Forgot to address two things: As for an 'optimal file structure', I'm not certain what exactly you're looking for. Our clusters that we run here are fairly standard linux installs (barebones, admittedly, but nothing fancy with the FS and layout), one large partition and one swap partition taking up a 4gb drive in each node. Node0 is kinda fancy (RAID and such), but it doesn't have to be.
As for the required software... you need MPICH (if that's the MPI stuff you run), rsh, and BootP/DHCP (Node0 is your server, and propagates to Nodex). Beyond that, just firewall Node0 heavily. The beowulf stuff really isn't much different from a barebones linux install with MPI code running. The only reason for the BootP and DHCP stuff is that here we use remote propagation of the OS to the nodes for security reasons. ~Warren
