def call_xenon(job,
n_processes=1,
cache="cache.json",
user_name="x2sun",
adapter="slurm",
queue_name=None,
host_name="cartesius.surfsara.nl",
workdir=None,
timeout=60000,
**kwargs):
"""
See :
https://github.com/NLeSC/Xenon-examples/raw/master/doc/tutorial/xenon-tutorial.pdf
"""
dict_properties = {
"slurm": {
"xenon.adaptors.slurm.ignore.version": "true"
},
"pbs": {
"xenon.adaptors.pbs.ignore.version": "true"
},
}
with XenonKeeper(log_level="DEBUG") as Xe:
certificate = Xe.credentials.newCertificateCredential(
"ssh", os.environ["HOME"] + "/.ssh/id_rsa", user_name, "", None)
xenon_config = XenonConfig(
jobs_scheme=adapter,
location=host_name,
credential=certificate,
jobs_properties=dict_properties[adapter],
)
print(xenon_config.__dict__)
if workdir is None:
workdir = "/home/" + user_name
job_config = RemoteJobConfig(
registry=registry,
init=plams.init,
finish=plams.finish,
queue=queue_name,
time_out=timeout,
working_dir=workdir,
)
with NCDisplay() as display:
result = run_xenon_prov(job,
Xe,
cache,
n_processes,
xenon_config,
job_config,
display=display)
return result
def test_ssh_job_submission():
with XenonKeeper() as x:
certificate = x.credentials.newCertificateCredential(
'ssh', path + '/id_rsa', 'joe', '', None)
config = XenonConfig(jobs_scheme='ssh',
location='0.0.0.0:10022',
credential=certificate)
perform_submission(x, config)
def test_slurm_job_submission():
with XenonKeeper() as x:
certificate = x.credentials.newCertificateCredential(
'ssh', path + '/id_rsa', 'joe', '', None)
config = XenonConfig(
jobs_scheme='slurm',
location='0.0.0.0:10022',
credential=certificate,
jobs_properties={'xenon.adaptors.slurm.ignore.version': 'true'})
perform_submission(x, config)
def call_xenon(job,
n_processes=1,
cache='cache.json',
user_name='x2sun',
adapter='slurm',
queue_name=None,
host_name='cartesius.surfsara.nl',
workdir=None,
timeout=60000,
**kwargs):
"""
See :
https://github.com/NLeSC/Xenon-examples/raw/master/doc/tutorial/xenon-tutorial.pdf
"""
dict_properties = {
'slurm': {
'xenon.adaptors.slurm.ignore.version': 'true'
},
'pbs': {
'xenon.adaptors.pbs.ignore.version': 'true'
}
}
with XenonKeeper(log_level='DEBUG') as Xe:
certificate = Xe.credentials.newCertificateCredential(
'ssh', os.environ["HOME"] + '/.ssh/id_rsa', user_name, '', None)
xenon_config = XenonConfig(jobs_scheme=adapter,
location=host_name,
credential=certificate,
jobs_properties=dict_properties[adapter])
print(xenon_config.__dict__)
if workdir is None:
workdir = '/home/' + user_name
job_config = RemoteJobConfig(registry=registry,
init=plams.init,
finish=plams.finish,
queue=queue_name,
time_out=timeout,
working_dir=workdir)
with NCDisplay() as display:
result = run_xenon_prov(job,
Xe,
cache,
n_processes,
xenon_config,
job_config,
display=display)
return result
def test_xenon_42():
A = log_add(1, 1)
B = sub(3, A)
multiples = [mul(log_add(i, B), A) for i in range(6)]
C = accumulate(noodles.gather(*multiples))
xenon_config = XenonConfig(jobs_scheme='local')
job_config = RemoteJobConfig(registry=serial.base, time_out=1000)
with XenonKeeper() as Xe, NCDisplay() as display:
result = run_xenon(C,
Xe,
"cache.json",
2,
xenon_config,
job_config,
display=display)
assert (result == 42)
# returns a set of results object containing the output of
# each point in the scan
lt = PES_scan([dftb, adf], settings, cnc, scan)
# Gets the object presenting the molecule
# with the maximum energy calculated from the scan
apprTS = select_max(lt, "energy")
# Run the TS optimization, using the default TS template
workflow = adf(templates.ts.overlay(settings), apprTS.molecule)
from noodles.run.xenon import (XenonKeeper, XenonConfig, RemoteJobConfig,
run_xenon)
with XenonKeeper() as Xe:
xenon_config = XenonConfig(jobs_scheme='slurm', location=None)
job_config = RemoteJobConfig(
registry=registry,
prefix='/home/jhidding/venv',
# the working_dir should exist and contain a file called worker.sh
working_dir='/home/jhidding/qm-test',
init=init,
finish=finish,
time_out=1)
ts = run_xenon(Xe, 1, xenon_config, job_config, workflow)
# Retrieve the molecular coordinates
mol = ts.molecule