[gpaw-users] Vibration analysis with GPAW
Chang Liu
chang.liu at fysik.su.se
Wed Aug 22 10:49:19 CEST 2018
Hi,
Here is the result for 1.3.0:
--------------------------------------------------------------------------
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: [[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<mailto: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/
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