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Life Science Supercomputers on Top500 List Hold Steady at Four Despite Top 10 'Shakeup'

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Four supercomputers dedicated to life science research currently rank among the fastest systems in the world, according to the most recent version of the Top500 list released this week at Supercomputing 2006 in Tampa, Fla. 
 
Two life science systems included on the last Top500 list, released in June [BioInform 06-30-06], did not meet the performance cutoff for the current version — 2.737 Tflop/s measured on the Linpack benchmark.
 
These systems — a 2.5 Tflop/s Sun cluster at Cedars-Sinai and a 2.4 Tflop/s IBM cluster at the Wellcome Trust Sanger Institute — were replaced by two other systems. Eli Lilly made its debut on the list at No. 75 with a 1,072-processer 8.6 Tflop/s IBM BladeCenter HS21, and an undisclosed US biotech ranked No. 100 with a 2,688-processor 6.6 Tflop/s IBM BladeCenter LS20.
 
IBM’s 18.2 Tflop/s “Blue Protein” Blue Gene system at Japan’s Computational Biology Research Center retained its ranking as the fastest life science computer, although it dropped from No. 15 in the June list to No. 21 in the current version of the Top500.
 
A 3.1 Tflop/s HP cluster at India’s Institute of Genomics and Integrative Biology dropped from No. 255 to No. 382.
 
The shuffling in the life science computing sector mirrored that of the top 10 systems in the list, which the Top500 organizers described as a “major shakeup.”
 
IBM’s BlueGene/L system, installed at DOE’s Lawrence Livermore National Laboratory, retained the No. 1 spot with a Linpack performance of 280.6 Tflop/s. But two new systems joined the top 10, several others moved up or down, and NEC’s Earth Simulator, which held the No. 1 spot for five lists, slipped out of the top 10 to the No. 14 spot.
 
Clusters are still the most common architecture in the current list, but growth has slowed. The current list includes 361 cluster computers, a drop of three from June. This is the first time cluster architectures have lost ground in the ranking since the first cluster — the University of Berkeley NOW system — debuted on the June 1997 list.
 
After that, clusters steadily gained ground until they surpassed massively parallel architectures for the first time in the Top500 list [BioInform 11-24-03], reaching a high of 364 systems in the June list.
 
If the current list is any indication, the high-performance computing field may be seeing a resurgence in MPP architectures — the current list boasts 10 more MPP systems than the June ranking.
 
Another recent trend — toward Intel chips — appears to be reversing as well. Since July 2004, more than half of all the Top500 systems have used Intel chips. While Intel processors are still used in 261 systems in the current list, that is down from 301 in June and 333 a year ago.
 
AMD’s Opteron family, meanwhile, surpassed IBM’s Power processors to become the second most common processor family with 113 systems, up from 55 systems a year ago. IBM Power processors make up 93 systems in the current list, up from 73 systems a year ago.
 
Dual core processors are also gaining in popularity. In the current list, 75 systems use Opteron dual core processors and 31 use Intel’s new Woodcrest dual core chips.
 
Linux continues to gain ground as the operating system of choice, claiming 376, or 75 percent, of the Top500 in the current list — up from 367 in the June list. This was followed by 86 Unix systems, 32 “mixed” systems, 3 BSD systems, and 3 Mac OS systems.
 
The Top500 list is compiled every six months by Hans Meuer of the University of Mannheim; Erich Strohmaier and Horst Simon of NERSC/Lawrence Berkeley National Laboratory; and Jack Dongarra of the University of Tennessee. The complete list is available at http://www.top500.org/.
 
 
Top-Ranking Life Science Supercomputers, Nov. 2006
Rank Nov. 2006
Rank June 2006
Installation Site
Manufacturer/
Computer
Number
of Processors
Tflop/s (max)
Year installed
21
15
Computational Biology Research Center, AIST (Japan) IBM/"Blue Protein" eServer Blue Gene Solution
8,192
18.2
2005
75
Eli Lilly and Co. IBM/BladeCenter HS21 Cluster (3.0 GHz Xeon dual core)
1,072
8.6
2006
100
Undisclosed US biotech IBM/BladeCenter LS20 (2.2 GHz Opteron dual core)
2,688
6.6
2006
382
255
Institute of Genomics and Integrative Biology (India) Hewlett-Packard/Cluster Platform 3000 (3.6 GHz Xeon)
576
3.1
2005

 

Top500 Supercomputer Manufacturer Ranking, Nov. 2006
Manufacturer
Rank Nov. 2006
Rank June
2006
Change in Rank
Count Nov. 2006
Count June
2006
Change in
Count
IBM 1 1 236 239 -3
Hewlett-Packard 2 2 158 157 +1
SGI 3 5 +2 20 12 +8
Dell 4 3 -1 18 22 -4
Cray Inc. 5 4 -1 15 16 -1
Sun Microsystems 6 7 +1 9 7 +2
Linux Networx 7 6 -1 7 8 -1
Hitachi 8 8 6 6
Fujitsu 9 10 +1 5 4 +1
Self-made 10 9 -1 5 6 -1
Atipa Technology 11 12 +1 4 3 +1
NEC 12 11 -1 3 4 -1
Appro International 13 15* +2 2 1 +1
HPTi 14* 15* +1 1 1
Intel 14* 13 -1 1 2 -1
lenovo 14* 15* +1 1 1
California Digital Corporation 14* 15* +1 1 1
Dawning 14* 15* +1 1 1
Bull SA 14* 15* +1 1 1
Galactic Computing 14* 15* +1 1 1
Rackable Systems 14* 14 1 2 -1
NEC/Sun 14* 15* +1 1 1
Hitachi/Fujitsu 14* 15* +1 1 1
DALCO AG Switzerland 14* 1 0 +1
IBM/HP 14* 1 0 +1
* Tied, with one installed system
† Number of installed systems in the Top500

 

Top500 Architecture Ranking, Nov. 2006
Computer Architecture
Count
Nov. 2006
Count
June 2006
Change
Cluster
(Beowulf, NOW, etc.)
361 364 -3
MPP
(homogeneous architecture)
108 98 +10
Constellations
(cluster of symmetrical processors)
31 38 -7
† Number of installed systems in the Top500  

 

Top500 Processor Ranking, Nov. 2006
Processor Generation
Count
Nov. 2006
Count
June 2006
Change
Pentium 4 Xeon 118 144 -26
Xeon EM64T 76 118 -42
Opteron Dual Core 76 34 +42
Opteron 37 46 -9
Itanium 2 35 37 -2
Xeon 51xx (Woodcrest) 31 0 +31
PowerPC 440 29 25 +4
PowerPC 970 18 13 +5
POWER5 17 19 -2
POWER5+ 12 3 +9
POWER4+ 11 14 -3
PA-8700+ 9 4 +5
PA-8900 8 8
Cray X1 4 4
Alpha 3 4 -1
NEC 3 4 -1
PA-8800 3 7 -4
SPARC64 V 3 3
POWER4 2 6 -4
POWER3 2 3 -1
Pentium 4 1 2 -1
Low Voltage Pentium Xeon 1 1
Xeon 50xx (Dempsy) 1 0 +1
† Number of installed systems in the Top500

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