HPC PROJECTS: VISUALISATION
HPCX supercomputers and is also one of the UK National Grid Service’s (NGS) nodes. In addition, Dr Sastry uses a powerful dedicated visualisation cluster, optimised for handling very large amounts of data through the use of InfiniBand interconnects. Scientists wishing to use the visualisation capacity offered connect via the grid, and the computational workload is distributed across the visualisation cluster and other resources as available. ‘In order to do this, we partition the data and farm out the processing to different nodes. It’s then brought back together, and it creates a full image. We build-in the intelligence to stitch all of the images back together dynamically, in the correct way.’ The resulting visualisation data is then sent back to the scientists running the application.
‘Computational steering is best achieved with 3D visualisation’
Lost worlds
Visualisation techniques are often the only way for researchers to gain an understanding of real-world scans. It would be nearly impossible for oil prospectors to identify the regions they’re looking for by examining raw seismological data, and so information from seismic surveys is turned into a 3D map of an area’s geology. As a result of these accessible, intuitive visualisations, the tried and tested surveying techniques of petrochemical prospectors have found new applications in other disciplines, including archaeology. The IBM Visual and Spatial Technology Centre (VISTA) at the University of Birmingham, UK, has used HPC-driven visualisation to uncover details of an area of land that was reclaimed by the North Sea more than 10,000 years ago. Seismic data, produced by Petroleum Geo-Services (PGS), was analysed by the Birmingham group using Avizo visualisation software, produced by VSG. Daniel Lichau, a product expert at VSG, explains that the group used the data to conduct an extensive sub-surface survey of the ground underneath the North Sea. Again, hundreds of gigabytes of data had to be processed, necessitating an HPC-driven approach. ‘The first use for Avizo is to inspect and
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browse very large data sets,’ says Lichau. ‘The technology to achieve this is based on a multi-resolution approach, allowing the user to display data progressively, which may not fit on memory storage. The Avizo software manages data between disk memory and the graphics board in order to bring a visualisation to the user.’ In addition, the software allowed the group to label parts of the data, such as an ancient riverbed running through the area under investigation. In this way, archaeologists at the university were able to identify areas of the sea floor that were once inhabited by Mesolithic people. Both Avizo and the seismic surveying techniques used were developed with oil and gas prospecting in mind, but archaeology has been able to take advantage of these powerful tools, with some fascinating results.
Peeling statues
In a similar way, while computerised X-ray tomography (CT scanning) has become an invaluable tool in clinical medicine, its applications are not limited to medicine. Researchers at the Department of Physics, of the University of Bologna, Italy, have used HPC-driven visualisation to analyse CT data in order to investigate hidden aspects of several ancient works of art, with a view to better preservation of the artefacts. The CT technique is not new, but Professor Franco Casali and his group have developed innovative methods of analysing the data produced – techniques specifically suitable for studying large works of art. The team explains that one particular analysis of a two-metre high wooden Japanese statue (known as a Kongo¯rikishi) generated more than 24,000 individual radiographic images, amounting to 120GB of data. Prior to the adoption of an HPC solution, processing the images of the Kongo¯rikishi took up to two months using a single dual- core machine running Windows XP and the group’s C++ based software. The researchers were able to achieve resolution better than the standard in medicine, but they added that processing times of this length negated the usefulness of the analysis, especially considering that researchers have to travel to the art to take these scans. The university therefore needed a system that was capable of dealing with the complex algorithms involved, at much higher speeds, and
HPC-driven visualisation has been used to analyse ancient works of art, such as this Kongo¯ rikishi statue. By switching to a cluster running Microsoft’s Windows HPC Server 2008, the team at the University of Bologna’s Department of Physics increased data processing performance by a factor of 75.
capable of doing so wherever the artefacts were located. Having already written its algorithms, the university also wanted a solution that did not require their developers to re-write the software. Vince Mendillo, director of HPC at Microsoft, recalls the difficulties of the application: ‘The tomographic images they were making essentially used a frequency sensor’s input, cut into slices; it’s a very complex approach. Their requirements were to employ something that was capable of large sweeps of analysis, and able to process large quantities of data.’ The department now conducts its calculations on a four-node, eight-core cluster, running the Windows HPC Server 2008 operating system. ‘We’re seeing Windows HPC Server applied in some cutting-edge areas,’ says Mendillo. ‘The group experienced a speed- up in performance of a factor of 75 when they switched to a fairly modestly-sized cluster configuration running Windows HPC Server, and they didn’t have to re-write their code; it is portable between the Windows client, the server, and our future Cloud versions.’
The benefits of the increased visualisation
capacity are comparable to those offered by Sastry’s work, in that it allows the researchers to make the most of their time through real-time analysis of their work. Mendillo states that the performance of the new system exceeded the group’s expectations. ‘We have a key focus on
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