[gmx-users] Performance of 4.6.1 vs. 4.5.5

[Mark Abraham]

On Sat, Mar 9, 2013 at 6:53 AM, Christopher Neale <
chris.neale at mail.utoronto.ca> wrote:

> 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.
>

What's the processor and network for those runs?

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.
>

Not sure what you mean by "reliable 10% performance boost." Reporting
actual ns/day rates would be clearer. Is a "140% performance boost" a
factor of 1.4 more ns/day or a factor of 2.4 more ns/day?

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.


Indeed.


> 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.
>

Finding the answer would start by examining the changes in the timing
breakdowns in your .log files. Switching from using in-memory MPI to
network MPI is a significant cost on busy/weak networks.

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.
>

Your system is probably not calculating energies very much. 4.6 uses
force-only kernels if that's all you need from it.

Mark

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
>
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