[gpaw-users] running different calculations in parallel

[Punit Kumar]

On Tue, 2 Jun 2020 at 13:24, Jens Jørgen Mortensen <jjmo at dtu.dk> wrote:

> On 5/30/20 1:43 PM, Punit Kumar wrote:
> > Hi Jens
> >
> > Thanks a lot for your response and for clarifying my doubts. The
> > calculation runs correctly and I got four output and four trajectory
> > files separately. But,
> >
> > On Wed, 27 May 2020 at 13:11, Jens Jørgen Mortensen <jjmo at dtu.dk
> > <mailto:jjmo at dtu.dk>> wrote:
> >
> >     Den 26.05.2020 kl. 12.06 skrev Punit Kumar via gpaw-users:
> >      > Dear gpaw-users
> >      >
> >      > I have made four different initial structures of H atom
> >     adsorption on
> >      > Ni(111) surface and club all these structures into a single
> >     trajectory
> >      > file (attached below). Now, I want to perform the structure
> >     optimization
> >      > calculation for all the initial structures parallelly over 40
> cores
> >      > (with each structure running on 10 cores). While doing this I
> don't
> >      > want my final outputs and trajectories to be mixed. I have
> >     searched for
> >      > this problem (or tutorial) in gpaw documentation
> >      >
> >     (
> https://wiki.fysik.dtu.dk/gpaw/documentation/parallel_runs/parallel_runs.html#parallel-runs
> )
> >      > and write down a piece of code for the same which looks like that
> >
> >     You have this line:
> >
> >           qn = BFGS(images[i],logfile='opt%d.log' % j)
> >
> >     but i is always 3.  Also, you don't need the for-loop.  And you
> should
> >     add this:
> >
> >           master=(comm.rank == 0)
> >
> >     when you create the BFGS object.
> >
> >     Here is my version:
> >
> >     from gpaw import GPAW, PW, mpi
> >     from ase import Atoms
> >     from ase.io <http://ase.io> import Trajectory
> >     from ase.optimize import BFGS
> >
> >     images = [Atoms('HH',
> >                       [(0, 0, 0), (0, 0, d)],
> >                       pbc=1,
> >                       cell=(2, 2, 3))
> >                 for d in [0.7, 0.725, 0.75, 0.775]]
> >
> >     n = mpi.size // 4
> >     j = 1 + mpi.rank // n
> >     assert 4 * n == mpi.size
> >     i = j - 1
> >     ranks = range(i * n, (i + 1) * n)
> >     print(i, ranks)
> >     comm = mpi.world.new_communicator(ranks)
> >     calc = GPAW(mode=PW(340),
> >                   txt='H_ads_%d.txt' % j,
> >                   communicator=comm)
> >     images[i].set_calculator(calc)
> >
> >     qn = BFGS(images[i], logfile='opt%d.log' % j, master=(comm.rank ==
> 0))
> >
> >
> > one thing I have observed that after the calculation is finished only
> > one log file is generated. Since there are four structures in images
> > atom object there should be four log files also. But after the
> > calculation is done I'm getting only one log file i.e. opt1.log. Do you
> > have any idea why it produces only one log file in spite of the fact
> > that *"% j " *is mentioned in the above line of code in order to
> > generate four different log files?
>
> No, I don't understand that.  I get four log-files.
>
> Jens Jørgen
>
> Thanks for the reply. I'm still getting only one log file and unable to
figure out where I'm doing it wrong. The gpaw version I'm currently using
is 1.2.0.

Punit

> >     traj = Trajectory('H_ads_%d.traj' % j, 'w', images[i],
> >     master=(comm.rank
> >     == 0))
> >
> >     qn.attach(traj)
> >     qn.run(fmax=0.5)
> >
> >     Jens Jørgen
> >
> >      > *f/rom ase.io <http://ase.io> <http://ase.io> import read,
> Trajectory
> >      > from ase.optimize import *
> >      > from ase.parallel import rank, size
> >      > from ase.visualize import view
> >      > from gpaw import GPAW, PW, Mixer, FermiDirac, Davidson, mpi
> >      >
> >      > bands = -60
> >      >
> >      > images = read('initial.traj at -4:')/*
> >      > /*
> >      > n = size // 4      # number of cpu's per image
> >      > j = 1 + rank // n  # my image number
> >      > assert 4 * n == size*/
> >      > /*
> >      > for i in range(len(images)):
> >      >      ranks = range(i * n, (i+1) * n)
> >      >      print(i,ranks)
> >      >      comm = mpi.world.new_communicator(ranks)
> >      >      calc = GPAW(mode=PW(340),xc='RPBE',spinpol=False,kpts=(6, 6,
> >      > 1),maxiter=1000,
> >      >
> >     nbands=bands,mixer=Mixer(beta=0.05,nmaxold=5,weight=50),
> >      >                  eigensolver='rmm-diis',symmetry={'point_group':
> >     False},
> >      >
> >      >
> occupations=FermiDirac(0.1),txt='H_ads_%d.txt'%j,communicator=comm)
> >      >      images[i].set_calculator(calc)
> >      >
> >      > qn = BFGS(images[i],logfile='opt%d.log' % j)
> >      >
> >      > traj = Trajectory('H_ads_%d.traj' % j, 'w', images[j],
> >     master=(rank % n
> >      > == 0))
> >      >
> >      > qn.attach(traj)
> >      > qn.run(fmax=0.5)
> >      > #view(slab)*/
> >      >
> >      > After running the calculation I'm not able to get different
> >     outputs and
> >      > trajectories. Since it is the first time I'm trying something
> >     like this
> >      > maybe I have made errors in my code. Can someone help me out to
> >     resolve
> >      > my problem? Any help or suggestion is highly appreciated.
> >      >
> >      > Thank you
> >      > Punit
> >      >
> >      > _______________________________________________
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> >      > gpaw-users at listserv.fysik.dtu.dk
> >     <mailto:gpaw-users at listserv.fysik.dtu.dk>
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> >      >
> >
>
>
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