Problems in new parsers
These are the top 20 exception from the last reprocessing of aims, exciting, abinit, crystal.
In addition to these, there are many calculations that produce incomplete results. This is most easily to spot, if you look at the system metadata. Many calculations have no formula. This indicates they have no system. This indicates the parser (even through running successfully) did not match much. Probably these calculation require slightly more relaxed regexps due to code version differences.
-
16879, parsers/fhi-aims, xx9izr2yRputru0JleV7-Q:t-ZPO5zE2Jw9DkP0m8fGQgR6vC-7
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1499, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1475, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1302, in parse_method
sec_method.x_fhi_aims_controlInOut_number_of_spin_channels = self.out_parser.get_number_of_spin_channels()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 710, in get_number_of_spin_channels
return array_size.get('Number of spin channels', 1)
AttributeError: 'NoneType' object has no attribute 'get'-
5891, in normalizer, qhx0VdcgS3inMmKECuN3KA:zw5o6RH9ZBAyDlsc4CXhWml09CLc
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 558, in normalizing
normalizer(self._parser_results).normalize(logger=logger)
File "/app/nomad/normalizing/encyclopedia/encyclopedia.py", line 286, in normalize
self.fill(context)
File "/app/nomad/normalizing/encyclopedia/encyclopedia.py", line 188, in fill
struct.normalize(context)
File "/app/nomad/normalizing/encyclopedia/material.py", line 739, in normalize
self.periodicity(ideal, prim_atoms)
File "/app/nomad/normalizing/encyclopedia/material.py", line 577, in periodicity
raise ValueError("Could not detect the periodic dimensions in a 1D system.")
ValueError: Could not detect the periodic dimensions in a 1D system.-
3084, parsers/lammps, DDZKox_nQ_CLTPPaGSr0_w:zzStifnyE7SwZuV3SGagFAfCtekQ
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/lammpsparser/lammps_parser.py", line 787, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/lammpsparser/lammps_parser.py", line 766, in parse
sec_md.with_trajectory = self.traj_parser.with_trajectory()
File "/usr/local/lib/python3.7/site-packages/lammpsparser/lammps_parser.py", line 199, in with_trajectory
return self.get('atoms_info') is not None
File "/app/nomad/parsing/file_parser/file_parser.py", line 78, in get
val = self.results.get(key, None)
File "/app/nomad/parsing/file_parser/file_parser.py", line 47, in results
self.parse(self._key, **self._kwargs)
File "/app/nomad/parsing/file_parser/text_parser.py", line 501, in parse
if self.file_mmap is None:
File "/app/nomad/parsing/file_parser/text_parser.py", line 345, in file_mmap
with open(self.mainfile) as f:
TypeError: expected str, bytes or os.PathLike object, not NoneType-
2711, parsers/fhi-aims, o-8XYG0JS5OJU59uchgA7w:zjS-6QqvVUrBNsQgaQGNEHRcipV1
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1499, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1473, in parse
sec_parallel_task_assignement.x_fhi_aims_parallel_task_host = task_hosts[i]
File "/app/nomad/metainfo/metainfo.py", line 849, in __setattr__
return super().__setattr__(name, value)
File "/app/nomad/metainfo/metainfo.py", line 2221, in __set__
(value, type(value), self, self.type))
TypeError: The value ['Task' '0' 'of' '512' '(0,0,0,0,0,0)' 'R1B-M0-N00-J00'] with type <class 'numpy.ndarray'> for quantity fhiaimsparser.metainfo.fhi_aims.x_fhi_aims_section_parallel_task_assignement.x_fhi_aims_parallel_task_host:Quantity is not of type <class 'str'>-
2271, parsers/fhi-aims, zb79w_T9Q_qbstffWBW46g:JHXpfS4E6piQw8ohphNqL8VglHyr
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1499, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1475, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1342, in parse_method
sec_xc_func.XC_functional_weight = weight(hybrid_coeff)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 766, in <lambda>
'name': 'GGA_X_PBE', 'weight': lambda x: 0.75 if x is None else 1.0 - x},
TypeError: unsupported operand type(s) for -: 'float' and 'str'-
1105, parsers/exciting, pvRdA8EBQ--7UQdVou5s-w:xrP0AfYb8-JsPChh0t0OthNP7K1X
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2153, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2128, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2053, in parse_configurations
self.parse_file(f, sec_scc)
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1332, in parse_file
parser_function(section)
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1171, in _parse_eigenvalues
sec_eigenvalues.eigenvalues_values = get_data('eigenvalues')
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1164, in get_data
res = np.hstack([v[key] for v in data])
File "<__array_function__ internals>", line 6, in hstack
File "/usr/local/lib/python3.7/site-packages/numpy/core/shape_base.py", line 346, in hstack
return _nx.concatenate(arrs, 1)
File "<__array_function__ internals>", line 6, in concatenate
ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 0, the array at index 0 has size 2 and the array at index 18 has size 1-
1080, in normalizer, uCSlNMEWQfOS5TMvsQXz1A:ziSEudHjaTYIe3Jzj-MKRZn4VkDt
Traceback (most recent call last):
File "/app/nomad/normalizing/dos.py", line 149, in normalize
n_atoms=number_of_atoms
File "/usr/local/lib/python3.7/site-packages/nomad_dos_fingerprints/DOSfingerprint.py", line 25, in calculate
self.indices, self.bins = self._calculate_bytes(raw_energies, raw_dos, grid)
File "/usr/local/lib/python3.7/site-packages/nomad_dos_fingerprints/DOSfingerprint.py", line 88, in _calculate_bytes
energy, dos = np.transpose([(e,d) for e,d in zip(energy, dos) if (e >= grid_array[0][0] and e <= grid_array[-1][0])])
ValueError: not enough values to unpack (expected 2, got 0)-
768, parsers/fhi-aims, iZGJdsGSRm6DYERVpo74fA:0iEfV-_AQA6wlw6mneY5ol8ia1vj
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1499, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1475, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1259, in parse_method
for key, val in self.control_parser.items():
File "/app/nomad/parsing/file_parser/text_parser.py", line 365, in items
yield key, self.get(key)
File "/app/nomad/parsing/file_parser/file_parser.py", line 78, in get
val = self.results.get(key, None)
File "/app/nomad/parsing/file_parser/file_parser.py", line 47, in results
self.parse(self._key, **self._kwargs)
File "/app/nomad/parsing/file_parser/text_parser.py", line 501, in parse
if self.file_mmap is None:
File "/app/nomad/parsing/file_parser/text_parser.py", line 345, in file_mmap
with open(self.mainfile) as f:
TypeError: expected str, bytes or os.PathLike object, not NoneType-
341, parsers/fhi-aims, wKiS4s-NS9Ky5o1OtYKI2w:2IIcVSSBI5ktFmjUyfMISbWYaOiI
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1499, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1475, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1315, in parse_method
self.parse_topology()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1424, in parse_topology
species = self.out_parser['control_inout']['species']
TypeError: 'NoneType' object is not subscriptable-
278, parsers/fhi-aims, qSCiRCcYSaifBVn00EFOQA:yHb3bEu31Sb24V5eRXcOJ63XX3bk
Traceback (most recent call last):
File "/app/nomad/parsing/file_parser/text_parser.py", line 406, in _parse_quantities
value_processed = quantities[i].to_data(values)
File "/app/nomad/parsing/file_parser/text_parser.py", line 220, in to_data
val_out = [process(val) for val in val_in]
File "/app/nomad/parsing/file_parser/text_parser.py", line 220, in <listcomp>
val_out = [process(val) for val in val_in]
File "/app/nomad/parsing/file_parser/text_parser.py", line 158, in process
val = self.str_operation(val)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 480, in str_to_energy_components
unit = {'Ha': 'hartree', 'eV': 'eV'}.get(vi[1], None)
IndexError: list index out of range
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1499, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1459, in parse
value = self.out_parser.get(key)
File "/app/nomad/parsing/file_parser/file_parser.py", line 78, in get
val = self.results.get(key, None)
File "/app/nomad/parsing/file_parser/file_parser.py", line 47, in results
self.parse(self._key, **self._kwargs)
File "/app/nomad/parsing/file_parser/text_parser.py", line 524, in parse
self._parse_quantity(quantity)
File "/app/nomad/parsing/file_parser/text_parser.py", line 463, in _parse_quantity
value.append(sub_parser.parse())
File "/app/nomad/parsing/file_parser/text_parser.py", line 516, in parse
self._parse_quantities(quantities_findall)
File "/app/nomad/parsing/file_parser/text_parser.py", line 419, in _parse_quantities
self.logger.warn('Error setting value', data=dict(quantity=quantities[i].name))
File "/usr/local/lib/python3.7/logging/__init__.py", line 1982, in warn
warning(msg, *args, **kwargs)
File "/usr/local/lib/python3.7/logging/__init__.py", line 1977, in warning
root.warning(msg, *args, **kwargs)
File "/usr/local/lib/python3.7/logging/__init__.py", line 1390, in warning
self._log(WARNING, msg, args, **kwargs)
TypeError: _log() got an unexpected keyword argument 'data'-
213, parsers/crystal, gddy5rHgRceN2sZZ6yTnrA:zbuT8J3-vcIknvze4gbDSWQDPEfP
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/crystalparser/crystal_parser.py", line 566, in parse
dist, minor = distribution.split(" : ", 1)
AttributeError: 'NoneType' object has no attribute 'split'-
199, parsers/phonopy, z369XxTOT5S3db4Q2vrbqg:xeYjLT2hhwWskUCXdeqVg3bkND6h
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 498, in process_phonon
raise ValueError("No method information available in referenced calculation.")
ValueError: No method information available in referenced calculation.-
171, parsers/exciting, vDg3jiguSsau7B2R9XjxMQ:o9pLQY2RAWuFd58rYJVgrzvO9SuO
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2153, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2126, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1802, in parse_method
xc_functional_names = self.info_parser.get_xc_functional_name()
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1002, in get_xc_functional_name
xc_functional = self.get('initialization').get('x_exciting_xc_functional', None)
AttributeError: 'NoneType' object has no attribute 'get'-
160, parsers/phonopy, win2cjTvRF6t_KjDmfVlZw:IxR6Cf1HLzo8zeedPFUHzO0t74BN
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 185, in parse
phonopy_obj = self.phonopy_obj
File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 50, in phonopy_obj
self._build_phonopy_object_fhi_aims()
File "/usr/local/lib/python3.7/site-packages/phonopyparser/phonopy_parser.py", line 77, in _build_phonopy_object_fhi_aims
cell_obj, supercell_matrix, displacement, sym)
File "/usr/local/lib/python3.7/site-packages/phonopyparser/fhiaims_io.py", line 137, in read_forces_aims
raise Exception("No phonon calculations found")
Exception: No phonon calculations found-
144, in normalizer, uCSlNMEWQfOS5TMvsQXz1A:xp4iSuT8IXqePP_KNuQaR0pOeC9z
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 558, in normalizing
normalizer(self._parser_results).normalize(logger=logger)
File "/app/nomad/normalizing/band_structure.py", line 63, in normalize
self.add_band_gaps(band, energy_reference)
File "/app/nomad/normalizing/band_structure.py", line 181, in add_band_gaps
energies = np.concatenate(energies, axis=2)
File "<__array_function__ internals>", line 6, in concatenate
ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 1, the array at index 0 has size 9 and the array at index 6 has size 27-
126, parsers/fhi-aims, jSSVtYWfTZacc7HjWPSqHQ:a8r8KkvKXWams50UhzMGCxY0IGqH
TypeError: only size-1 arrays can be converted to Python scalars
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1499, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1477, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1190, in parse_configurations
parse_section(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1147, in parse_section
forces_raw[-len(forces):], 'eV/angstrom')
File "/app/nomad/metainfo/metainfo.py", line 849, in __setattr__
return super().__setattr__(name, value)
File "/app/nomad/metainfo/metainfo.py", line 2111, in __set__
obj.m_set(self, value)
File "/app/nomad/metainfo/metainfo.py", line 956, in m_set
value = self.__to_np(quantity_def, value)
File "/app/nomad/metainfo/metainfo.py", line 920, in __to_np
value = value.astype(quantity_def.type)
File "/usr/local/lib/python3.7/site-packages/pint/quantity.py", line 1654, in _numpy_method_wrap
value = func(*args, **kwargs)
ValueError: setting an array element with a sequence.-
107, parsers/exciting, pzD88LYnTty-c_Xg07dqwg:wRtykAr2p9qUNTGDT-fZabQozNB4
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2153, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2128, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2061, in parse_configurations
sec_scc.x_exciting_geometry_optimization_method = optimization_step.get('method')
AttributeError: 'NoneType' object has no attribute 'x_exciting_geometry_optimization_method'-
101, parsers/fhi-aims, ZFNMJDbJQ9aUq3o-aMq7lw:n43gSkg2cIhEM60wbmipsKQo1rig
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1499, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1477, in parse
self.parse_configurations()
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1190, in parse_configurations
parse_section(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1163, in parse_section
parse_dos(section)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 941, in parse_dos
energies, dos = read_projected_dos(proj_dos_files)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 897, in read_projected_dos
energies = pint.Quantity(data[0], 'eV')
TypeError: 'NoneType' object is not subscriptable-
61, parsers/exciting, ff8C1I9LTuiNVu5fyPVxnw:xHhm3RgE-DzKTJ8X1qYc2xm01Ld6
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2153, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2132, in parse
self.parse_xs()
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1631, in parse_xs
self.parse_file('input.xml', sec_method)
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1332, in parse_file
parser_function(section)
File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1368, in _parse_input_xs
sec_method.x_exciting_xs_screening_rgkmax = rgkmax
File "/app/nomad/metainfo/metainfo.py", line 849, in __setattr__
return super().__setattr__(name, value)
File "/app/nomad/metainfo/metainfo.py", line 2111, in __set__
obj.m_set(self, value)
File "/app/nomad/metainfo/metainfo.py", line 956, in m_set
value = self.__to_np(quantity_def, value)
File "/app/nomad/metainfo/metainfo.py", line 917, in __to_np
(quantity_def, value))
nomad.metainfo.metainfo.MetainfoError: The quantity excitingparser.metainfo.exciting.section_method.x_exciting_xs_screening_rgkmax:Quantity has not a unit, but value 3.5 bohr has.-
15, parsers/crystal, llZrblH4THCuJvVjEBXBFA:VdOUqF-aHTwlDSRcuoubmNBPFxHo
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/crystalparser/crystal_parser.py", line 618, in parse
atomic_numbers,
UnboundLocalError: local variable 'atomic_numbers' referenced before assignment-
13, parsers/fhi-aims, w8VbMKDwSb27iSM2oCE4Kg:kEp6pGbAJfjwn5r1PuvciCi1IIPd
Traceback (most recent call last):
File "/app/nomad/parsing/file_parser/text_parser.py", line 406, in _parse_quantities
value_processed = quantities[i].to_data(values)
File "/app/nomad/parsing/file_parser/text_parser.py", line 220, in to_data
val_out = [process(val) for val in val_in]
File "/app/nomad/parsing/file_parser/text_parser.py", line 220, in <listcomp>
val_out = [process(val) for val in val_in]
File "/app/nomad/parsing/file_parser/text_parser.py", line 158, in process
val = self.str_operation(val)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 467, in str_to_eigenvalues
eig, occ = eigs[1:3]
ValueError: not enough values to unpack (expected 2, got 0)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 453, in parsing
self._parser_results, logger=logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1499, in parse
parser.parse(filepath, archive, logger)
File "/usr/local/lib/python3.7/site-packages/fhiaimsparser/fhiaims_parser.py", line 1459, in parse
value = self.out_parser.get(key)
File "/app/nomad/parsing/file_parser/file_parser.py", line 78, in get
val = self.results.get(key, None)
File "/app/nomad/parsing/file_parser/file_parser.py", line 47, in results
self.parse(self._key, **self._kwargs)
File "/app/nomad/parsing/file_parser/text_parser.py", line 524, in parse
self._parse_quantity(quantity)
File "/app/nomad/parsing/file_parser/text_parser.py", line 463, in _parse_quantity
value.append(sub_parser.parse())
File "/app/nomad/parsing/file_parser/text_parser.py", line 516, in parse
self._parse_quantities(quantities_findall)
File "/app/nomad/parsing/file_parser/text_parser.py", line 419, in _parse_quantities
self.logger.warn('Error setting value', data=dict(quantity=quantities[i].name))
File "/usr/local/lib/python3.7/logging/__init__.py", line 1982, in warn
warning(msg, *args, **kwargs)
File "/usr/local/lib/python3.7/logging/__init__.py", line 1977, in warning
root.warning(msg, *args, **kwargs)
File "/usr/local/lib/python3.7/logging/__init__.py", line 1390, in warning
self._log(WARNING, msg, args, **kwargs)
TypeError: _log() got an unexpected keyword argument 'data'Old issues description:
These are exceptions thrown by parsers during reprocessing all non staging exciting and abinit code runs. I only checked the first one, but it reproduces with nomad parse ....
| exception_hash.keyword: Descending | # | calc_id | upload_id | mainfile | parser | exception |
|---|---|---|---|---|---|---|
| s7J4tcDHcGPdLgK2ZnnzqhE56hd3 | 1105 | xrP0AfYb8-JsPChh0t0OthNP7K1X | pvRdA8EBQ--7UQdVou5s-w | volume-1.5/0.965489384605630/INFO.OUT | parsers/exciting | Traceback (most recent call last): File "/app/nomad/processing/data.py", line 453, in parsing self._parser_results, logger=logger) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2126, in parse self.parse_configurations() File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2058, in parse_configurations self.parse_file(f, sec_scc) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1337, in parse_file parser_function(section) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1176, in _parse_eigenvalues sec_eigenvalues.eigenvalues_values = get_data('eigenvalues') File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1169, in get_data res = np.hstack([v[key] for v in data]) File "<array_function internals>", line 6, in hstack File "/usr/local/lib/python3.7/site-packages/numpy/core/shape_base.py", line 346, in hstack return _nx.concatenate(arrs, 1) File "<array_function internals>", line 6, in concatenate ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 0, the array at index 0 has size 2 and the array at index 18 has size 1 |
| hwe7MyzCotT17K4FWIlLLnLyII3_ | 171 | yEqUiNBD7iu3P4YZmzgvpj2CbFV6 | QLFt5odgS1S1LQ_MDbZgpQ | silver-tddft/silver-loss/6/INFOXS.OUT | parsers/exciting | Traceback (most recent call last): File "/app/nomad/processing/data.py", line 453, in parsing self._parser_results, logger=logger) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2124, in parse self.parse_method() File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1807, in parse_method xc_functional_names = self.info_parser.get_xc_functional_name() File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1002, in get_xc_functional_name xc_functional = self.get('initialization').get('x_exciting_xc_functional', None) AttributeError: 'NoneType' object has no attribute 'get' |
| MEQ6y79UyB-M8DAu-NR4SBHzEJIq | 107 | wRtykAr2p9qUNTGDT-fZabQozNB4 | pzD88LYnTty-c_Xg07dqwg | home1/UTE/ETERRNAL/DATA/FINISHED/CGeSn/000016/GG/L_GAMMA/INFO.OUT | parsers/exciting | Traceback (most recent call last): File "/app/nomad/processing/data.py", line 453, in parsing self._parser_results, logger=logger) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2126, in parse self.parse_configurations() File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2066, in parse_configurations sec_scc.x_exciting_geometry_optimization_method = optimization_step.get('method') AttributeError: 'NoneType' object has no attribute 'x_exciting_geometry_optimization_method' |
| HXW2tu3a-mtJmMCuvzjUTwTvISba | 62 | xHhm3RgE-DzKTJ8X1qYc2xm01Ld6 | ff8C1I9LTuiNVu5fyPVxnw | AB@Graphene/azobenzene/cis/BSE/rpa/INFO_QMT001.OUT | parsers/exciting | Traceback (most recent call last): File "/app/nomad/processing/data.py", line 453, in parsing self._parser_results, logger=logger) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2130, in parse self.parse_xs() File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1636, in parse_xs self.parse_file('input.xml', sec_method) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1337, in parse_file parser_function(section) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1373, in _parse_input_xs sec_method.x_exciting_xs_screening_rgkmax = rgkmax File "/app/nomad/metainfo/metainfo.py", line 849, in setattr return super().setattr(name, value) File "/app/nomad/metainfo/metainfo.py", line 2111, in set obj.m_set(self, value) File "/app/nomad/metainfo/metainfo.py", line 956, in m_set value = self.__to_np(quantity_def, value) File "/app/nomad/metainfo/metainfo.py", line 917, in __to_np (quantity_def, value)) nomad.metainfo.metainfo.MetainfoError: The quantity excitingparser.metainfo.exciting.section_method.x_exciting_xs_screening_rgkmax:Quantity has not a unit, but value 3.5 bohr has. |
| 3kmtj-uvUs_AtxPSd_mgAoWmUY5i | 14 | LuH6KeBENcz3_mwE8HOwvYKJyqLw | 0NR0E6gqQ2yVicJCMEP4SA | c-Si-OCTSF/12x12x12-BSE-PBE/INFO_QMT001.OUT | parsers/exciting | Traceback (most recent call last): File "/app/nomad/processing/data.py", line 453, in parsing self._parser_results, logger=logger) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2130, in parse self.parse_xs() File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1636, in parse_xs self.parse_file('input.xml', sec_method) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1337, in parse_file parser_function(section) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1360, in _parse_input_xs sec_method.x_exciting_xs_rgkmax = rgkmax File "/app/nomad/metainfo/metainfo.py", line 849, in setattr return super().setattr(name, value) File "/app/nomad/metainfo/metainfo.py", line 2111, in set obj.m_set(self, value) File "/app/nomad/metainfo/metainfo.py", line 956, in m_set value = self.__to_np(quantity_def, value) File "/app/nomad/metainfo/metainfo.py", line 917, in __to_np (quantity_def, value)) nomad.metainfo.metainfo.MetainfoError: The quantity excitingparser.metainfo.exciting.section_method.x_exciting_xs_rgkmax:Quantity has not a unit, but value 8.0 bohr has. |
| 2khWqBfkrqi65UqODhX0_U-Dp5qs | 6 | fwG3jU4_PBV1uWdAzFtXotFs293m | dkZ_BRDqSA2DeGsH3ItFyw | conv_ecut/Si.out0006 | parsers/abinit | Traceback (most recent call last): File "/app/nomad/processing/data.py", line 453, in parsing self._parser_results, logger=logger) File "/usr/local/lib/python3.7/site-packages/abinitparser/abinit_parser.py", line 983, in parse self.parse_dataset(dataset) File "/usr/local/lib/python3.7/site-packages/abinitparser/abinit_parser.py", line 847, in parse_dataset sec_method = self.parse_method(dataset) File "/usr/local/lib/python3.7/site-packages/abinitparser/abinit_parser.py", line 759, in parse_method sec_method.number_of_spin_channels = int(self.out_parser.get_input_var('nsppol', nd, 1)) TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType' |
| h04dOeanRAxBsfNPaVUnydXG8kSu | 5 | mVpv7QL-IkSnnbPdZB0CxrPjhtwG | ML2qGfRqSnmxDLvPKkrLMQ | LiH-pbc/130/INFO.OUT | parsers/exciting | Traceback (most recent call last): File "/app/nomad/processing/data.py", line 453, in parsing self._parser_results, logger=logger) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2126, in parse self.parse_configurations() File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2051, in parse_configurations sec_scc = parse_configuration(self.info_parser.get('groundstate')) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2042, in parse_configuration sec_system = self.parse_system(section) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1995, in parse_system setattr(sec_system, name, val) File "/app/nomad/metainfo/metainfo.py", line 849, in setattr return super().setattr(name, value) File "/app/nomad/metainfo/metainfo.py", line 2111, in set obj.m_set(self, value) File "/app/nomad/metainfo/metainfo.py", line 956, in m_set value = self.__to_np(quantity_def, value) File "/app/nomad/metainfo/metainfo.py", line 934, in __to_np value = quantity_def.type.type(value) ValueError: invalid literal for int() with base 10: '********' |
| cfgruvgumKUmo3jBj8wCYAPfsg7e | 2 | Ukv9vOpmfindZocfvucn3eYOFFZq | bBwLURrsQzyT-avIDAsNhA | silicon-gw/INFO.OUT | parsers/exciting | Traceback (most recent call last): File "/app/nomad/processing/data.py", line 453, in parsing self._parser_results, logger=logger) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2128, in parse self.parse_gw() File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1712, in parse_gw self.parse_file(f, sec_method) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1337, in parse_file parser_function(section) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1665, in _parse_input_gw 'gw/selfenergy/npol', 0) File "/app/nomad/metainfo/metainfo.py", line 849, in setattr return super().setattr(name, value) File "/app/nomad/metainfo/metainfo.py", line 2221, in set (value, type(value), self, self.type)) TypeError: The value 2 with type <class 'numpy.int64'> for quantity nomad.datamodel.metainfo.common_dft.Method.gw_self_energy_c_number_of_poles:Quantity is not of type <class 'int'> |
| QptEjMdzQgru7wm-iUM0sYRQktG0 | 1 | 9UM_CpSzaystbWPZoghgjg3dZmC8 | CgtgzCMXTUyY0tjfBYXAnA | TiO2/anatese/K/nomad/INFO.OUT | parsers/exciting | Traceback (most recent call last): File "/app/nomad/processing/data.py", line 453, in parsing self._parser_results, logger=logger) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2126, in parse self.parse_configurations() File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2058, in parse_configurations self.parse_file(f, sec_scc) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1337, in parse_file parser_function(section) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1106, in _parse_dos if self.dos_parser.get('totaldos', None) is None: File "/app/nomad/parsing/file_parser/file_parser.py", line 78, in get val = self.results.get(key, None) File "/app/nomad/parsing/file_parser/file_parser.py", line 47, in results self.parse(self._key, **self._kwargs) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 505, in parse if not self.total_dos: File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 471, in total_dos self._total_dos = self.root.findall('./%s/%s' % (self._totaldos_key, self._diagram_key)) File "/app/nomad/parsing/file_parser/xml_parser.py", line 52, in root self._file_handler = ElementTree.parse(self.mainfile).getroot() File "/usr/local/lib/python3.7/xml/etree/ElementTree.py", line 1197, in parse tree.parse(source, parser) File "/usr/local/lib/python3.7/xml/etree/ElementTree.py", line 598, in parse self._root = parser._parse_whole(source) File "", line None xml.etree.ElementTree.ParseError: no element found: line 111468, column 0 |
| g4xYYjGHqxmbahc5Xk0jQrB2BvLv | 1 | B7YX4kB9f1PSwYbeJeUcExy-UKZw | cdAK5_-gQ4GLFbZrgBRpQQ | conv/workdir/ngridk_08-rgkmax_05/INFO.OUT | parsers/exciting | Traceback (most recent call last): File "/app/nomad/processing/data.py", line 453, in parsing self._parser_results, logger=logger) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2126, in parse self.parse_configurations() File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2058, in parse_configurations self.parse_file(f, sec_scc) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1337, in parse_file parser_function(section) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1162, in _parse_eigenvalues if self.eigval_parser.get('eigenvalues_occupancies', None) is None: File "/app/nomad/parsing/file_parser/file_parser.py", line 78, in get val = self.results.get(key, None) File "/app/nomad/parsing/file_parser/file_parser.py", line 47, in results self.parse(self._key, **self._kwargs) File "/app/nomad/parsing/file_parser/text_parser.py", line 501, in parse if self.file_mmap is None: File "/app/nomad/parsing/file_parser/text_parser.py", line 348, in file_mmap offset=self._file_offset) ValueError: cannot mmap an empty file |
| iwirABQpTlKQWqHEg7jS-2l-oA5w | 1 | qQbcfYsilb40jkYEN5hoW9PUdUrY | mcyQ9xEwQu2uNrkEtKNobg | volumes-rgkmax13/volume-2.1/1.01315940382018/INFO.OUT | parsers/exciting | Traceback (most recent call last): File "/app/nomad/processing/data.py", line 453, in parsing self._parser_results, logger=logger) File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 2124, in parse self.parse_method() File "/usr/local/lib/python3.7/site-packages/excitingparser/exciting_parser.py", line 1813, in parse_method correlation = self.input_xml_parser.get('libxc/correlation', None) File "/app/nomad/parsing/file_parser/file_parser.py", line 78, in get val = self.results.get(key, None) File "/app/nomad/parsing/file_parser/file_parser.py", line 47, in results self.parse(self._key, **self._kwargs) File "/app/nomad/parsing/file_parser/xml_parser.py", line 76, in parse if not self.root: File "/app/nomad/parsing/file_parser/xml_parser.py", line 52, in root self._file_handler = ElementTree.parse(self.mainfile).getroot() File "/usr/local/lib/python3.7/xml/etree/ElementTree.py", line 1197, in parse tree.parse(source, parser) File "/usr/local/lib/python3.7/xml/etree/ElementTree.py", line 598, in parse self._root = parser._parse_whole(source) File "", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 |
In addition, there are plenty of ABINIT calc that do not have a section_system, but no parser errors: https://nomad-lab.eu/prod/rae/reprocess/gui/search?visualization=system&dft.code_name=ABINIT&dft.system=unavailable
I am not sure if this is all, because the numbers do not add up. There are roughly ~2500 exciting runs with missing formulas/systems, but only ~2000 exceptions. We will see after bug fixes.