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One New Life Science Computer Makes Top500 List; Clusters, BlueGene Continue to Advance

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An SGI Altix system installed at the National Cancer Institute marks the only new life science system to join the most recent ranking of the 500 most powerful supercomputers in the world based on the Linpack benchmark.

The latest Top500 list, released at the Supercomputing 2005 conference last week, includes nine systems that are dedicated to life science research. Only one of those — IBM's "Blue Protein" system at the Computational Biology Research Center at Japan's National Institute of Advanced Industrial Science and Technology — made it into the top 20 this time around. The 18.2-teraflop system, ranked at No. 12, held the No. 8 spot six months ago.

The next highest-ranked life science system came in at No. 268. The computer, a 2.4-gigaflop IBM HS20 Cluster at the Wellcome Trust Sanger Institute, was ranked No. 137 in June.

The new NCI arrival, weighing in at 1.7 teraflops, debuted on the Top500 list at No. 483. Only one life science computer from the June list — a 1.3-teraflop system at an undisclosed UK biotech company — didn't make the 1.6-teraflop cutoff for the November 2005 ranking, so the total number of life science systems remains level at nine (see table below for details on all the life science systems on the list).

Top Ranking Life Science Supercomputers, November 2005
Rank
Nov.
2005
Rank June
2005
Installation Site
Manufacturer/
Computer
Number of
Processors
Gflop/s
(max)
Year
Installed
12
8
Computational Biology Research Center, AIST (Japan) IBM/"Blue Protein" eServer Blue Gene Solution
8,192
18,200
2005
268
137
Wellcome Trust Sanger Institute IBM/HS20 Cluster,
(3.2 GHz Xeon)
600
2,405
2005
293
158
Institute of Genomics and Integrative Biology (India) Hewlett-Packard/Cluster Platform 3000
(3.6 GHz Xeon)
576
2,156
2005
361
200
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
407
242
University at Buffalo, SUNY, Center for Computational Research (Center of Excellence in Bioinformatics) IBM/BladeCenter
(2.8 GHz Xeon)
546
1,817
2004
435
249
Arizona State University/Translational Genomics Research Institute IBM/xSeries cluster (2.4 GHz Xeon)
1,048
1,755
2003
462
259
University of Wales Swansea, Institute of Life Science IBM/ eServer pSeries 690 (1.9 GHz Power4+)
352
1,714
2005
483
National Cancer Institute SGI/Altix (1.5 GHz Itanium 2)
320
1,667
2005
488
268
US life science company (name withheld) IBM/ xSeries
(3.2 GHz Xeon)
400
1,657
2005

The most recent version of the ranking, which is released every six months, indicates that the recent trend in favor of cluster-based computing has not diminished. Clusters now comprise 360 systems on the list — up from 304 in June (see table below for details on computational architectures in the list).

Top 500 Supercomputer Architecture Ranking, November 2005
Computer Architecture
Count
Nov. 2005
Count
June 2005
Change
Cluster
(Beowulf, NOW, etc.)
360
304
+56
MPP (homogeneous architecture)
104
117
-13
Constellations (cluster of symmetrical processors)
36
79
-43

IBM's BlueGene/L system, which the company originally designed for protein-folding simulations, now claims 19 of the top 500 spots, up from 16 in June. The fastest computer in the list is a 280.6-teraflop BlueGene/L system at the Department of Energy's Lawrence Livermore National Laboratory, which has doubled in size since June. This system is the only supercomputer to break the 100-teraflop mark, and is nearly triple the speed of the No. 2 system on the list — another BlueGene system at IBM's Thomas J. Watson Research Center with a Linpack performance of 91.3 teraflops.

IBM dominates the current list, claiming almost half (43.8 percent) of all systems, but this is down slightly from the June ranking, in which IBM claimed 52 percent of the supercomputers in the top 500. Hewlett-Packard retains its No. 2 position with 33.8 percent of all systems — up a bit from 26.2 percent in June — while Cray takes the No. 3 position over from SGI with 3.6 of all installed systems (see table below for details on manufacturer rankings).

Top 500 Supercomputer Manufacturer Ranking, November 2005
Manufacturer
Rank
Nov. 2005
Rank
June
2005
Change in
Rank
Count
Nov.
2005
Count
June
2005*
Change
in
Count
IBM
1
1
219
259
-40
Hewlett-Packard
2
2
169
131
+38
Cray Inc.
3
5
+2
18
16
+2
SGI
4
3
-1
18
24
-6
Dell
5
4
-1
17
21
-4
Linux Networx
6
9
+3
16
5
+11
NEC
7
6
-1
6
8
-2
Hitachi
8
12
+4
5
4
+1
Atipa Technology
9
8
-1
5
5
Self-made
10
7
-3
5
6
-1
Fujitsu
11
11
4
4
Sun Microsystems
12
10
-2
4
5
-1
Intel
13
21
+8
2
1
+1
HPTi
14
20
+6
1
1
Fujitsu-Siemens
15
18
+3
1
1
Appro International
16
1
0
+1
lenovo
17
13
-4
1
2
-1
California Digital Corporation
18
16
-2
1
1
Angstrom Microsystems
19
14
-5
1
1
Dawning
20
17
-3
1
1
Bull SA
21
1
0
+1
Apple
22
15
-7
1
1
Galactic Computing
23
19
-4
1
1
GraphStream
24
1
0
+1
Rackable Systems
25
1
0
+1

IBM also remains the leading manufacturer among life science computers, with six out of nine on the list — compared to seven out of nine six months ago.

Linux is the most popular operating system in the Top500, claiming 372 of the systems on the list. Unices came in second with 100 systems. The balance is made up of 5 Mac OS, 4 BSD, and 19 "mixed" operating systems.

Windows 2003 Server claims one system on the list — a 2.1-teraflop Dell system at the Cornell Theory Center that holds the No. 310 spot.

Intel processors remain the most common among the top 500, claiming 333 of the systems on the list, of which 82 are the company's new EM64T processors. The second most commonly used processors remain IBM Power processors, with 73 systems in the current list. AMD's Opterons gained the most ground with 55 systems in the current list compared to 25 six months ago. Hewlett-Packard's PA-RISC processors, which came in third six months ago with 36 systems, were included in only 17 systems in the current list.

The Top500 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.

— Bernadette Toner ([email protected])

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