Hi all,
I am new to AiiDA in general and I want to calculate Raman from aiida-vibroscopy.
I prepared following overrides.yaml and submit.py files (please see below). When I check the status, I feel like it wasnt running successfully. Can you please suggest me what I am doing wrong here and how may I fix this?
The submit.py was successfully submitted with PK=42
I am not sure what is wrong there but something is not right. Can you please tell me whats going on here?
Then when I check the status:
(aiidaENV) rkarkee@ch-fe1:/lustre/scratch5/rkarkee> verdi process status 42
IRamanSpectraWorkChain<42> Finished [400] [1:inspect_process]
└── HarmonicWorkChain<44> Finished [400] [2:inspect_processes]
├── generate_preprocess_data<45> Finished [0]
├── PhononWorkChain<50> Finished [400] [3:inspect_base_supercell]
│ ├── generate_preprocess_data<51> Finished [0]
│ ├── get_supercell<57> Finished [0]
│ └── PwBaseWorkChain<60> Finished [301] [2:while_(should_run_process)(2:inspect_process)]
│ └── PwCalculation<63> Excepted
└── DielectricWorkChain<55> Excepted [2:run_base_scf]
And Process report 44 shows:
(aiidaENV) rkarkee@ch-fe1:/lustre/scratch5/rkarkee> verdi process report 44
2024-02-14 20:49:59 [5 | REPORT]: [44|HarmonicWorkChain|run_phonon]: submitting `PhononWorkChain` <PK=50>
2024-02-14 20:49:59 [6 | REPORT]: [44|HarmonicWorkChain|run_dielectric]: submitting `DielectricWorkChain` <PK=55>
2024-02-14 20:50:00 [7 | REPORT]: [55|DielectricWorkChain|on_except]: Traceback (most recent call last):
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/engine/base.py”, line 1969, in _exec_single_context
self.dialect.do_execute(
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/engine/default.py”, line 922, in do_execute
cursor.execute(statement, parameters)
sqlite3.OperationalError: database is locked
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/plumpy/base/state_machine.py”, line 324, in transition_to
self._enter_next_state(new_state)
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/plumpy/base/state_machine.py”, line 388, in _enter_next_state
self._fire_state_event(StateEventHook.ENTERED_STATE, last_state)
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/plumpy/base/state_machine.py”, line 300, in _fire_state_event
callback(self, hook, state)
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/plumpy/processes.py”, line 331, in
lambda _s, <em>h, from_state: self.on_entered(cast(Optional[process_states.State], from_state)),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/aiida/engine/processes/process.py”, line 424, in on_entered
set_process_state_change_timestamp(self)
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/aiida/engine/utils.py”, line 287, in set_process_state_change</em> timestamp
backend.set_global_variable(key, value, description)
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/aiida/storage/psql_dos/backend.py”, line 411, in set_global_va riable
session.query(DbSetting).filter(DbSetting.key == key).update(dict(val=value))
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/orm/query.py”, line 3271, in update
result: CursorResult[Any] = self.session.execute(
^^^^^^^^^^^^^^^^^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/orm/session.py”, line 2308, in execute
return self._execute_internal(
^^^^^^^^^^^^^^^^^^^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/orm/session.py”, line 2190, in _execute_internal
result: Result[Any] = compile_state_cls.orm_execute_statement(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/orm/bulk_persistence.py”, line 1617, in orm_execute _statement
return super().orm_execute_statement(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/orm/context.py”, line 293, in orm_execute_statement
result = conn.execute(
^^^^^^^^^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/engine/base.py”, line 1416, in execute
return meth(
^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/sql/elements.py”, line 517, in _execute_on_connecti on
return connection._execute_clauseelement(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/engine/base.py”, line 1639, in _execute_clauseeleme nt
ret = self._execute_context(
^^^^^^^^^^^^^^^^^^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/engine/base.py”, line 1848, in _execute_context
return self._exec_single_context(
^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/engine/base.py”, line 1988, in _exec_single_context
self._handle_dbapi_exception(
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/engine/base.py”, line 2344, in _handle_dbapi_except ion
raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/engine/base.py”, line 1969, in _exec_single_context
self.dialect.do_execute(
File “/users/rkarkee/conda/envs/aiidaENV/lib/python3.11/site-packages/sqlalchemy/engine/default.py”, line 922, in do_execute
cursor.execute(statement, parameters)
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked
[SQL: UPDATE db_dbsetting SET val=?, time=? WHERE db_dbsetting.“key” = ?]
[parameters: (‘“2024-02-14T13:50:00.839680-07:00”’, ‘2024-02-14 13:50:00.842878’, ‘process|state_change|work’)]
(Background on this error at: [Error Messages — SQLAlchemy 2.0 Documentation](https://sqlalche.me/e/20/e3q8))
2024-02-14 20:50:00 [8 | REPORT]: [55|DielectricWorkChain|on_terminated]: remote folders will not be cleaned
2024-02-14 20:50:01 [9 | REPORT]: [50|PhononWorkChain|run_base_supercell]: launching base supercell scf PwBaseWorkChain<60>
2024-02-14 20:50:02 [10 | REPORT]: [60|PwBaseWorkChain|run_process]: launching PwCalculation<63> iteration #1
2024-02-14 20:50:02 [12 | REPORT]: [60|PwBaseWorkChain|on_terminated]: remote folders will not be cleaned
2024-02-14 20:50:02 [13 | REPORT]: [50|PhononWorkChain|inspect_base_supercell]: base supercell scf failed with exit status 301
2024-02-14 20:50:03 [14 | REPORT]: [50|PhononWorkChain|on_terminated]: remote folders will not be cleaned
2024-02-14 20:50:03 [15 | REPORT]: [44|HarmonicWorkChain|inspect_processes]: the child `PhononWorkChain` with <PK=50> failed
2024-02-14 20:50:03 [16 | REPORT]: [44|HarmonicWorkChain|on_terminated]: remote folders will not be cleaned
My inputs for this run is as follow:
I have overrides.yaml file and then a python file (see below)
%%%%%%%%%%%%% overrides.yaml %%%%%%%%%%%%%%%%
clean_workdir: false # whether to clean the working directiories
dielectric:
clean_workdir: false
kpoints_parallel_distance: 0.2 # kpoints distance in Angstrom^-1 to sample the BZ parallel to the electric field. If used, it should help in converging faster the final results
property: raman
# central_difference: # if you know what you are doing, custom numerical derivatives with respect to electric field
# accuracy: 2
# electric_field_step: 0.0005
scf:
pseudo_family: new_PBE
kpoints_distance: 0.4 # kpoints distance in Angstrom^-1 to sample the BZ
kpoints_force_parity: false
max_iterations: 5
pw:
metadata:
options:
max_wallclock_seconds: 43200
resources:
num_machines: 1
num_mpiprocs_per_machine: 256
#queue_name: standard # for SLURM
# account: account_name # for SLURM, also for project etc
withmpi: true
parameters:
ELECTRONS:
conv_thr: 2.0e-10
electron_maxstep: 100
mixing_beta: 0.2
SYSTEM:
ecutrho: 280.0
ecutwfc: 70.0
vdw_corr: Grimme-D2
settings:
sleep_submission_time: 1.0
phonon:
clean_workdir: false
displacement_generator:
distance: 0.01 # atomic displacements for phonon calculation, in Angstrom
scf:
pseudo_family: new_PBE
kpoints_distance: 0.15 # kpoints distance in Angstrom^-1 to sample the BZ
kpoints_force_parity: false
max_iterations: 5
pw:
metadata:
options:
max_wallclock_seconds: 43200
resources:
num_machines: 1
num_mpiprocs_per_machine: 1
# queue_name: partition_name # for SLURM
# account: account_name # for SLURM, also for project etc
withmpi: true
settings:
cmdline: [‘-nk’, ‘8’]
# gamma_only: True # to use only if KpointsData has only a mesh 1 1 1 0 0 0 (i.e. Gamma not shifted)
parameters:
ELECTRONS:
conv_thr: 2.0e-12
electron_maxstep: 80
mixing_beta: 0.4
SYSTEM:
ecutwfc: 70.0
ecutrho: 280
vdw_corr: Grimme-D2
settings:
sleep_submission_time: 1.0 # waiting time in seconds between different submission of SCF calculation. Recommended to be at least 1 second, to not overload.
settings:
run_parallel: true
use_primitive_cell: false
symmetry:
distinguish_kinds: false
is_symmetry: true
symprec: 1.0e-05
%%%%% submit.py %%%%%%%%%%%%%%%%%
# -*- coding: utf-8 -*-
# pylint: disable=line-too-long,wildcard-import,pointless-string-statement,unused-wildcard-import
“”“Submit an IRamanSpectraWorkChain via the get_builder_from_protocol using the overrides.”“”
from pathlib import Path
from aiida import load_profile
from aiida.engine import submit
from aiida.orm import *
from aiida_quantumespresso.common.types import ElectronicType
from aiida_vibroscopy.workflows.spectra.iraman import IRamanSpectraWorkChain
load_profile()
# =============================== INPUTS ===============================
# Please, change the following inputs.
mesh = [[4, 4, 2], [0.5, 0.5, 0.5]]
pseudo_family_name=‘pbe_psp’
pw_code_label = ‘qe-7.3@newhpc’
structure_id = 21 # PK or UUID of your AiiDA StructureData
protocol = ‘fast’ # also ‘moderate’ and ‘precise’; ‘moderate’ should be good enough in general
overrides_filepath = ‘./overrides.yaml’ # should be a path, e.g. /path/to/overrides.yaml. Format is YAML
# Consult the documentation for HOW-TO for how to use properly the overrides.
# !!! FOR FULL INPUT NESTED STRUCTURE: [IRamanSpectraWorkChain — aiida-vibroscopy 1.0.2 documentation](https://aiida-vibroscopy.readthedocs.io/en/latest/topics/workflows/spectra/iraman.html)
# You can follow the input structure provided on the website to fill further the overrides.
# ======================================================================
# If you don’t have a StructureData, but you have a CIF or XYZ, or similar, file
# you can import your structure uncommenting the following:
# from [ase.io](http://ase.io/) import read
# atoms = read(‘/path/to/file.cif’)
# structure = StructureData(ase=atoms)
# structure.store()
# structure_id = structure.pk
# print(f"Your structure has been stored in the database with PK={structure_id}")
def main():
“”“Submit an IRamanSpectraWorkChain calculation.”“”
code = load_code(pw_code_label)
structure = load_node(structure_id)
kwargs = {‘electronic_type’: ElectronicType.INSULATOR}
kpoints = KpointsData()
kpoints.set_kpoints_mesh(mesh[0], mesh[1])
#pseudo_family = load_group(pseudo_family_name)
#pseudos = pseudo_family.get_pseudos(structure=structure)
builder = IRamanSpectraWorkChain.get_builder_from_protocol(
code=code,
structure=structure,
protocol=protocol,
overrides=Path(overrides_filepath),
**kwargs,
)
builder.dielectric.scf.kpoints = kpoints
builder.dielectric.pop('kpoints_parallel_distance', None)
builder.dielectric.scf.pop('kpoints_distance', None)
builder.phonon.scf.kpoints = kpoints
#builder.dielectric.scf.pw.pseudos = pseudos
#builder.phonon.scf.pw.pseudos = pseudos
calc = submit(builder)
print(f'Submitted IRamanSpectraWorkChain with PK={calc.pk} and UUID={calc.uuid}')
print('Register *at least* the PK number, e.g. in you submit script.')
print('You can monitor the status of your calculation with the following commands:')
print(' * verdi process status PK')
print(' * verdi process list -L IRamanSpectraWorkChain # list all running IRamanSpectraWorkChain')
print(
' * verdi process list -ap1 -L IRamanSpectraWorkChain # list all IRamanSpectraWorkChain submitted in the previous 1 day'
)
print('If the WorkChain finishes with exit code 0, then you can inspect the outputs and post-process the data.')
print('Use the command')
print(' * verdi process show PK')
print('To show further information about your WorkChain. When finished, you should see some outputs.')
print('The main output can be accessed via `load_node(PK).outputs.vibrational_data.numerical_accuracy_*`.')
print('You have to complete the remaning `*`, which depends upond the accuracy of the calculation.')
print('See also the documentation and the reference paper for further details.')
if **name** == ‘**main**’:
“”“Run script.”“”
main()