import json
import os
import shutil
from config import base_path, data_path
from multiarea_model.default_params import nested_update, sim_params
try:
from multiarea_model.sumatra_helpers import register_record
sumatra_found = True
except ImportError:
sumatra_found = False
def start_job(label, submit_cmd, jobscript_template, sumatra=False, reason=None, tag=None):
"""
Start job on a compute cluster.
Parameters
----------
label : str
Simulation label identifying the simulation to be run.
The function loads all necessary files from the subfolder
identified by the label.
submit_cmd : str
Submit command of the queueing system used.
jobscript_template : formatted str
Formatted string defining the template for the job script.
Can include the following keyword arguments:
sim_dir : str
Directory of the simulation
label : str
Simulation label
num_processes : int
Total number of MPI processes, defined in sim_params
local_num_threads : int
Number of OpenMP threads per MPI process, defined in sim_params
base_path : str
Base path of the library defined in config.py
"""
# Copy run_simulation script to simulation folder
shutil.copy2(os.path.join(base_path, 'run_simulation.py'),
os.path.join(data_path, label))
# Load simulation parameters
fn = os.path.join(data_path,
label,
'_'.join(('custom_params',
label)))
with open(fn, 'r') as f:
custom_params = json.load(f)
nested_update(sim_params, custom_params['sim_params'])
# Copy custom param file for each MPI process
for i in range(sim_params['num_processes']):
shutil.copy(fn, '_'.join((fn, str(i))))
# Collect relevant arguments for job script
num_vp = sim_params['num_processes'] * sim_params[
'local_num_threads']
d = {'label': label,
'network_label': custom_params['network_label'],
'base_path': base_path,
'sim_dir': os.path.join(data_path, label),
'local_num_threads': sim_params['local_num_threads'],
'num_processes': sim_params['num_processes'],
'num_vp': num_vp}
# Write job script
job_script_fn = os.path.join(data_path,
label,
'_'.join(('job_script',
'.'.join((label, 'sh')))))
with open(job_script_fn, 'w') as f:
f.write(jobscript_template.format(**d))
# If chosen, register simulation to sumatra
if sumatra:
if sumatra_found:
register_record(label, reason=reason, tag=tag)
else:
raise ImportWarning('Sumatra is not installed, so'
'cannot register simulation record.')
# Submit job
os.system('{submit_cmd} {job_script_fn}'.format(submit_cmd=submit_cmd,
job_script_fn=job_script_fn))