Linux PC Cluster III - Umbriel
Our third Linux cluster, made up of Athlon MPs and collectively known as the Umbriel cluster, was designed and configured in 2003. At purchase it consisted of 72 dual-processor Athlon machines with 512MB of memory each, divided into three independent 24-node clusters. It went into service in May 2003, and is still in service.
System Specifications
- 2x AMD Athlon MP 2600+ CPUs
- Gigabyte GA-7DPXDW-P Motherboard
- Antec SX835II ATX Case
- 512MB PC2100 ECC DDR SDRAM (one DIMM)
- Intel PRO/1000MT Server Gigabit Network Card (64-bit)
- Sony 1.44MB floppy drive
- Western Digital 40GB Special Edition HD (root nodes only)
- 16x Sony DVD-ROM drive (root nodes only)
- nVidia TNT2 32MB AGP Video Board
- Runs Clustermatic on a RedHat 8.0
- Built by Champaign Computer
umbriel, miranda, caliban
Each of these clusters consists of twenty-four dual-processor Athlon systems. Only the root node of each system has a hard drive and DVD-ROM; the rest only have floppy drives.
Each cluster is controlled as a single root node, which is controlled much like a standard Linux box. Computations are divided up and transferred to the rest of the cluster by a single front end machine. The other machines have no keyboard, mouse, or monitor; they only connect via the network. The machines are connected through three 24-port managed gigabit switches.
We also purchased four additional nodes, configured for serial use but usable as spare root nodes if necessary. These systems have 2GB of RAM (in two DIMMs) but are otherwise identical to the root nodes of the above systems.
Performance
Using the molecular dynamics code NAMD we achieved these speedups on a 92,000 atom system on our clusters (as of March 2004, benchmarked with NAMD 2.5):
| CPUs | Sec/Step | Speed-Up | Efficiency |
|---|---|---|---|
| 1 | 4.41 | 1 | 100% |
| 2 | 2.26 | 1.96 | 97.8% |
| 4 | 1.21 | 3.64 | 91.0% |
| 8 | 0.624 | 7.07 | 88.4% |
| 16 | 0.323 | 7.07 | 88.6% |
| 24 | 0.222 | 19.8 | 82.6% |
| 32 | 0.170 | 25.9 | 81.0% |
| 48 | 0.122 | 36.4 | 75.83% |
Breakdown of Costs (at time of purchase)
| Count | Unit Cost | Total | Description | |
|---|---|---|---|---|
| Systems, Round 1 | 24 | $1,135.00 | $27,240.00 | umbriel |
| Systems, Round 2 | 24 | $1,061.00 | $25,464.00 | caliban |
| Systems, Round 3 | 24 | $1,050.00 | $25,200.00 | miranda |
| Extra Root Node Parts | 3 | $144.00 | $432.00 | Hard Drive, CD-ROM |
| Serial Nodes | 4 | $1,792.00 | $7,168.00 | lyon, istanbul, kiev, budapest |
| Gigabit Switches | 3 | $2,575.00 | $7,725.00 | SMC TigerSwitch 8624T |
| Shelves, Cables, Etc | ~$ 2,000.00 | |||
| Total | $95,229.00 | |||
