[gmx-users] Excessive compute time using PME
Jordi Camps
jcamps at lsi.upc.edu
Wed May 18 13:26:43 CEST 2005
Hello list!
Yes, you were right on the problem. I computed bad box vectors which makes
the box extra-large. Now I reduced the box to it's real size, but now I get
some kind of error. GXM writes an step-1.pdb and a step0.pdb files (the
second one shows that all the molecules exploded) and core dumps. I'm
working to find the cause.
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 van der Spoel
Enviado el: martes, 17 de mayo de 2005 12:48
Para: Discussion list for GROMACS users
Asunto: RE: [gmx-users] Excessive compute time using PME
On Tue, 2005-05-17 at 12:13 +0200, Jordi Camps wrote:
> Hello,
>
> Yes, this is correct. If I'm not wrong, the box is 67nm.
Then that explains it. It is 1000 times larger than "normal" so it will take
a while to perform MD simulations.
>
> --
> 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 van der
> Spoel Enviado el: martes, 17 de mayo de 2005 9:47
> Para: Discussion list for GROMACS users
> Asunto: RE: [gmx-users] Excessive compute time using PME
>
>
> 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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