HI all,
I am trying to run aiida-vibroscopy but ran into this error.
aiidaENV) rkarkee@ch-fe1:/lustre/scratch5/rkarkee> verdi process report 189
2024-03-04 16:18:58 [91 | REPORT]: [189|IRamanSpectraWorkChain|run_spectra]: submitting `HarmonicWorkChain` <PK=191>
2024-03-04 16:19:00 [92 | REPORT]: [191|HarmonicWorkChain|run_phonon]: submitting `PhononWorkChain` <PK=197>
2024-03-04 16:19:00 [93 | REPORT]: [191|HarmonicWorkChain|run_dielectric]: submitting `DielectricWorkChain` <PK=201>
2024-03-04 16:19:01 [94 | REPORT]: [201|DielectricWorkChain|run_base_scf]: launching base scf PwBaseWorkChain<208>
2024-03-04 16:19:01 [95 | REPORT]: [197|PhononWorkChain|run_base_supercell]: launching base supercell scf PwBaseWorkChain<210>
2024-03-04 16:19:02 [96 | REPORT]: [210|PwBaseWorkChain|run_process]: launching PwCalculation<213> iteration #1
2024-03-04 16:19:02 [97 | REPORT]: [208|PwBaseWorkChain|run_process]: launching PwCalculation<216> iteration #1
2024-03-04 16:19:47 [102 | REPORT]: [208|PwBaseWorkChain|report_error_handled]: PwCalculation<216> failed with exit status 305: Both the stdout and XML output files could not be read or parsed.
2024-03-04 16:19:47 [103 | REPORT]: [208|PwBaseWorkChain|report_error_handled]: Action taken: unrecoverable error, aborting...
2024-03-04 16:19:48 [104 | REPORT]: [208|PwBaseWorkChain|inspect_process]: PwCalculation<216> failed but a handler detected an unrecoverable problem, aborting
2024-03-04 16:19:48 [105 | REPORT]: [208|PwBaseWorkChain|on_terminated]: remote folders will not be cleaned
2024-03-04 16:19:48 [106 | REPORT]: [201|DielectricWorkChain|inspect_base_scf]: base scf failed with exit status 300
2024-03-04 16:19:48 [107 | REPORT]: [201|DielectricWorkChain|on_terminated]: remote folders will not be cleaned
2024-03-04 16:19:58 [112 | REPORT]: [210|PwBaseWorkChain|report_error_handled]: PwCalculation<213> failed with exit status 305: Both the stdout and XML output files could not be read or parsed.
2024-03-04 16:19:58 [113 | REPORT]: [210|PwBaseWorkChain|report_error_handled]: Action taken: unrecoverable error, aborting...
2024-03-04 16:19:58 [114 | REPORT]: [210|PwBaseWorkChain|inspect_process]: PwCalculation<213> failed but a handler detected an unrecoverable problem, aborting
2024-03-04 16:19:59 [115 | REPORT]: [210|PwBaseWorkChain|on_terminated]: remote folders will not be cleaned
2024-03-04 16:19:59 [116 | REPORT]: [197|PhononWorkChain|inspect_base_supercell]: base supercell scf failed with exit status 300
2024-03-04 16:19:59 [117 | REPORT]: [197|PhononWorkChain|on_terminated]: remote folders will not be cleaned
2024-03-04 16:19:59 [118 | REPORT]: [191|HarmonicWorkChain|inspect_processes]: the child `PhononWorkChain` with <PK=197> failed
2024-03-04 16:19:59 [119 | REPORT]: [191|HarmonicWorkChain|on_terminated]: remote folders will not be cleaned
2024-03-04 16:19:59 [120 | REPORT]: [189|IRamanSpectraWorkChain|inspect_process]: `HarmonicWorkChain` failed with exit status 400
I am using overrides.yaml as
aiidaENV) rkarkee@ch-fe1:~> less 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: PBE_PSP_new
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
settings:
cmdline: ['-pd', '.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: PBE_PSP_new
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: ['-pd', '.true.']
# 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
and submitting the job via
# -*- 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_new'
pw_code_label = 'qe-7.3@hpc'
structure_id = 4 # 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: 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 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()
I am running in HPC. I have created a code.yaml and configured.
label: 'qe-7.3'
description: 'quantum_espresso v7.3'
default_calc_job_plugin: 'quantumespresso.pw'
filepath_executable: '/users/rkarkee/q-e-qe-7.3/bin/pw.x'
computer: 'hpc'
prepend_text: |
module swap PrgEnv-cray PrgEnv-intel
module load cmake
append_text: ' '
I’ve installed aiida via conda environment. The status looks following:
(aiidaENV) rkarkee@ch-fe1:~> verdi status
✔ version: AiiDA v2.5.1
✔ config: /users/rkarkee/.aiida
✔ profile: quicksetup
✔ storage: Storage for 'quicksetup' [open] @ postgresql://aiida_qs_rkarkee_20554bcc4bead70a3479c4ef8d5f1f4e:***@localhost:5434/quicksetup_rkarkee_20554bcc4bead70a3479c4ef8d5f1f4e / DiskObjectStoreRepository: 983ccf2a46b74550938fdb7753c1117f | /users/rkarkee/.aiida/repository/quicksetup/container
✔ rabbitmq: Connected to RabbitMQ v3.8.14 as amqp://guest:guest@127.0.0.1:5672?heartbeat=600
✔ daemon: Daemon is running with PID 242406
Can you please help me resolve this issue?
Thanks
Best
Rijan