Exceptions and errors while processing MD entries
Reprocessing MD entries (c2pk, lammps, gromacs) for #677 (closed) revealed the following problems:
Exceptions during processing
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(1633 entries/2 uploads) parsers/lammps: E-NiLifGgF1_cJt4tbq3nyhBpVTc
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1088, in parsing
parser.parse(self.mainfile_file.os_path, self._parser_results, logger=logger, **kwargs)
File "/app/nomad/parsing/parser.py", line 283, in parse
self.mainfile_parser.parse(mainfile, archive, logger)
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/lammps/parser.py", line 1014, in parse
self.traj_parsers = TrajParsers(parsers)
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/lammps/parser.py", line 592, in __init__
parser.parse()
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/utils/mdanalysis.py", line 77, in parse
atoms = list(self.universe.atoms)
AttributeError: 'NoneType' object has no attribute 'atoms'
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(1494 entries/3 uploads) parsers/lammps: zNnUQHXJm5rlmNmkiY1_AU6qLkbH
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1088, in parsing
parser.parse(self.mainfile_file.os_path, self._parser_results, logger=logger, **kwargs)
File "/app/nomad/parsing/parser.py", line 283, in parse
self.mainfile_parser.parse(mainfile, archive, logger)
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/lammps/parser.py", line 1023, in parse
self.parse_method()
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/lammps/parser.py", line 890, in parse_method
if self.traj_parsers[0].mainfile is None or self.data_parser.mainfile is None:
AttributeError: 'NoneType' object has no attribute 'mainfile'
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(1446 entries/4 uploads) parsers/lammps: vEiU11z5x1faQ8fxxh8MTGpZW22C
example: upload_id: oF8t7vEhSwSnrTPnPhGbLQ, entry_id: HJqVgYr7onG0sP3hHREtf2mN5jkO, mainfile: GrSp/log.lammps
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1088, in parsing
parser.parse(self.mainfile_file.os_path, self._parser_results, logger=logger, **kwargs)
File "/app/nomad/parsing/parser.py", line 283, in parse
self.mainfile_parser.parse(mainfile, archive, logger)
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/lammps/parser.py", line 1025, in parse
self.parse_workflow()
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/lammps/parser.py", line 707, in parse_workflow
sec_md.ensemble_type = ensemble_type.upper()
File "/app/nomad/metainfo/metainfo.py", line 1250, in __setattr__
return super().__setattr__(name, value)
File "/app/nomad/metainfo/metainfo.py", line 2820, in __set__
obj.m_set(self, value)
File "/app/nomad/metainfo/metainfo.py", line 1371, in m_set
value = self.__set_normalize(quantity_def, value)
File "/app/nomad/metainfo/metainfo.py", line 1294, in __set_normalize
(value, quantity_def))
TypeError: The value is not an enum value for quantity nomad.datamodel.metainfo.workflow.MolecularDynamics.ensemble_type:Quantity.
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(62 entries/0 uploads) undefined: VwDFQBhfqjtRS_3AfXMwMSbXfQNS
example: upload_id: undefined, entry_id: bm1_uD4K_RUqgxCvbu-Ly-83uvev, mainfile: undefined
Traceback (most recent call last):
File "./nomad/files.py", line 817, in read_archive
return read_archive(self.archive_file_object(entry_id).os_path, use_blocked_toc=use_blocked_toc)
File "./nomad/archive/storage.py", line 551, in read_archive
return ArchiveReader(file_or_path, **kwargs)
File "./nomad/archive/storage.py", line 337, in __init__
BytesIO, open(self._file_or_path, 'rb', buffering=archive.read_buffer_size))
FileNotFoundError: [Errno 2] No such file or directory: '.volumes/fs/staging/p/p7IeDfNfTC-PPuMmkatlig/archive/bm1_uD4K_RUqgxCvbu-Ly-83uvev-v1.msg'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./nomad/app/v1/routers/entries.py", line 705, in _read_entry_from_archive
with upload_files.read_archive(entry_id, True) as archive:
File "./nomad/files.py", line 820, in read_archive
raise KeyError(entry_id)
KeyError: 'bm1_uD4K_RUqgxCvbu-Ly-83uvev'
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(62 entries/0 uploads) undefined: aUTdWd0aoJtPRXyfxXFWV0gqvR4u
example: upload_id: undefined, entry_id: SQ44la1WMqa-4elizXmJE_rgi0gP, mainfile: undefined
Traceback (most recent call last):
File "./nomad/files.py", line 817, in read_archive
return read_archive(self.archive_file_object(entry_id).os_path, use_blocked_toc=use_blocked_toc)
File "./nomad/archive/storage.py", line 551, in read_archive
return ArchiveReader(file_or_path, **kwargs)
File "./nomad/archive/storage.py", line 337, in __init__
BytesIO, open(self._file_or_path, 'rb', buffering=archive.read_buffer_size))
FileNotFoundError: [Errno 2] No such file or directory: '.volumes/fs/staging/l/lVnsVRtvQHa6c9tgeMJ8cw/archive/SQ44la1WMqa-4elizXmJE_rgi0gP-v1.msg'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./nomad/app/v1/routers/entries.py", line 705, in _read_entry_from_archive
with upload_files.read_archive(entry_id, True) as archive:
File "./nomad/files.py", line 820, in read_archive
raise KeyError(entry_id)
KeyError: 'SQ44la1WMqa-4elizXmJE_rgi0gP'
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(38 entries/8 uploads) parsers/cp2k: ptjms53HHijTqzdqgnDFOVo8w1uE
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1088, in parsing
parser.parse(self.mainfile_file.os_path, self._parser_results, logger=logger, **kwargs)
File "/app/nomad/parsing/parser.py", line 283, in parse
self.mainfile_parser.parse(mainfile, archive, logger)
File "/usr/local/lib/python3.7/site-packages/electronicparsers/cp2k/parser.py", line 1557, in parse
self.parse_configurations_quickstep()
File "/usr/local/lib/python3.7/site-packages/electronicparsers/cp2k/parser.py", line 1250, in parse_configurations_quickstep
parse_calculations(md_steps)
File "/usr/local/lib/python3.7/site-packages/electronicparsers/cp2k/parser.py", line 1220, in parse_calculations
parse_md_step(calculation)
File "/usr/local/lib/python3.7/site-packages/electronicparsers/cp2k/parser.py", line 1190, in parse_md_step
step = int(md_output.get("step"))
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'
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(13 entries/0 uploads) undefined: 9F3Xwhu7P0NU1Cqvt32EcZmnWqU_
example: upload_id: undefined, entry_id: NdSnG1dnjLAe06ZVz4Uri2ZyehGY, mainfile: undefined
Traceback (most recent call last):
File "./nomad/files.py", line 817, in read_archive
return read_archive(self.archive_file_object(entry_id).os_path, use_blocked_toc=use_blocked_toc)
File "./nomad/archive/storage.py", line 551, in read_archive
return ArchiveReader(file_or_path, **kwargs)
File "./nomad/archive/storage.py", line 337, in __init__
BytesIO, open(self._file_or_path, 'rb', buffering=archive.read_buffer_size))
FileNotFoundError: [Errno 2] No such file or directory: '.volumes/fs/staging/u/uFZEdlf8TYyIpcLj1jsaEg/archive/NdSnG1dnjLAe06ZVz4Uri2ZyehGY-v1.msg'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./nomad/app/v1/routers/entries.py", line 705, in _read_entry_from_archive
with upload_files.read_archive(entry_id, True) as archive:
File "./nomad/files.py", line 820, in read_archive
raise KeyError(entry_id)
KeyError: 'NdSnG1dnjLAe06ZVz4Uri2ZyehGY'
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(13 entries/0 uploads) undefined: J3M_rPhtECRMA2CIivXMZctmlx48
example: upload_id: undefined, entry_id: fmdQZp7h-GNUi1eEpr6jEGFbgmV3, mainfile: undefined
Traceback (most recent call last):
File "./nomad/files.py", line 817, in read_archive
return read_archive(self.archive_file_object(entry_id).os_path, use_blocked_toc=use_blocked_toc)
File "./nomad/archive/storage.py", line 551, in read_archive
return ArchiveReader(file_or_path, **kwargs)
File "./nomad/archive/storage.py", line 337, in __init__
BytesIO, open(self._file_or_path, 'rb', buffering=archive.read_buffer_size))
FileNotFoundError: [Errno 2] No such file or directory: '.volumes/fs/staging/g/gcUapevORuap1ldv1UcNdw/archive/fmdQZp7h-GNUi1eEpr6jEGFbgmV3-v1.msg'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./nomad/app/v1/routers/entries.py", line 705, in _read_entry_from_archive
with upload_files.read_archive(entry_id, True) as archive:
File "./nomad/files.py", line 820, in read_archive
raise KeyError(entry_id)
KeyError: 'fmdQZp7h-GNUi1eEpr6jEGFbgmV3'
-
(11 entries/4 uploads) parsers/cp2k: RRoDQ6tMsv5byKulreK4cPcHWPU6
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/billiard/pool.py", line 1267, in mark_as_worker_lost
human_status(exitcode), job._job),
billiard.exceptions.WorkerLostError: Worker exited prematurely: signal 9 (SIGKILL) Job: 3138.
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(10 entries/1 uploads) parsers/archive: TEEa4cIFzY_8m3HzeD_jRYXy8YuT
Traceback (most recent call last):
File "/app/nomad/parsing/parser.py", line 309, in parse_file
archive_data = json.load(f)
File "/usr/local/lib/python3.7/json/__init__.py", line 296, in load
parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
File "/usr/local/lib/python3.7/json/__init__.py", line 348, in loads
return _default_decoder.decode(s)
File "/usr/local/lib/python3.7/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/local/lib/python3.7/json/decoder.py", line 353, in raw_decode
obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting property name enclosed in double quotes: line 2 column 5 (char 6)
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(10 entries/1 uploads) parsers/archive: qOO77DcK8jWSCqi_WAA7WoNQ6XW6
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1088, in parsing
parser.parse(self.mainfile_file.os_path, self._parser_results, logger=logger, **kwargs)
File "/app/nomad/parsing/parser.py", line 348, in parse
self.parse_file(mainfile, f, archive, logger)
File "/app/nomad/parsing/parser.py", line 316, in parse_file
raise e
File "/app/nomad/parsing/parser.py", line 309, in parse_file
archive_data = json.load(f)
File "/usr/local/lib/python3.7/json/__init__.py", line 296, in load
parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
File "/usr/local/lib/python3.7/json/__init__.py", line 348, in loads
return _default_decoder.decode(s)
File "/usr/local/lib/python3.7/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/local/lib/python3.7/json/decoder.py", line 353, in raw_decode
obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting property name enclosed in double quotes: line 2 column 5 (char 6)
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(2 entries/1 uploads) parsers/gromacs: WkT97UhwXboPpdE6ff7B6X4CPDQw
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1088, in parsing
parser.parse(self.mainfile_file.os_path, self._parser_results, logger=logger, **kwargs)
File "/app/nomad/parsing/parser.py", line 283, in parse
self.mainfile_parser.parse(mainfile, archive, logger)
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/gromacs/parser.py", line 972, in parse
self.parse_system()
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/gromacs/parser.py", line 791, in parse_system
rdf_results = self.traj_parser.calc_molecular_rdf()
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/utils/mdanalysis.py", line 195, in calc_molecular_rdf
exclusion_block=exclusion_block, nbins=n_bins).run()
File "/usr/local/lib/python3.7/site-packages/MDAnalysis/analysis/base.py", line 303, in run
self._single_frame()
File "/usr/local/lib/python3.7/site-packages/MDAnalysis/analysis/rdf.py", line 355, in _single_frame
pairs, dist = distances.capped_distance(self.g1.positions,
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/utils/mdanalysis.py", line 433, in positions
unwrap=True, compound=self.compound)
File "/usr/local/lib/python3.7/site-packages/MDAnalysis/lib/util.py", line 1900, in wrapper
return groupmethod(group, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/MDAnalysis/core/groups.py", line 446, in wrapped
return function(group, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/MDAnalysis/core/groups.py", line 456, in wrapped
return function(group, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/MDAnalysis/core/topologyattrs.py", line 1518, in center_of_mass
unwrap=unwrap)
File "/usr/local/lib/python3.7/site-packages/MDAnalysis/lib/util.py", line 1900, in wrapper
return groupmethod(group, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/MDAnalysis/core/groups.py", line 446, in wrapped
return function(group, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/MDAnalysis/core/groups.py", line 456, in wrapped
return function(group, *args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/MDAnalysis/core/groups.py", line 1081, in center
coords = atoms.unwrap(compound=comp, reference=None, inplace=False)
File "/usr/local/lib/python3.7/site-packages/MDAnalysis/core/groups.py", line 1874, in unwrap
positions = unique_atoms.positions
File "/usr/local/lib/python3.7/site-packages/MDAnalysis/core/groups.py", line 2534, in __getattr__
raise NoDataError('This Universe has no coordinates')
MDAnalysis.exceptions.NoDataError: This Universe has no coordinates
-
(2 entries/1 uploads) parsers/charmm: jIMpSavB0KSwsHvpYVNdleBnRY5-
Traceback (most recent call last):
File "/app/nomad/normalizing/system.py", line 256, in system_type_analysis
cls = classifier.classify(atoms)
File "/usr/local/lib/python3.7/site-packages/matid/classification/classifier.py", line 242, in classify
global_min_dist = dist_matrix_mod.min()
File "/usr/local/lib/python3.7/site-packages/numpy/core/_methods.py", line 44, in _amin
return umr_minimum(a, axis, None, out, keepdims, initial, where)
ValueError: zero-size array to reduction operation minimum which has no identity
-
(2 entries/1 uploads) parsers/charmm: w5UgK41gaLBJ618jWoksm0meisfv
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1113, in normalizing
normalizer(self._parser_results).normalize(logger=logger)
File "/app/nomad/normalizing/results.py", line 107, in normalize
self.normalize_run(logger=self.logger)
File "/app/nomad/normalizing/results.py", line 221, in normalize_run
logger
File "/app/nomad/normalizing/material.py", line 62, in material
symbols, reduced_counts = atomutils.get_hill_decomposition(self.repr_system.atoms.labels, reduced=True)
File "/app/nomad/atomutils.py", line 446, in get_hill_decomposition
greatest_common_divisor = reduce(math.gcd, counts)
TypeError: reduce() of empty sequence with no initial value
-
(1 entries/1 uploads) parsers/dl-poly: -QMdYvx7_bPO-VtsALmzyP4prI45
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 835, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 906, in process_entry
self._process_entry_local()
File "/app/nomad/processing/data.py", line 981, in _process_entry_local
entry.archiving()
File "/app/nomad/processing/data.py", line 1152, in archiving
archive_size = self.write_archive(self._parser_results)
File "/app/nomad/processing/data.py", line 1186, in write_archive
return self.upload_files.write_archive(self.entry_id, archive.m_to_dict())
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1876, in items
yield name, sub_section.m_to_dict(**kwargs)
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1858, in items
yield name, serialize_quantity(quantity, is_set, False, path)
File "/app/nomad/metainfo/metainfo.py", line 1783, in serialize_quantity
return serialize(value)
File "/app/nomad/metainfo/metainfo.py", line 1734, in _serialize
(value, quantity, self))
nomad.metainfo.metainfo.MetainfoError: Only python primitives are allowed for Any typed non virtual quantities: [2.54435e+03 3.15450e+00 2.34000e+00 1.01170e+04 4.81770e+03] of quantity nomad.datamodel.metainfo.simulation.method.Interaction.parameters:Quantity in section Interaction(atom_labels, functional_form, parameters)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1056, in _on_fail
self.write_archive(self._parser_results)
File "/app/nomad/processing/data.py", line 1186, in write_archive
return self.upload_files.write_archive(self.entry_id, archive.m_to_dict())
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1876, in items
yield name, sub_section.m_to_dict(**kwargs)
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1858, in items
yield name, serialize_quantity(quantity, is_set, False, path)
File "/app/nomad/metainfo/metainfo.py", line 1783, in serialize_quantity
return serialize(value)
File "/app/nomad/metainfo/metainfo.py", line 1734, in _serialize
(value, quantity, self))
nomad.metainfo.metainfo.MetainfoError: Only python primitives are allowed for Any typed non virtual quantities: [2.54435e+03 3.15450e+00 2.34000e+00 1.01170e+04 4.81770e+03] of quantity nomad.datamodel.metainfo.simulation.method.Interaction.parameters:Quantity in section Interaction(atom_labels, functional_form, parameters)
-
(1 entries/1 uploads) parsers/phonopy: 60CFzD6iCO2WxEBIle0fNAkngP1c
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 835, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 906, in process_entry
self._process_entry_local()
File "/app/nomad/processing/data.py", line 981, in _process_entry_local
entry.archiving()
File "/app/nomad/processing/data.py", line 1152, in archiving
archive_size = self.write_archive(self._parser_results)
File "/app/nomad/processing/data.py", line 1186, in write_archive
return self.upload_files.write_archive(self.entry_id, archive.m_to_dict())
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1858, in items
yield name, serialize_quantity(quantity, is_set, False, path)
File "/app/nomad/metainfo/metainfo.py", line 1786, in serialize_quantity
return [serialize(item, f"{path}/{index}") for index, item in enumerate(value)]
File "/app/nomad/metainfo/metainfo.py", line 1786, in <listcomp>
return [serialize(item, f"{path}/{index}") for index, item in enumerate(value)]
File "/app/nomad/metainfo/metainfo.py", line 1690, in reference_serialize
return quantity_type.serialize(self, quantity, value)
File "/app/nomad/metainfo/metainfo.py", line 651, in serialize
return context.create_reference(section, quantity_def, value)
File "/app/nomad/datamodel/context.py", line 146, in create_reference
assert entry_id is not None, 'Only archives with entry_id can be referenced'
AssertionError: Only archives with entry_id can be referenced
-
(1 entries/1 uploads) parsers/dl-poly: HGWnEaoE1Ahb-uTJgfbbdXOQIebN
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 835, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 906, in process_entry
self._process_entry_local()
File "/app/nomad/processing/data.py", line 981, in _process_entry_local
entry.archiving()
File "/app/nomad/processing/data.py", line 1152, in archiving
archive_size = self.write_archive(self._parser_results)
File "/app/nomad/processing/data.py", line 1186, in write_archive
return self.upload_files.write_archive(self.entry_id, archive.m_to_dict())
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1876, in items
yield name, sub_section.m_to_dict(**kwargs)
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1858, in items
yield name, serialize_quantity(quantity, is_set, False, path)
File "/app/nomad/metainfo/metainfo.py", line 1783, in serialize_quantity
return serialize(value)
File "/app/nomad/metainfo/metainfo.py", line 1734, in _serialize
(value, quantity, self))
nomad.metainfo.metainfo.MetainfoError: Only python primitives are allowed for Any typed non virtual quantities: [2.54435e+03 3.15450e+00 2.34000e+00 1.01170e+04 4.81770e+03] of quantity nomad.datamodel.metainfo.simulation.method.Interaction.parameters:Quantity in section Interaction(atom_labels, functional_form, parameters)
-
(1 entries/1 uploads) parsers/dftbplus: HPaOQmVbiL5fRyauuw6DW3EF49YZ
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1088, in parsing
parser.parse(self.mainfile_file.os_path, self._parser_results, logger=logger, **kwargs)
File "/app/nomad/parsing/parser.py", line 283, in parse
self.mainfile_parser.parse(mainfile, archive, logger)
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/dftbplus/parser.py", line 346, in parse
if input_file.endswith('.hsd'):
AttributeError: 'NoneType' object has no attribute 'endswith'
-
(1 entries/1 uploads) parsers/phonopy: Om-KCzY1jPFzvRvSNcSEQdRuZaNk
Traceback (most recent call last):
File "/app/nomad/processing/base.py", line 835, in proc_task
rv = unwrapped_func(proc, *args, **kwargs)
File "/app/nomad/processing/data.py", line 906, in process_entry
self._process_entry_local()
File "/app/nomad/processing/data.py", line 981, in _process_entry_local
entry.archiving()
File "/app/nomad/processing/data.py", line 1152, in archiving
archive_size = self.write_archive(self._parser_results)
File "/app/nomad/processing/data.py", line 1186, in write_archive
return self.upload_files.write_archive(self.entry_id, archive.m_to_dict())
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1858, in items
yield name, serialize_quantity(quantity, is_set, False, path)
File "/app/nomad/metainfo/metainfo.py", line 1786, in serialize_quantity
return [serialize(item, f"{path}/{index}") for index, item in enumerate(value)]
File "/app/nomad/metainfo/metainfo.py", line 1786, in <listcomp>
return [serialize(item, f"{path}/{index}") for index, item in enumerate(value)]
File "/app/nomad/metainfo/metainfo.py", line 1690, in reference_serialize
return quantity_type.serialize(self, quantity, value)
File "/app/nomad/metainfo/metainfo.py", line 651, in serialize
return context.create_reference(section, quantity_def, value)
File "/app/nomad/datamodel/context.py", line 146, in create_reference
assert entry_id is not None, 'Only archives with entry_id can be referenced'
AssertionError: Only archives with entry_id can be referenced
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1056, in _on_fail
self.write_archive(self._parser_results)
File "/app/nomad/processing/data.py", line 1186, in write_archive
return self.upload_files.write_archive(self.entry_id, archive.m_to_dict())
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1872, in items
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1872, in <listcomp>
for item in self.m_get_sub_sections(sub_section_def)]
File "/app/nomad/metainfo/metainfo.py", line 1878, in m_to_dict
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1878, in <dictcomp>
return {key: value for key, value in items()}
File "/app/nomad/metainfo/metainfo.py", line 1858, in items
yield name, serialize_quantity(quantity, is_set, False, path)
File "/app/nomad/metainfo/metainfo.py", line 1786, in serialize_quantity
return [serialize(item, f"{path}/{index}") for index, item in enumerate(value)]
File "/app/nomad/metainfo/metainfo.py", line 1786, in <listcomp>
return [serialize(item, f"{path}/{index}") for index, item in enumerate(value)]
File "/app/nomad/metainfo/metainfo.py", line 1690, in reference_serialize
return quantity_type.serialize(self, quantity, value)
File "/app/nomad/metainfo/metainfo.py", line 651, in serialize
return context.create_reference(section, quantity_def, value)
File "/app/nomad/datamodel/context.py", line 146, in create_reference
assert entry_id is not None, 'Only archives with entry_id can be referenced'
AssertionError: Only archives with entry_id can be referenced
-
(1 entries/1 uploads) parsers/tinker: ZgOEDGbXS0orwJ4MyloZ-5TGQnjN
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1113, in normalizing
normalizer(self._parser_results).normalize(logger=logger)
File "/app/nomad/normalizing/results.py", line 107, in normalize
self.normalize_run(logger=self.logger)
File "/app/nomad/normalizing/results.py", line 211, in normalize_run
properties, conv_atoms, wyckoff_sets, spg_number = self.properties(repr_system, repr_symmetry)
File "/app/nomad/normalizing/results.py", line 565, in properties
geometry_optimization = self.geometry_optimization()
File "/app/nomad/normalizing/results.py", line 412, in geometry_optimization
structure_optimized = self.nomad_system_to_structure(StructureOptimized, system_ref)
File "/app/nomad/normalizing/results.py", line 803, in nomad_system_to_structure
struct.dimension_types = np.array(system.atoms.periodic).astype(int)
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'
-
(2 entries/2 uploads) parsers/tinker: other
Traceback (most recent call last):
File "/app/nomad/processing/data.py", line 1088, in parsing
parser.parse(self.mainfile_file.os_path, self._parser_results, logger=logger, **kwargs)
File "/app/nomad/parsing/parser.py", line 283, in parse
self.mainfile_parser.parse(mainfile, archive, logger)
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/tinker/parser.py", line 468, in parse
parameters = {key.lower(): val for key, val in self.key_parser.get('key_val', [])}
File "/usr/local/lib/python3.7/site-packages/atomisticparsers/tinker/parser.py", line 468, in <dictcomp>
parameters = {key.lower(): val for key, val in self.key_parser.get('key_val', [])}
ValueError: too many values to unpack (expected 2)
Other errors
-
(40918 entries/n.n. uploads) parsers/cp2k: Error reading trajectory.
-
(36108 entries/n.n. uploads) parsers/cp2k: no lattice vectors but periodicity
-
(38 entries/n.n. uploads) parsers/cp2k: Error reading MD energies.
-
(28 entries/n.n. uploads) parsers/cp2k: Cannot resolve xc functional
-
(10 entries/n.n. uploads) parsers/archive: Cannot parse archive json or yaml.
-
(2 entries/n.n. uploads) parsers/dl-poly: could not write archive after processing failure
-
(2 entries/n.n. uploads) parsers/phonopy: could not write archive after processing failure
-
(2 entries/n.n. uploads) parsers/charmm: matid project system classification failed
-
(1 entries/n.n. uploads) parsers/phonopy: Error generating phonopy object.
-
(1 entries/n.n. uploads) parsers/phonopy: Error running phonopy.
-
(1 entries/n.n. uploads) parsers/phonopy: could not write mongodb archive entry