def test_prepare_inputs_with_eeg_monitor(self, operation_factory,
simulator_factory,
surface_index_factory,
sensors_index_factory,
region_mapping_index_factory,
connectivity_index_factory):
surface_idx, surface = surface_index_factory(cortical=True)
sensors_idx, sensors = sensors_index_factory()
proj = ProjectionSurfaceEEG(sensors=sensors,
sources=surface,
projection_data=numpy.ones(3))
op = operation_factory()
storage_path = FilesHelper().get_project_folder(op.project, str(op.id))
prj_db_db = h5.store_complete(proj, storage_path)
prj_db_db.fk_from_operation = op.id
dao.store_entity(prj_db_db)
connectivity = connectivity_index_factory(76, op)
rm_index = region_mapping_index_factory(conn_gid=connectivity.gid,
surface_gid=surface_idx.gid)
eeg_monitor = EEGViewModel(projection=proj.gid, sensors=sensors.gid)
eeg_monitor.region_mapping = rm_index.gid
sim_folder, sim_gid = simulator_factory(op=op,
monitor=eeg_monitor,
conn_gid=connectivity.gid)
hpc_client = HPCSchedulerClient()
input_files = hpc_client._prepare_input(op, sim_gid)
assert len(input_files) == 11
def _operation_finished(operation, simulator_gid):
op_ident = dao.get_operation_process_for_operation(operation.id)
# TODO: Handle login
job = Job(
Transport(os.environ[HPCSchedulerClient.CSCS_LOGIN_TOKEN_ENV_KEY]),
op_ident.job_id)
operation = dao.get_operation_by_id(operation.id)
folder = HPCSchedulerClient.storage_interface.get_project_folder(
operation.project.name)
storage_interface = StorageInterface()
if storage_interface.encryption_enabled():
storage_interface.inc_project_usage_count(folder)
storage_interface.sync_folders(folder)
try:
sim_h5_filenames, metric_op, metric_h5_filename = \
HPCSchedulerClient.stage_out_to_operation_folder(job.working_dir, operation, simulator_gid)
operation.mark_complete(STATUS_FINISHED)
dao.store_entity(operation)
HPCSchedulerClient().update_db_with_results(
operation, sim_h5_filenames, metric_op, metric_h5_filename)
except OperationException as exception:
HPCOperationService.LOGGER.error(exception)
HPCOperationService._operation_error(operation)
finally:
if storage_interface.encryption_enabled():
storage_interface.sync_folders(folder)
storage_interface.set_project_inactive(operation.project)
def test_prepare_inputs(self, operation_factory, simulator_factory):
op = operation_factory(test_user=self.test_user,
test_project=self.test_project)
sim_folder, sim_gid = simulator_factory(op=op)
hpc_client = HPCSchedulerClient()
input_files = hpc_client._prepare_input(op, sim_gid)
assert len(input_files) == 6
def _operation_finished(operation, simulator_gid):
op_ident = dao.get_operation_process_for_operation(operation.id)
# TODO: Handle login
job = Job(
Transport(os.environ[HPCSchedulerClient.CSCS_LOGIN_TOKEN_ENV_KEY]),
op_ident.job_id)
sim_h5_filenames, metric_op, metric_h5_filename = \
HPCSchedulerClient.stage_out_to_operation_folder(job.working_dir, operation, simulator_gid)
operation.mark_complete(STATUS_FINISHED)
dao.store_entity(operation)
HPCSchedulerClient().update_db_with_results(operation,
sim_h5_filenames,
metric_op,
metric_h5_filename)
def test_stage_out_to_operation_folder(self, mocker, operation_factory,
simulator_factory,
pse_burst_configuration_factory):
burst = pse_burst_configuration_factory(self.test_project)
op = operation_factory(test_user=self.test_user,
test_project=self.test_project)
op.fk_operation_group = burst.fk_operation_group
dao.store_entity(op)
sim_folder, sim_gid = simulator_factory(op=op)
burst.simulator_gid = sim_gid.hex
dao.store_entity(burst)
output_path = self._do_operation_launch(op,
sim_gid,
mocker,
is_pse=True)
def _stage_out_dummy(dir, sim_gid):
return [
os.path.join(output_path, enc_file)
for enc_file in os.listdir(output_path)
]
mocker.patch.object(HPCSchedulerClient, '_stage_out_results',
_stage_out_dummy)
sim_results_files, metric_op, metric_file = HPCSchedulerClient.stage_out_to_operation_folder(
None, op, sim_gid)
assert op.id != metric_op.id
assert os.path.exists(metric_file)
assert len(sim_results_files) == 1
assert os.path.exists(sim_results_files[0])
def _do_operation_launch(self, op, sim_gid, mocker, is_pse=False):
# Prepare encrypted dir
self.encryption_handler = EncryptionHandler(sim_gid)
job_encrypted_inputs = HPCSchedulerClient()._prepare_input(op, sim_gid)
self.encryption_handler.encrypt_inputs(job_encrypted_inputs)
encrypted_dir = self.encryption_handler.get_encrypted_dir()
mocker.patch('tvb.core.operation_hpc_launcher._request_passfile',
_request_passfile_dummy)
mocker.patch(
'tvb.core.operation_hpc_launcher._update_operation_status',
_update_operation_status)
# Call do_operation_launch similarly to CSCS env
plain_dir = self.files_helper.get_project_folder(
self.test_project, 'plain')
do_operation_launch(sim_gid.hex, 1000, is_pse, '', op.id, plain_dir)
assert len(os.listdir(encrypted_dir)) == 7
output_path = os.path.join(encrypted_dir,
HPCSimulatorAdapter.OUTPUT_FOLDER)
assert os.path.exists(output_path)
expected_files = 2
if is_pse:
expected_files = 3
assert len(os.listdir(output_path)) == expected_files
return output_path
def _get_backend_client():
# type: () -> BackendClient
if TvbProfile.current.hpc.IS_HPC_RUN:
# Return an entity capable to submit jobs to HPC.
return HPCSchedulerClient()
if TvbProfile.current.cluster.IS_DEPLOY:
# Return an entity capable to submit jobs to the cluster.
return ClusterSchedulerClient()
# Return a thread launcher.
return StandAloneClient()
def _get_backend_client():
# type: () -> BackendClient
if TvbProfile.current.hpc.IS_HPC_RUN:
if not TvbProfile.current.hpc.CAN_RUN_HPC:
raise InvalidSettingsException(
"We can not enable HPC run. Most probably pyunicore is not installed!"
)
# Return an entity capable to submit jobs to HPC.
return HPCSchedulerClient()
if TvbProfile.current.cluster.IS_DEPLOY:
# Return an entity capable to submit jobs to the cluster.
return ClusterSchedulerClient()
# Return a thread launcher.
return StandAloneClient()
def _get_backend_client(adapter_instance):
# type: (ABCAdapter) -> BackendClient
# For the moment run only simulations on HPC
if TvbProfile.current.hpc.IS_HPC_RUN and type(adapter_instance) is get_class_by_name(
"{}.{}".format(SIMULATOR_MODULE, SIMULATOR_CLASS)):
if not TvbProfile.current.hpc.CAN_RUN_HPC:
raise InvalidSettingsException("We can not enable HPC run. Most probably pyunicore is not installed!")
# Return an entity capable to submit jobs to HPC.
return HPCSchedulerClient()
if TvbProfile.current.cluster.IS_DEPLOY:
# Return an entity capable to submit jobs to the cluster.
return ClusterSchedulerClient()
# Return a thread launcher.
return StandAloneClient()