pyiron_base
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Published
20 hours ago •
pyiron
pyiron
Restarting old jobs does not work anymore with the latest update
All restart functionality is broken for old jobs (not sure how to allow others to reproduce this)
error: rror saving warn (key /Ni111_Mo_surface_sub1_cov/input/vasp_dict/eddrmm_handling): h5io_browser doesn't support saving elements of type "<class 'str'>" to HDF!
- switching pyiron versions to the old ones did not work
- manually changing h5io_browser did not work
- old problematic jobs: type(job_test['input/vasp_dict']) -> dict
- new working jobs: type(job_test['input/vasp_dict']) -> pyiron_base.storage.hdfio.ProjectHDFio
Can you be a bit more specific how old these jobs are? Which version of pyiron_atomistics did you use to create those?
how to do that for a job? since !conda list pyiron will print out those for the loaded kernel
Can you post the output of job.to_dict() for both the old and the new job? Maybe we can write a converter from the old format to the new one. Do you know when the old job was calculated?
Old job -> restart not working -> creation date: 2024-01-03
{'NAME': 'Vasp',
'TYPE': "<class 'pyiron_atomistics.vasp.vasp.Vasp'>",
'OBJECT': 'Vasp',
'DICT_VERSION': '0.1.0',
'VERSION': '6.4.0_mpi',
'HDF_VERSION': '0.2.0',
'status': 'finished',
'input/generic_dict': {'restart_file_list': [],
'restart_file_dict': {},
'exclude_nodes_hdf': [],
'exclude_groups_hdf': []},
'server': {'NAME': 'Server',
'TYPE': "<class 'pyiron_base.jobs.job.extension.server.generic.Server'>",
'OBJECT': 'Server',
'DICT_VERSION': '0.1.0',
'user': 'aabdelkawy',
'host': 'cmti001',
'run_mode': 'queue',
'queue': 'cm',
'qid': 6803227,
'cores': 80,
'threads': 1,
'new_h5': True,
'structure_id': None,
'run_time': None,
'memory_limit': None,
'accept_crash': False},
'executable': {'NAME': 'Executable',
'TYPE': "<class 'pyiron_base.jobs.job.extension.executable.Executable'>",
'OBJECT': 'Executable',
'DICT_VERSION': '0.1.0',
'executable': {'NAME': 'DataContainer',
'TYPE': "<class 'pyiron_base.storage.datacontainer.DataContainer'>",
'OBJECT': 'DataContainer',
'HDF_VERSION': '0.2.0',
'VERSION': '0.1.0',
'READ_ONLY': False,
'version': '6.4.0_mpi',
'name': 'vasp',
'operation_system_nt': 0,
'executable': None,
'mpi': 1,
'accepted_return_codes': [0]}},
'input/generic/NAME': 'GenericInput',
'input/generic/TYPE': "<class 'pyiron_atomistics.atomistics.job.atomistic.GenericInput'>",
'input/generic/OBJECT': 'GenericInput',
'input/generic/DICT_VERSION': '0.1.0',
'input/generic/VERSION': '0.1',
'input/generic/data_dict': {'Parameter': ['calc_mode',
'structure',
'fix_symmetry',
'k_mesh_spacing',
'k_mesh_center_shift',
'reduce_kpoint_symmetry',
'max_iter',
'pressure'],
'Value': ['minimize', 'atoms', 'True', 'None', 'None', 'True', None, None],
'Comment': ['static, minimize, md',
'atoms, continue_final',
'',
'',
'',
'',
'',
'']},
'input/structure/TYPE': "<class 'pyiron_atomistics.atomistics.structure.atoms.Atoms'>",
'input/structure/units': {'length': 'A', 'mass': 'u'},
'input/structure/dimension': 3,
'input/structure/positions': array([[ 0. , 0. , 0. ],
[ 2.4876017 , 1.43621752, 2.03111828],
[ 1.24380078, 0.71810871, 4.05734758],
[ 0. , 0. , 6.08684106],
[ 2.4876017 , 1.43621752, 8.11469364],
[ 1.24380078, 0.71810871, 10.11913593],
[ 1.24380083, 2.15432623, 0. ],
[ 3.73140253, 3.59054375, 2.03111828],
[ 2.48760161, 2.87243494, 4.05734758],
[ 1.24380083, 2.15432623, 6.08684106],
[ 3.73140253, 3.59054375, 8.11469364],
[ 2.48760161, 2.87243494, 10.11913593],
[ 2.48760166, 4.30865246, 0. ],
[ 4.97520336, 5.74486998, 2.03111828],
[ 3.73140243, 5.02676117, 4.05734758],
[ 2.48760166, 4.30865246, 6.08684106],
[ 4.97520336, 5.74486998, 8.11469364],
[ 3.73140243, 5.02676117, 10.11913593],
[ 3.73140248, 6.46297869, 0. ],
[ 6.21900419, 7.89919621, 2.03111828],
[ 4.97520326, 7.1810874 , 4.05734758],
[ 3.73140248, 6.46297869, 6.08684106],
[ 6.21900419, 7.89919621, 8.11469364],
[ 4.97520326, 7.1810874 , 10.11913593],
[ 2.48760166, 0. , 0. ],
[ 4.97520336, 1.43621752, 2.03111828],
[ 3.73140243, 0.71810871, 4.05734758],
[ 2.48760166, 0. , 6.08684106],
[ 4.97520336, 1.43621752, 8.11469364],
[ 3.73140243, 0.71810871, 10.11913593],
[ 3.73140248, 2.15432623, 0. ],
[ 6.21900419, 3.59054375, 2.03111828],
[ 4.97520326, 2.87243494, 4.05734758],
[ 3.73140248, 2.15432623, 6.08684106],
[ 6.21900419, 3.59054375, 8.11469364],
[ 4.97520326, 2.87243494, 10.11913593],
[ 4.97520331, 4.30865246, 0. ],
[ 7.46280501, 5.74486998, 2.03111828],
[ 6.21900409, 5.02676117, 4.05734758],
[ 4.97520331, 4.30865246, 6.08684106],
[ 7.46280501, 5.74486998, 8.11469364],
[ 6.21900409, 5.02676117, 10.11913593],
[ 6.21900414, 6.46297869, 0. ],
[ 8.70660584, 7.89919621, 2.03111828],
[ 7.46280492, 7.1810874 , 4.05734758],
[ 6.21900414, 6.46297869, 6.08684106],
[ 8.70660584, 7.89919621, 8.11469364],
[ 7.46280492, 7.1810874 , 10.11913593],
[ 4.97520331, 0. , 0. ],
[ 7.46280501, 1.43621752, 2.03111828],
[ 6.21900409, 0.71810871, 4.05734758],
[ 4.97520331, 0. , 6.08684106],
[ 7.46280501, 1.43621752, 8.11469364],
[ 6.21900409, 0.71810871, 10.11913593],
[ 6.21900414, 2.15432623, 0. ],
[ 8.70660584, 3.59054375, 2.03111828],
[ 7.46280492, 2.87243494, 4.05734758],
[ 6.21900414, 2.15432623, 6.08684106],
[ 8.70660584, 3.59054375, 8.11469364],
[ 7.46280492, 2.87243494, 10.11913593],
[ 7.46280497, 4.30865246, 0. ],
[ 9.95040667, 5.74486998, 2.03111828],
[ 8.70660574, 5.02676117, 4.05734758],
[ 7.46280497, 4.30865246, 6.08684106],
[ 9.95040667, 5.74486998, 8.11469364],
[ 8.70660574, 5.02676117, 10.11913593],
[ 8.70660579, 6.46297869, 0. ],
[11.1942075 , 7.89919621, 2.03111828],
[ 9.95040657, 7.1810874 , 4.05734758],
[ 8.70660579, 6.46297869, 6.08684106],
[11.1942075 , 7.89919621, 8.11469364],
[ 9.95040657, 7.1810874 , 10.11913593],
[ 7.46280496, 0. , 0. ],
[ 9.95040667, 1.43621752, 2.03111828],
[ 8.70660574, 0.71810871, 4.05734758],
[ 7.46280496, 0. , 6.08684106],
[ 9.95040667, 1.43621752, 8.11469364],
[ 8.70660574, 0.71810871, 10.11913593],
[ 8.70660579, 2.15432623, 0. ],
[11.1942075 , 3.59054375, 2.03111828],
[ 9.95040657, 2.87243494, 4.05734758],
[ 8.70660579, 2.15432623, 6.08684106],
[11.1942075 , 3.59054375, 8.11469364],
[ 9.95040657, 2.87243494, 10.11913593],
[ 9.95040662, 4.30865246, 0. ],
[12.43800832, 5.74486998, 2.03111828],
[11.1942074 , 5.02676117, 4.05734758],
[ 9.95040662, 4.30865246, 6.08684106],
[12.43800832, 5.74486998, 8.11469364],
[11.1942074 , 5.02676117, 10.11913593],
[11.19420745, 6.46297869, 0. ],
[13.68180915, 7.89919621, 2.03111828],
[12.43800823, 7.1810874 , 4.05734758],
[11.19420745, 6.46297869, 6.08684106],
[13.68180915, 7.89919621, 8.11469364],
[12.43800823, 7.1810874 , 10.11913593]]),
'input/structure/info': {},
'input/structure/species': ['Ni', 'Mo'],
'input/structure/indices': array([0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0]),
'input/structure/tags/initial_magmoms': [0.634,
0.636,
0.59,
0.59,
0.635,
0.0,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
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0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
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0.636,
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0.59,
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0.636,
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0.634,
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0.636,
0.59,
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0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634],
'input/structure/tags/selective_dynamics': [[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True],
[False, False, False],
[False, False, False],
[True, True, True],
[True, True, True],
[True, True, True],
[True, True, True]],
'input/structure/tags/spin': [0.634,
0.636,
0.59,
0.59,
0.635,
0.0,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634,
0.634,
0.636,
0.59,
0.59,
0.635,
0.634],
'input/structure/cell/cell': array([[ 9.95040662, 0. , 0. ],
[ 4.97520331, 8.61730492, 0. ],
[ 0. , 0. , 25.15559124]]),
'input/structure/cell/pbc': array([ True, True, True]),
'input/structure/spins': array([0.634, 0.636, 0.59 , 0.59 , 0.635, 0. , 0.634, 0.636, 0.59 ,
0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634,
0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 ,
0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634,
0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 ,
0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634,
0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 ,
0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634,
0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 ,
0.59 , 0.635, 0.634, 0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634,
0.634, 0.636, 0.59 , 0.59 , 0.635, 0.634]),
'input/vasp_dict/eddrmm_handling': 'warn',
'input/incar/NAME': 'Incar',
'input/incar/TYPE': "<class 'pyiron_atomistics.vasp.base.Incar'>",
'input/incar/OBJECT': 'Incar',
'input/incar/DICT_VERSION': '0.1.0',
'input/incar/VERSION': '0.1',
'input/incar/data_dict': {'Parameter': ['SYSTEM',
'PREC',
'ALGO',
'LREAL',
'LWAVE',
'LORBIT',
'ENCUT',
'ISPIN',
'MAGMOM',
'NCORE',
'ISIF',
'IBRION',
'NELM',
'NSW',
'EDIFFG',
'EDIFF'],
'Value': ['Ni111_Mo_surface_sub1_cov',
'Accurate',
'Normal',
'Auto',
False,
'11',
450,
2,
'1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ',
8,
2,
2,
400,
100,
'-0.01',
1e-06],
'Comment': ['jobname',
'',
'',
'',
'',
'',
'',
'',
'',
'',
'',
'',
'',
'',
'',
'']},
'input/kpoints/NAME': 'Kpoints',
'input/kpoints/TYPE': "<class 'pyiron_atomistics.vasp.base.Kpoints'>",
'input/kpoints/OBJECT': 'Kpoints',
'input/kpoints/DICT_VERSION': '0.1.0',
'input/kpoints/VERSION': '0.1',
'input/kpoints/data_dict': {'Parameter': ['', '', '', '', ''],
'Value': ['Kpoints file generated with pyiron_atomistics',
'0',
'Monkhorst_Pack',
'2 2 1',
'0 0 0'],
'Comment': ['', '', '', '', '']},
'input/potcar/NAME': 'Potcar',
'input/potcar/TYPE': "<class 'pyiron_atomistics.vasp.potential.Potcar'>",
'input/potcar/OBJECT': 'Potcar',
'input/potcar/DICT_VERSION': '0.1.0',
'input/potcar/VERSION': '0.1',
'input/potcar/data_dict': {'Parameter': ['xc'],
'Value': ['GGA'],
'Comment': ['LDA, GGA']},
'input/potential_dict': {'Mo': None, 'Ni': None}}
New job -> restart is working -> created today (different structure/setup just a test job)
{'NAME': 'Vasp',
'TYPE': "<class 'pyiron_atomistics.vasp.vasp.Vasp'>",
'OBJECT': 'Vasp',
'DICT_VERSION': '0.1.0',
'VERSION': '6.4.0_mpi',
'HDF_VERSION': '0.2.0',
'status': 'finished',
'input/generic_dict': {'restart_file_list': [],
'restart_file_dict': {},
'exclude_nodes_hdf': [],
'exclude_groups_hdf': []},
'server': {'NAME': 'Server',
'TYPE': "<class 'pyiron_base.jobs.job.extension.server.generic.Server'>",
'OBJECT': 'Server',
'DICT_VERSION': '0.1.0',
'user': 'aabdelkawy',
'host': 'cmti001',
'run_mode': 'queue',
'queue': 'cmti',
'qid': 8332741,
'cores': 10,
'threads': 1,
'new_h5': True,
'structure_id': None,
'run_time': None,
'memory_limit': None,
'accept_crash': False},
'executable': {'NAME': 'Executable',
'TYPE': "<class 'pyiron_base.jobs.job.extension.executable.Executable'>",
'OBJECT': 'Executable',
'DICT_VERSION': '0.1.0',
'executable': {'NAME': 'DataContainer',
'TYPE': "<class 'pyiron_base.storage.datacontainer.DataContainer'>",
'OBJECT': 'DataContainer',
'HDF_VERSION': '0.2.0',
'VERSION': '0.1.0',
'READ_ONLY': False,
'version': '6.4.0_mpi',
'name': 'vasp',
'operation_system_nt': False,
'executable': None,
'mpi': True,
'accepted_return_codes': [0]}},
'input/generic/NAME': 'GenericInput',
'input/generic/TYPE': "<class 'pyiron_atomistics.atomistics.job.atomistic.GenericInput'>",
'input/generic/OBJECT': 'GenericInput',
'input/generic/DICT_VERSION': '0.1.0',
'input/generic/VERSION': '0.1',
'input/generic/data_dict': OrderedDict([('Parameter',
['calc_mode',
'structure',
'fix_symmetry',
'k_mesh_spacing',
'k_mesh_center_shift',
'reduce_kpoint_symmetry']),
('Value', ['static', 'atoms', 'True', None, None, True]),
('Comment',
['static, minimize, md',
'atoms, continue_final',
'',
'',
'',
''])]),
'input/structure/TYPE': "<class 'pyiron_atomistics.atomistics.structure.atoms.Atoms'>",
'input/structure/units': {'length': 'A', 'mass': 'u'},
'input/structure/dimension': 3,
'input/structure/positions': array([[0. , 0. , 0. ],
[0. , 2.025, 2.025],
[2.025, 0. , 2.025],
[2.025, 2.025, 0. ]]),
'input/structure/info': {},
'input/structure/species': ['Al'],
'input/structure/indices': array([0, 0, 0, 0]),
'input/structure/cell/cell': array([[4.05, 0. , 0. ],
[0. , 4.05, 0. ],
[0. , 0. , 4.05]]),
'input/structure/cell/pbc': array([ True, True, True]),
'input/vasp_dict/eddrmm_handling': 'ignore',
'input/incar/NAME': 'Incar',
'input/incar/TYPE': "<class 'pyiron_atomistics.vasp.base.Incar'>",
'input/incar/OBJECT': 'Incar',
'input/incar/DICT_VERSION': '0.1.0',
'input/incar/VERSION': '0.1',
'input/incar/data_dict': OrderedDict([('Parameter',
['SYSTEM',
'PREC',
'ALGO',
'LREAL',
'LWAVE',
'LORBIT',
'IBRION',
'NELM',
'NSW']),
('Value',
['test_job',
'Accurate',
'Fast',
False,
False,
'0',
-1,
100,
0]),
('Comment', ['jobname', '', '', '', '', '', '', '', ''])]),
'input/kpoints/NAME': 'Kpoints',
'input/kpoints/TYPE': "<class 'pyiron_atomistics.vasp.base.Kpoints'>",
'input/kpoints/OBJECT': 'Kpoints',
'input/kpoints/DICT_VERSION': '0.1.0',
'input/kpoints/VERSION': '0.1',
'input/kpoints/data_dict': OrderedDict([('Parameter', ['', '', '', '', '']),
('Value',
['Kpoints file generated with pyiron_atomistics',
'0',
'Monkhorst_Pack',
'4 4 4',
'0 0 0']),
('Comment', ['', '', '', '', ''])]),
'input/potcar/NAME': 'Potcar',
'input/potcar/TYPE': "<class 'pyiron_atomistics.vasp.potential.Potcar'>",
'input/potcar/OBJECT': 'Potcar',
'input/potcar/DICT_VERSION': '0.1.0',
'input/potcar/VERSION': '0.1',
'input/potcar/data_dict': OrderedDict([('Parameter', ['xc', 'Al', 'pot_0']),
('Value',
['GGA',
'Al-gga-pbe',
'/cmmc/u/aabdelkawy/pyiron-resources-cmmc/vasp/potentials/potpaw_PBE/Al/POTCAR']),
('Comment', ['LDA, GGA', '', ''])]),
'input/potential_dict': {'Al': None}}