def setUpModule():
global WARNING_CONTEXT
global PROVIDER
global TEMPDIR
global KEYPATH
WARNING_CONTEXT = warnings.catch_warnings()
WARNING_CONTEXT.__enter__()
warnings.simplefilter('ignore', ResourceWarning)
PROVIDER = DummySlurmBackend(n_workers=5, staging_dir=STAGING_DIR)
PROVIDER.__enter__()
TEMPDIR = tempfile.TemporaryDirectory()
KEYPATH = os.path.join(TEMPDIR.name, 'id_rsa')
subprocess.check_call(
'ssh-keygen -q -b 2048 -t rsa -f {} -N ""'.format(KEYPATH), shell=True)
subprocess.check_call('docker exec {} mkdir -p -m 600 /root/.shh'.format(
PROVIDER.controller.short_id),
shell=True)
subprocess.check_call('docker cp {}.pub {}:/root/tmpkey'.format(
KEYPATH, PROVIDER.controller.short_id),
shell=True)
subprocess.check_call(
'docker exec {} bash -c "cat /root/tmpkey >> /root/.ssh/authorized_keys"'
.format(PROVIDER.controller.short_id),
shell=True)
subprocess.check_call(
'docker exec {} chown root:root /root/.ssh/authorized_keys'.format(
PROVIDER.controller.short_id),
shell=True)
def setUpModule():
global WARNING_CONTEXT
global BACKEND
WARNING_CONTEXT = warnings.catch_warnings()
WARNING_CONTEXT.__enter__()
warnings.simplefilter('ignore', ResourceWarning)
BACKEND = DummySlurmBackend(n_workers=1, staging_dir=STAGING_DIR)
BACKEND.__enter__()
def setUpModule():
global WARNING_CONTEXT
global BACKEND
WARNING_CONTEXT = warnings.catch_warnings()
WARNING_CONTEXT.__enter__()
warnings.simplefilter('ignore', ResourceWarning)
BACKEND = DummySlurmBackend(n_workers=1, staging_dir=STAGING_DIR)
BACKEND.__enter__()
with BACKEND.transport() as transport:
if not transport.isdir(BACKEND.bind_path.name):
if not transport.isdir(os.path.dirname(BACKEND.bind_path.name)):
transport.makedirs(os.path.dirname(BACKEND.bind_path.name))
transport.mklink('/mnt/nfs', BACKEND.bind_path.name)
def test_container_invokation(self):
"""
Tests that commands can be invoked in a container
"""
container = self.dkr.containers.run('gcr.io/broad-cga-aarong-gtex/slurmind', '/bin/bash', detach=True, tty=True)
self.assertIsInstance(container, docker.models.containers.Container)
callback = DummySlurmBackend.exec_run(container, 'ls')
self.assertTrue(callable(callback))
result = callback()
self.assertEqual(result.exit_code, 0)
self.assertEqual(
result.output,
b'bin\nboot\nconf_templates\ncontroller.py\ndev\netc\ngcsdk\nhome'
b'\nlib\nlib32\nlib64\nlibx32\nmedia\nmnt\nopt\nproc\nroot\nrun'
b'\nsbin\nsrv\nsys\ntmp\nusr\nvar\nworker.sh\n'
)
container.stop(timeout=1)
def test_xargs(self):
"""
Runs a quick test of the xargs orchestrator
"""
with DummySlurmBackend(n_workers=1,
staging_dir=STAGING_DIR) as backend:
with backend.transport() as transport:
transport.sendtree(
os.path.dirname(os.path.dirname(
os.path.dirname(__file__))), '/opt/canine')
rc, stdout, stderr = backend.invoke(
"bash -c 'pip3 install -e /opt/canine && pip3 install pyopenssl; echo foo | canine-xargs -d /mnt/nfs echo @'"
)
self.assertFalse(rc)
time.sleep(5)
sacct = backend.sacct()
self.assertIn('2_0', sacct.index.values)
self.assertTrue((sacct['ExitCode'] == '0:0').all())
with backend.transport() as transport:
self.assertTrue(transport.isfile('/mnt/nfs/2.0.stdout'))
with transport.open('/mnt/nfs/2.0.stdout', 'r') as r:
self.assertEqual(r.read().strip(), 'foo')
def setUpClass(cls):
cls.backend = DummySlurmBackend(n_workers=5, staging_dir=STAGING_DIR)
cls.backend.__enter__()