OpenGL® API-Based Analysis of Large Datasets in a Cloud Environment

Introduction

Due to the ability of X-rays to penetrate materials, they are highly appropriate to visualize internal structures of opaque objects. Moreover, X-ray-computed tomography provides the opportunity to visualize internal structures of optically dense materials in 3D. The intensity of X-rays emitted by synchrotron light sources is several orders of magnitudes higher than from laboratory sources and provide brilliant and partially coherent radiation for fast imaging with synchrotron radiation (Cloetens, Bolle, Ludwig, Baruchel, & Schlenke, 2001). The application of synchrotron-based X-ray-micro-tomography for biological samples was the onset of a new era of morphological research on millimetre-sized animals like small arthropods (e.g. Heethoff & Norton, 2009; van de Kamp, Vagovič, Baumbach, & Riedel, 2011; Schmelzle, Norton, & Heethoff,2015). In recent years, new setups enabled unrivalled opportunities of high-throughput measurements, 3D/4D-tomographic imaging of dynamic systems, and even living organisms (dos Santos Rolo, 2014). Online data evaluation became possible by the usage of advanced graphic processors for scientific computing (Chilingaryan, Kopmann, Mirone, dos Santos Rolo, & Vogelgesang, 2011). These new technologies, however, result in large amounts of data: currently up to 100 GByte per volume summing up to 15 TByte/day. Technical limitations are reached regarding data acquisition, storage, and organization. Analysis of tomographic data is usually time-consuming and many analysis steps relies on commercial applications that provide visual output based on the OpenGL® API for Microsoft operating systems (Mauch et al., 2014). An example for frequently used commercial applications are AMIRA™ and VG Studio MAX™, which are costly and might not be available at all user’s home institutions. In order to simplify the access to efficient analysis tools the idea was born to analyse the tomographic datasets in a cloud environment. This environment is based on a computing centre that is located directly at the data producing synchrotron facility. A tailored analysis tool chain should be pre-installed, licensed products could be used more effectively and complex installation procedures of open source tools or custom developments are avoided. But such an approach faces several difficulties for a virtual instantiation:

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  Possible lag of virtual machine desktops.

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  Analysis software like Amira requires GPU support for the OpenGL® and DirectX API as well as NVIDIA® CUDA™ support.

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  Interactive operation with 3D objects requires high frame rates.

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  Users might have only small bandwidth.

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  Very large VM RAM requirements for datasets in the magnitude of 50 to 100 GB.

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  High speed network interconnect from the VM to the data storage for loading and saving such datasets in a few minutes.

In order to deal with the challenges presented by fast state-of-the art synchrotron X-ray imaging, partners from the University of Darmstadt, the University of Heidelberg and Karlsruhe Institute of Technology (KIT) established the project ASTOR (“Arthropod Structure revealed by ultra-fast Tomography and Online Reconstruction), which is funded by the German Federal Ministry of Education and Research. In this chapter an overview of ASTOR’s cloud concept is given and different aspects are presented in detail.

Astor Workflow, Overview

Figure 1.

The scientific analysis workflow