Notes:
=============================================================================
"jac" == Joint Amber/Charrm DHFR benchmark. This is the protein DHFR,
solvated with TIP3 water, in a periodic box. There are 23,558 total atoms,
and PME used with a direct space cutoff of 9 Ang. This is the benchmark
in benchmarks/jac subdirectory of the Amber 7 distribution.
--------------------------------------------------------------------------------
node-name CPU OS compiler npcu time-per-step
--------------------------------------------------------------------------------
boneyard 450 MHz G4 Mac OSX g77 1 5.17
quine 1.2 Ghz Mobile PIII Windows XP g77-3 1 2.01
quine 1.3 Ghz Pentium M Windows XP absoft 1 1.79
--------------------------------------------------------------------------------
troll 1.2 Ghz AMD RH 7.1 g77-3 1 1.83
(ethernet, lam 6.5.6) 2 0.91
4 0.73
8 0.52 (3.5)
vandy 1.0 GHz PIII RH7.3 ifc 7 1 2.70
(myrinet 2000, MPICH) 2 1.52
4 0.80
8 0.44 (6.0)
16 0.25 (10.7)
32 0.17 (16.3)
redfish 2.4 GHz PIV RH8.0 ifc 7 1 1.09
(gigabit, lam 6.5.7) 2 0.56
4 0.35
8 0.20 (5.4)
16 0.18 (6.0)
bohr 2.0 Ghz PIV Xeon RH 7.3 ifc 1 1.41
2 0.79
euler2 833 MHz Itanium HP-UX f90 1 1.06
2 0.55
wigner 900 MHz Itanium2 HP-UX f90 1 0.61
(rx2600) 2 0.30
SGI-altix 1 GHz Itanium2 Linux efc 7 1 0.68
(b2-stepping, 3Mb L3 cache) 2 0.34
4 0.18
8 0.10 (6.8)
16 0.07 (9.7)
Bull 1.3 GHz Itanium2 Linux efc 7 1 0.46
Novascale 5160 (Madison) 2 0.24
4 0.13
8 0.08
16 0.05
SGI-altix 1.5 GHz Itanium2 Linux efc 7 1 0.44
(Madison) 2 0.23
4 0.12
8 0.07 (6.3)
16 0.04 (10.0)
--------------------------------------------------------------------------------
p630 1.0 GHz Power 4 AIX xlf90 1 1.16
2 0.60
4 0.34 (3.5)
thing2 500 Mhz Origin 2400 IRIX f90 1 1.410
2 0.731
4 0.400
8 0.230 (6.1)
16 0.147 (9.6)
32 0.101 (14.0)
primepwr 450 MHz Ultrasprac4 Solaris frt 1 2.88
2 1.54
4 0.83
8 0.50 (5.8)
bluefish 500 Mhz R14K Origin 3800 IRIX f90 1 1.397
2 .686
4 .374
8 .206
16 .126 (11.1)
32 .093 (15.0)
64 .078 (17.9)
BlueHorizon IBM 375MHz Power3 Node AIX5L xlf90 1 2.538
2 1.229
4 .658
8 .375 (6.8)
16 .228 (11.1)
32 .162 (15.7)
64 .124 (20.5)
lemieux 667 MHz Compaq Alphaserver ES40 Tru64 f90 1 1.02
2 .46
4 .25
8 .15 (6.8)
16 .10 (10.2)
32 .07 (14.6)
64 .06 (17)
jaromir Cray T3E 450 MHz Unicosmk f90 1 ---- Not enough memory
2 ---- for 23,000 atoms
4 2.14 (assume 4)
8 1.11 (7.7)
16 .59 (14.5)
32 .33 (25.9)
64 .20 (42.8)
128 .16 (53.5)
=============================================================================
"gb_mb" == Generalized Born myoglobin simulation. This protein has 2492
atoms, and is run with a 20 Ang. cutoff and a salt concentration of 0.2 M,
with nrespa=4 (long range forces computed every 4 steps.) This is the
test case in the benchmarks/gb_mb subdirectory of the Amber 7 distribution.
--------------------------------------------------------------------------------
node-name CPU OS compiler npcu time-per-step
--------------------------------------------------------------------------------
boneyard 450 MHz G4 Mac OSX g77 1 4.90
quine 1.2 Ghz Mobile PIII Windows XP g77 1 2.62
--------------------------------------------------------------------------------
troll 1.2 Ghz AMD RH 7.1 ifc 1 1.00
vandy 1.0 GHz PIII RH7.3 ifc 7 1 1.61
(myrinet 2000, MPICH) 2 0.84
4 0.41
8 0.21 (7.6)
16 0.11 (14.5)
32 0.06 (25.5)
bohr 2.0 Ghz PIV Xeon RH 7.3 g77_3.1 1 1.64
ifc 1 0.62
2 0.32
euler2 833 MHz Itanium HP-UX f90 1 1.18
2 0.60
wigner 900 MHz Itanium2 HP-UX f90 1 0.62
(rx2600) 2 0.32
SGI-altix 1 GHz Itanium2 Linux efc 7 1 0.69
(b2-stepping, 3Mb L3 cache) 2 0.35
4 0.18
8 0.09 (7.7)
16 0.05 (13.8)
Bull 1.3 GHz Itanium2 Linux efc 7 1 0.52
Novascale 5160 (Madison) 2 0.26
4 0.13
8 0.07
16 0.04
SGI-altix 1.5 GHz Itanium2 Linux efc 7 1 0.46
(Madison) 2 0.23
4 0.12
8 0.06 (7.7)
16 0.03 (14.4)
--------------------------------------------------------------------------------
p630 1.0 GHz Power 4 AIX xlf90 1 0.99
2 0.50
4 0.26 (3.8)
thing2 500 Mhz Origin 2400 IRIX f90 1 1.315
2 0.662
4 0.338
8 0.172
16 0.091 (14.5)
32 0.051 (25.8)
primepwr 450 MHz Ultrasprac4 Solaris frt 1 2.49
2 1.22
4 0.63
8 0.33 (7.6)