteReality2 graphics pipeline

GODIVA2: interactive visualization of environmental data on the Web

GODIVA2 is a dynamic website that provides visual access to several terabytes of physically distributed, four-dimensional environmental data. It allows users to explore large datasets interactively without the need to install new software or download and understand complex data. Through the use of open international standards, GODIVA2 maintains a high level of interoperability with third-party systems, allowing diverse datasets to be mutually compared. Scientists can use the system to search for features in large datasets and to diagnose the output from numerical simulations and data processing algorithms. Data providers around Europe have adopted GODIVA2 as an INSPIRE-compliant dynamic quick-view system for providing visual access to their data

Hardware-accelerated interactive data visualization for neuroscience in Python.

Large datasets are becoming more and more common in science, particularly in neuroscience where experimental techniques are rapidly evolving. Obtaining interpretable results from raw data can sometimes be done automatically; however, there are numerous situations where there is a need, at all processing stages, to visualize the data in an interactive way. This enables the scientist to gain intuition, discover unexpected patterns, and find guidance about subsequent analysis steps. Existing visualization tools mostly focus on static publication-quality figures and do not support interactive visualization of large datasets. While working on Python software for visualization of neurophysiological data, we developed techniques to leverage the computational power of modern graphics cards for high-performance interactive data visualization. We were able to achieve very high performance despite the interpreted and dynamic nature of Python, by using state-of-the-art, fast libraries such as NumPy, PyOpenGL, and PyTables. We present applications of these methods to visualization of neurophysiological data. We believe our tools will be useful in a broad range of domains, in neuroscience and beyond, where there is an increasing need for scalable and fast interactive visualization

Pycortex: an interactive surface visualizer for fMRI.

Surface visualizations of fMRI provide a comprehensive view of cortical activity. However, surface visualizations are difficult to generate and most common visualization techniques rely on unnecessary interpolation which limits the fidelity of the resulting maps. Furthermore, it is difficult to understand the relationship between flattened cortical surfaces and the underlying 3D anatomy using tools available currently. To address these problems we have developed pycortex, a Python toolbox for interactive surface mapping and visualization. Pycortex exploits the power of modern graphics cards to sample volumetric data on a per-pixel basis, allowing dense and accurate mapping of the voxel grid across the surface. Anatomical and functional information can be projected onto the cortical surface. The surface can be inflated and flattened interactively, aiding interpretation of the correspondence between the anatomical surface and the flattened cortical sheet. The output of pycortex can be viewed using WebGL, a technology compatible with modern web browsers. This allows complex fMRI surface maps to be distributed broadly online without requiring installation of complex software

Somoclu: An Efficient Parallel Library for Self-Organizing Maps

Somoclu is a massively parallel tool for training self-organizing maps on large data sets written in C++. It builds on OpenMP for multicore execution, and on MPI for distributing the workload across the nodes in a cluster. It is also able to boost training by using CUDA if graphics processing units are available. A sparse kernel is included, which is useful for high-dimensional but sparse data, such as the vector spaces common in text mining workflows. Python, R and MATLAB interfaces facilitate interactive use. Apart from fast execution, memory use is highly optimized, enabling training large emergent maps even on a single computer.Comment: 26 pages, 9 figures. The code is available at https://peterwittek.github.io/somoclu