[gpaw-users] RuntimeError: inverse_cholesky error: 1
Marcin Dulak
Marcin.Dulak at fysik.dtu.dk
Tue Nov 25 13:32:31 CET 2014
On 11/25/2014 12:41 PM, d.davelou at materials.uoc.gr wrote:
> I forgot to say that I have added two Sulfurs at the W-end in order to
> have a stable structure.So the total width includes the addatoms.
there was a similar problem in the past but with a vdw functional:
https://listserv.fysik.dtu.dk/pipermail/gpaw-users/2010-December/000550.html
On the other hand this error can be also due to an incorrectly installed
GPAW.
Please run the tests in parallel first:
mpiexec -np 8 gpaw-python `which gpaw-test`
If the tests pass please attach the full script and the txt output so we
can have a look at the structure.
There should be no need for the slow cg eigensolver in a recent GPAW
(0.10.0 or later) - use the default 'dav'.
Best regards,
Marcin
>
> Davelou Dafni
>
> Quoting d.davelou at materials.uoc.gr:
>
>> Hello again,
>>
>> This is the calculator I use for a structure with a width of four WS2
>> on the y axis.The parameters here are the right parameters according
>> to the MoS2 structure.Also I have adding to the program an occasional
>> writer for the .gpw files and the calculation stops long after some
>> .gpw files are created.
>>
>> --------------------------------------------------------------------
>> nb=272
>> gx=16
>> gy=4*round((gx/4.0)*flake.cell[1][1]/flake.cell[0][0])
>> gz=4*round((gx/4.0)*flake.cell[2][2]/flake.cell[0][0])
>>
>> calc = GPAW(gpts=(gx,gy,gz),
>> kpts=(4,1,1),
>> xc = 'PBE',
>> nbands=nb,
>> convergence = {'bands':-200},
>> occupations = FermiDirac(width = 0.015),
>> eigensolver = 'cg',
>> spinpol = False,
>> txt = name + '.txt',
>> )
>> flake.set_calculator(calc)
>>
>> -------------------------------------------------------------------
>>
>> Davelou Dafni
>>
>>
>> Quoting Tristan Maxson <tgmaxson at gmail.com>:
>>
>>> A more detailed input file / starting set up would be helpful to debug
>>> here. Please attach something so we can look at how you are running
>>> the
>>> calculation.
>>>
>>> Thank you,
>>> Tristan Maxson
>>>
>>> On Tue, Nov 25, 2014 at 5:52 AM, <d.davelou at materials.uoc.gr> wrote:
>>>
>>>> Hello,
>>>>
>>>> I'm a new gpaw user and I've come against this inverse cholesky
>>>> error.I am
>>>> studying dichalcogenide ribbons and I try to calculate the relaxed
>>>> structures' wavefunctions but I keep getting this error.I have already
>>>> tried changing the number of bands in the calculation, the width in
>>>> the
>>>> fermidirac equation and the eigensolver parameter I use is 'cg'.In
>>>> the past
>>>> I studied the relaxed structure in MoS2, so I have an idea in what
>>>> should
>>>> be the correct calculation parameters but they don't seem to work for
>>>> WS2.If anyone could guide me on what should I do I would appreciate
>>>> it!
>>>>
>>>> This is what my error.txt file shows:
>>>>
>>>> "Traceback (most recent call last):
>>>> Traceback (most recent call last):
>>>> Traceback (most recent call last):
>>>> Traceback (most recent call last):
>>>> Traceback (most recent call last):
>>>> Traceback (most recent call last):
>>>> File "230_kohn_017.py", line 86, in ?
>>>> relax.run(fmax=0.05)
>>>> File "230_kohn_017.py", line 86, in ?
>>>> relax.run(fmax=0.05)
>>>> File "230_kohn_017.py", line 86, in ?
>>>> File "/usr/lib/python2.4/site-packages/ase/optimize/optimize.py",
>>>> line
>>>> 114, in run
>>>> f = self.atoms.get_forces()
>>>> File "/usr/lib/python2.4/site-packages/ase/optimize/optimize.py",
>>>> line
>>>> 114, in run
>>>> relax.run(fmax=0.05)
>>>> f = self.atoms.get_forces()
>>>> File "/usr/lib/python2.4/site-packages/ase/atoms.py", line 568, in
>>>> get_forces
>>>> File "/usr/lib/python2.4/site-packages/ase/optimize/optimize.py",
>>>> line
>>>> 114, in run
>>>> f = self.atoms.get_forces()
>>>> File "230_kohn_017.py", line 86, in ?
>>>> File "/usr/lib/python2.4/site-packages/ase/atoms.py", line
>>>> 568, in
>>>> get_forces
>>>> File "/usr/lib/python2.4/site-packages/ase/atoms.py", line 568, in
>>>> get_forces
>>>> File "230_kohn_017.py", line 86, in ?
>>>> relax.run(fmax=0.05)
>>>> relax.run(fmax=0.05)
>>>> File "/usr/lib/python2.4/site-packages/ase/optimize/optimize.py",
>>>> line
>>>> 114, in run
>>>> File "230_kohn_017.py", line 86, in ?
>>>> forces = self._calc.get_forces(self)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/aseinterface.py", line
>>>> 71, in get_forces
>>>> File "/usr/lib/python2.4/site-packages/ase/optimize/optimize.py",
>>>> line
>>>> 114, in run
>>>> f = self.atoms.get_forces()
>>>> File "/usr/lib/python2.4/site-packages/ase/atoms.py", line 568, in
>>>> get_forces
>>>> relax.run(fmax=0.05)
>>>> force_call_to_set_positions=force_call_to_set_positions)
>>>> f = self.atoms.get_forces()
>>>> File "/usr/lib/python2.4/site-packages/ase/optimize/optimize.py",
>>>> line
>>>> 114, in run
>>>> f = self.atoms.get_forces()
>>>> File "/usr/lib/python2.4/site-packages/ase/atoms.py", line 568, in
>>>> get_forces
>>>> forces = self._calc.get_forces(self)
>>>> forces = self._calc.get_forces(self)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/aseinterface.py", line
>>>> 71, in get_forces
>>>> force_call_to_set_positions=force_call_to_set_positions)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/paw.py", line 261, in
>>>> calculate
>>>> File "/usr/lib/python2.4/site-packages/ase/atoms.py", line 568, in
>>>> get_forces
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/paw.py", line 261, in
>>>> calculate
>>>> forces = self._calc.get_forces(self)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/aseinterface.py", line
>>>> 71, in get_forces
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/aseinterface.py", line
>>>> 71, in get_forces
>>>> force_call_to_set_positions=force_call_to_set_positions)
>>>> self.occupations):
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/scf.py", line 46, in
>>>> run
>>>> wfs.eigensolver.iterate(hamiltonian, wfs)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/paw.py", line 261, in
>>>> calculate
>>>> force_call_to_set_positions=force_call_to_set_positions)
>>>> self.occupations):
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/scf.py", line 46, in
>>>> run
>>>> wfs.eigensolver.iterate(hamiltonian, wfs)
>>>> File
>>>> "/usr/lib64/python2.4/site-packages/gpaw/eigensolvers/eigensolver.py",
>>>> line 71, in iterate
>>>> wfs.orthonormalize()
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/wavefunctions/fdpw.py",
>>>> line 234, in orthonormalize
>>>> File
>>>> "/usr/lib64/python2.4/site-packages/gpaw/eigensolvers/eigensolver.py",
>>>> line 71, in iterate
>>>> wfs.orthonormalize()
>>>> forces = self._calc.get_forces(self)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/aseinterface.py", line
>>>> 71, in get_forces
>>>> force_call_to_set_positions=force_call_to_set_positions)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/paw.py", line 261, in
>>>> calculate
>>>> forces = self._calc.get_forces(self)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/aseinterface.py", line
>>>> 71, in get_forces
>>>> force_call_to_set_positions=force_call_to_set_positions)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/paw.py", line 261, in
>>>> calculate
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/wavefunctions/fdpw.py",
>>>> line 234, in orthonormalize
>>>> self.occupations):
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/scf.py", line 46, in
>>>> run
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/paw.py", line 261, in
>>>> calculate
>>>> self.occupations):
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/scf.py", line 46, in
>>>> run
>>>> wfs.eigensolver.iterate(hamiltonian, wfs)
>>>> self.overlap.orthonormalize(self, kpt)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/overlap.py", line
>>>> 94, in
>>>> orthonormalize
>>>> self.occupations):
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/scf.py", line 46, in
>>>> run
>>>> self.overlap.orthonormalize(self, kpt)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/overlap.py", line
>>>> 94, in
>>>> orthonormalize
>>>> self.occupations):
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/scf.py", line 46, in
>>>> run
>>>> File
>>>> "/usr/lib64/python2.4/site-packages/gpaw/eigensolvers/eigensolver.py",
>>>> line 71, in iterate
>>>> wfs.orthonormalize()
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/wavefunctions/fdpw.py",
>>>> line 234, in orthonormalize
>>>> wfs.eigensolver.iterate(hamiltonian, wfs)
>>>> File
>>>> "/usr/lib64/python2.4/site-packages/gpaw/eigensolvers/eigensolver.py",
>>>> line 71, in iterate
>>>> wfs.orthonormalize()
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/wavefunctions/fdpw.py",
>>>> line 234, in orthonormalize
>>>> self.ksl.inverse_cholesky(S_nn)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 148, in inverse_cholesky
>>>> self._inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 155, in _inverse_cholesky
>>>> wfs.eigensolver.iterate(hamiltonian, wfs)
>>>> File
>>>> "/usr/lib64/python2.4/site-packages/gpaw/eigensolvers/eigensolver.py",
>>>> line 71, in iterate
>>>> wfs.orthonormalize()
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/wavefunctions/fdpw.py",
>>>> line 234, in orthonormalize
>>>> wfs.eigensolver.iterate(hamiltonian, wfs)
>>>> File
>>>> "/usr/lib64/python2.4/site-packages/gpaw/eigensolvers/eigensolver.py",
>>>> line 71, in iterate
>>>> wfs.orthonormalize()
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/wavefunctions/fdpw.py",
>>>> line 234, in orthonormalize
>>>> self.ksl.inverse_cholesky(S_nn)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 148, in inverse_cholesky
>>>> self._inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 155, in _inverse_cholesky
>>>> self.overlap.orthonormalize(self, kpt)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/overlap.py", line
>>>> 94, in
>>>> orthonormalize
>>>> self.ksl.inverse_cholesky(S_nn)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 148, in inverse_cholesky
>>>> inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/utilities/lapack.py",
>>>> line 99, in inverse_cholesky
>>>> self.overlap.orthonormalize(self, kpt)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/overlap.py", line
>>>> 94, in
>>>> orthonormalize
>>>> self.ksl.inverse_cholesky(S_nn)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 148, in inverse_cholesky
>>>> inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/utilities/lapack.py",
>>>> line 99, in inverse_cholesky
>>>> raise RuntimeError('inverse_cholesky error: %d' % info)
>>>> self.overlap.orthonormalize(self, kpt)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/overlap.py", line
>>>> 94, in
>>>> orthonormalize
>>>> self.ksl.inverse_cholesky(S_nn)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 148, in inverse_cholesky
>>>> self._inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 155, in _inverse_cholesky
>>>> inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/utilities/lapack.py",
>>>> line 99, in inverse_cholesky
>>>> raise RuntimeError('inverse_cholesky error: %d' % info)
>>>> RuntimeError self._inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 155, in _inverse_cholesky
>>>> RuntimeError: inverse_cholesky error: 1
>>>> self.overlap.orthonormalize(self, kpt)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/overlap.py", line
>>>> 94, in
>>>> orthonormalize
>>>> self.ksl.inverse_cholesky(S_nn)
>>>> self._inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 155, in _inverse_cholesky
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 148, in inverse_cholesky
>>>> raise RuntimeError('inverse_cholesky error: %d' % info)
>>>> : inverse_cholesky error: 1
>>>> inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/utilities/lapack.py",
>>>> line 99, in inverse_cholesky
>>>> raise RuntimeError('inverse_cholesky error: %d' % info)
>>>> GPAW CLEANUP (node 9): exceptions.RuntimeError occurred. Calling
>>>> MPI_Abort!
>>>> self._inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 155, in _inverse_cholesky
>>>> RuntimeError: inverse_cholesky error: 1
>>>> GPAW CLEANUP (node 7): exceptions.RuntimeError occurred. Calling
>>>> MPI_Abort!
>>>> inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/utilities/lapack.py",
>>>> line 99, in inverse_cholesky
>>>> raise RuntimeError('inverse_cholesky error: %d' % info)
>>>> RuntimeError: GPAW CLEANUP (node 8): exceptions.RuntimeError occurred.
>>>> Calling MPI_Abort!
>>>> RuntimeError: inverse_cholesky error: 1
>>>> inverse_cholesky(S_NN)
>>>> inverse_cholesky error: 1
>>>> GPAW CLEANUP (node 10): exceptions.RuntimeError occurred. Calling
>>>> MPI_Abort!
>>>> GPAW CLEANUP (node 6): exceptions.RuntimeError occurred. Calling
>>>> MPI_Abort!
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/utilities/lapack.py",
>>>> line 99, in inverse_cholesky
>>>> raise RuntimeError('inverse_cholesky error: %d' % info)
>>>> RuntimeError: inverse_cholesky error: 1
>>>> GPAW CLEANUP (node 11): exceptions.RuntimeError occurred. Calling
>>>> MPI_Abort!
>>>> Traceback (most recent call last):
>>>> Traceback (most recent call last):
>>>> Traceback (most recent call last):
>>>> Traceback (most recent call last):
>>>> Traceback (most recent call last):
>>>> Traceback (most recent call last):
>>>> File "230_kohn_017.py", line 86, in ?
>>>> relax.run(fmax=0.05)
>>>> File "/usr/lib/python2.4/site-packages/ase/optimize/optimize.py",
>>>> line
>>>> 114, in run
>>>> f = self.atoms.get_forces()
>>>> File "/usr/lib/python2.4/site-packages/ase/atoms.py", line 568, in
>>>> get_forces
>>>> forces = self._calc.get_forces(self)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/aseinterface.py", line
>>>> 71, in get_forces
>>>> force_call_to_set_positions=force_call_to_set_positions)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/paw.py", line 261, in
>>>> calculate
>>>> self.occupations):
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/scf.py", line 46, in
>>>> run
>>>> wfs.eigensolver.iterate(hamiltonian, wfs)
>>>> File
>>>> "/usr/lib64/python2.4/site-packages/gpaw/eigensolvers/eigensolver.py",
>>>> line 71, in iterate
>>>> File "230_kohn_017.py", line 86, in ?
>>>> wfs.orthonormalize()
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/wavefunctions/fdpw.py",
>>>> line 234, in orthonormalize
>>>> relax.run(fmax=0.05)
>>>> self.overlap.orthonormalize(self, kpt)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/overlap.py", line
>>>> 94, in
>>>> orthonormalize
>>>> File "/usr/lib/python2.4/site-packages/ase/optimize/optimize.py",
>>>> line
>>>> 114, in run
>>>> f = self.atoms.get_forces()
>>>> self.ksl.inverse_cholesky(S_nn)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 148, in inverse_cholesky
>>>> File "/usr/lib/python2.4/site-packages/ase/atoms.py", line 568, in
>>>> get_forces
>>>> self._inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 155, in _inverse_cholesky
>>>> forces = self._calc.get_forces(self)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/aseinterface.py", line
>>>> 71, in get_forces
>>>> inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/utilities/lapack.py",
>>>> line 99, in inverse_cholesky
>>>> raise RuntimeError('inverse_cholesky error: %d' % info)
>>>> RuntimeError: inverse_cholesky error: 1
>>>> force_call_to_set_positions=force_call_to_set_positions)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/paw.py", line 261, in
>>>> calculate
>>>> File "230_kohn_017.py", line 86, in ?
>>>> GPAW CLEANUP (node 0): exceptions.RuntimeError occurred. Calling
>>>> MPI_Abort!
>>>> self.occupations):
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/scf.py", line 46, in
>>>> run
>>>> relax.run(fmax=0.05)
>>>> wfs.eigensolver.iterate(hamiltonian, wfs)
>>>> File
>>>> "/usr/lib64/python2.4/site-packages/gpaw/eigensolvers/eigensolver.py",
>>>> line 71, in iterate
>>>> wfs.orthonormalize()
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/wavefunctions/fdpw.py",
>>>> line 234, in orthonormalize
>>>> File "/usr/lib/python2.4/site-packages/ase/optimize/optimize.py",
>>>> line
>>>> 114, in run
>>>> f = self.atoms.get_forces()
>>>> File "/usr/lib/python2.4/site-packages/ase/atoms.py", line 568, in
>>>> get_forces
>>>> self.overlap.orthonormalize(self, kpt)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/overlap.py", line
>>>> 94, in
>>>> orthonormalize
>>>> File "230_kohn_017.py", line 86, in ?
>>>> relax.run(fmax=0.05)
>>>> self.ksl.inverse_cholesky(S_nn)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 148, in inverse_cholesky
>>>> File "/usr/lib/python2.4/site-packages/ase/optimize/optimize.py",
>>>> line
>>>> 114, in run
>>>> self._inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 155, in _inverse_cholesky
>>>> forces = self._calc.get_forces(self)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/aseinterface.py", line
>>>> 71, in get_forces
>>>> f = self.atoms.get_forces()
>>>> File "/usr/lib/python2.4/site-packages/ase/atoms.py", line 568, in
>>>> get_forces
>>>> inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/utilities/lapack.py",
>>>> line 99, in inverse_cholesky
>>>> raise RuntimeError('inverse_cholesky error: %d' % info)
>>>> force_call_to_set_positions=force_call_to_set_positions)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/paw.py", line 261, in
>>>> calculate
>>>> RuntimeError: inverse_cholesky error: 1
>>>> File "230_kohn_017.py", line 86, in ?
>>>> GPAW CLEANUP (node 1): exceptions.RuntimeError occurred. Calling
>>>> MPI_Abort!
>>>> relax.run(fmax=0.05)
>>>> self.occupations):
>>>> File "/usr/lib/python2.4/site-packages/ase/optimize/optimize.py",
>>>> line
>>>> 114, in run
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/scf.py", line 46, in
>>>> run
>>>> wfs.eigensolver.iterate(hamiltonian, wfs)
>>>> File
>>>> "/usr/lib64/python2.4/site-packages/gpaw/eigensolvers/eigensolver.py",
>>>> line 71, in iterate
>>>> forces = self._calc.get_forces(self)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/aseinterface.py", line
>>>> 71, in get_forces
>>>> f = self.atoms.get_forces()
>>>> File "/usr/lib/python2.4/site-packages/ase/atoms.py", line 568, in
>>>> get_forces
>>>> wfs.orthonormalize()
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/wavefunctions/fdpw.py",
>>>> line 234, in orthonormalize
>>>> force_call_to_set_positions=force_call_to_set_positions)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/paw.py", line 261, in
>>>> calculate
>>>> forces = self._calc.get_forces(self)
>>>> File "230_kohn_017.py", line 86, in ?
>>>> relax.run(fmax=0.05)
>>>> self.occupations):
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/scf.py", line 46, in
>>>> run
>>>> self.overlap.orthonormalize(self, kpt)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/overlap.py", line
>>>> 94, in
>>>> orthonormalize
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/aseinterface.py",
>>>> line 71, in get_forces
>>>> force_call_to_set_positions=force_call_to_set_positions)
>>>> File "/usr/lib/python2.4/site-packages/ase/optimize/optimize.py",
>>>> line
>>>> 114, in run
>>>> f = self.atoms.get_forces()
>>>> wfs.eigensolver.iterate(hamiltonian, wfs)
>>>> File
>>>> "/usr/lib64/python2.4/site-packages/gpaw/eigensolvers/eigensolver.py",
>>>> line 71, in iterate
>>>> self.ksl.inverse_cholesky(S_nn)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 148, in inverse_cholesky
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/paw.py", line 261, in
>>>> calculate
>>>> File "/usr/lib/python2.4/site-packages/ase/atoms.py", line 568, in
>>>> get_forces
>>>> wfs.orthonormalize()
>>>> self._inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 155, in _inverse_cholesky
>>>> inverse_cholesky(S_NN)
>>>> self.occupations):
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/scf.py", line 46, in
>>>> run
>>>> wfs.eigensolver.iterate(hamiltonian, wfs)
>>>> File
>>>> "/usr/lib64/python2.4/site-packages/gpaw/eigensolvers/eigensolver.py",
>>>> line 71, in iterate
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/wavefunctions/fdpw.py",
>>>> line 234, in orthonormalize
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/utilities/lapack.py",
>>>> line 99, in inverse_cholesky
>>>> wfs.orthonormalize()
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/wavefunctions/fdpw.py",
>>>> line 234, in orthonormalize
>>>> self.overlap.orthonormalize(self, kpt)
>>>> raise RuntimeError('inverse_cholesky error: %d' % info)
>>>> RuntimeError: inverse_cholesky error: 1
>>>> forces = self._calc.get_forces(self)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/aseinterface.py", line
>>>> 71, in get_forces
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/overlap.py",
>>>> line 94,
>>>> in orthonormalize
>>>> self.ksl.inverse_cholesky(S_nn)
>>>> self.overlap.orthonormalize(self, kpt)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/overlap.py", line
>>>> 94, in
>>>> orthonormalize
>>>> self.ksl.inverse_cholesky(S_nn)
>>>> GPAW CLEANUP (node 3): exceptions.RuntimeError occurred. Calling
>>>> MPI_Abort!
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/paw.py", line 261, in
>>>> calculate
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 148, in inverse_cholesky
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 148, in inverse_cholesky
>>>> self.occupations):
>>>> self._inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 155, in _inverse_cholesky
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/scf.py", line 46, in
>>>> run
>>>> wfs.eigensolver.iterate(hamiltonian, wfs)
>>>> self._inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 155, in _inverse_cholesky
>>>> inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/utilities/lapack.py",
>>>> line 99, in inverse_cholesky
>>>> File
>>>> "/usr/lib64/python2.4/site-packages/gpaw/eigensolvers/eigensolver.py",
>>>> line 71, in iterate
>>>> wfs.orthonormalize()
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/wavefunctions/fdpw.py",
>>>> line 234, in orthonormalize
>>>> inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/utilities/lapack.py",
>>>> line 99, in inverse_cholesky
>>>> raise RuntimeError('inverse_cholesky error: %d' % info)
>>>> RuntimeError: inverse_cholesky error: 1
>>>> self.overlap.orthonormalize(self, kpt)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/overlap.py", line
>>>> 94, in
>>>> orthonormalize
>>>> GPAW CLEANUP (node 5): exceptions.RuntimeError occurred. Calling
>>>> MPI_Abort!
>>>> self.ksl.inverse_cholesky(S_nn)
>>>> raise RuntimeError('inverse_cholesky error: %d' % info)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 148, in inverse_cholesky
>>>> self._inverse_cholesky(S_NN)
>>>> RuntimeError: inverse_cholesky error: 1
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/kohnsham_layouts.py",
>>>> line 155, in _inverse_cholesky
>>>> GPAW CLEANUP (node 2): exceptions.RuntimeError occurred. Calling
>>>> MPI_Abort!
>>>> inverse_cholesky(S_NN)
>>>> File "/usr/lib64/python2.4/site-packages/gpaw/utilities/lapack.py",
>>>> line 99, in inverse_cholesky
>>>> raise RuntimeError('inverse_cholesky error: %d' % info)
>>>> RuntimeError: inverse_cholesky error: 1
>>>> GPAW CLEANUP (node 4): exceptions.RuntimeError occurred. Calling
>>>> MPI_Abort!
>>>> --------------------------------------------------------------------------
>>>>
>>>> MPI_ABORT was invoked on rank 6 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.
>>>> --------------------------------------------------------------------------
>>>>
>>>> --------------------------------------------------------------------------
>>>>
>>>> mpirun has exited due to process rank 7 with PID 24307 on
>>>> node mst-11a exiting without calling "finalize". This may
>>>> have caused other processes in the application to be
>>>> terminated by signals sent by mpirun (as reported here).
>>>> --------------------------------------------------------------------------
>>>>
>>>> [mst-11a:24299] 5 more processes have sent help message
>>>> help-mpi-api.txt /
>>>> mpi-abort
>>>> [mst-11a:24299] Set MCA parameter "orte_base_help_aggregate" to 0
>>>> to see
>>>> all help / error messages"
>>>>
>>>> Thank you very much,
>>>> Davelou Dafni
>>>>
>>>>
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>>>> gpaw-users at listserv.fysik.dtu.dk
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