Clustering Is Not Rocket Science
About 12 months after receiving our first 66 nodes, we had the opportunity to purchase 60 more dual-Opteron nodes, thanks to funding from the University of Queensland. Applying the same tools and techniques just described, we were able to integrate the additional 60 nodes into our cluster with minimal time and effort. The main technical difficulty we faced as we scaled up the compute resources was the additional load on the file server. It is well known that the present NFS version (v3) that is bundled with Linux does not scale well with increasing nodes. We have circumvented this situation by employing two file servers to share the load. The ideal situation would have been to invest in a dedicated storage area network (SAN). With 66 nodes, this would have been overkill, and due to the capricious nature of research funding in a university environment, we could never predict that we would have the money to buy an additional 60 nodes.
Although there is a little more detail involved with the cluster setup, such as setting common time across the cluster with NTP, the collection of tools just described forms the basis of cluster operation and administration. This leaves time for research and the chance to use the cluster for some interesting science and engineering.
At the Centre for Hypersonics at the University of Queensland, there are two primary areas of research: planetary-entry vehicles and scramjets. Planetary-entry vehicles experience enormous heat loads during atmospheric entry, and this is a primary design concern for the aerospace engineer. Using the cluster, we can do large-scale parallel computations of the high-temperature gaseous flow around typical spacecraft. So far, we have studied spacecraft re-entering Earth, entering Mars and Titan, the largest moon of Saturn. In addition to computations of realistic spacecraft configurations, we also study simplified geometries like spheres and cylinders in order to better understand the fundamental flow physics at these high temperatures.
The other main focus of research at the Centre for Hypersonics is the study, design and optimization of scramjet engines. When traveling at speeds many times faster than the Concorde, scramjets suffer from large amounts of aerodynamic drag. The drag forces experienced play a leading role in determining the performance capabilities of these engines. The cluster allows for theories of drag reduction, such as near wall hydrogen combustion, to be examined in very fine detail. Using complex three-dimensional turbulence models, we can study the very fine scales of the flow that govern the amount of drag.
Figure 1 shows an example of the results of computations inside a scramjet combustion chamber. The colored contours represent vorticity, which is an indication of mixing, and the shaded pattern shows flow density variations.
The Centre for Computational Molecular Science (CCMS) engages in interdisciplinary research in areas where molecular scale computations are involved. The areas of research are diverse and include studies of electronic structure, quantum and molecular dynamics, computational nanotechnology and biomolecular modelling. Among the current projects is the computational modelling of red fluorescent proteins found in coral reefs that have application in deep-tissue biomedical imaging. Another project is investigating materials for hydrogen storage in future fuel cell technologies.
The quantum and molecular dynamics group conducts research into the detailed dynamics and mechanisms of gas phase reactions. These reactions involving only a few atoms often play the key role in atmospheric or combustion cycles. The detailed quantum-level calculations are parallel in nature and are impractical to do serially as the memory requirements far exceed the average desktop. Of current interest is the study of the reaction of hydrogen with molecular oxygen. It is one of the most important reactions in the combustion of hydrocarbon fuels.
Figure 2 provides a graphical representation of quantum dynamic collision of an hydrogen atom and an oxygen molecule. The figure shows the wavefunction and the potential energy for the HOO system. From right to left: the hydrogen atom approaches the oxygen molecule, the HOO complex is formed (a deep well can be seen in the potential energy surface), the complex breaks apart and the products O and OH (hydroxyl radical) are formed.