[gmx-users] speed issue, gmx runtime estimate = f(t)

[Szilárd Páll]

Hi,

As Justin said, it's probably the imbalance which is causing the
slowdown. You can take a look at the statistics at the end of the log
file. One simple thing you could do is to compare the log file of your
long, gradually slowing down run with a shorter run to see which part
takes more time.

--
Szilárd



On Wed, Apr 6, 2011 at 3:26 PM, Michael Brunsteiner <mbx0009 at yahoo.com> wrote:
>
> Dear all,
>
> I am trying to optimize runtimes/speed for a series of
> calculations i plan to do with a rather complex system.
> When looking at runtimes I observed one peculiar issue:
> the estimated runtime written to stderr by mdrun with the "-v"
> option keepsgrowing ... in my experience this estimate normally
> converges to a fairly accurate value within a few hundred
> steps. not so here ..
> for example, starting a job at 12:14 gromacs writes to stderr:
>
> step 100, will finish Wed Apr  6 12:40:35 2011vol 0.97  imb F  1%
> step 200, will finish Wed Apr  6 12:39:42 2011vol 0.95  imb F  2%
> step 300, will finish Wed Apr  6 12:39:47 2011vol 0.95  imb F  1%
> step 400, will finish Wed Apr  6 12:39:52 2011vol 0.96  imb F  1%
> ...
> step 38400, will finish Wed Apr  6 14:09:11 2011vol 0.91  imb F 29%
>
> so the estimated run time grows steadily from 25 to 110 minutes
> within about one hour...
> this is mdrun_d (gmx-4.5.3) running on a linux PC with
> 2 processores/4 nodes/8 threads. There's a couple of other programs (X, editor,
> ...)
> running at the same time but none of them uses a lot of CPU.
>
> Anyway, what i see lets me expect there might be a way
> to speed up these calculations. I'd appreciate any suggestions!
> (below is my mdp file.)
>
> cheers,
> Michael
>
>
> mdp file:
>
> integrator           = md
> ;
> dt                   = 0.001
> tinit                = 0
> nsteps               = 100000
> nstxtcout            = 0
> nstxout              = 1000
> nstvout              = 0
> nstfout              = 0
> nstenergy            = 1000
> ;
> constraint_algorithm = lincs
> constraints          = hbonds
> ;
> comm_mode            = Linear
> nstcomm              = 1
> pbc                  = xyz
> nstlist              = 10
> ns_type              = grid
> rlist                = 1.4
> rcoulomb             = 1.4
> rvdw                 = 1.4
> ;
> coulombtype          = PME
> vdwtype              = User
> fourierspacing       = 0.2
> optimize_fft         = yes
> ;
> Tcoupl               = nose-hoover
> tc_grps              = System
> ref_t                = 300.0
> tau_t                = 0.4
> gen_vel              = yes
> gen_temp             = 240.0
> gen_seed             = 222222
> ;
> pull                 = umbrella
> pull_geometry        = distance
> pull_dim             = N N Y
> pull_start           = yes
> pull_ngroups         = 1
> pull_group0          = f1
> pull_group1          = f2
> pull_rate1           = -0.015
> pull_k1              = 1000
> pull_nstxout         = 100
> pull_nstfout         = 100
> pull_pbcatom0        = 241
> pull_pbcatom1        = 482
> ;
> freezegrps           = c1 c2
> freezedim            = Y Y N Y Y N
> ;
> energygrps           = SOL CC CF
> energygrp_table      = CF CF  CF SOL  CF CC
> --
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