def setUpClass(cls):
if not MPControl.is_initialized:
MPControl.set_multiprocess_engine("local")
MPControl.connect()
DotProduct.set_mkl(True)
def set_up_dask(n_jobs=2):
MPControl.set_multiprocess_engine("dask-cluster")
MPControl.client.use_default_configuration("rusty_ccb", n_jobs=n_jobs)
MPControl.client.add_worker_conda(
"source ~/.local/anaconda3/bin/activate inferelator")
MPControl.client.add_slurm_command_line("--constraint=broadwell")
MPControl.connect()
def initialize_multiprocessing(self):
"""
Register the multiprocessing controller if set and run .connect()
"""
if self.multiprocessing_controller is not None:
MPControl.set_multiprocess_engine(self.multiprocessing_controller)
MPControl.connect()
def setUpClass(cls):
cls.tempdir = tempfile.mkdtemp()
MPControl.shutdown()
MPControl.set_multiprocess_engine(cls.name)
# Create a wrapper for LocalCluster so that the HPC controller can be tested locally
# And then bind it so that it works in py27 right
def fake_cluster(*args, **kwargs):
replace_args = dict()
replace_args["n_workers"] = kwargs.pop("n_workers", 0)
replace_args["threads_per_worker"] = kwargs.pop(
"threads_per_worker", 1)
replace_args["processes"] = kwargs.pop("processes", True)
replace_args["local_dir"] = kwargs.pop("local_directory", None)
clust = distributed.LocalCluster(**replace_args)
clust._active_worker_n = 0
def _count_active_workers(self):
val = self._active_worker_n
self._active_worker_n += 1
return val
clust._count_active_workers = types.MethodType(
_count_active_workers, clust)
return clust
MPControl.client._cluster_controller_class = types.MethodType(
fake_cluster, MPControl.client)
MPControl.client.set_job_size_params(n_jobs=1,
n_cores_per_job=1,
mem_per_job="1gb")
MPControl.client._local_directory = cls.tempdir
MPControl.connect()
def start_mpcontrol_dask(n_cores=N_CORES):
utils.Debug.set_verbose_level(1)
MPControl.set_multiprocess_engine("dask-cluster")
MPControl.client.minimum_cores = n_cores
MPControl.client.maximum_cores = n_cores
MPControl.client.walltime = '48:00:00'
MPControl.client.add_worker_env_line('module load slurm')
MPControl.client.add_worker_env_line('module load gcc/8.3.0')
MPControl.client.add_worker_env_line('source ' + CONDA_ACTIVATE_PATH)
MPControl.client.cluster_controller_options.append("-p ccb")
MPControl.connect()
def __init__(self, *args, **kwargs):
super(TestBBSRrunnerPython, self).__init__(*args, **kwargs)
# Extra behavior: only run if KVSClient can reach the host:
try:
MPControl.connect()
except Exception as e:
if str(e) == 'Missing host':
print(
'Test test_bbsr.py exiting since KVS host is not running')
print(
'Try rerunning tests with python $LOCALREPO/kvsstcp.py --execcmd "nosetests --nocapture -v"'
)
self.missing_kvs_host = True
# Mock out Slurm process IDs so that KVS can access this process ID in bbsr_python.py
os.environ['SLURM_PROCID'] = str(0)
os.environ['SLURM_NTASKS'] = str(1)
from inferelator.distributed.inferelator_mp import MPControl
MPControl.set_multiprocess_engine("local")
MPControl.connect()
def tearDownClass(cls):
MPControl.shutdown()
MPControl.set_multiprocess_engine("local")
MPControl.connect()
if cls.tempdir is not None:
shutil.rmtree(cls.tempdir)
def setUpClass(cls):
cls.tempdir = tempfile.mkdtemp()
MPControl.shutdown()
MPControl.set_multiprocess_engine("dask-local")
MPControl.connect(local_dir=cls.tempdir, n_workers=1, processes=False)
def set_up_dask(n_jobs=1):
MPControl.set_multiprocess_engine("dask-cluster")
MPControl.client.use_default_configuration("rusty_rome", n_jobs=n_jobs)
MPControl.client.add_worker_conda("source ~/.local/anaconda3/bin/activate inferelator")
MPControl.client.set_job_size_params(walltime="168:00:00")
MPControl.connect()
def setUpClass(cls):
if not MPControl.is_initialized:
MPControl.connect()
def tearDownClass(cls):
MPControl.shutdown()
MPControl.set_multiprocess_engine("local")
MPControl.connect()
def setUpClass(cls):
MPControl.shutdown()
MPControl.set_multiprocess_engine(cls.name)
MPControl.connect()
def setUpClass(cls):
cls.tempdir = tempfile.mkdtemp()
MPControl.shutdown()
MPControl.set_multiprocess_engine(cls.name)
MPControl.connect(local_dir=cls.tempdir, n_workers=1)
def setUpClass(cls):
cls.temp_dir = tempfile.mkdtemp()
cls.server = kvsstcp.KVSServer("", 0)
MPControl.shutdown()
MPControl.set_multiprocess_engine(cls.name)
MPControl.connect(host=cls.server.cinfo[0], port=cls.server.cinfo[1])
def start_mpcontrol_dask(n_cores=N_CORES):
MPControl.set_multiprocess_engine("dask-cluster")
MPControl.client.use_default_configuration("rusty_ccb", n_jobs=2)
MPControl.client.add_worker_conda(
"source /mnt/ceph/users/sysbio/.anaconda3/bin/activate inferelator")
MPControl.connect()