[gpaw-users] Error in running calculation with "rmm-diis" as well for band parallelization

[mohnish pandey]

Dear GPAW users and Developers,

I asked a question a week ago regarding running the calculation with
band-parallelization. Marcin suggested that it doesn't work in 'cg' method.
So for bigger systems I am trying to use 'rmm-diis'. But unfortunately with
no luck. I am pasting my input and error message I am getting. I really
appreciate your help. Thanks a lot in advance.

*INPUT:*

from ase.parallel import paropen
from ase.io import read
from ase.lattice.spacegroup import crystal
from ase.lattice.spacegroup.spacegroup import spacegroup_from_data
from ase.units import Hartree
from ase.io import PickleTrajectory
from ase import Atom, Atoms, visualize
from ase.structure import bulk
from ase.constraints import UnitCellFilter as StrainFilter
from ase.optimize.fire import FIRE as QuasiNewton
from ase import *

from gpaw.test import equal
from gpaw import GPAW,FermiDirac,restart
from gpaw import PW
from gpaw.mixer import Mixer
from gpaw.wavefunctions.pw import PW
from gpaw.mpi import serial_comm, rank, size, world
from gpaw import *

import numpy as np
import shlex
import re
from glob import glob
import pprint
import datetime
import os
import commands

ITl = read('/home/camp/mohpa/cif-mat-proj/non_spinpol/TlI.cif', index=-1,
format='cif')

length_a = (np.dot(ITl.get_cell()[0],ITl.get_cell()[0]))**0.5
length_b = (np.dot(ITl.get_cell()[1],ITl.get_cell()[1]))**0.5
length_c = (np.dot(ITl.get_cell()[2],ITl.get_cell()[2]))**0.5

kx = int(27.0/length_a+0.5)
ky = int(27.0/length_b+0.5)
kz = int(27.0/length_c+0.5)

calc = GPAW(mode=PW(600),
            xc = 'PBE',
            kpts=(kx,ky,kz),
            nbands = 40,
            usesymm=True,
            communicator=world,
            convergence = {'bands' : 'all'},
            maxiter=600,

            basis='dzp',
            eigensolver='rmm-diis',
            txt = 'ITl_opt_bulk_PBE.out',
            occupations=FermiDirac(width=0.05))

ITl.set_calculator(calc)
sf = StrainFilter(ITl)
qn = QuasiNewton(sf, logfile = 'ITl'+'.log')
qn.run(fmax=0.05)

#Calculation with optimized structure
calc = GPAW(mode=PW(600),
            xc = 'PBE',
            kpts=(kx,ky,kz),
            nbands = 40,
            usesymm=True,
            basis='dzp',
            communicator=world,
            maxiter=600,
            eigensolver='rmm-diis',
            txt = 'ITl_bulk_PBE.out',
            occupations=FermiDirac(width=0.05))

ITl.set_calculator(calc)
en = ITl.get_potential_energy()
calc.write('ITl'+'_PBE.gpw')
p = paropen('tot_en.txt','a')
p.write('ITl'+'  '+str(en)+'\n')

*ERROR:*
*
*
Traceback (most recent call last):
  File "ITl.py", line 56, in ?
    qn.run(fmax=0.05)
  File "/home/camp/mohpa/ase/ase/optimize/optimize.py", line 114, in run
    f = self.atoms.get_forces()
  File "/home/camp/mohpa/ase/ase/constraints.py", line 1116, in get_forces
Traceback (most recent call last):
Traceback (most recent call last):
  File "ITl.py", line 56, in ?
    qn.run(fmax=0.05)
  File "ITl.py", line 56, in ?
    qn.run(fmax=0.05)
  File "/home/camp/mohpa/ase/ase/optimize/optimize.py", line 114, in run
    f = self.atoms.get_forces()
    stress = self.atoms.get_stress()
  File "/home/camp/mohpa/ase/ase/optimize/optimize.py", line 114, in run
    f = self.atoms.get_forces()
  File "/home/camp/mohpa/ase/ase/constraints.py", line 1116, in get_forces
Traceback (most recent call last):
    stress = self.atoms.get_stress()
  File "/home/camp/mohpa/ase/ase/atoms.py", line 668, in get_stress
  File "ITl.py", line 56, in ?
    qn.run(fmax=0.05)
  File "/home/camp/mohpa/ase/ase/constraints.py", line 1116, in get_forces
    stress = self.atoms.get_stress()
Traceback (most recent call last):
  File "/home/camp/mohpa/ase/ase/atoms.py", line 668, in get_stress
  File "/home/camp/mohpa/ase/ase/optimize/optimize.py", line 114, in run
  File "ITl.py", line 56, in ?
    f = self.atoms.get_forces()
    qn.run(fmax=0.05)
  File "/home/camp/mohpa/ase/ase/atoms.py", line 668, in get_stress
  File "/home/camp/mohpa/ase/ase/constraints.py", line 1116, in get_forces
  File "/home/camp/mohpa/ase/ase/optimize/optimize.py", line 114, in run
    f = self.atoms.get_forces()
    stress = self._calc.get_stress(self)
    stress = self.atoms.get_stress()
    stress = self._calc.get_stress(self)
    stress = self._calc.get_stress(self)
  File "/home/camp/mohpa/ase/ase/constraints.py", line 1116, in get_forces
  File "/home/camp/mohpa/ase/ase/atoms.py", line 668, in get_stress
  File "/home/camp/mohpa/Software/gpaw.9554/gpaw/aseinterface.py", line 82,
in get_stress
    stress = self._calc.get_stress(self)
    stress = self.atoms.get_stress()
Traceback (most recent call last):
Traceback (most recent call last):
  File "/home/camp/mohpa/ase/ase/atoms.py", line 668, in get_stress
  File "/home/camp/mohpa/Software/gpaw.9554/gpaw/aseinterface.py", line 82,
in get_stress
  File "ITl.py", line 56, in ?
    self.calculate(atoms, converge=True)
    qn.run(fmax=0.05)
    self.calculate(atoms, converge=True)
    stress = self._calc.get_stress(self)
  File "/home/camp/mohpa/ase/ase/optimize/optimize.py", line 114, in run
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 228, in calculate
  File "/home/camp/mohpa/Software/gpaw.9554/gpaw/aseinterface.py", line 82,
in get_stress
    f = self.atoms.get_forces()
    self.calculate(atoms, converge=True)
  File "ITl.py", line 56, in ?
    qn.run(fmax=0.05)
Traceback (most recent call last):
  File "/home/camp/mohpa/ase/ase/constraints.py", line 1116, in get_forces
  File "ITl.py", line 56, in ?
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 228, in calculate
    qn.run(fmax=0.05)
  File "/home/camp/mohpa/Software/gpaw.9554/gpaw/aseinterface.py", line 82,
in get_stress
    stress = self.atoms.get_stress()
    self.calculate(atoms, converge=True)
  File "/home/camp/mohpa/ase/ase/optimize/optimize.py", line 114, in run
    f = self.atoms.get_forces()
  File "/home/camp/mohpa/Software/gpaw.9554/gpaw/aseinterface.py", line 82,
in get_stress
  File "/home/camp/mohpa/ase/ase/optimize/optimize.py", line 114, in run
    self.calculate(atoms, converge=True)
  File "/home/camp/mohpa/ase/ase/atoms.py", line 668, in get_stress
    f = self.atoms.get_forces()
    self.set_positions(atoms)
    self.set_positions(atoms)
    stress = self._calc.get_stress(self)
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 228, in calculate
    self.set_positions(atoms)
  File "/home/camp/mohpa/ase/ase/constraints.py", line 1116, in get_forces
    stress = self.atoms.get_stress()
  File "/home/camp/mohpa/Software/gpaw.9554/gpaw/aseinterface.py", line 82,
in get_stress
  File "/home/camp/mohpa/ase/ase/constraints.py", line 1116, in get_forces
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 228, in calculate
    self.calculate(atoms, converge=True)
    self.set_positions(atoms)
  File "/home/camp/mohpa/ase/ase/atoms.py", line 668, in get_stress
    stress = self.atoms.get_stress()
    stress = self._calc.get_stress(self)
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 228, in calculate
  File "/home/camp/mohpa/Software/gpaw.9554/gpaw/aseinterface.py", line 82,
in get_stress
  File "/home/camp/mohpa/ase/ase/atoms.py", line 668, in get_stress
    self.set_positions(atoms)
    self.calculate(atoms, converge=True)
    stress = self._calc.get_stress(self)
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 304, in set_positions
  File "/home/camp/mohpa/Software/gpaw.9554/gpaw/aseinterface.py", line 82,
in get_stress
    self.calculate(atoms, converge=True)
    self.wfs.initialize(self.density, self.hamiltonian, spos_ac)
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 304, in set_positions
    self.wfs.initialize(self.density, self.hamiltonian, spos_ac)
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 67, in
initialize
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 304, in set_positions
    self.wfs.initialize(self.density, self.hamiltonian, spos_ac)
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 67, in
initialize
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 228, in calculate
    self.initialize_wave_functions_from_basis_functions(
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 67, in
initialize
    self.initialize_wave_functions_from_basis_functions(
    self.set_positions(atoms)
    self.initialize_wave_functions_from_basis_functions(
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 75, in
initialize_wave_functions_from_basis_functions
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 304, in set_positions
    lcaoksl, lcaobd = self.initksl, self.initksl.bd
AttributeError: 'NoneType' object has no attribute 'bd'
    self.wfs.initialize(self.density, self.hamiltonian, spos_ac)
GPAW CLEANUP (node 2): exceptions.AttributeError occurred.  Calling
MPI_Abort!
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 304, in set_positions
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 67, in
initialize
    self.initialize_wave_functions_from_basis_functions(
    self.wfs.initialize(self.density, self.hamiltonian, spos_ac)
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 75, in
initialize_wave_functions_from_basis_functions
    lcaoksl, lcaobd = self.initksl, self.initksl.bd
AttributeError: 'NoneType' object has no attribute 'bd'
GPAW CLEANUP (node 5): exceptions.AttributeError occurred.  Calling
MPI_Abort!
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 228, in calculate
    self.set_positions(atoms)
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 75, in
initialize_wave_functions_from_basis_functions
    lcaoksl, lcaobd = self.initksl, self.initksl.bd
AttributeError: 'NoneType' object has no attribute 'bd'
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 228, in calculate
GPAW CLEANUP (node 3): exceptions.AttributeError occurred.  Calling
MPI_Abort!
    self.set_positions(atoms)
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 67, in
initialize
    self.initialize_wave_functions_from_basis_functions(
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 304, in set_positions
    self.wfs.initialize(self.density, self.hamiltonian, spos_ac)
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 75, in
initialize_wave_functions_from_basis_functions
    lcaoksl, lcaobd = self.initksl, self.initksl.bd
AttributeError: 'NoneType' object has no attribute 'bd'
GPAW CLEANUP (node 6): exceptions.AttributeError occurred.  Calling
MPI_Abort!
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 304, in set_positions
    self.wfs.initialize(self.density, self.hamiltonian, spos_ac)
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 67, in
initialize
    self.initialize_wave_functions_from_basis_functions(
  File "/home/niflheim/mohpa/gpaw/gpaw/paw.py", line 304, in set_positions
    self.wfs.initialize(self.density, self.hamiltonian, spos_ac)
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 75, in
initialize_wave_functions_from_basis_functions
    lcaoksl, lcaobd = self.initksl, self.initksl.bd
AttributeError: 'NoneType' object has no attribute 'bd'
GPAW CLEANUP (node 4): exceptions.AttributeError occurred.  Calling
MPI_Abort!
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 67, in
initialize
    self.initialize_wave_functions_from_basis_functions(
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 75, in
initialize_wave_functions_from_basis_functions
    lcaoksl, lcaobd = self.initksl, self.initksl.bd
AttributeError: 'NoneType' object has no attribute 'bd'
GPAW CLEANUP (node 7): exceptions.AttributeError occurred.  Calling
MPI_Abort!
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 67, in
initialize
    self.initialize_wave_functions_from_basis_functions(
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 75, in
initialize_wave_functions_from_basis_functions
    lcaoksl, lcaobd = self.initksl, self.initksl.bd
AttributeError: 'NoneType' object has no attribute 'bd'
GPAW CLEANUP (node 0): exceptions.AttributeError occurred.  Calling
MPI_Abort!
  File "/home/niflheim/mohpa/gpaw/gpaw/wavefunctions/fdpw.py", line 75, in
initialize_wave_functions_from_basis_functions
    lcaoksl, lcaobd = self.initksl, self.initksl.bd
AttributeError: 'NoneType' object has no attribute 'bd'
GPAW CLEANUP (node 1): exceptions.AttributeError occurred.  Calling
MPI_Abort!
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
with errorcode 42.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec has exited due to process rank 2 with PID 14004 on
node a055.dcsc.fysik.dtu.dk exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpiexec (as reported here).
--------------------------------------------------------------------------
[a055.dcsc.fysik.dtu.dk:14001] 7 more processes have sent help message
help-mpi-api.txt / mpi-abort
[a055.dcsc.fysik.dtu.dk:14001] Set MCA parameter "orte_base_help_aggregate"
to 0 to see all help / error messages




-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey,
PhD Student,
Center for Atomic Scale Materials Design,
Department of Physics,
Technical University of Denmark
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