On 17/07/2012 5:00 PM, DeChang Li wrote:
Dear all,
I am running a 9000 atom system with GBSA (Gromacs 4.5.5) in a
Blue Gene/Q cluster. I got the speed 1.002 ns/day with 8 cores.
However, in my own workstation with 8 cores the same system can reach
nearly 10 ns/day (Intel(R) Xeon(R) CPU E5620 @ 2.40GHz). Can anyone
tell me what's wrong in my simulation? Any suggestion will be
appreciated.
Your workstation is running highly effective optimized SSE loops.
BlueGene/Q is not using its multiple FPU because that code hasn't been
written (for explicit or implicit solvation), and BlueGene's processors
are probably slower too.
Mark
Following is my md.mdp file:
constraints = hbonds
constraint_algorithm = LINCS
lincs_order = 4
comm_mode = Angular
comm_grps = system
integrator = sd
;annealing = single single
;annealing_npoints = 2 2
;annealing_time = 0 500 0 500
;annealing_temp = 200 300 200 300
dt = 0.002 ; ps !
nsteps = 5000000 ; total 5000 ps.
nstcomm = 10
nstcalcenergy = 10
nstxout = 10000 ; collect data every 1 ps
nstenergy = 10000
nstvout = 10000
nstlog = 1000
;nstxtcout = 50000
;xtc_grps = system
nstfout = 0
nstlist = 10
ns_type = grid
pbc = no
rlist = 1.2
coulombtype = cut-off
rcoulomb = 1.2
rvdw = 1.2
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
;energygrps = alpha1 alpha2 alpha3 beta1 beta2 beta3 gamma
;DispCorr = EnerPres
; Berendsen temperature coupling is on in two groups
Tcoupl =
tau_t = 0.5
tc-grps = system
ref_t = 300
; Pressure coupling is on
Pcoupl = no ;berendsen
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300
gen_seed = -1
implicit_solvent = GBSA
gb_algorithm = OBC
rgbradii = 1.2
sa_surface_tension = 2.25936
Here is the preformace info:
M E G A - F L O P S A C C O U N T I N G
RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
NF=No Forces
Computing: M-Number M-Flops % Flops
-----------------------------------------------------------------------------
Generalized Born Coulomb 61.482892 2951.179 0.4
GB Coulomb + LJ 2565.481100 156494.347 19.4
Outer nonbonded loop 152.268546 1522.685 0.2
1,4 nonbonded interactions 116.143224 10452.890 1.3
Born radii (HCT/OBC) 2868.222234 524884.669 64.9
Born force chain rule 2868.222234 43023.334 5.3
NS-Pairs 516.814696 10853.109 1.3
Reset In Box 4.464788 13.394 0.0
CG-CoM 4.482576 13.448 0.0
Bonds 22.174434 1308.292 0.2
Angles 80.586114 13538.467 1.7
Propers 160.742142 36809.951 4.6
Virial 4.636254 83.453 0.0
Update 44.478894 1378.846 0.2
Stop-CM 4.455894 44.559 0.0
Calc-Ekin 44.487788 1201.170 0.1
Lincs 44.951630 2697.098 0.3
Lincs-Mat 261.822552 1047.290 0.1
Constraint-V 44.951630 359.613 0.0
Constraint-Vir 2.251163 54.028 0.0
-----------------------------------------------------------------------------
Total 808731.820 100.0
-----------------------------------------------------------------------------
D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
av. #atoms communicated per step for force: 2 x 660.5
av. #atoms communicated per step for LINCS: 2 x 34.3
Average load imbalance: 1.7 %
Part of the total run time spent waiting due to load imbalance: 1.4 %
R E A L C Y C L E A N D T I M E A C C O U N T I N G
Computing: Nodes Number G-Cycles Seconds %
-----------------------------------------------------------------------
Domain decomp. 8 502 59.421 37.1 0.5
DD comm. load 8 8 0.004 0.0 0.0
Comm. coord. 8 5001 16.575 10.4 0.2
Neighbor search 8 502 136.093 85.1 1.2
Force 8 5001 9744.582 6090.7 88.3
Wait + Comm. F 8 5001 90.905 56.8 0.8
Write traj. 8 2 0.954 0.6 0.0
Update 8 5001 72.936 45.6 0.7
Constraints 8 10002 171.445 107.2 1.6
Comm. energies 8 502 10.427 6.5 0.1
Rest 8 732.742 458.0 6.6
-----------------------------------------------------------------------
Total 8 11036.086 6897.9 100.0
-----------------------------------------------------------------------
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 862.243 862.243 100.0
14:22
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 3.047 937.940 1.002 23.946
Finished mdrun on node 0 Tue Jul 17 16:06:48 2012
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