Supercomputers/Systems/Bio-X2
USA · operational · hpc
Bio-X2
Also known as Bio-X2 cluster; Stanford Bio-X squared
Operated by Stanford University .
Phase 1 seed dataset, compiled by hand. These rows were built from public operator, laboratory and vendor sources. A mechanical second-reader pass has since fetched every cited source: 1092 of 1153 systems have a readable citation that names them, and 40 are genuinely weakly sourced. Every claim carries its source and a confidence tier. Treat anything below verified as a lead, not a citation.
Measured performance
- Rmax
- 15.57 TFlop/s
- Rpeak
- 20.58 TFlop/s
- Rmax ÷ Rpeak
- 75.7%
- Cores
- 2,208
- Power
- -
- Per watt
- - GF/W
Figures are as last publicly reported for the configuration described below, not a live measurement. Where a system was upgraded in place, the post-upgrade configuration is shown and the earlier one appears in the timeline.
What this machine is made of
One row per supplier relationship. “Supplier at build” is the company that shipped the part at the time; where that company has since been acquired, the parent it rolls up to today is shown beside it. That distinction is what makes ticker-level aggregation possible across a thirty-year dataset.
| Role | Part | Supplier at build | Quantity | Confidence | Source |
|---|---|---|---|---|---|
| Integrator | - Dell PowerEdge 1950 cluster | Dell Technologies | - | Reported | top500.org |
| CPU | - Intel Xeon E5345 quad-core 2.33 GHz, 2,208 cores | Intel | - | Reported | top500.org |
| Interconnect | Mellanox InfiniBand DDR Interconnect Fat tree · 20 Gb/s per 4x port · About 2 microseconds 4x InfiniBand DDR | NVIDIA | - | Reported | top500.org |
The read
NSF-funded biological computing cluster at Stanford, a Dell PowerEdge 1950 system with 2,208 Xeon E5345 quad-core 2.33 GHz cores on InfiniBand DDR in the Stanford Biomedical Computational Facility. The Bio-X2 site describes 20 teraflops of 8-core nodes with 4x DDR InfiniBand, housed in the James H. Clark Center, funded by an NSF proposal from 21 Bio-X faculty with hardware donated by Dell and Cisco, and says it ranked number 54 on the June 2007 TOP500. TOP500 lists 15.57 TFlop/s Rmax and 20.58 TFlop/s Rpeak; it was 54th in June 2007, 73rd, 164th and 361st in November 2008, its last appearance.
Timeline
Public list appearances
Pointers only: rank and edition, linking to the canonical entry. We do not reproduce list tables. See sourcing policy.
Change history
- 2026-10-09 Added Bio-X2
Source check
We fetched this system's own citations and recorded whether each page actually mentions it. This is a corroboration signal, not a fact check, and it is published so you can see how well the sourcing holds up rather than take it on trust.
| Cited source | Result | Found on the page |
|---|---|---|
| web.archive.org | names system and part | Mellanox InfiniBand DDR |
| top500.org | names system and part | Mellanox InfiniBand DDR |
Checked 2026-10-09 by pnpm verify. Re-run it and the table changes with the web.
Further reading
Operating a supercomputer
Acceptance testing, why "installed" and "in production" are six months apart, and the machine lifecycle.
Inside a node
Latency-optimised versus throughput-optimised processors, NUMA, and the end of the host-to-device copy.
The interconnect
Topologies, why latency and tail behaviour matter more than bandwidth, and how the fabric market consolidated.