[gpaw-users] BSSE parallel issue

[Ask Hjorth Larsen]

Also: Please attach full scripts (written so as to demonstrate the
error) and logfiles so I don't have to guess which parameters to
change.  For example I don't know how many CPUs you were using.

Regards
Ask

2013/9/1 Ask Hjorth Larsen <asklarsen at gmail.com>:
> Hello
>
> It works for me.
>
> Note that 17 atoms is not enough for scalapack to be a good idea.
>
> The first parameter in your mixer should be 0.04, not 0.4.
>
> Best regards
> Ask
>
>
> 2013/9/1 Glen Jenness <glenjenness at gmail.com>:
>> Hi GPAW users!
>> I ran into a curious problem when running GPAW in parallel while specifying
>> ghost centers for a BSSE correction.
>>
>> I will be able to run my dimer system (in this case a CO molecule on a Rh
>> (111) surface), but then when I specify calc.set(setups={'Rh': 'ghost"
>> etc.), it'll enter the memory estimate part, and then freeze if I run over 1
>> node.
>>
>> A colleague suggested setting the parallel option sl_auto to True, but doing
>> so gives:
>>
>> ] [27] gpaw-python(PyObject_Call+0x5d) [0x49128d]
>> [compute-0-6:29024] [28] gpaw-python(PyEval_EvalFrameEx+0x399d) [0x50dbfd]
>> [compute-0-6:29024] [29] gpaw-python(PyEval_EvalCodeEx+0x89b) [0x511ffb]
>> [compute-0-6:29024] *** End of error message ***
>> [compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
>> base/pls_base_orted_cmds.c at line 275
>> [compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
>> pls_tm_module.c at line 572
>> [compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
>> errmgr_hnp.c at line 90
>> mpirun noticed that job rank 0 with PID 17481 on node compute-0-9 exited on
>> signal 11 (Segmentation fault).
>> [compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
>> base/pls_base_orted_cmds.c at line 188
>> [compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
>> pls_tm_module.c at line 603
>>
>>
>> Any idea what could cause either issue?
>>
>> Thanks!
>>
>> My python input is:
>>
>> from ase.atoms import Atoms
>> from ase.lattice.surface import fcc111, add_adsorbate
>> from ase.constraints import FixAtoms
>> from ase.optimize.lbfgs import LBFGS
>> from ase.parallel import parprint
>>
>> from gpaw import GPAW, Mixer, FermiDirac
>>
>> PL = {'sl_auto': True}
>>
>> verb = False
>> mix = Mixer(beta=0.40, nmaxold=45, weight=50.0)
>> occ = FermiDirac(0.1)
>>
>> calc = GPAW(mode='lcao', basis='dzp', txt='rhodium.txt', kpts=(5,5,1),
>> occupations=occ, xc='PBE', verbose=verb, mixer=mix, parallel=PL)
>>
>> rhodium = fcc111('Rh', (1,1,4), vacuum=8.0)
>> constraint = FixAtoms([0, 1])
>> rhodium.set_constraint(constraint)
>> rhodium *= (2,2,1)
>>
>> co = Atoms('CO', positions=[(0,0,0), (0,0,1.14)])
>> add_adsorbate(rhodium, co, 1.8, position='ontop')
>>
>> rhodium.set_calculator(calc)
>>
>> opt = LBFGS(rhodium, trajectory='co-rhodium.traj')
>> opt.run(fmax=0.01)
>> e_ads = rhodium.get_potential_energy()
>> parprint('e_ads = %f' % e_ads)
>>
>> calc.set(setups={'Rh': 'ghost', 'C': 'paw', 'O': 'paw'})
>> rhodium.set_calculator(calc)
>> e_co = rhodium.get_potential_energy()
>> parprint('e_co = %s' % e_co)
>>
>> calc.set(setups={'Rh': 'paw', 'C': 'ghost', 'O': 'ghost'})
>> rhodium.set_calculator(calc)
>> e_surf = rhodium.get_potential_energy()
>> parprint('e_surf = %s' % e_surf)
>>
>> parprint('E_BE = %f' % ( e_ads - e_co - e_surf))
>>
>> --
>> Dr. Glen Jenness
>> Schmidt Group/Morgan Group
>> Department of Chemistry/Materials Science and Engineering (MSAE)
>> University of Wisconsin - Madison
>>
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