Berk Hess wrote:
Hi,
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.
From the .mdp file I posted before, grompp gave the following:
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 56x60x50, spacing 0.238 0.230 0.240
Estimate for the relative computational load of the PME mesh part: 0.34
Should it have advised me about anything else? It seems that the PME load is
reasonable, given what I understand about the matter. I suppose that does
indicate to the PP/PME ratio I should be using.
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).
Which cut-offs, rlist/rcoulomb? I thought these were force field-dependent.
Please correct me if I'm wrong.
Hopefully mdrun should choose the proper number of pme nodes for you
when you do not use -npme.
I have never gotten mdrun to cooperate without specifically defining -npme;
maybe it's just me or something that I'm doing. For example, output from two
runs I tried (using 64 cores):
1. With fourierspacing = 0.12 (only difference from the posted .mdp file)
-------------------------------------------------------
Program mdrun_4.0_rc2_mpi, VERSION 4.0_rc2
Source code file: domdec_setup.c, line: 132
Fatal error:
Could not find an appropriate number of separate PME nodes. i.e. >=
0.563840*#nodes (34) and <= #nodes/2 (32) and reasonable performance wise
(grid_x=112, grid_y=117).
Use the -npme option of mdrun or change the number of processors or the PME grid
dimensions, see the manual for details.
-------------------------------------------------------
2. With fourierspacing = 0.24 (the posted .mdp file)
-------------------------------------------------------
Program mdrun_4.0_rc2_mpi, VERSION 4.0_rc2
Source code file: domdec_setup.c, line: 132
Fatal error:
Could not find an appropriate number of separate PME nodes. i.e. >=
0.397050*#nodes (24) and <= #nodes/2 (32) and reasonable performance wise
(grid_x=56, grid_y=60).
Use the -npme option of mdrun or change the number of processors or the PME grid
dimensions, see the manual for details.
-------------------------------------------------------
Thanks.
-Justin
Berk
------------------------------------------------------------------------
> Date: Wed, 1 Oct 2008 17:18:24 -0400
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Improving scaling - Gromacs 4.0 RC2
>
>
> Hi,
>
> 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.
>
> -Justin
>
> =======test.mdp=========
> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
------------------------------------------------------------------------
Express yourself instantly with MSN Messenger! MSN Messenger
<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
