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

[Nichols A. Romero]

In the real space code, if nbands > lcao basis the extra bands would be filled with random wave functions. I don't know about the PW code.

----- Original Message -----
> From: "Marcin Dulak" <Marcin.Dulak at fysik.dtu.dk>
> To: "mohnish pandey" <mohnish.iitk at gmail.com>
> Cc: gpaw-users at listserv.fysik.dtu.dk
> Sent: Saturday, December 8, 2012 7:56:10 AM
> Subject: Re: [gpaw-users] Error in running calculation with "rmm-diis" as well for band parallelization
> Hi,
> 
> i guess this means you are asking for more bands (40) than is
> available in the basis set.
> It will be also impossible to converge rmm-diis with convergence =
> {'bands' : 'all'}.
> 
> For the systems of this size in planewave mode, in order to have also
> access to cg,
> i recommend you run in serial or leave the default number of dzp bands
> and set a number of k-points that is divisible by
> the number of cores you are planning to use.
> 
> Best regards,
> 
> Marcin
> 
> On 12/08/12 12:34, mohnish pandey wrote:
> 
> 
> 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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> 
> 
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-- 
Nichols A. Romero, Ph.D.
Argonne Leadership Computing Facility
Argonne National Laboratory
Building 240 Room 2-127
9700 South Cass Avenue
Argonne, IL 60490
(630) 252-3441