Python run_xenon Examples

Example #1

def test_xenon_42_multi():
    A = add(1, 1)
    B = sub(3, A)

    multiples = [mul(add(i, B), A) for i in range(6)]
    C = schedule(sum)(gather_all(multiples))

    machine = Machine(
        scheduler_adaptor='slurm',
        location='ssh://fs0.das5.cs.vu.nl/home/jhidding',
        credential=xenon.CertificateCredential(
            username='******', certfile='/home/johannes/.ssh/id_rsa'),
        jobs_properties={
            'xenon.adaptors.schedulers.ssh.strictHostKeyChecking': 'false'
        })
    worker_config = XenonJobConfig(
        prefix=Path('/home/jhidding/.local/share/workon/mcfly'),
        working_dir='/home/jhidding/',
        time_out=1000000000000,
        verbose=False)  # , options=['-C', 'TitanX', '--gres=gpu:1'])

    result = run_xenon(C,
                       machine=machine,
                       worker_config=worker_config,
                       n_processes=2)

    print("The answer is:", result)

Example #2

File: test_numpy.py Project: NLeSC/noodles

def run(wf):
    xenon_config = XenonConfig(
        jobs_scheme='local'
    )

    job_config = RemoteJobConfig(
        registry=registry,
        time_out=1000
    )

    with XenonKeeper() as Xe, NCDisplay() as display:
        result = run_xenon(
            wf, Xe, "cache.json", 2, xenon_config, job_config,
            display=display, deref=True)

    return result

Example #3

File: test_run_xenon.py Project: romulogoncalves/noodles

def test_xenon_42_multi(xenon_server):
    A = add(1, 1)
    B = sub(3, A)

    multiples = [mul(add(i, B), A) for i in range(6)]
    C = schedule(sum)(gather_all(multiples))

    machine = Machine()
    worker_config = XenonJobConfig(queue_name='multi', verbose=True)

    result = run_xenon(C,
                       machine=machine,
                       worker_config=worker_config,
                       n_processes=2)

    assert (result == 42)

Example #4

File: test_xenon_local.py Project: cwmeijer/noodles

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)

Example #5

File: test_xenon_local.py Project: NLeSC/noodles

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)

Example #6

File: linear_TS_xenon.py Project: miroi/qmworks

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
r1 = mol.atoms[0].coords
r2 = mol.atoms[4].coords

print("TS Bond distance:", bond_distance(r1, r2))
print("TS Energy:", ts.energy)