X-ray imaging software tools for HPC clusters and the Cloud

Abstract

Computed Tomography (CT) is a non-destructive imaging technique widely used across many scientific, industrial and medical fields. It is both computationally and data intensive, and therefore can benefit from infrastructure in the “supercomputing” domain for research purposes, such as Synchrotron science. Our group within CSIRO has been actively developing X-ray tomography and image processing software and systems for HPC clusters. We have also leveraged the use of GPU's (Graphical Processing Units) for several codes enabling speedups by an order of magnitude or more over CPU-only implementations. A key goal of our systems is to enable our targeted “end users”, researchers, easy access to the tools, computational resources and data via familiar interfaces and client applications such that specialized HPC expertise and support is generally not required in order to initiate and control data processing, analysis and visualzation workflows. We have strived to enable the use of HPC facilities in an interactive fashion, similar to the familiar Windows desktop environment, in contrast to the traditional batch-job oriented environment that is still the norm at most HPC installations. Several collaborations have been formed, and we currently have our systems deployed on two clusters within CSIRO, Australia. A major installation at the Australian Synchrotron (MASSIVE GPU cluster) where the system has been integrated with the Imaging and Medical Beamline (IMBL) detector to provide rapid on-demand CT-reconstruction and visualization capabilities to researchers whilst on-site and remotely. A smaller-scale installation has also been deployed on a mini-cluster at the Shanghai Synchrotron Radiation Facility (SSRF) in China. All clusters run the Windows HPC Server 2008 R2 operating system. The two large clusters running our software, MASSIVE and CSIRO Bragg are currently configured as “hybrid clusters” in which individual nodes can be dual-booted between Linux and Windows as demand requires. We have also recently explored the adaptation of our CT-reconstruction code to Cloud infrastructure, and have constructed a working “proof-of-concept” system for the Microsoft Azure Cloud. However, at this stage several challenges remain to be met in order to make it a truly viable alternative to our HPC cluster solution. Recently, CSIRO was successful in its proposal to develop eResearch tools for the Australian Government funded NeCTAR Research Cloud. As part of this project our group will be contributing CT and imaging processing components.