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Top500 List Sees One Less Life Science System, But Stanford Makes Green Top 10

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Only four life science systems made the most recent Top500 list of the world’s fastest supercomputers, but one of these machines — installed at Stanford University’s Biomedical Computational Facility — placed within the top 10 in the inaugural “Green500” list of energy-efficient supercomputers.
 
The last version of the twice-annual Top500 roster, released in June, included five systems dedicated to life science research. Two of those systems did not make the performance requirement for the current list, which was released this week at the SC07 supercomputing conference in Reno, Nev. — 5.9 teraflops on the Linpack benchmark, compared to 4 teraflops for the previous version [BioInform, June 29, 2007].
 
One new life science machine — placed at an undisclosed US biotechnology firm — joined the current version of the Top500 list at the No. 318 spot. The system, an IBM/xSeries x3550 cluster, has 1,248 processors and a kick of 7.5 teraflops (see Table 1, below, for details).
 
The fastest life science offering, IBM’s “Blue Protein” system at the AIST Computational Biology Research Center in Japan, boasts 18.7 teraflops of performance and 8,192 processors. Its ranking in the Top500 fell to No. 52 in the current list from the No. 21 spot in June.
 
For the fifth time in a row, the No. 1 spot in the Top500 is held by a BlueGene/L system developed by IBM and the Department of Energy’s National Nuclear Security Administration and installed at DOE’s Lawrence Livermore National Laboratory. The system has been enhanced since June, and reached a Linpack benchmark performance of 478.2 teraflops, compared to 280.6 teraflops six months ago.
 
While life science supercomputers may not have had much of a showing in the Top500 list, the Dell "Bio-X2" machine at the Stanford Biomedical Computational Facility ranked No. 6 in the first-ever Green500 roster, which is intended to complement the Top500 list and emphasizes performance metrics other than speed, such as performance per watt and energy efficiency.
 
The Green500 list ranks systems based on megaflops per watt. The Stanford system came in at No. 6 with 245.27 megaflops/watt, while the AIST system ranked No. 15 with 208.31 megaflops/watt. The BlueGene/L system that holds the No. 1 spot in the Top500 ranks No. 22 in the Green500 with 205.27 megaflops/watt.
 
In a conversation with BioInform, Erich Strohmaier of Lawrence Berkeley National Laboratory and one of the Top500 list’s compilers, said that even though only four supercomputers on the list are used solely for life science research, it does not reflect how important high-performance supercomputing is to the field.
 
“If you don’t see that many [supercomputers on the list] dedicated to life science, I would suggest it isn’t because applications aren’t there, but because the researchers who run these applications use facilities which are more general-purpose, like our center, [the National Energy Research Scientific Computing Center], or Oak Ridge, which has a variety of users, not just a single label,” Strohmaier said.
 

“If you don’t see that many [supercomputers on the list] dedicated to life science, I would suggest it isn’t because applications aren’t there, but because the researchers who run these applications use facilities which are more general-purpose.”

Strohmaier said that while none of the top six positions in the Top500 is occupied by life science offerings, slots seven through 10 likely handle some work that is related to life sciences. For example, he said that the No. 9 system, an 85.4-teraflop Cray XT4 installed at DOE’s Lawrence Berkeley National Laboratory, falls into this category.
 
IBM, Clusters Dominate
 
IBM regained the lead over HP in terms of the most installed systems on the Top500 list, with 232 machines, or 46 percent of all systems, compared to 192, or 38 percent of all systems, in June. HP’s count, meanwhile, slipped to 166, or a 33-percent share, in the current list from 202 systems, or a 40-percent share, in June. IBM, which had been ahead of HP since June 2004, lost the lead in the number of systems six months ago (see table 2, below, for details).
 
The trend toward cluster computing is also going strong, with cluster architectures comprising 406 systems on the current list, or 81 percent of all systems — up from 373, or 75 percent share, in June (see table 3, below, for details).
 
Linux continues to gain ground as the favored supercomputing operating system, moving to 426 systems, or 85.2 percent of the total list, from 389 systems six months ago. Unix usage, meantime, fell to 30 systems from 60 in June. There are two Mac OS and six Windows systems in the current Top500.
 
A total of 354 systems in the current Top500 list, or 71 percent, use Intel processors — the largest share for Intel chips ever in the Top500 —compared with 289 systems and 57.8 percent six months ago.
 
The AMD Opteron family remained the second most-common processor family, pulling in 78 systems, or 15.6 percent, down from 105 systems, or 21 percent, six months ago.
 
IBM Power processors make up 61 systems, or 12.2 percent of the current list, down from 85 systems and 17 percent six months ago (see table 4, below, for details).  
 
 
Table 1: Life Science Supercomputers, by Rank, Nov. 2007
Rank Nov. 2007
Rank June 2007
Installation Site Manufacturer/Computer Number of Processors
Tflop/s (max)
52
21
Computational Biology Research Center, AIST (Japan) IBM/"Blue Protein" eServer Blue Gene Solution 8,192
18.7
73
54
Stanford University Biomedical Computational Facility Dell/"Bio-X2" PowerEdge 1950 (2.33 GHz) 2,208
15.6
318
Undisclosed US biotechnology firm IBM/xSeries x3550 cluster (2.66 Xeon quad core) 1,248
7.5
411
188
Merck & Co. IBM/BladeCenter LS20 (2.2 GHz Opteron dual core) 2,688
6.6
 
 
Table 2: Top500 Supercomputer Manufacturer Ranking, Nov. 2007
Manufacturer
Rank Nov. 2007
Rank June 2007
Change in Rank
Count Nov. 2007
Count June 2007
Change in Count
IBM
1
2
+1
232
192
+40
Hewlett-Packard
2
1
-1
166
202
-36
Dell
3
3
24
23
+1
SGI
4
4
22
19
+3
Cray Inc.
5
5
14
11
+3
Linux Networx
6
6
9
8
+1
Hitachi
7*
8
+1
4
6
-2
Appro International
7*
11*
+4
4
2
+2
Self-made
7*
9
+2
4
5
-1
Fujitsu
8*
10*
+2
3
4
-1
Sun Microsystems
8*
7
-1
3
7
-4
NEC
9*
10*
+1
2
4
-2
Bull SA
9*
11*
+2
2
2
Intel
10*
11*
+1
1
2
-1
NEC/Sun
10*
11*
+1
1
2
-1
Megware
10*
12*
+2
1
1
California Digital Corporation
10*
12*
+2
1
1
Dawning
10*
12*
+2
1
1
T-Platforms
10*
12*
+2
1
1
Hitachi/Fujitsu
10*
12*
+2
1
1
DALCO AG Switzerland
10*
12*
+2
1
1
Koi Computers
10*
1
0
+1
TeamHPC of M&A Technology
10*
1
0
+1
Transtec AG
10*
1
0
+1

* Tie
Number of installed systems in the Top500

 
 
Table 3: Top500 Architecture Ranking, Nov. 2007
Computer Architecture
Count Nov. 2007
Count June 2007
Change
Cluster (Beowulf, NOW, etc.)
406
373
+33
MPP (homogeneous architecture)
91
107
-16
Constellations (cluster of symmetrical processors)
3
20
-17
Number of installed systems in the Top500
 
 
Table 4: Top500 Processor Generation Ranking, Nov. 2007
Processor Generation
Count Nov. 2007
Count June 2007
Change
Xeon 51xx (Woodcrest)
215
204
+11
Xeon 53xx (Clovertown)
102
19
+83
Opteron Dual Core
69
91
-22
PowerPC 440
21
34
-13
Itanium 2
18
25
-7
POWER5+
18
20
-2
Pentium 4 Xeon
12
27
-15
Opteron
9
16
-7
PowerPC 970
8
11
-3
POWER5
5
10
-5
PowerPC 450
5
1
+4
Xeon EM64T
4
7
-3
POWER4+
3
6
-3
NEC
2
4
-2
Cray X1
2
2
SPARC64 V
1
3
-2
Itanium 2 Dual Core
1
3
-2
Alpha
1
2
-1
POWER3
1
2
-1
Low Voltage Pentium Xeon
1
1
Xeon 50xx (Dempsy)
1
1
Opteron Quad Core
1
0
+1

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