HPC PROJECTS: VISUALISATION
A picture says a thousand words
Visualisation is a vital component of many HPC applications, but rendering huge datasets is no easy task,
as Stephen Mounsey discovers
W
hen the results of an abstract, intractable, or complicated system are visualised successfully, the results can make for some of the most engaging aspects of HPC today. Dr Lakshmi Sastry is a senior software engineer at the UK’s Science and Technology Facilities Council (STFC). Among her many interests, Dr Sastry works on optimising HPC data-processing for users of the STFC’s Isis neutron spectroscopy facility, and the Diamond Light Source synchrotron. ‘One of the results of high performance computing is extremely large amounts of data,’ she explains. ‘We’re talking about many gigabytes of data, and hundreds of megabytes per hour. This could come from simulations or observed data.’
Facilities such as Diamond and Isis are expensive: ‘When researchers are conducting experiments, they want to look at the data and see whether or not the experimental set-up is good, and to see whether they’re producing useful data,’ says Sastry. ‘Up until very recently, they would pay lots of money for a day at the facility, and then take the data back to their organisation, and only then find out if the work was useful. We’re now moving towards real time analysis and visualisation data,’ Sastry says, adding that researchers may also run simulations alongside their experiments to compare generated results to those they expect. A degree of in-line, real-time fine tuning is now possible.
Modelling the heart
Sastry’s techniques allow researchers to use computationally demanding visualisation algorithms without having their own on-site access to the expensive HPC equipment necessary. Sastry believes that the approach could have revolutionary applications in
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a clinical diagnostic setting – an area of medical science that has seldom taken advantage of HPC. A project called Integrated Biology, recently completed by the team, examined ways of improving the prognosis for heart attack patients through more accurate diagnosis of the extent of their heart attack. ‘Some people suffer a heart attack and go through treatment, and then make a full recovery, but some people pass away after suffering the first heart attack. The differences often depend on which parts of the heart tissue are damaged. Given that treatment is very uniform from outside [the body], it can actually miss [the affected area] – if, for example, the doctor tries to inject adrenaline, but it is injected into the ischemic tissue [the parts that have died due to lack of oxygen], it is not going to have a good effect.’ A group at Oxford University has created an anatomically correct mathematical model of the human heart, with a view to better understanding where these ischemic
areas are likely to be after a heart attack. ‘If they then run the model on the best supercomputer they have, using 2,000 processors, for 24 hours, they get seven seconds of simulation data,’ says Sastry, adding that this is insufficient to gain an understanding of the processes involved. Furthermore, supercomputing resources are limited, meaning that this approach might not allow the opportunity to adapt the simulation: ‘A big part of the project money would be used up, and it might not even give you any new information.’
Computational steering techniques, using
snapshots taken at intermediate times, allow the researchers to check that the simulation is proceeding in the correct direction, ensuring that computer resources are not wasted. ‘Computational steering is best achieved with 3D visualisation,’ states Sastry. ‘Again, the data produced is in very large quantities, and so real-time visualisation using a single machine is not possible.’ The ultimate aim of the Integrated
Biology project is to provide an accurate, mathematical model of how a healthy heart functions. Failing hearts can then be compared to this model in order to provide clinicians with an idea of where the damage is, and how best to treat it. A grid service would allow the demanding computation to be done wherever the resources exist, meaning that HPC facilities need not be co-located with the point of care. The computing resources required are significant: SCFC, alongside Edinburgh University, runs the UK’s Blue Gene and
HPC-driven visualisation has allowed archaeologists at the University of Birmingham, UK, to harness data from seismic surveys. The image shows an ancient river bed on the floor of the North Sea, where archaeologists believe Mesolithic people once lived. Image courtesy of VSG.
SCIENTIFIC COMPUTING WORLD APRIL/MAY 2010
www.scientific-computing.com
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