[gmx-users] Improving scaling - Gromacs 4.0 RC2
gmx3 at hotmail.com
Thu Oct 2 10:06:44 CEST 2008
Looking at your 64 core results, it seems that your PP:PME load ratio is about 1:1.
In most cases 3:1 is much better performance wise.
grompp probably also printed a note about this and also how to fix it.
I have also described this shortly in the parallelization section of the pdf manual.
You should probably increase your cut-offs and pme grid spacing by the same factor
(something around 1.2).
Hopefully mdrun should choose the proper number of pme nodes for you
when you do not use -npme.
> Date: Wed, 1 Oct 2008 17:18:24 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Improving scaling - Gromacs 4.0 RC2
> I've been playing around with the latest release candidate of version 4.0, and I
> was hoping someone out there more knowledgeable than me might tell me how to
> improve a bit on the performance I'm seeing. To clarify, the performance I'm
> seeing is a ton faster than 3.3.x, but I still seem to be getting bogged down
> with the PME/PP balance. I'm using mostly the default options with the new mdrun:
> mdrun_mpi -s test.tpr -np 64 -npme 32
> The system contains about 150,000 atoms - a membrane protein surrounded by
> several hundred lipids and solvent (water). The protein parameters are GROMOS,
> lipids are Berger, and water is SPC. My .mdp file (adapted from a generic 3.3.x
> file that I always used to use for such simulations) is attached at the end of
> this mail. It seems that my system runs fastest on 64 CPU's. Almost all tests
> with 128 or 256 seem to run slower. The nodes are dual-core 2.3 GHz Xserve G5,
> connected by Infiniband.
> Here's a summary of some of the tests I've run:
> -np -npme -ddorder ns/day % performance loss from imbalance
> 64 16 interleave 5.760 19.6
> 64 32 interleave 9.600 40.9
> 64 32 pp_pme 5.252 3.9
> 64 32 cartesian 5.383 4.7
> All other mdrun command line options are defaults.
> I get ~10.3 ns/day with -np 256 -npme 64, but since -np 64 -npme 32 seems to
> give almost that same performance there seems to be no compelling reason to tie
> up that many nodes.
> Any hints on how to speed things up any more? Is it possible? Not that I'm
> complaining...the same system under GMX 3.3.3 gives just under 1 ns/day :) I'm
> really curious about the 40.9% performance loss I'm seeing with -np 64 -npme 32,
> even though it gives the best overall performance in terms of ns/day.
> Thanks in advance for your attention, and any comments.
> title = NPT simulation for a membrane protein
> ; Run parameters
> integrator = md
> dt = 0.002
> nsteps = 10000 ; 20 ps
> nstcomm = 1
> ; Output parameters
> nstxout = 500
> nstvout = 500
> nstfout = 500
> nstlog = 500
> nstenergy = 500
> ; Bond parameters
> constraint_algorithm = lincs
> constraints = all-bonds
> continuation = no ; starting up
> ; Twin-range cutoff scheme, parameters for Gromos96
> nstlist = 5
> ns_type = grid
> rlist = 0.8
> rcoulomb = 0.8
> rvdw = 1.4
> ; PME electrostatics parameters
> coulombtype = PME
> fourierspacing = 0.24
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; V-rescale temperature coupling is on in three groups
> Tcoupl = V-rescale
> tc_grps = Protein POPC SOL_NA+_CL-
> tau_t = 0.1 0.1 0.1
> ref_t = 310 310 310
> ; Pressure coupling is on
> Pcoupl = Berendsen
> pcoupltype = semiisotropic
> tau_p = 2.0
> compressibility = 4.5e-5 4.5e-5
> ref_p = 1.0 1.0
> ; Generate velocities is on
> gen_vel = yes
> gen_temp = 310
> gen_seed = 173529
> ; Periodic boundary conditions are on in all directions
> pbc = xyz
> ; Long-range dispersion correction
> DispCorr = EnerPres
> ========end test.mdp==========
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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