Only four supercomputers dedicated to life science research rank among the fastest systems in the world, according to the most recent version of the Top500 list released this week at the International Supercomputing Conference in Dresden, Germany.
The previous version of the ranking, released in November, included nine life science systems [BioInform 11-21-05]. The new list includes one new life science entry -- an 800-processor Sun cluster at Cedars-Sinai with Linpack benchmark performance of 2.5 teraflop/s. Six systems that qualified for the November ranking fell short of the 2.026 TFlop/s entry point for the current list, however: the Center of Excellence in Bioinformatics at the University at Buffalo (two separate systems); Arizona State University/Translational Genomics Research Institute; the Institute of Life Science at the University of Wales Swansea; the National Cancer Institute; and an undisclosed US life science company.
The highest-ranking life science computer, an 18.2 TFlop/s IBM BlueGene system at the Computational Biology Research Center at Japan's National Institute of Advanced Industrial Science and Technology, holds the No. 15 spot in the current list (see table below for details on all the life science systems on the list). This system was ranked No. 12 six months ago.
Another BlueGene system, the BlueGene/L at DOE's Lawrence Livermore National Laboratory, claimed the No. 1 spot for the third time in a row with a Linpack benchmark performance of 280.6 TFlop/s.
IBM now has 24 BlueGene systems on the list, up from 19 in November, and dominates the list overall, with nearly half the computers in the current ranking -- 239. Hewlett-Packard claims 31 percent of the top 500 supercomputers, with 157 systems, while Dell comes in a distant third, with 22 (see table below for details on manufacturer rankings).
While clusters are still the most common architecture, with 364 of the systems on the list, growth appears to have tapered off in the last six months, with only four more cluster-based systems making it into the top 500 since November (see table below for details on computational architectures in the list).
In terms of processors, Intel chips are at the core of 301 of all 500 systems, down slightly from 333 systems six months ago. IBM's Power processor family is the second most common processor family, with 84 systems, while AMD's Opterons are gaining ground, with 81 systems using them compared to 55 six months ago (see table below for details on processor generations on the list).
Linux remains the most popular operating system for high-performance computing, claiming 367 of the top 500, followed by 98 Unix-based systems, 24 "mixed" systems, 5 Mac OS, 4 BSD, and 2 Windows systems, including a 4.1 TFlop/s system at the National Center for Supercomputer Applications running Microsoft Computer Cluster 2003, ranked at No. 130.
The Top500 list is compiled every six months. Complete details are available at http://www.top500.org/.
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Top-Ranking Life Science Supercomputers, June 2006
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Rank June 2006
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Rank Nov. 2005
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Installation Site
|
Manufacturer/
Computer |
Number
of Processors |
Tflop/s (max)
|
Year installed
|
|
15
|
12
|
Computational Biology Research Center, AIST (Japan)
|
IBM/"Blue Protein" eServer Blue Gene Solution |
8,192
|
18.2
|
2005
|
|
255
|
293
|
Institute of Genomics and Integrative Biology (India)
|
Hewlett-Packard/Cluster Platform 3000 (3.6 GHz Xeon) |
576
|
2.2
|
2005
|
|
412
|
--
|
Cedars-Sinai
|
Sun Microsystems/Fire x2100 Cluster (2.2 GHz dual core Opteron) |
800
|
2.5
|
2006
|
|
431
|
268
|
Wellcome Trust Sanger Institute
|
IBM/HS20 Cluster, (3.2 GHz Xeon) |
600
|
2.4
|
2005
|
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Top500 Supercomputer Manufacturer Ranking, June 2006
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Manufacturer
|
Rank June 2006
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Rank Nov. 2005
|
Change in Rank
|
Count June 2006
|
Count Nov. 2005
|
Change in
Count |
| IBM | 1 | 1 | -- | 239 | 219 | +20 |
| Hewlett-Packard | 2 | 2 | -- | 157 | 169 | -12 |
| Dell | 3 | 5 | +2 | 22 | 21 | +1 |
| Cray Inc. | 4 | 3 | -1 | 16 | 18 | -2 |
| SGI | 5 | 4 | -1 | 12 | 18 | -6 |
| Linux Networx | 6 | 6 | -- | 8 | 16 | -8 |
| Sun Microsystems | 7 | 12 | +5 | 7 | 4 | +3 |
| Hitachi | 8 | 8 | -- | 6 | 5 | +1 |
| Self-made | 9 | 10 | +1 | 6 | 5 | +1 |
| Fujitsu | 10 | 11 | +1 | 4 | 4 | -- |
| NEC | 11 | 7 | -4 | 4 | 6 | -2 |
| Atipa Technology | 12 | 9 | -3 | 3 | 5 | -2 |
| Intel | 13 | 13 | -- | 2 | 2 | -- |
| Rackable Systems | 14 | 25 | +11 | 2 | 1 | +1 |
| HPTi | 15 | 14 | -1 | 1 | 1 | -- |
| Appro International | 16 | 16 | -- | 1 | 1 | -- |
| lenovo | 17 | 17 | -- | 1 | 1 | -- |
| California Digital Corporation | 18 | 18 | -- | 1 | 1 | -- |
| Angstrom Microsystems | 19 | 19 | -- | 1 | 1 | -- |
| Dawning | 20 | 20 | -- | 1 | 1 | -- |
| Bull SA | 21 | 21 | -- | 1 | 1 | -- |
| Exadron | 22 | -- | -- | 1 | 0 | +1 |
| Apple | 23 | 22 | -1 | 1 | 1 | -- |
| Galactic Computing | 24 | 23 | -1 | 1 | 1 | -- |
| NEC/Sun | 25 | -- | -- | 1 | 0 | +1 |
| Hitachi/Fujitsu | 26 | -- | -- | 1 | 0 | +1 |
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Top500 Architecture Ranking, Nov. 2005
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|
Computer Architecture
|
Count
June 2006 |
Count
Nov. 2005 |
Change
|
|||
| Cluster (Beowulf, NOW, etc.) |
364 | 360 | +4 | |||
| MPP (homogeneous architecture) |
98 | 104 | -6 | |||
| Constellations (cluster of symmetrical processors) |
38 | 36 | +2 | |||
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Top500 Processor Ranking, June 2006
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Processor Generation
|
Count
June 2006 |
Count
Nov. 2005 |
Change
|
|||
| Pentium 4 Xeon | 144 | 203 | -124 | |||
| Xeon EM64T | 118 | 82 | +36 | |||
| Opteron | 46 | 50 | -4 | |||
| Itanium | 2 | 37 | -9 | |||
| Opteron Dual Core | 34 | 5 | +29 | |||
| PowerPC 440 | 25 | 19 | +6 | |||
| POWER5 | 19 | 16 | +3 | |||
| POWER4+ | 14 | 16 | -2 | |||
| PowerPC 970 | 13 | 9 | +4 | |||
| PA-8900 | 8 | -- | +8 | |||
| PA-8800 | 7 | 8 | -1 | |||
| POWER4 | 6 | 9 | -3 | |||
| Alpha | 4 | 4 | -- | |||
| NEC | 4 | 4 | -- | |||
| Cray X1 | 4 | 8 | -4 | |||
| PA-8700+ | 4 | 9 | -5 | |||
| POWER3 | 3 | 3 | -- | |||
| SPARC64 V | 3 | 3 | -- | |||
| POWER5+ | 3 | 1 | +2 | |||
| Pentium 4 | 2 | 1 | +1 | |||
| UltraSPARC IV | 1 | 1 | -- | |||
| Low Voltage Pentium Xeon | 1 | 0 | +1 | |||