[gpaw-users] Vibration analysis with GPAW
Jens Jørgen Mortensen
jjmo at dtu.dk
Wed Aug 22 11:19:51 CEST 2018
On 08/22/2018 10:49 AM, Chang Liu wrote:
>
> Hi,
>
>
> Here is the result for 1.3.0:
>
Looks like all your test runs are timing out for some reason. I don't
know what the problem is. Maybe start from scratch with version 1.4.1b1
and check that the tests pass in serial.
Jens Jørgen
>
> --------------------------------------------------------------------------
> A process has executed an operation involving a call to the
> "fork()" system call to create a child process. Open MPI is currently
> operating in a condition that could result in memory corruption or
> other system errors; your job may hang, crash, or produce silent
> data corruption. The use of fork() (or system() or other calls that
> create child processes) is strongly discouraged.
>
> The process that invoked fork was:
>
> Local host: [[50631,1],0] (PID 698801)
>
> If you are *absolutely sure* that your application will successfully
> and correctly survive a call to fork(), you may disable this warning
> by setting the mpi_warn_on_fork MCA parameter to 0.
> --------------------------------------------------------------------------
> python-2.7.14
> /hpc2n/eb/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/GPAW/1.3.0-Python-2.7.14/bin/gpaw-python
> gpaw-1.3.0
> /hpc2n/eb/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/GPAW/1.3.0-Python-2.7.14/lib/python2.7/site-packages/gpaw/
> ase-3.15.0
> /hpc2n/eb/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/ASE/3.15.0-Python-2.7.14/lib/python2.7/site-packages/ase-3.15.0-py2.7.egg/ase/
> numpy-1.13.1
> /hpc2n/eb/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/numpy-1.13.1-py2.7-linux-x86_64.egg/numpy/
> scipy-0.19.1
> /hpc2n/eb/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/scipy-0.19.1-py2.7-linux-x86_64.egg/scipy/
> _gpaw built-in
> parallel
> /hpc2n/eb/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/GPAW/1.3.0-Python-2.7.14/bin/gpaw-python
> FFTW yes
> scalapack yes
> libvdwxc yes
> PAW-datasets 1: /hpc2n/eb/software/Core/GPAW-setups/0.9.20000
> Running tests in /tmp/gpaw-test-eDDCuQ
> Jobs: 1, Cores: 4, debug-mode: False
> =============================================================================
> linalg/gemm_complex.py 0.012 OK
> ase_features/ase3k_version.py 0.007 OK
> kpt.py 0.010 OK
> mpicomm.py 0.008 OK
> pathological/numpy_core_multiarray_dot.py 0.007 OK
> eigen/cg2.py 0.010 OK
> fd_ops/laplace.py 0.000 SKIPPED
> linalg/lapack.py 0.009 OK
> linalg/eigh.py 0.009 OK
> parallel/submatrix_redist.py 0.010 OK
> lfc/second_derivative.py 0.013 OK
> parallel/parallel_eigh.py 0.009 OK
> lfc/gp2.py 0.013 OK
> linalg/blas.py 0.011 OK
> Gauss.py 0.016 OK
> symmetry/check.py 0.351 OK
> fd_ops/nabla.py 0.096 OK
> linalg/dot.py 0.008 OK
> linalg/mmm.py 0.008 OK
> xc/lxc_fxc.py 0.008 OK
> xc/pbe_pw91.py 0.007 OK
> fd_ops/gradient.py 0.009 OK
> maths/erf.py 0.007 OK
> lfc/lf.py 0.009 OK
> maths/fsbt.py 0.035 OK
> parallel/compare.py 0.010 OK
> vdw/libvdwxc_functionals.py 0.061 OK
> radial/integral4.py 0.035 OK
> linalg/zher.py 0.018 OK
> fd_ops/gd.py 0.009 OK
> pw/interpol.py 0.008 OK
> poisson/screened_poisson.py 0.113 OK
> xc/xc.py 0.024 OK
> xc/XC2.py 0.038 OK
> radial/yukawa_radial.py 0.007 OK
> vdw/potential.py 0.008 OK
> radial/lebedev.py 0.014 OK
> occupations.py 0.028 OK
> lfc/derivatives.py 0.011 OK
> parallel/realspace_blacs.py 0.051 OK
> pw/reallfc.py 0.129 OK
> parallel/pblas.py RuntimeError: MPI barrier
> timeout.
> To get a full traceback, use: gpaw -T test ...
>
> The output for 1.4.0:
>
>
> --------------------------------------------------------------------------
> A process has executed an operation involving a call to the
> "fork()" system call to create a child process. Open MPI is currently
> operating in a condition that could result in memory corruption or
> other system errors; your job may hang, crash, or produce silent
> data corruption. The use of fork() (or system() or other calls that
> create child processes) is strongly discouraged.
>
> The process that invoked fork was:
>
> Local host: [[55354,1],0] (PID 701537)
>
> If you are *absolutely sure* that your application will successfully
> and correctly survive a call to fork(), you may disable this warning
> by setting the mpi_warn_on_fork MCA parameter to 0.
> --------------------------------------------------------------------------
> python-2.7.14 /home/c/chliu/pfs/gpaw-ase/gpaw-1.4.0/build/bin/gpaw-python
> gpaw-1.4.0
> /home/c/chliu/pfs/gpaw-ase/gpaw-1.4.0/build/lib/python2.7/site-packages/gpaw/
> ase-3.16.0
> /home/c/chliu/pfs/gpaw-ase/ase-3.16.0/build/lib/python2.7/site-packages/ase-3.16.0-py2.7.egg/ase/
> numpy-1.13.1
> /pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/numpy-1.13.1-py2.7-linux-x86_64.egg/numpy/
> scipy-0.19.1
> /pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/scipy-0.19.1-py2.7-linux-x86_64.egg/scipy/
> _gpaw built-in
> parallel /home/c/chliu/pfs/gpaw-ase/gpaw-1.4.0/build/bin//gpaw-python
> FFTW yes
> scalapack no
> libvdwxc no
> PAW-datasets 1: /hpc2n/eb/software/Core/GPAW-setups/0.9.20000
> Running tests in /tmp/gpaw-test-a5FilR
> Jobs: 1, Cores: 4, debug-mode: False
> =============================================================================
> linalg/gemm_complex.py 0.070 OK
> ase_features/ase3k_version.py 0.030 OK
> kpt.py 0.029 OK
> mpicomm.py 0.026 OK
> pathological/numpy_core_multiarray_dot.py 0.024 OK
> eigen/cg2.py 0.077 OK
> fd_ops/laplace.py 0.000 SKIPPED
> linalg/lapack.py 0.032 OK
> linalg/eigh.py 0.029 OK
> parallel/submatrix_redist.py 0.000 SKIPPED
> lfc/second_derivative.py 0.041 OK
> parallel/parallel_eigh.py 0.029 OK
> lfc/gp2.py 0.028 OK
> linalg/blas.py 0.016 OK
> Gauss.py 0.046 OK
> symmetry/check.py 0.602 OK
> fd_ops/nabla.py 0.136 OK
> linalg/dot.py 0.023 OK
> linalg/mmm.py 0.029 OK
> xc/lxc_fxc.py 0.031 OK
> xc/pbe_pw91.py 0.031 OK
> fd_ops/gradient.py 0.025 OK
> maths/erf.py 0.032 OK
> lfc/lf.py 0.043 OK
> maths/fsbt.py 0.061 OK
> parallel/compare.py 0.033 OK
> vdw/libvdwxc_functionals.py 0.000 SKIPPED
> radial/integral4.py 0.655 OK
> linalg/zher.py 0.043 OK
> fd_ops/gd.py 0.028 OK
> pw/interpol.py 0.033 OK
> poisson/screened_poisson.py 0.225 OK
> xc/xc.py 0.042 FAILED! (rank 0,1,2,3)
> #############################################################################
> RANK 0,1,2,3:
> Traceback (most recent call last):
> File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-1.4.0/build/lib/python2.7/site-packages/gpaw/test/__init__.py",
> line 643, in run_one
> exec(compile(fd.read(), filename, 'exec'), loc)
> File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-1.4.0/build/lib/python2.7/site-packages/gpaw/test/xc/xc.py",
> line 83, in <module>
> equal(error, 0, 6e-9)
> File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-1.4.0/build/lib/python2.7/site-packages/gpaw/test/__init__.py",
> line 29, in equal
> raise AssertionError(msg)
> AssertionError: inf != 0 (error: |inf| > 6e-09)
> #############################################################################
> xc/XC2.py 0.065 OK
> radial/yukawa_radial.py 0.030 OK
> vdw/potential.py 0.027 OK
> radial/lebedev.py 0.037 OK
> occupations.py 0.064 OK
> lfc/derivatives.py 0.028 OK
> pw/reallfc.py 0.200 OK
> parallel/pblas.py 0.044 OK
> fd_ops/non_periodic.py 0.029 OK
> spectrum.py 0.102 OK
> pw/lfc.py 0.140 OK
> gauss_func.py 0.302 OK
> multipoletest.py 0.153 OK
> cluster.py 1.722 OK
> poisson/poisson.py 0.079 OK
> poisson/poisson_asym.py 0.173 OK
> parallel/arraydict_redist.py 0.028 OK
> parallel/scalapack.py 0.019 OK
> gauss_wave.py 0.259 OK
> fd_ops/transformations.py 0.042 OK
> parallel/blacsdist.py 0.037 OK
> pbc.py 0.910 OK
> atoms_too_close.py 0.636 OK
> ext_potential/harmonic.py 0.559 OK
> atoms_mismatch.py 0.031 OK
> setup_basis_spec.py 0.054 OK
> overlap.py 1.602 OK
> pw/direct.py 0.020 OK
> vdw/libvdwxc_spin.py 0.000 SKIPPED
> timing.py 0.485 OK
> parallel/ut_parallel.py 1.059 OK
> lcao/density.py 0.880 OK
> pw/stresstest.py 0.620 OK
> pw/fftmixer.py 0.909 OK
> symmetry/usesymm.py 1.082 OK
> coulomb.py 0.288 OK
> xc/xcatom.py 0.685 OK
> force_as_stop.py 0.656 OK
> vdwradii.py 0.669 OK
> ase_features/ase3k.py 0.974 OK
> pathological/numpy_zdotc_graphite.py 0.749 OK
> utilities/eed.py [b-an01.hpc2n.umu.se:701531] 1 more process has sent
> help message help-opal-runtime.txt / opal_init:warn-fork
> [b-an01.hpc2n.umu.se:701531] Set MCA parameter
> "orte_base_help_aggregate" to 0 to see all help / error messages
> 1.440 OK
> lcao/dos.py 1.132 OK
> solvation/nan_radius.py 1.195 OK
> solvation/pbc_pos_repeat.py 0.282 OK
> lcao/generate_ngto.py 0.000 SKIPPED
> linalg/gemv.py 1.368 OK
> fileio/idiotproof_setup.py [b-an01.hpc2n.umu.se:701531] 2 more
> processes have sent help message help-opal-runtime.txt /
> opal_init:warn-fork
> 2.065 OK
> radial/ylexpand.py 1.101 OK
> eigen/keep_htpsit.py 1.298 OK
> xc/gga_atom.py 0.908 OK
> generic/hydrogen.py 1.756 OK
> aeatom.py 0.785 OK
> ase_features/plt.py 1.619 OK
> ds_beta.py 2.141 OK
> multipoleH2O.py 2.132 OK
> spinorbit_Kr.py 0.000 SKIPPED
> stdout.py 1.659 OK
> lcao/largecellforce.py 1.516 OK
> parallel/scalapack_diag_simple.py 0.027 OK
> fixdensity.py 2.102 OK
> pseudopotential/ah.py RuntimeError: MPI barrier
> timeout.
> To get a full traceback, use: gpaw -T test ...
>
> The output for 1.4.1b1:
>
>
> --------------------------------------------------------------------------
> A process has executed an operation involving a call to the
> "fork()" system call to create a child process. Open MPI is currently
> operating in a condition that could result in memory corruption or
> other system errors; your job may hang, crash, or produce silent
> data corruption. The use of fork() (or system() or other calls that
> create child processes) is strongly discouraged.
>
> The process that invoked fork was:
>
> Local host: [[54483,1],0] (PID 702648)
>
> If you are *absolutely sure* that your application will successfully
> and correctly survive a call to fork(), you may disable this warning
> by setting the mpi_warn_on_fork MCA parameter to 0.
> --------------------------------------------------------------------------
> python-2.7.14
> /home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/bin/gpaw-python
> gpaw-1.4.1b1
> /home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/
> ase-3.16.3b1
> /home/c/chliu/pfs/gpaw-ase/ase-master-180815/build/lib/python2.7/site-packages/ase-3.16.3b1-py2.7.egg/ase/
> numpy-1.13.1
> /pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/numpy-1.13.1-py2.7-linux-x86_64.egg/numpy/
> scipy-0.19.1
> /pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/scipy-0.19.1-py2.7-linux-x86_64.egg/scipy/
> _gpaw built-in
> parallel
> /home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/bin//gpaw-python
> FFTW yes
> scalapack no
> libvdwxc no
> PAW-datasets 1: /hpc2n/eb/software/Core/GPAW-setups/0.9.20000
> Running tests in /tmp/gpaw-test-zOKgfP
> Jobs: 1, Cores: 4, debug-mode: False
> =============================================================================
> linalg/gemm_complex.py 0.029 OK
> ase_features/ase3k_version.py 0.028 OK
> kpt.py 0.026 OK
> mpicomm.py 0.026 OK
> pathological/numpy_core_multiarray_dot.py 0.029 OK
> eigen/cg2.py 0.058 OK
> fd_ops/laplace.py 0.000 SKIPPED
> linalg/lapack.py 0.023 OK
> linalg/eigh.py 0.025 OK
> parallel/submatrix_redist.py 0.000 SKIPPED
> lfc/second_derivative.py 0.035 OK
> parallel/parallel_eigh.py 0.025 OK
> lfc/gp2.py 0.023 OK
> linalg/blas.py 0.020 OK
> Gauss.py 0.021 OK
> symmetry/check.py 0.570 OK
> fd_ops/nabla.py 0.136 OK
> linalg/dot.py 0.021 OK
> linalg/mmm.py 0.026 OK
> xc/pbe_pw91.py 0.015 OK
> fd_ops/gradient.py 0.030 OK
> maths/erf.py 0.029 OK
> lfc/lf.py 0.019 OK
> maths/fsbt.py 0.062 OK
> parallel/compare.py 0.027 OK
> vdw/libvdwxc_functionals.py 0.000 SKIPPED
> radial/integral4.py 0.371 OK
> linalg/zher.py 0.034 OK
> fd_ops/gd.py 0.010 OK
> pw/interpol.py 0.021 OK
> poisson/screened_poisson.py 0.169 OK
> xc/xc.py 0.048 FAILED! (rank 0,1,2,3)
> #############################################################################
> RANK 0,1,2,3:
> Traceback (most recent call last):
> File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/test/__init__.py",
> line 656, in run_one
> exec(compile(fd.read(), filename, 'exec'), loc)
> File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/test/xc/xc.py",
> line 83, in <module>
> equal(error, 0, 6e-9)
> File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/test/__init__.py",
> line 29, in equal
> raise AssertionError(msg)
> AssertionError: inf != 0 (error: |inf| > 6e-09)
> #############################################################################
> xc/XC2.py 0.077 OK
> radial/yukawa_radial.py 0.032 OK
> vdw/potential.py 0.010 OK
> radial/lebedev.py 0.048 OK
> occupations.py 0.044 OK
> lfc/derivatives.py 0.032 OK
> pw/reallfc.py 0.142 OK
> parallel/pblas.py 0.029 OK
> fd_ops/non_periodic.py 0.023 OK
> spectrum.py 0.084 OK
> pw/lfc.py 0.128 OK
> gauss_func.py 0.262 OK
> multipoletest.py 0.145 OK
> cluster.py 1.504 OK
> poisson/poisson.py 0.069 OK
> poisson/poisson_asym.py 0.207 OK
> parallel/arraydict_redist.py 0.200 OK
> parallel/scalapack.py 0.206 OK
> gauss_wave.py 0.267 OK
> fd_ops/transformations.py 0.044 OK
> parallel/blacsdist.py 0.030 OK
> pbc.py 0.815 OK
> atoms_too_close.py 0.026 OK
> ext_potential/harmonic.py 0.630 OK
> atoms_mismatch.py 0.019 OK
> setup_basis_spec.py 0.073 OK
> pw/direct.py 0.024 OK
> vdw/libvdwxc_spin.py 0.000 SKIPPED
> timing.py 0.465 OK
> parallel/ut_parallel.py 1.060 OK
> lcao/density.py 0.797 OK
> pw/stresstest.py 0.608 OK
> pw/fftmixer.py 0.912 OK
> lcao/fftmixer.py 0.960 FAILED! (rank 0,1,2,3)
> #############################################################################
> RANK 0,1,2,3:
> Traceback (most recent call last):
> File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/test/__init__.py",
> line 656, in run_one
> exec(compile(fd.read(), filename, 'exec'), loc)
> File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/test/lcao/fftmixer.py",
> line 14, in <module>
> equal(e, -1.710365540, 1.0e-6)
> File
> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/test/__init__.py",
> line 29, in equal
> raise AssertionError(msg)
> AssertionError: -1.7103632097 != -1.71036554 (error:
> |2.33029705465e-06| > 1e-06)
> #############################################################################
> symmetry/usesymm.py 1.032 OK
> coulomb.py 0.394 OK
> xc/xcatom.py 0.621 OK
> force_as_stop.py 0.548 OK
> vdwradii.py 0.597 OK
> ase_features/ase3k.py 0.997 OK
> pathological/numpy_zdotc_graphite.py usage: gpaw [-h] [--version]
> [-T] [-P N]
> {help,run,info,dos,gpw,completion,test,atom,diag,python,sbatch,dataset,symmetry,rpa,install-data}
> ...
> gpaw: error: RuntimeError: MPI barrier timeout.
> To get a full traceback, use: gpaw -T test ...
>
>
>
> Best wishes,
> Chang Liu
> ----------------------------------------------------------
> Chang Liu
> PhD student
> Fysikum, Albanova, Stockholm University
> S-106 91 Stockholm, Sweden
> +46 767159891
> http://xsolasgroup.fysik.su.se/
> ------------------------------------------------------------------------
> *From:* Jens Jørgen Mortensen <jjmo at dtu.dk>
> *Sent:* Wednesday, August 22, 2018 8:58:03 AM
> *To:* Chang Liu; gpaw-users
> *Subject:* Re: [gpaw-users] Vibration analysis with GPAW
> On 08/21/2018 01:47 PM, Chang Liu via gpaw-users wrote:
>>
>> Hi,
>>
>>
>> I am trying to run vibration analysis on a few trajectories obtained
>> from NEB calculations. Below is one of the input files:
>>
>>
>> from gpaw import *
>> from ase.vibrations import Vibrations
>> from ase.io import *
>> from ase.units import Pascal, m, Bohr
>> from gpaw.utilities import h2gpts
>> import numpy as np
>>
>> name = '2co'
>> state = 0
>> xc = 'BEEF-vdW'
>>
>> mixer = Mixer(0.1, 5, weight = 100.0)
>> calc = GPAW(#gpts = h2gpts(0.2, slab.get_cell(), idiv=8),
>> poissonsolver = {'dipolelayer':'xy','eps':1e-12},
>> kpts = {'density':2},
>> xc = xc,
>> symmetry = {'point_group':False},
>> mixer = mixer,
>> eigensolver=Davidson(3),
>> spinpol = False,
>> occupations = FermiDirac(0.1),
>> maxiter = 1000,
>> )
>> neb_states = read('%s_neb.traj@:'%name)
>> slab = neb_states[state]
>> slab.center(vacuum=5.,axis=2)
>> slab.cell[2][2]+=10.
>> slab.pbc = (1,1,0)
>>
>> calc.set(gpts = h2gpts(0.2, slab.get_cell(), idiv=8),txt =
>> '%s_%d_gpaw.out' % (name,state))
>> slab.set_calculator(calc)
>> e_f = slab.get_potential_energy()
>> rho = slab.calc.get_all_electron_density(gridrefinement=4)
>> write('%s_%d.cube'% (name,state), slab, data=rho * Bohr**3)
>> f = open('Energy_%s_%d.txt' % (name,state), 'w')
>> f.write('%.3f\n' % e_f)
>> f.close()
>>
>> vib = Vibrations(slab,range(45,49),'vib_%s_%d'%(name,state))
>> vib.run()
>> vib.summary(log='vib_%s_%d.log'%(name,state))
>> vib.write_mode()
>> vib_energies = vib.get_energies()
>>
>> With GPAW-1.3.0, the calculation was finished without any problem.
>> However, with both 1.4.0 and 1.4.1b1, all the calculations crash with
>> such an error:
>>
>>
>>
>> ___ ___ ___ _ _ _
>> | | |_ | | | |
>> | | | | | . | | | |
>> |__ | _|___|_____| 1.4.1b1
>> |___|_|
>>
>> User: chliu at b-cn0521.hpc2n.umu.se
>> Date: Mon Aug 20 21:55:05 2018
>> Arch: x86_64
>> Pid: 68732
>> Python: 2.7.14
>> gpaw:
>> /home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw
>> _gpaw:
>> /home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/bin/gpaw-python
>> ase:
>> /home/c/chliu/pfs/gpaw-ase/ase-master-180815/build/lib/python2.7/site-packages/ase-3.16.3b1-py2.7.egg/ase
>> (version 3.16.3b1)
>> numpy:
>> /pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/numpy-1.13.1-py2.7-linux-x86_64.egg/numpy
>> (version 1.13.1)
>> scipy:
>> /pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/scipy-0.19.1-py2.7-linux-x86_64.egg/scipy
>> (version 0.19.1)
>> units: Angstrom and eV
>> cores: 84
>>
>> Input parameters:
>> eigensolver: {name: dav,
>> niter: 3}
>> kpts: {density: 2}
>> maxiter: 1000
>> mixer: {backend: pulay,
>> beta: 0.1,
>> method: separate,
>> nmaxold: 5,
>> weight: 100.0}
>> occupations: {name: fermi-dirac,
>> width: 0.1}
>> poissonsolver: {dipolelayer: xy,
>> eps: 1e-12}
>> spinpol: False
>> symmetry: {point_group: False}
>> xc: BEEF-vdW
>>
>> Writing vib_2co_0.eq.pckl
>> rank=00 L00: Traceback (most recent call last):
>> rank=00 L01: File
>> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/__init__.py",
>> line 200, in main
>> rank=00 L02: runpy.run_path(gpaw_args.script, run_name='__main__')
>> rank=00 L03: File
>> "/hpc2n/eb/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/runpy.py",
>> line 252, in run_path
>> rank=00 L04: return _run_module_code(code, init_globals, run_name,
>> path_name)
>> rank=00 L05: File
>> "/hpc2n/eb/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/runpy.py",
>> line 82, in _run_module_code
>> rank=00 L06: mod_name, mod_fname, mod_loader, pkg_name)
>> rank=00 L07: File
>> "/hpc2n/eb/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/runpy.py",
>> line 72, in _run_code
>> rank=00 L08: exec code in run_globals
>> rank=00 L09: File "2co_0.py", line 40, in <module>
>> rank=00 L10: vib.run()
>> rank=00 L11: File
>> "/home/c/chliu/pfs/gpaw-ase/ase-master-180815/build/lib/python2.7/site-packages/ase-3.16.3b1-py2.7.egg/ase/vibrations/vibrations.py",
>> line 131, in run
>> rank=00 L12: self.calculate(atoms, filename, fd)
>> rank=00 L13: File
>> "/home/c/chliu/pfs/gpaw-ase/ase-master-180815/build/lib/python2.7/site-packages/ase-3.16.3b1-py2.7.egg/ase/vibrations/vibrations.py",
>> line 168, in calculate
>> rank=00 L14: forces = self.calc.get_forces(atoms)
>> rank=00 L15: File
>> "/home/c/chliu/pfs/gpaw-ase/ase-master-180815/build/lib/python2.7/site-packages/ase-3.16.3b1-py2.7.egg/ase/calculators/calculator.py",
>> line 515, in get_forces
>> rank=00 L16: return self.get_property('forces', atoms)
>> rank=00 L17: File
>> "/home/c/chliu/pfs/gpaw-ase/ase-master-180815/build/lib/python2.7/site-packages/ase-3.16.3b1-py2.7.egg/ase/calculators/calculator.py",
>> line 548, in get_property
>> rank=00 L18: self.calculate(atoms, [name], system_changes)
>> rank=00 L19: File
>> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/calculator.py",
>> line 297, in calculate
>> rank=00 L20: self.log, self.call_observers)
>> rank=00 L21: File
>> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/scf.py",
>> line 62, in run
>> rank=00 L22: wfs.eigensolver.iterate(ham, wfs)
>> rank=00 L23: File
>> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/eigensolvers/eigensolver.py",
>> line 84, in iterate
>> rank=00 L24: wfs.orthonormalize(kpt)
>> rank=00 L25: File
>> "/home/c/chliu/pfs/gpaw-ase/ase-master-180815/build/lib/python2.7/site-packages/ase-3.16.3b1-py2.7.egg/ase/utils/timing.py",
>> line 173, in new_method
>> rank=00 L26: x = method(slf, *args, **kwargs)
>> rank=00 L27: File
>> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/wavefunctions/fdpw.py",
>> line 396, in orthonormalize
>> rank=00 L28: S.invcholesky()
>> rank=00 L29: File
>> "/home/c/chliu/pfs/gpaw-ase/gpaw-master-180815/build/lib/python2.7/site-packages/gpaw/matrix.py",
>> line 248, in invcholesky
>> rank=00 L30: check_finite=debug)
>> rank=00 L31: File
>> "/pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/scipy-0.19.1-py2.7-linux-x86_64.egg/scipy/linalg/decomp_cholesky.py",
>> line 81, in
>> cholesky
>> rank=00 L32: check_finite=check_finite)
>> rank=00 L33: File
>> "/pfs/software/eb/amd64_ubuntu1604_bdw/software/MPI/GCC/6.4.0-2.28/OpenMPI/2.1.1/Python/2.7.14/lib/python2.7/site-packages/scipy-0.19.1-py2.7-linux-x86_64.egg/scipy/linalg/decomp_cholesky.py",
>> line 30, in
>> _cholesky
>> rank=00 L34: raise LinAlgError("%d-th leading minor not positive
>> definite" % info)
>> rank=00 L35: LinAlgError: 21-th leading minor not positive definite
>> GPAW CLEANUP (node 0): <class 'numpy.linalg.linalg.LinAlgError'>
>> occurred. Calling MPI_Abort!
>> --------------------------------------------------------------------------
>> MPI_ABORT was invoked on rank 0 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.
>> --------------------------------------------------------------------------
>>
>> The GPAW versions 1.3.0, 1.4.0 and 1.4.1b1 were all installed with
>> the same modules (OpenMPI, Scipy, Numpy, etc.). It seems to be
>> related with the change from 1.3.0 to 1.4.0... Could you please help
>> me? Thanks a lot!
>>
>
> Could you try to run the GPAW tests in parallel and show us the output?
>
> $ gpaw -P 4 test
>
> Jens Jørgen
>
>>
>> Best wishes,
>> Chang Liu
>> ----------------------------------------------------------
>> Chang Liu
>> PhD student
>> Fysikum, Albanova, Stockholm University
>> S-106 91 Stockholm, Sweden
>> +46 767159891
>> http://xsolasgroup.fysik.su.se/
>>
>>
>> _______________________________________________
>> gpaw-users mailing list
>> gpaw-users at listserv.fysik.dtu.dk
>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/gpaw-users/attachments/20180822/0c9bc069/attachment-0001.html>
More information about the gpaw-users
mailing list