This projects was underwritten by a grant from the
National Science Foundation for Professor Jeffrey Fox, Mathematics, and Professor Robert C. Eaton as co-principal investigator. The cluster is housed in the Departments of Biology (EPO),
Center for Neuroscience, under the management of Professor Eaton.
With unique parallel Fortran code written by Professor Fox and his students, the cluster will assist researchers who are interested in understanding the biophysics of computation in neural dendrites at the molecular dynamics level.
"From my point of view, there is going to be explosive growth in demand for HPC in the biological sciences. The very nature of the people using this technology requires as little assembly of the hardware and software as possible, otherwise small labs will not be able to afford the time and expense of using cluster computing. While cluster computing is not a yet turn key affair ... the closer it gets to workstation status the more it will be incorporated into small labs," states Professor Fox.
Terra Soft provided a single source HPC solution for Fox, with expertise and support for the Yellow Dog Linux operating system, Black Lab cluster management suite, and Apple hardware.
We went with Black Lab ... to minimize our effort
Fox continues, "None of the people working on the project are experts in parallel computation, computer science, or applied mathematics. Our focus is on the biology and biophysics, so we went with Yellow Dog/Blacklab [in order to] minimize the amount of time and effort needed to set up a cluster for scientific computing."
While the Apple Xserve does serve as a headless HPC node with as many as four or no local drives at all, the
30 nodes (60 CPUs) in this cluster have the following components:
dual 1GHz G4 CPUs per node
1GB RAM per node
single 60GB drive per node
a local YDL OS built by the Black Lab server
gig-e internode communication fabric
The internode communication is made possible by an HP ProCurve Gig-e Switch with:
dual hot-swap power supplies
6 bays each with 6 gig-e ports, total 36 gig-e ports
The cluster is housed in a hand-built Bud Industries rack case with:
removable front and rear doors and side panels
industrial strength casters
internal cabling channels
overhead cooling fan
Black Lab eliminates the need for keyboard and monitor switches, provides automated server to node process migration, and is immediately scalable to several hundred nodes. Yellow Dog Linux provides a professional open-source distribution substantiated by a large, growing PowerPC userbase.
The G4 was chosen [for its] price/performance ratio.
Fox concludes, "We were very aggressive in our plans for the model in terms of computation, yet we had a very modest budget for hardware. The G4 was chosen [for its] price/performance ratio. The Xserve with gigabit ethernet is ideal for the current message passing requirements."
Terra Soft promotes a hands-on design and build experience that is educational, enjoyable, and professional.
Terra Soft's customers are given an opportunity to be involved with every step of the process (Professor Fox, above, bottom-right). Terra Soft worked with Fox in September '02 to build a 4-node, code development cluster comprised of Apple PowerPC G4s that were at one time used as desktop workstations. This cluster is housed in Fox's office, Department of Mathematics, while he maintains a LAN connection to the primary cluster which is housed in the Department of Biology.
For this project, Terra Soft's services included purchase and delivery of all components; assembly, cable management, testing; node building (via Black Lab) and instruction for Fox and his students. The entire cluster, internode communication components, case, installation, and training were provided for less than $150,000.
2002
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