March 2008
Urgent Computing: Exploring Supercomputing's New Role
Steven Manos
Stefan Zasada
Peter V. Coveney, Centre for Computational Science, Chemistry Department, University College London

2.1 The need for resource reservation and urgent computing

When used as part of the clinical decision making process, computational resources often need to support more exotic scheduling policies than simple first come, first served, batch scheduling, which is the typical scenario seen in high-performance research computing today. Clinicians who require interactive access to machines (for example, for steering and visualisation, as well as cross-site applications, for example when performing cerebral blood flow simulations using the HemeLB code discussed later in this article) also need to be able to both schedule time on specific resources - compute and networking - and access tools to allow them to easily co-reserve those resources, so they are available when needed. This in turn leads to a demand on resource providers to implement policies and tools that allow such reservations to be made as needed and when required, so that such methodologies can be incorporated into a user's normal research activities, rather than just providing such facilities on an ad hoc basis. Moreover, the resources provided by a single grid may not always be sufficiently powerful or appropriate to run large-scale distributed models, and resources provided by multiple grids may need to be federated in order for a particular investigation to be conducted.

If these resources need to be used interactively, the problem of reservation becomes compounded since each grid has its own policies and systems for making advanced reservations, if it has any at all. Additionally, the high performance network provision between grids may also be limited or non-existent. Nevertheless, such obstacles must be overcome to make efficient use of available federated systems.

The key factor that transcends all of the current patient-specific medical simulation scenarios described in this article is the need to turn simulations around fast enough to make the result clinically relevant. This in turn means that the results can be obtained and interpreted within a timeframe on which a clinical decision is made; for example, in the HIV case described later this is roughly two weeks – the time it takes to get the results of a genotypic assay. To achieve the required turn around factor, such simulations cannot be run in a resource’s normal batch mode; they need to be given a higher priority and they require some form of on-demand computing to succeed.

3. Different paradigms for on-demand computing

We consider two different urgent computing paradigms in order to make use of supercomputing resources, provided by a grid, in clinical scenarios; the advance reservation of CPU time on a compute resource at some specific point in the future, and the pre-emption of running jobs on a machine by some ‘higher priority’ work. The two paradigms apply to slightly different situations; the former would be of most use when a clinician knows in advance that a simulation needs to be performed at a specific time, for example an interactive brain blood-flow simulation run for a surgeon while planning or conducting a surgical procedure. The second paradigm is most useful when a medical simulation needs to be performed urgently, but the need for the simulation is not known in advance. An example of this latter simulation would be where a clinician encounters a HIV patient and urgently needs to compute the efficacy of a series of inhibitor drugs in relation to the patient’s specific HIV mutation.

There is crossover between the two different urgent computing paradigms considered, and to a certain extent both apply to each of the situations mentioned. We favour a combination of both paradigms, to give clinicians and scientists the greatest amount of flexibility possible for the work they need to conduct. We discuss the technical aspects of the two paradigms in greater detail below.

Pages: 1 2 3 4 5 6 7 8 9

Reference this article
Manos, S., Zasada, S., Coveney, P. V. "Life or Death Decision-making: The Medical Case for Large-scale, On-demand Grid Computing," CTWatch Quarterly, Volume 4, Number 1, March 2008. http://www.ctwatch.org/quarterly/articles/2008/03/life-or-death-decision-making-the-medical-case-for-large-scale-on-demand-grid-computing/

Any opinions expressed on this site belong to their respective authors and are not necessarily shared by the sponsoring institutions or the National Science Foundation (NSF).

Any trademarks or trade names, registered or otherwise, that appear on this site are the property of their respective owners and, unless noted, do not represent endorsement by the editors, publishers, sponsoring institutions, the National Science Foundation, or any other member of the CTWatch team.

No guarantee is granted by CTWatch that information appearing in articles published by the Quarterly or appearing in the Blog is complete or accurate. Information on this site is not intended for commercial purposes.