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Five New Life Science Supercomputers Join Top500 List; Blue Gene Dominates the Field

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Five new supercomputers dedicated to life science research have joined the ranks of the world's most powerful computing systems, according to the most recent Top500 ranking, with one — an 18.2-teraflop IBM Blue Gene system at the Computational Biology Research Center at Japan's National Institute of Advanced Industrial Science and Technology — breaking into the top 10.

New systems installed at the Wellcome Trust Sanger Institute, India's Institute of Genomics and Integrative Biology, the Institute of Life Science at the University of Wales, and an undisclosed US life science company all debuted in the top 300 (see chart for a complete list of life science systems in the Top500).

But rapid advances in high-performance computing have bumped eight life science systems off the list. The fastest of these, an IBM Blade Center installed at the Sanger Institute with a Linpack benchmark performance of 1,122 Gflop/s, was ranked No. 321 in the last version of the Top500 just six months ago [BioInform 11-15-04], but didn't make the 1,166-Gflop/s cutoff for the June 2005 ranking.


IBM systems make up more than half — 52 percent — of the 500 supercomputers on the list. HP follows with 26.2 percent of the systems, and SGI is third with a 5-percent share of the top 500.

The total number of life science machines in the top 500 has dropped to nine from 13 six months ago. Supercomputers at Bayer CropScience, Celera, and Singapore's Bioinformatics Institute were among the life science systems that didn't make it to the Top500 this time around.

IBM's Blue Gene system, which the company initially designed for protein-folding simulations, dominates the list, claiming the No. 1 spot as well as four other spots in the top 10 and 11 more in the top 70. A BlueGene/L system at the US Department of Energy's Lawrence Livermore National Laboratory claimed the No. 1 position for the second time in a row, but the system has doubled in size during the last six months to reach a new record Linpack benchmark performance of 136.8 Tflop/s.

IBM plans to double the size of this system again, and the organizers of the Top500 list expect it to retain the No. 1 spot "for the next few editions" of the biannual ranking.

IBM systems make up more than half (52 percent) of the 500 supercomputers on the list (see chart for details on manufacturer rankings). HP follows with 26.2 percent of the systems, and SGI is third with a 5-percent share of the top 500.

IBM is also the leading manufacturer among life science computers, with seven out of nine systems on the list.

Cluster-based systems continue to make up the most common architecture in the top 500, with 304 systems in the current list labeled as clusters, up from 294 in November (see chart for details on computational architectures).

Intel processors are used in 333 of the 500 systems, up from 320 Intel-based systems six months ago and 287 last June. The second most commonly used processors are the IBM Power processors (77 systems), ahead of Hewlett-Packard's PA Risc processors (36) and AMD processors (25).

The TOP 500 list is compiled by Hans Meuer of the University of Mannheim, Germany; Erich Strohmaier and Horst Simon of NERSC/Lawrence Berkeley National Laboratory; and Jack Dongarra of the University of Tennessee, Knoxville.

The complete list is available at http://www.top500.org/.

— Bernadette Toner ([email protected])

Top Ranking Life Science Supercomputers, June 2005
Rank
June
2005
Rank Nov.
2004
Installation Site
Manufacturer/
Computer
Number of
Processors
Gflop/s
(max)
Year
Installed
8 —
Computational Biology Research Center,
AIST (Japan)
IBM/"Blue Protein" eServer Blue
Gene Solution
8,192 18,200 2005
137 —
Wellcome Trust
Sanger Institute
IBM/HS20 Cluster
(3.2 GHz Xeon)
600 2,405 2005
158 —
Institute of Genomics
and Integrative Biology
Hewlett-Packard/
Cluster Platform 3000
(3.6 GHz Xeon)
576 2,156 2005
200 123
University at Buffalo, SUNY, Center for Computational Research (Center of Excellence in Bioinformatics)
Dell/ PowerEdge
2650 Cluster
(2.4 GHz Xeon)
600 2,004 2002
242 152 University at Buffalo, SUNY, Center for Computational Research (Center of Excellence in Bioinformatics) IBM/BladeCenter
(2.8 GHz Xeon)
546 1,817 2004
249 159 Arizona State University/Translational Genomics Research Institute IBM/xSeries cluster
(2.4 GHz Xeion)
1,048 1,755 2003
259 — University of Wales Swansea, Institute of
Life Science
IBM/ eServer pSeries 690 (1.9 GHz Power4+) 352 1,714 2005
268 — US life science company (name withheld) IBM/ xSeries
(3.2 GHz Xeon)
400 1,657 2005
380 219 UK biotech company (name withheld) IBM/BladeCenter
(2.8 GHz Xeon)
400 1,335 2004

 

Top 500 Supercomputer Manufacturer Ranking, June 2005
Manufacturer
Rank
June 2005
Rank
Nov.
2004
Change in
Rank
Count June 2005*
Count
Nov. 2004*
Change
in
Count
IBM 1 1 — 259 216 +43
HP 2 2 — 131 173 -42
SGI 3 3 — 24 20 +4
Dell 4 4 — 21 14 +7
Cray Inc. 5 8 +3 16 9 +7
NEC 6 5 -1 8 12 -4
Self-made 7 7 — 6 10 -4
Atipa 8 10 +2 5 4 +1
Linux Network 9 6 -3 5 11 -6
Sun 10 11 — 5 4 +1
Fujitsu 11 12 — 4 3 +1
Hitachi 12 9 — 4 6 -2
Lenovo 13 13 — 2 2 —
Angstrom 14 14 — 1 2 -1
Apple 15 — — 1 0 +1
California Digital Corporation 16 16 — 1 1 —
Dawning 17 17 — 1 1 —
Fujitsu-Siemens 18 — — 1 0 +1
Galactic Computing 19 — — 1 0 +1
HPTi 20 18 -2 1 1 —
Intel 21 19 -2 1 1 —
Verari 22 21 -1 1 1 —
Visual Technology 23 22 -1 1 1 —

* Number of installed systems on the Top 500 list of supercomputers

 

Top 500 Supercomputer Architecture Ranking, June 2005
Computer Architecture
Count
June 2005
Count
Nov. 2004
Change
Cluster
(Beowulf, NOW, etc.)
304
294
+10
Constellations
(cluster of symmetrical multiprocessors)
79
106
-27
MPP
(homogeneous architecture)
117
100
+17

 

 

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