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Six Life Science Computers Cut from Top500 Ranking as IBM's BlueGene Gains Ground

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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/.

Top-Ranking Life Science Supercomputers, June 2006
Rank June 2006
Rank Nov. 2005
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
Top500 Supercomputer Manufacturer Ranking, June 2006
Manufacturer
Rank June 2006
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
Top500 Architecture Ranking, Nov. 2005
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
Top500 Processor Ranking, June 2006
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

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