[ase-users] Cores
Tadeu Leonardo Soares e Silva
tsilva at peq.coppe.ufrj.br
Tue Apr 26 18:32:44 CEST 2011
Dear Marcin
Thank you very much.
It works much better.
Sincerely,
Tadeu Leonardo
On Tue, 26 Apr 2011 10:20:40 +0200, Marcin Dulak wrote
> Hi,
>
> please continue on the mailing list.
> dyn or qn is just a name of a variable - this is how you name the
optimizer.
> It's sometimes safer to avoid symmetry=True (see
> https://listserv.fysik.dtu.dk/pipermail/ase-users/2010-
> October/000871.html), As the manual says stay_alive=True saves on
> writing to disk: see https://wiki.fysik.dtu.dk/dacapo/Manual#dacapo-
> fortran-program-python-interface-communication Try out the options
> to see which ones work better for your jobs.
>
> Best regards,
>
> Marcin
>
> Tadeu Leonardo Soares e Silva wrote:
> > Dear Marcin
> >
> > Thank you very much. It works much better! By the way what is the differ
> > between dyn = BFGS and qn= BFGS for geometry optimizations? Would I
need to
> > use symmetry=True and stay_alive=True for my geometry optimizations?
> >
> > Sincerely,
> >
> > Tadeu
> >
> >
> > On Tue, 19 Apr 2011 18:07:54 +0200, Marcin Dulak wrote
> >
> >> Hi,
> >>
> >> Tadeu Leonardo Soares e Silva wrote:
> >>
> >>> Dear Marcin
> >>>
> >>> Thank you very much. But I have a doubt. I would like to make the
follow
> >>>
> > job.
> >
> >>> #!/usr/bin/env python
> >>> import ase
> >>> from ase import *
> >>> from ase.lattice.surface import *
> >>> from ase.calculators.jacapo import *
> >>>
> >>> slab = fcc111('Pd',a=3.92, size=(5,5,4), vacuum=10.0, orthogonal=False)
> >>> slab.center()
> >>>
> >>> calc = Jacapo(nc='superficiePd.nc',
> >>> pw=400,
> >>> kpts=(3,3,1),
> >>> xc='RPBE',
> >>> dipole=True,
> >>> symmetry=True,
> >>> stay_alive=True,
> >>> ft=0.1,
> >>> atoms=slab)
> >>>
> >>> #here we select atoms with tag not equal to 1 and 2 to fix
> >>>
> >>>
> >>> constraint = ase.constraints.FixAtoms(mask=[a.get_tag() > 2 for a in
> >>>
> > slab])
> >
> >>> slab.set_constraint(constraint)
> >>>
> >>> dyn = ase.optimize.QuasiNewton(slab, trajectory='superficiePd.traj')
> >>> dyn.run(fmax=0.05)
> >>>
> >>> print slab.get_potential_energy()
> >>> print slab.get_forces()
> >>> ase.io.write ('superficiePd.xyz',slab)
> >>>
> >>> The .txt file:
> >>>
> >>> KPT: 9 BZ kpoints specified in file
> >>> KPT: k-points in the irriducible Brillouin zone (nkprun) : 5
> >>> KPT: ----------------------------------------------------------
> >>> KPT: k-point k-point in units of k-point
> >>> KPT: number B1 B2 B3 weigth
> >>> KPT: ----------------------------------------------------------
> >>> KPT: 1 -0.333333 -0.333333 0.000000 0.222222
> >>> KPT: 2 -0.333333 0.000000 0.000000 0.222222
> >>> KPT: 3 -0.333333 0.333333 0.000000 0.222222
> >>> KPT: 4 0.000000 -0.333333 0.000000 0.222222
> >>> KPT: 5 0.000000 0.000000 0.000000 0.111111
> >>> KPT: ----------------------------------------------------------
> >>> KPT:
> >>> KPT: Chadi-Cohen asymptotic error estimate: 0.000096675384
> >>> KPT: (see PRB 8, 5747 (1973); 13, 5188 (1976))
> >>> KPT: nkpmem : 1
> >>>
> >>> In this .txt file I would have just 5 five kpoint (100 Pd atoms), then
I
> >>> could to use until 15 cores ( 3 cores or processors per k point). But
I
> >>>
> > have
> >
> >>> 400 cores in my cluster. Could I to use more cores for this job? I
> >>>
> > belive
> >
> >>> that with 15 cores it will take much.
> >>>
> >>>
> >> the job run on many more cores than k-points will be just slower
> >> that a job run on the number of cores equal to the number of k-
> >> points - try it. I would set kpts=(4,4,1) (unless you really need (3,
> >> 3,1)), so the number of k-points reduced by symmetry would be even,
> >> and then use an even number of cores, kpts, maybe kpts*2 - you need
> >> to test this.
> >>
> >> Best regards,
> >>
> >> Marcin
> >>
> >>> What do you think about this?
> >>>
> >>> Sincerely,
> >>>
> >>> Tadeu
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Tue, 19 Apr 2011 10:59:04 +0200, Marcin Dulak wrote
> >>>
> >>>
> >>>> Hi,
> >>>>
> >>>> if you use k-points please have a look at the vasp recommendation
> >>>> from http://www.raunvis.hi.is/~finnboo/bjolfur/ (last section:
> >>>> running in parallel): one processor per k-point (the number of k-
> >>>> points is printed in the txt output). Make an experiment to verify
> >>>> that this holds for the configuration of your cluster. If you don't
> >>>> have k-points then you have to make experiments described at
> >>>> https://listserv.fysik.dtu.dk/pipermail/ase-users/2011-
March/000976.html
> >>>> Usually people run dacapo jobs on 8-32 cores.
> >>>>
> >>>> Best regards,
> >>>>
> >>>> Marcin
> >>>>
> >>>> Tadeu Leonardo Soares e Silva wrote:
> >>>>
> >>>>
> >>>>> Dear Marcin
> >>>>>
> >>>>> How do I do to calculate how many cores should I to use in Jacapo? I
> >>>>>
> >>>>>
> >>> have a
> >>>
> >>>
> >>>>> cluster with 400 cores. Could I to use all cores for a job?
> >>>>>
> >>>>>
> >>>>> Sincerely,
> >>>>>
> >>>>> Tadeu
> >>>>>
> >>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>>>
> >>>>> PEQ/COPPE renova o nivel de curso 7, maximo na CAPES:
> >>>>> 45 anos de excelencia no ensino e pesquisa de pos-graduação em
> >>>>> Engenharia Quimica.
> >>>>>
> >>>>> ************************************
> >>>>>
> >>>>> PEQ/COPPE : 45 years of commitment to excellence in teaching and
> >>>>> research in Chemical Engineering.
> >>>>>
> >>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>>>
> >>>>>
> >>>>>
> >>>> --
> >>>> ***********************************
> >>>>
> >>>> Marcin Dulak
> >>>> Technical University of Denmark
> >>>> Department of Physics
> >>>> Building 307, Room 229
> >>>> DK-2800 Kongens Lyngby
> >>>> Denmark
> >>>> Tel.: (+45) 4525 3157
> >>>> Fax.: (+45) 4593 2399
> >>>> email: Marcin.Dulak at fysik.dtu.dk
> >>>>
> >>>> ***********************************
> >>>>
> >>>>
> >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>
> >>> PEQ/COPPE renova o nivel de curso 7, maximo na CAPES:
> >>> 45 anos de excelencia no ensino e pesquisa de pos-graduação em
> >>> Engenharia Quimica.
> >>>
> >>> ************************************
> >>>
> >>> PEQ/COPPE : 45 years of commitment to excellence in teaching and
> >>> research in Chemical Engineering.
> >>>
> >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++
> >>>
> >>>
> >> --
> >> ***********************************
> >>
> >> Marcin Dulak
> >> Technical University of Denmark
> >> Department of Physics
> >> Building 307, Room 229
> >> DK-2800 Kongens Lyngby
> >> Denmark
> >> Tel.: (+45) 4525 3157
> >> Fax.: (+45) 4593 2399
> >> email: Marcin.Dulak at fysik.dtu.dk
> >>
> >> ***********************************
> >>
> >
> >
> > +++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > PEQ/COPPE renova o nivel de curso 7, maximo na CAPES:
> > 45 anos de excelencia no ensino e pesquisa de pos-graduação em
> > Engenharia Quimica.
> >
> > ************************************
> >
> > PEQ/COPPE : 45 years of commitment to excellence in teaching and
> > research in Chemical Engineering.
> >
> > +++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
>
> --
> ***********************************
>
> Marcin Dulak
> Technical University of Denmark
> Department of Physics
> Building 307, Room 229
> DK-2800 Kongens Lyngby
> Denmark
> Tel.: (+45) 4525 3157
> Fax.: (+45) 4593 2399
> email: Marcin.Dulak at fysik.dtu.dk
>
> ***********************************
+++++++++++++++++++++++++++++++++++++++++++++++++++++
PEQ/COPPE renova o nivel de curso 7, maximo na CAPES:
45 anos de excelencia no ensino e pesquisa de pos-graduação em
Engenharia Quimica.
************************************
PEQ/COPPE : 45 years of commitment to excellence in teaching and
research in Chemical Engineering.
+++++++++++++++++++++++++++++++++++++++++++++++++++++
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