Dear Users/Developers,
I have installed AiiDA and created the profile, setup the computer and pre-installed vasp code. For this, I used vasp and slurm installed locally on my workstation; vasp and slurm works fine individually. I am running AiiDA through API (5. Test a VASP run — AiiDA-VASP 3.1.0 documentation).
I have uploaded potcar files also. I have performed verdi computer and code test; they are perfectly fine. When I am launching the python script, AiiDA lauches VASP job, but it does not generate any data in the database directory. It is unable to create _aiidasubmit.sh file, _scheduler-stderr.txt or _scheduler-stdout.txt in the database directory.
import numpy as np
from aiida import load_profile
from aiida.common.extendeddicts import AttributeDict
from aiida.engine import submit
from aiida.orm import Bool, Code, Str
from aiida.plugins import DataFactory, WorkflowFactory
load_profile()
###code_to_used = load_code(128)
def get_structure():
“”"
Set up Si primitive cell
Si
5.431
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
Si
2
Direct
0.8750000000000000 0.8750000000000000 0.8750000000000000
0.1250000000000000 0.1250000000000000 0.1250000000000000
"""
structure_data = DataFactory('core.structure')
alat = 5.431
lattice = np.array([[.5, 0, .5], [.5, .5, 0], [0, .5, .5]]) * alat
structure = structure_data(cell=lattice)
for pos_direct in ([0.875, 0.875, 0.875], [0.125, 0.125, 0.125]):
pos_cartesian = np.dot(pos_direct, lattice)
structure.append_atom(position=pos_cartesian, symbols='Si')
return structure
def main(code_string, incar, kmesh, structure, potential_family, potential_mapping, options):
“”“Main method to setup the calculation.”“”
# First, we need to fetch the AiiDA datatypes which will
# house the inputs to our calculation
dict_data = DataFactory('core.dict')
kpoints_data = DataFactory('core.array.kpoints')
# Then, we set the workchain you would like to call
workchain = WorkflowFactory('vasp.vasp')
# And finally, we declare the options, settings and input containers
settings = AttributeDict()
inputs = AttributeDict()
# Organize settings
settings.parser_settings = {'output_params': ['total_energies', 'maximum_force']}
# Set inputs for the following WorkChain execution
# Set code
inputs.code = Code.get_from_string(code_string)
# Set structure
inputs.structure = structure
# Set k-points grid density
kpoints = kpoints_data()
kpoints.set_kpoints_mesh(kmesh)
inputs.kpoints = kpoints
# Set parameters
inputs.parameters = dict_data(dict=incar)
# Set potentials and their mapping
inputs.potential_family = Str(potential_family)
inputs.potential_mapping = dict_data(dict=potential_mapping)
# Set options
inputs.options = dict_data(dict=options)
# Set settings
inputs.settings = dict_data(dict=settings)
# Set workchain related inputs, in this case, give more explicit output to report
inputs.verbose = Bool(True)
# Submit the requested workchain with the supplied inputs
submit(workchain, **inputs)
if name == ‘main’:
# Code_string is chosen among the list given by ‘verdi code list’
CODE_STRING = ‘vasp-ws@workstation’
# POSCAR equivalent
# Set the silicon structure
STRUCTURE = get_structure()
# INCAR equivalent
# Set input parameters
INCAR = {'incar': {'prec': 'NORMAL', 'encut': 200, 'ediff': 1E-4, 'ialgo': 38, 'ismear': -5, 'sigma': 0.1}}
# KPOINTS equivalent
# Set kpoint mesh
KMESH = [9, 9, 9]
# POTCAR equivalent
# Potential_family is chosen among the list given by
# 'verdi data vasp-potcar listfamilies'
POTENTIAL_FAMILY = 'PBE.54'
# The potential mapping selects which potential to use, here we use the standard
# for silicon, this could for instance be {'Si': 'Si_GW'} to use the GW ready
# potential instead
POTENTIAL_MAPPING = {'Si': 'Si'}
# Jobfile equivalent
# In options, we typically set scheduler options.
# See https://aiida.readthedocs.io/projects/aiida-core/en/latest/scheduler/index.html
# AttributeDict is just a special dictionary with the extra benefit that
# you can set and get the key contents with mydict.mykey, instead of mydict['mykey']
OPTIONS = AttributeDict()
OPTIONS.account = ''
OPTIONS.qos = ''
OPTIONS.resources = {'num_machines': 1, 'tot_num_mpiprocs': 1}
OPTIONS.queue_name = 'workstation'
OPTIONS.max_wallclock_seconds = 3600
OPTIONS.max_memory_kb = 10240000
main(CODE_STRING, INCAR, KMESH, STRUCTURE, POTENTIAL_FAMILY, POTENTIAL_MAPPING, OPTIONS)
Somehow, by struggling with slurm and JobIDs, I found that AiiDA momentarily generates _aiidasubmit.sh (I grep it using scontrol show JobID as long as Slurm shows jobs’ status running). But, it vanishes including the directory “1b6f-e832-455d-82dd-1e6791ddd6be” given in the path below.
cat /home/msajjad/gautam/project/aiida/c5/dc/1b6f-e832-455d-82dd-1e6791ddd6be/_aiidasubmit.sh
#!/bin/bash
#SBATCH --no-requeue
#SBATCH --job-name=“aiida-1299”
#SBATCH --get-user-env
#SBATCH --output=_scheduler-stdout.txt
#SBATCH --error=_scheduler-stderr.txt
#SBATCH --partition=workstation
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --time=01:00:00
#SBATCH --mem=10000
source /opt/intel/oneapi/setvars.sh
‘mpirun’ ‘-np’ ‘1’ ‘/home/msajjad/gautam/software/vasp/vasp.6.2.0/bin/vasp_std’ > ‘vasp_output’ 2>&1
I took this job script, and tried running vasp calculation with it separately, it runs fine. But, AiiDA is unable to produce any results.
Please suggest me what could be the issue here. I would grateful to you.
With Regards,
Gautam Sharma,
Postdoctoral fellow,
Khalifa University of Science and Technology,
Abu Dhabi, UAE.