Phono3py example fails
Summary
The phono3py example in the tutorial fails when phono3py tries to read a fail in hdf5 format.
This error was uncovered after adding the scripts in the examples
directory to the CI (#363).
The full output can be found here.
Steps to reproduce
One can run the CI but that will also run all the other tests. A more efficient approach is to focus on the failing part.
In examples/basic_tutorial
-
1_prepare_reference_data.py
OK -
2_construct_fcp.py
OK -
3_compute_harmonic_thermal_properties.py
OK -
4_compute_third_order_properties.py
FAILS
What is the current bug behavior?
Partial output written to stdout by phono3py
Traceback (most recent call last):
File "/usr/local/bin/phono3py", line 709, in <module>
settings.get_write_phonon())))
File "/usr/local/lib/python3.6/dist-packages/phono3py/phonon3/__init__.py", line 201, in set_phph_interaction
verbose=self._log_level)
File "/usr/local/lib/python3.6/dist-packages/phono3py/phonon3/interaction.py", line 285, in set_dynamical_matrix
self.set_phonons(verbose=verbose)
File "/usr/local/lib/python3.6/dist-packages/phono3py/phonon3/interaction.py", line 329, in set_phonons
self._set_phonon_c(_grid_points, verbose=verbose)
File "/usr/local/lib/python3.6/dist-packages/phono3py/phonon3/interaction.py", line 393, in _set_phonon_c
verbose=verbose)
File "/usr/local/lib/python3.6/dist-packages/phono3py/phonon/solver.py", line 14, in set_phonon_c
import phono3py._phono3py as phono3c
ImportError: /usr/local/lib/python3.6/dist-packages/phono3py/_phono3py.cpython-36m-x86_64-linux-gnu.so: undefined symbol: LAPACKE_dsyevd
Traceback (most recent call last):
File "4_compute_third_order_properties.py", line 51, in <module>
with h5py.File('kappa-m{0}{0}{0}.hdf5'.format(mesh), 'r') as hf:
File "/usr/local/lib/python3.6/dist-packages/h5py/_hl/files.py", line 394, in __init__
swmr=swmr)
File "/usr/local/lib/python3.6/dist-packages/h5py/_hl/files.py", line 170, in make_fid
fid = h5f.open(name, flags, fapl=fapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5f.pyx", line 85, in h5py.h5f.open
OSError: Unable to open file (unable to open file: name = 'kappa-m141414.hdf5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
The full output can be found here.
What is the expected correct behavior?
Test passes without warnings and test_benchmarks_tutorial
job passes without warnings/errors.
Possible fixes
Run the sequence of scripts manually in the docker image used by the CI. Check what happens to the file.
Edited by Paul Erhart