[gmx-users] Excessive compute time using PME

[Jordi Camps]

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
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.