[gmx-users] Excessive compute time using PME
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 17 09:46:46 CEST 2005
On Tue, 2005-05-17 at 00:52 +0200, Jordi Camps wrote:
> Hi all!
>
> I've tried turning off the optimize_fft parameter, and the running time
> changed to 140s, while when running with optimize_fft=yes the time was 141s.
> It doesn't make a big change.
>
> The grid generated is:
> Using a fourier grid of 567x539x462, spacing 0.119 0.118 0.119
> which has the next dimensions:
> 567==(3^4)*7
> 539==(7^2)*11
> 462==2*3*7*11
This means your box is 60 nm. Is that correct?
> All of them can be computed with the default FFT optimizations of the FFTW
> libraries. How the grid should look like?
>
> Anyone has another suggestion? This long times are killing us :-(
>
> Thanks for all,
>
> --
> Jordi Camps Puchades
> Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
> UPC-CIRI
> c/. Jordi Girona 1-3
> Modul C6-E201 Tel. : 934 011 650
> E-08034 Barcelona Fax : 934 017 014
> Catalunya (Spain) e-mail: jcamps at lsi.upc.edu
>
> -----Mensaje original-----
> De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] En
> nombre de David
> Enviado el: sábado, 14 de mayo de 2005 9:24
> Para: Discussion list for GROMACS users
> Asunto: RE: [gmx-users] Excessive compute time using PME
>
>
> On Sat, 2005-05-14 at 03:29 +0200, Jordi Camps wrote:
> > Hello!
> >
> > The box is full of waters (plus the protein) and not specially large.
> > It is a truncated octahedron box. The grid spacing is the standard:
> > fourierspacing=0.12
>
> Check the grid anyway, but the first steps are extra costly because you
> turned on optimize_fft. Try it without.
>
> > Either way, this line is commented out.
> >
> > The parameters are:
> > title = Simulation
> > cpp = /lib/cpp
> > integrator = md
> > dt = 0.002
> > nsteps = 2
> > nstlog = 500
> > nstxout = 500
> > nstenergy = 500
> > nstvout = 500
> > nstxtcout = 500
> > constraint_algorithm= shake
> > constraints = hbonds
> > pbc = xyz
> >
> > ;;;; Pressure coupling is on
> > Pcoupl = berendsen
> > pcoupltype = isotropic
> > ;;;;tau_p = 0.5
> > compressibility = 4.5e-5
> > ref_p = 1.01325
> >
> > ;;;; Berendsen temperature coupling is on in three groups
> > Tcoupl = berendsen
> > tau_t = 0.1
> > tc_grps = System
> > ref_t = 300
> >
> >
> > coulombtype = PME
> > rcoulomb = 1.0
> > rvdw = 1.0
> > rlist = 1.0
> > optimize_fft = yes
> > ;;;; Generate velocites is on at 300 K.
> > gen_vel = no
> >
> > Thanks for your help,
> >
> > --
> > Jordi Camps Puchades
> > Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
> > UPC-CIRI
> > c/. Jordi Girona 1-3
> > Modul C6-E201 Tel. : 934 011 650
> > E-08034 Barcelona Fax : 934 017 014
> > Catalunya (Spain) e-mail: jcamps at lsi.upc.edu
> >
> > -----Mensaje original-----
> > De: gmx-users-bounces at gromacs.org
> > [mailto:gmx-users-bounces at gromacs.org] En nombre de David Enviado el:
> > viernes, 13 de mayo de 2005 19:20
> > Para: Discussion list for GROMACS users
> > Asunto: Re: [gmx-users] Excessive compute time using PME
> >
> >
> > On Fri, 2005-05-13 at 18:05 +0200, Jordi Camps wrote:
> > > Dear sirs,
> > >
> > > I'm trying to run some simulations with PME, but the time that them
> > > takes are unusually long. Finally I reduced the number of steps to
> > > compute to only two (2) steps and one system with about 20000 atoms
> > > takes about 140 seconds to compute (spending 98% of the time "solving
> > > PME"). But if I take out the coulombtype=PME parameter (so I simulate
> > > with a cut-off), the time needed for the same two steps is about 3
> > > seconds. Adding PME calculus should increase the compute time, but not
> > > in this magnitude order.
> > > If I let the simulation run for more time, I get about 1500 steps in 12
> > > hours (approx.).
> > >
> > > Is this normal? Could it be a compilation problem? An uncorrected
> > > bug?
> > > A parameter definition problem?
> >
> > Is your box nearly empty and very large? Or are you using a very fine
> > spaced grid?
> >
> > >
> > > I can supply the .mdp and the other files if necessary.
> > >
> > > I've been simulating on one processor (in multiple processors
> > > behaves
> > > similarly). I'm using PBC too.
> > >
> > > Thanks for your help.
> > >
> > > Sincerely,
> > >
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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