Under benchmark results there are 4 columns of results for each processor, two for Protin and two for Prolsq. Each program then has results for a small and large problem. Times are given in seconds and represent CPU plus system time. The numbers in parentheses are performance relative to a VAX 11/780. Since the VAX 11/780 was an approximately one MIP machine the numbers in paranetheses represent approximate MIP ratings.
To a first approximation Protin is a scalar program operating predominantly on integers and Prolsq a highly vectorized program with good parallelism operating predominantly on floating point numbers.
In the majority of cases the manufacturers themselves have run the codes and while I believe the numbers to be accurate in all cases I would strongly suggest you use these numbers as a guide and not as a sole purchasing decision!
How much effort has gone into modifying the codes also varies, although in the majority of cases there has been little modification. Where there have been modifications that code is available. I would encourage you to run the benchmarks on your own machines and feed me the numbers so the community may benefit. Thanks to all the interested parties who have run the benchmarks over the years.
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Benchmark Results
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Benchmark Submission Form
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Benchmark description
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Get benchmark programs
References:
Bourne & Hendrickson, Selecting a Processor for Computations in Molecular
Biophysics, Comput. Biol. Med. (1988) 18, 341-349
Bourne & Hendrickson, A Protein Crystallographic Benchmark, Comput. Biol.
Med. (1990) 20, 219-230.
Small Large
Erabutoxin b: Hexon
Post-synaptic neurotoxin Viral coat protein
Eur. J. Biochem. 153:521-527 (1985) Science 232:1148-1151 (1986)
6853 daltons 109077 daltons
3590 reflexions (2.5A) 19172 reflexions (2.9A)
P212121 P213
545 non-hydrogen atoms 6864 non-hydrogen atoms
Benchmark CPU Times
Times in seconds; time relative to a VAX 11/780 in parenthesis]
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Processor Linpack* PROTIN PROTIN PROLSQ PROLSQ
(Mflops) Small Large Small Large
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DEC 8400 (21164) 8CPU 2282 - - - 124(1642.6)
DEC 8400 (21164) 6CPU 1902 - - - 138(1475.9)
Convex C4640 4CPU - - - - 142(1434.4)
DEC 8200 (21164) 6CPU 1821 - - - 148(1376.2)
Convex C3880 8CPU 795 - - - 176(1157.3)
DEC 8400 (21164) 4CPU 1351 - - - 176(1157.3)
DEC 8200 (21164) 4CPU 1317 - - - 177(1150.7)
Convex C3860 6CPU - - 201(1013.3)
Convex C4620 2CPU - - - - 218.(934.3)
SGI R8000 6CPU - - - - 219.(930.1)
DEC 2100 (21164) 4CPU 1022 - - - 235.(866.7)
Convex C3840 4CPU 425 - - - 257.(792.5)
Convex SPP-1 8CPU - - - - 265.(768.6)
DEC 7000/710 275Mhz 6CPU 962 - - - 282.(722.3)
SGI R8000 4CPU - - - 8.4(169.1) 282.(722.3)
SGI Chal. L 150Mhz 12CPU - 0.6 (52.0) 7.6 (47.4) - 299.(681.2)
DEC 8400 (21164) 2CPU 757 - - - 312.(652.8)
DEC 8200 (21164) 2CPU 752 - - - 313.(650.7)
Convex C4610 1CPU - - - - 330.(617.2)
DEC 7000/710 275Mhz 4CPU 693 - - - 371.(549.0)
DEC 2100 (21164) 2CPU 578 - - - 423.(481.5)
DEC 7000/660 VMS 6CPU 754 - - - 431.(472.6)
Concex C3820 2CPU 222 - - - 435.(468.2)
SGI R8000 2CPU - - 9.0(157.9) 458.(444.7)
SGI Chal. L 100Mhz 12CPU - 0.9 (34.7) 10.0 (36.0) - 469.(434.3)
DEC 7000/640 VMS 4CPU 525 - - - 534.(381.4)
DEC 8400 (21164) 1CPU 410 - 6.6 (54.6) - 599.(340.0)
DEC 8200 (21164) 1CPU 410 - 6.6 (54.6) - 599.(340.0)
DEC A500MP 190Mhz 4CPU 358 - - - 605.(336.7)
SGI Chal. L 150Mhz 6CPU - - - - 614.(331.7)
DEC 7000/710 275Mhz 2CPU 361 - - - 636.(320.3)
SGI R8000 1CPU - - - 9.1(156.1) 700.(291.0)
DEC 2100 A500MP VMS 4CPU 356 - - - 711.(286.5)
Cray X-MP/416 218 - - 7.5(189.4) -
SGI Chal. L 150Mhz 4 CPU - - - 8.6(165.1) 768.(265.2)
SGI Chal. L 100Mhz 6 CPU - - - - 771.(264.2)
Convex C3810 1 CPU 113 - - - 795.(256.2)
DEC 2100 (21164) 1 CPU 317 - 7.1 (50.8) - 851.(239.3)
DEC 7000/620 VMS 2 CPU 279 - - - 914.(222.9)
DEC A500MP 190Mhz 2 CPU 209 - - - 984.(207.0)
DEC 2100 A500MP VMS 2CPU 207 - - - 1295.(157.3)
DEC 7000/610 OSF/1 1 CPU 155 0.8 (39.0) 9.4 (38.3) 9.8(145.0) 1502.(135.6)
SGI Chal. L 100Mhz 4 CPU - - - 11.0(129.2) 1131.(180.1)
DEC 7000/710 275Mhz 1CPU 208 - - - 1204.(169.2)
SGI Chal. L 150Mhz 2 CPU - - - 11.1(128.1) 1436.(141.8)
DEC 2100 190Mhz 1CPU 129 0.9 (34.7) 10.3 (35.0) 11.9(119.4) 2029.(100.4)
SGI 4D/460 40Mhz 6 CPU - - - - 1496.(136.1)
Convex SPP-1 1 CPU - - - - 1680.(121.2)
SGI Chal. L 150Mhz 1 CPU - - - 14.0(101.5) 2646. (77.0)
SGI Chal. L 100Mhz 2 CPU - - - 14.8(100.0) 2106. (96.7)
DEC 7000/610 VMS 1 CPU 1.1 (28.4) 12.0 (30.0) 15.1 (94.1) 1775.(114.8)
SGI Chal. 150Mhz 1 CPU 0.9 (34.7) - 17.7 (80.3) -
SGI 4D/440 40Mhz 4 CPU 42 - - 18.3 (77.6) 2066. (98.6)
DEC 2100 A500MP VMS 1CPU 127 1.5 (20.8) 17.7 (20.4) 18.6 (76.4) 2327. (87.5)
DEC 4000-610 AXP 114 1.3 (24.0) 16.1 (22.4) 18.9 (75.2) 2728. (74.7)
Convex C240 166 - - - 1211.(168.2)
Multiflow 28/300 69 - 34.7 (10.4) - 2189. (93.1)
STAR 910/VP - - - 19.9 (71.4) 1753.(116.2)
IBM 3090-300E VF - 1.7 (18.4) 11.6 (31.1) 20.2 (70.3) 2320. (87.8)
HP 9000/735 100Mhz 107 1.1 (28.4) 10.0 (36.0) 21.1 (67.3) 5002. (40.7)
SGI Chal. L 100Mhz 1 CPU - - - 21.3 (66.7) 3730. (54.6)
DEC 3000-500 AXP 107 1.5 (20.8) 18.7 (19.3) 21.5 (66.1) 3460. (58.9)
SGI Crimson R4000 100Mhz - 1.0 (31.2) 10.9 (33.1) 22.0 (64.6) 3616. (56.3)
Convex C220 89 2.9 (10.8) 29.6 (12.2) 23.0 (61.8) 2668. (76.3)
Cydrome Cydra 5 - 5.4 (5.8) - 23.9 (59.4) -
DEC 3400 AXP 90 1.6 (19.5) 19.5 (18.5) 24.8 (57.3) 3758. (54.2)
Multiflow 14/200 - 3.7 (8.4) - 25.8 (55.1) 3836. (53.1)
Multiflow 14/300 42 - 36.3 (9.9) - 3846. (53.0)
SGI 4D/420 2 CPU - - - 27.0 (52.6) 4183. (48.7)
Convex C210 44 2.6 (12.0) 30.2 (11.9) 30.0 (47.4) 3987. (51.1)
Sun SS1000 1.0 (31.2) 19.6 (18.4) 31.0 (45.8) 5982. (34.1)
Facom M780/10R - 0.7 (44.6) 4.6 (78.3) 36.2 (39.2) 5819. (35.0)
SGI Crimson R4000 50Mhz 32 1.4 (22.3) 37.3 (38.1)
Alliant FX/80 69 5.4 (5.8) - 41.0 (34.7) -
SGI 4D/410 40Mhz 1 CPU - - - 41.9 (33.9) 7798. (26.1)
VAXstation 4000-90 - 1.1 (28.4) 14.7 (24.5) 46.1 (30.8) 9961. (20.4)
FPS M64/60 34 5.1 (6.1) - 55.5 (25.6) -
Stellar GS1000 - 7.2 (4.3) - 56.5 (25.2) -
Alliant FX/40 33 5.6 (5.6) - 59.3 (24.0) -
Multiflow 7/300 22 - 37.4 (9.6) - 7680. (26.5)
E&S ESV20/33 - 4.3 (7.3) 55.7 (6.5) 61.0 (23.3) 27948. ( 7.3)
Ardent Titan-2 25 - - 61.0 (23.3) -
SGI 4D/240 25Mhz 4CPU 28 7.7 (4.1) 37.5 (9.6) 61.1 (23.3) 8607. (23.7)
Convex C1-XP - 8.5 (3.7) 100.5 (3.6) 61.9 (23.0) 8278. (24.6)
Convex C1-XL - 11.4 (2.7) - 79.8 (17.8) -
SGI 4D35 - 1.9 (16.4) - 85.5 (16.6) -
SGI 4D/310 33Mhz 1 CPU 10 2.3 (13.6) - 86.6 (16.4) -
SGI R3000 33Mhz - 2.1 (14.9) - 88.7 (16.0) -
SGI 4D/220 25Mhz 2 CPU 15 6.3 (5.0) - 94.6 (15.0) -
Alliant FX/8 - 12.0 (2.6) - 102.0 (13.9) -
STAR ST-100 - - - 108.2 (13.1) 4477. (45.5)
FPS M64/50 17 - - 110.0 (12.9) -
SGI Indigo R3000 33Mhz - 2.6 (12.0) - 112.7 (12.6) -
DEC DECstation 3100 - 13.0 (2.4) - 140.2 (10.1) -
DEC VAXstation 4000/60 - 3.3 (9.5) 36.5 (9.9) 145.6 (9.8) 29646. (6.9)
SGI 4D/80GT - 8.8 (3.6) - 182.9 (7.8) 38991. (5.2)
Masscomp MC6600 - - - 206.0 (6.9) -
DEC VAX 8800 2 CPU 2.5 6.0 (5.2) - 277.3 (5.1) -
DEC VAX 8700 (VMS) 1.3 5.7 (5.5) - 280.6 (5.1)
DEC VAX 8650 - 6.0 (5.2) 70.0 (5.2) 285.0 (5.0) 37996. (5.3)
SGI 4D/20 - 16.5 (1.9) - 304.5 (4.7) -
DEC VAX 8700 (ULTRIX) 1.3 14.3 (2.2) - 330.7 (4.3) -
Sun 4/280 - 8.7 (3.6) - 357.0 (4.0) -
SGI 4D/70GT - 11.1 (2.8) - 359.4 (4.0) -
Sun 4/260 0.5 10.4 (3.0) - 381.7 (3.7) -
Masscomp MC6600b - - - 412.0 (3.5) -
Alliant FX/1 - 12.0 (2.6) - 503.0 (2.8) -
Sun 4/110 - 11.7 (2.7) - 505.0 (2.8) -
DEC VAX 6310 - 9.1 (3.4) - 635.5 (2.2) -
Masscomp MC5450b - - - 745.4 (1.9) -
DEC VAX 3400 - 17.2 (1.8) - 638.4 (2.2) -
Sun 3/180 - 32.1 (1.0) - 780.3 (1.8) -
SGI 3020 - 30.1 (1.0) - 1260.7 (1.1) -
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DEC VAX 11/780 - 31.2 (1.0) 360.4 (1.0) 1420.7 (1.0)203680. (1.0)
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Masscomp MC6600a - - - 1510.2 (0.9) -
DEC VAXstation 2000 - 38.4 (0.8) 508.8 (0.7) 2326.0 (0.6)363069. (0.6)
DEC VAX 11/750 - 48.6 (0.6) 832.0 (0.4) 2037.0 (0.7) -
DEC VAXstation II - 36.9 (0.9) - 2271.8 (0.6) -
Masscomp MC5450a - - - 2727.7 (0.5) -
DEC MicroVAX II - 37.6 (0.8) - 3260.3 (0.4) -
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* Linpack results are for full precision optimized Linpack on a 1000x1000
matrix as reported by Dongarra (9/93).
BENCHMARK SUBMISSION FORM
Name: Date:
Institution:
Make/Model/Serial No:
Physical Memory (in Megabytes):
Disk Drive (Make and Model):
Operating System (Name and Version):
Fortran Compiler (Name and Version):
Small Problem PROTIN Compile Time:
Small Problem PROLSQ Compile Time:
Small Problem PROTIN CPU time (user + system--in Seconds):
Small Problem PROTIN Elapsed Time (in Seconds):
Small Problem PROTIN Page Faults:
Small Problem PROLSQ CPU time (user + system--in Seconds):
Small Problem PROLSQ Elapsed Time (in Seconds):
Small Problem PROLSQ Page Faults:
Large Problem PROTIN CPU time (user + system--in Seconds):
Large Problem PROTIN Elapsed Time (in Seconds):
Large Problem PROTIN Page Faults:
Large Problem PROLSQ CPU time (user + system--in Seconds):
Large Problem PROLSQ Elapsed Time (in Seconds):
Large Problem PROLSQ Page Faults:
Comments on Changes Made to Code:
Please return to:
Philip E. Bourne
San Diego Supercomputer Center
PO Box 85608
San Diego CA 92186-9784
Voice: (619) 534-8301
Fax: (619) 534-5117
Email: bourne@sdsc.edu