Supercomputers @ Home




"No matter how smart the algorithms - they are always too slow to do what they are supposed to do - overnight on a desktop PC" - that's a well known experience in bioinformatics. Luckily it turns out that most of the time, a simple scale up by one or two orders of magnitude is enough to get it running (probably our brains can only think at most two orders of magnitude ahead of current computer powers..).
If the task parallelizes very well (which is true for most areas covered by YASARA, but certainly not for all applications of interest), then there is only one simple way to obtain a maximum performance for each dollar invested: Buying a Linux cluster of cheap PCs, linked with Ethernet (Figure 1).

But the best performance / price ratio (i.e. infinite) can still be achieved by not buying anything at all - just abuse what is already present. At the CMBI, we turned our 26 Linux/Windows PCs into one big distributed computing cluster, using our software package Models@Home (Figure 2-4).



In principle, Models@Home is a screen saver that runs our jobs as soon as the computer is idle. The very general design allows to run whichever program one needs, as long as it is available for either of the two currently supported operating systems: Linux or Windows. It is aimed at course grained applications that can easily be split up into multiple jobs and do not require much data exchange. If you want to build your own cluster, Models@Home is available for free download.
Fortunately, most applications in structural bioinformatics are very course grained and thus ideally suited for our cluster: Model building, threading, docking, data base updates etc.