def immigrate_existing(builder, remote_data, seal=True):
"""Immigrate a Calculation that was not run using AiiDa.
:param builder: a populated builder instance for a CalcJob
:type builder: aiida.engine.processes.builder.ProcessBuilder
:param remote_data: a remote data folder,
containing the output files required for parsing
:type remote_data: aiida.orm.RemoteData
:param seal: whether to seal the calc node, from further attribute changes
:type seal: bool
:rtype: aiida.orm.CalcJobNode
"""
# initialise calcjob
runner = get_manager().get_runner()
pw_calc_cls = builder._process_class
process = instantiate_process(runner, pw_calc_cls, **builder)
calc_node = process.node
# prepare for submission
with SandboxFolder() as temp_folder:
calc_info = process.presubmit(temp_folder) # noqa F841
calc_node.put_object_from_tree(temp_folder.abspath, force=True)
# link remote folder to calc_node
if not remote_data.is_stored:
remote_data.store()
remote_data.add_incoming(
calc_node, link_type=LinkType.CREATE, link_label="remote_folder"
)
calc_node.set_remote_workdir(remote_data.get_remote_path())
transport = remote_data.computer.get_transport()
with SandboxFolder() as temp_retrieved:
# retrieved output files
retrieve_calculation(calc_node, transport, temp_retrieved.abspath)
# parse output
calc_node.set_state(CalcJobState.PARSING)
exit_code = process.parse(temp_retrieved.abspath)
# link outgoing nodes
process.update_outputs()
# finalise calc node
calc_node.delete_state()
calc_node.delete_checkpoint()
calc_node.set_process_state(ProcessState.FINISHED)
calc_node.set_exit_status(exit_code.status)
calc_node.set_exit_message(exit_code.message)
if seal:
calc_node.seal()
# record that the node was created via immigration
calc_node.set_extra("immigrated", True)
calc_node.set_extra("immigration_func", __name__)
return calc_node
def do_retrieve():
with transport_queue.request_transport(authinfo) as request:
transport = yield cancellable.with_interrupt(request)
# Perform the job accounting and set it on the node if successful. If the scheduler does not implement this
# still set the attribute but set it to `None`. This way we can distinguish calculation jobs for which the
# accounting was called but could not be set.
scheduler = node.computer.get_scheduler()
scheduler.set_transport(transport)
try:
detailed_job_info = scheduler.get_detailed_job_info(node.get_job_id())
except FeatureNotAvailable:
logger.info('detailed job info not available for scheduler of CalcJob<{}>'.format(node.pk))
node.set_detailed_job_info(None)
else:
node.set_detailed_job_info(detailed_job_info)
raise Return(execmanager.retrieve_calculation(node, transport, retrieved_temporary_folder))
nlcgcalc = CalculationFactory('sirius.py.nlcg')
calc = nlcgcalc(inputs)
with SandboxFolder() as sandbox_folder:
calc_info, script_filename = calc.presubmit(sandbox_folder)
calc_info.uuid = calc.node.uuid
# calc_info = calc.prepare_for_submission(folder=None)
from aiida.engine.daemon import execmanager
with computer.get_transport() as transport:
calc_info, script_filename = execmanager.upload_calculation(
calc.node, transport, calc_info, script_filename=script_filename)
# dummy submit
job_id = -1
calc.node.set_job_id(job_id)
# copy stdout to workdir instead of running the actual calculation
remote_workdir = calc.node.attributes['remote_workdir']
copyfile('sirius.py.nlcg.out',
os.path.join(remote_workdir, 'sirius.py.nlcg.out'))
calc.node.set_state(CalcJobState.RETRIEVING)
execmanager.retrieve_calculation(calc.node,
transport,
retrieved_temporary_folder=None)
calc.node.set_state(CalcJobState.PARSING)
execmanager.parse_results(calc)
for out in calc.outputs:
calc.outputs[out].store()
calc.kill()
def do_retrieve():
with transport_queue.request_transport(authinfo) as request:
transport = yield cancellable.with_interrupt(request)
raise Return(
execmanager.retrieve_calculation(node, transport,
retrieved_temporary_folder))
