[gpaw-users] Calculation freezes after memory estimate

[Juho Arjoranta]

Lainaus "Marcin Dulak" <Marcin.Dulak at fysik.dtu.dk>:

> On 06/26/12 08:41, Juho Arjoranta wrote:
>> Hello,
>>
>> I have been converging the vacuum around a copper surface with two
>> bottom layers fixed and with 4 and 6 layers of copper everything went
>> fine. Now I have an 8 layer surface and the calculation freezes after
>> the evaluation of memory usage is made. The calculation for the
>> surface was restarted from a bulk calculation where the initial state
>> for the surface was set. The bulk was relaxed to make sure that the
>> structure is really correct.
> could freezing be ralated to scalapack?
> I remember similar problems with scalapack on, for example
> this hangs:  
> https://trac.fysik.dtu.dk/projects/gpaw/browser/trunk/gpaw/test/parallel/scalapack_pdlasrt_hang.py
>
> Marcin
It would seem that the freezing was related to scalapack. I tried to  
run the same calculations with the default eigensolver and without  
scalapack and it seems to be working now. To get the density and wave  
functions to converge I also made some modifications to the calculator:

surface, calc = restart('bulk-8-initial.gpw',
                         txt = name + '.txt',
                         xc = 'PBE',
                         basis = 'szp(dzp)',
                         mixer=Mixer(beta=0.1, nmaxold=2, weight=100.0),
                         poissonsolver=PoissonSolver(nn=3, relax='GS',  
eps=1e-12),
                         parallel={'domain': (1,2,7)},
                         kpts = (8, 8, 1),
                         h = 0.12)

And for a different (but similiar system) I also increased the maximum  
number of iterations for the Poisson solver as explained in this  
thread:  
https://listserv.fysik.dtu.dk/pipermail/gpaw-users/2010-October/000408.html

Juho

>>
>> Initially when I used the same calculator options as for the 6 layer
>> surface the calculation for 8 layers froze. After that I have tried
>> less agressive mixing, different Poisson solvers, extracting the
>> single-zeta polarization basis set from the double-zeta polarization
>> basis sets, and eventually even a different eigensolver.
>>
>> These calculation were run at Louhi and the last one I tried was this one:
>>
>> from ase.parallel import paropen
>> from gpaw import restart, Mixer
>> from gpaw.poisson import PoissonSolver
>> from ase.constraints import FixAtoms
>> from ase.optimize import QuasiNewton
>> from numpy import zeros
>>
>> resultfile = paropen('8-layer-cg-results.txt', 'w')
>>
>> for vac in range(5, 15):
>>
>>          name = '8-layer-cg-%.i-vacuum' % vac
>>
>>          k = 8
>>          a = 3.643       # Lattice constant from the convergence  
>> calculations
>>
>>          surface, calc = restart('bulk-8-initial.gpw',
>>                          txt = name + '.txt',
>>                          eigensolver = 'cg',
>>                          mixer=Mixer(beta=0.1, nmaxold=2, weight=100.0),
>>                          poissonsolver=PoissonSolver(nn=3, relax='J'),
>>                          basis='szp(dzp)',
>>                          parallel={'sl_default': (5,1,64),
>>                                    'domain': (1,1,5)},
>>                          kpts = (k, k, 1))
>>
>>          # Fixing of the two bottom layers
>>
>>          fix = 2
>>
>>          positions = surface.get_positions()
>>          number = positions.size / 3
>>
>>          array = zeros([number])
>>          for i in range(0, number):
>>                  if (surface.positions[i][2]<  fix * a / 2):
>>                          array[i] = 1
>>                  surface.set_tags(array)
>>          c = FixAtoms(mask=[atom.tag == 1 for atom in surface])
>>          surface.set_constraint(c)
>>
>>          surface.pbc = (1, 1, 0)                         # Set PBC
>> false in z-direction
>>          surface.center(axis = 2, vacuum = vac)          # Center the
>> system in z-direction and add vacuum
>>
>>          surface.set_calculator(calc)
>>
>>          # Relaxation of the surface
>>
>>          relax = QuasiNewton(surface, trajectory = name + '.traj')
>>          relax.run(fmax = 0.05)
>>
>> Equivalent code worked with 4 and 6 layers just fine. Then of course
>> there were no need for different eigensolver or basis etc. For some
>> reason the only error message I get, is Louhi sending me this to my
>> email:
>>
>> PBS Job Id: 1098436.sdb
>> Job Name:   8-layer-cg
>> Post job file processing error; job 1098436.sdb on host nid00143
>>
>>
>> Unable to copy file /var/spool/PBS/spool/1098436.sdb.OU to
>> nid00139://wrk/arjoran/8-layer-cg.o1098436
>> error from copy
>> nid00139: Connection refused
>> end error output
>> Output retained on that host in: /var/spool/PBS/undelivered/1098436.sdb.OU
>>
>> Any ideas how the get that running?
>>
>> Juho Arjoranta
>>
>>
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>
>
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