[gmx-users] Performance of 4.6.1 vs. 4.5.5

[Christopher Neale]

Dear users:

I am seeing a 140% performance boost when moving from gromacs 4.5.5 to 4.6.1 when I run a simulation on a single node. However, I am "only" seeing a 110% performance boost when running on multiple nodes. Does anyone else see this? Note that I am not using the verlet cutoff scheme.

I'm not sure that this is a problem, but I was surprised to see how big the difference was between 1 and 2 nodes, while for 2-10 nodes I saw a reliable 10% performance boost.

Please note that, while I compiled the fftw (with sse2) and gromacs 4.6.1, I did not compile the 4.5.5 version that I am comparing to (or its fftw) so the difference might be in compilation options. Still, I wonder why the benefits of 4.6.1 are so fantastic on 1 node but fall off to good-but-not-amazing on > 1 node.

The system is about 43K atoms. I have not tested this with other systems or cutoffs.

My mdp file follows. Thank you for any advice.

Chris.

constraints = all-bonds
lincs-iter =  1
lincs-order =  6
constraint_algorithm =  lincs
integrator = sd
dt = 0.002
tinit = 0
nsteps = 2500000000
nstcomm = 1
nstxout = 2500000000
nstvout = 2500000000
nstfout = 2500000000
nstxtcout = 50000
nstenergy = 50000
nstlist = 10
nstlog=0
ns_type = grid
vdwtype = switch
rlist = 1.0
rlistlong = 1.6
rvdw = 1.5
rvdw-switch = 1.4
rcoulomb = 1.0
coulombtype = PME
ewald-rtol = 1e-5
optimize_fft = yes
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
tc_grps             =  System
tau_t               =  1.0
ld_seed             =  -1
ref_t = 310
gen_temp = 310
gen_vel = yes
unconstrained_start = no
gen_seed = -1
Pcoupl = berendsen
pcoupltype = semiisotropic
tau_p = 4 4
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
dispcorr = EnerPres