def retriever():
configure_logging(daemon=True, daemon_log_file=DAEMON_LOG_FILE)
from aiida.daemon.execmanager import retrieve_jobs
LOGGER.info('Checking for calculations to retrieve')
set_daemon_timestamp(task_name='retriever', when='start')
retrieve_jobs()
set_daemon_timestamp(task_name='retriever', when='stop')
def manual_tick_all():
from aiida.daemon.execmanager import submit_jobs, update_jobs, retrieve_jobs
from aiida.work.daemon import tick_workflow_engine
from aiida.daemon.workflowmanager import execute_steps
submit_jobs()
update_jobs()
retrieve_jobs()
execute_steps() # legacy workflows
tick_workflow_engine()
def retriever():
from aiida.daemon.execmanager import retrieve_jobs
print "aiida.daemon.tasks.retrieve: Checking for calculations to retrieve"
set_daemon_timestamp(task_name='retriever', when='start')
retrieve_jobs()
set_daemon_timestamp(task_name='retriever', when='stop')
def run_tests_on_calcs_with_prefixes(self, prefixes):
"""
Test immigration, retrieval, and parsing of calcs for all prefixes.
Prefixes should be a group of prefixes that refer to calculations whose
Aiida-generated input files should be identical.
:param prefixes: A group of prefixes that refer to calculations whose
Aiida-generated input files should be identical.
:type prefixes: list of str
"""
# Get the computer's transport and create instance.
Transport = self.computer.get_transport_class()
transport = Transport()
# Initialize arrays for storing data for each job.
inpt_txts = []
# Open the transport for the duration of immigrations, so it's not
# reopened for each one. This would really matter for ssh tranports.
with transport as t:
# Loop over all manual prefixes.
for prefix in prefixes:
# Define the calc's initialization parameters. These result in
# calling of the `set_` methods with the specified values.
init_params = {
'computer': self.computer,
'resources': {
'num_machines': 1,
'num_mpiprocs_per_machine': 1
},
'remote_workdir': TEST_JOB_DIR,
'input_file_name': prefix + '.in',
'output_file_name': prefix + '.out'
}
# Initialize the calculation using the `set_` methods.
calc = PwimmigrantCalculation(**init_params)
# Set the code.
calc.use_code(self.code)
# Create the input nodes.
try:
calc.create_input_nodes(t) # Open transport passed.
except Exception as error:
self.fail(
"Error creating input nodes for prefix '{}':\n{}\n\n"
"".format(prefix, error))
# Submit a test submission in a temporary directory and store
# the input file's contents. Need to do this before now,
# because calc's state is NEW.
with SandboxFolder() as folder:
# Submit test and get the subfolder containing the input
# file.
subfolder = calc.submit_test(folder, prefix)[0]
# Get the path of the input file.
inpt_path = os.path.join(subfolder.abspath, prefix + '.in')
# Open the input file, read and store it's contents.
with open(inpt_path) as f:
inpt_txts.append(f.read())
# Prepare the calc for retrieval and parsing.
calc.prepare_for_retrieval_and_parsing(transport)
# Call the daemon's retrieval function, so all immigrated calcs get
# retrieved and parsed.
try:
retrieve_jobs()
except Exception as error:
self.fail("Error during retrieval of immigrated calcs:\n{}\n\n"
"".format(error))
# Test the create_input_nodes method by comparing the input files
# generated above by the submit_test method. The first input file
# will serve as the reference.
ref_words = inpt_txts[0].split()
for txt, prefix in zip(inpt_txts[1:], prefixes[1:]):
# Loop over the words of the reference and current input files.
for w1, w2 in zip(ref_words, txt.split()):
# If the words are not the same, and the reference word is
# not the calculation's prefix parameter...
if w2 != w1 and w1.strip("'") not in prefixes:
# Try using the regex-based str2val function of
# pwinputparser to convert the word strings into python
# values.
try:
val1, val2 = [str2val(x) for x in (w1, w2)]
except Exception as error:
self.fail(
"The strings, '{}' and '{}', of the submit_test "
"input files for calcs with prefixes {} and {} "
"were not equal and could not be converted to "
"python values using the str2val function of "
"pwinputparser.\nThe exception thrown was:\n{"
"}\n\n".format(w1, w2, prefixes[0], prefix, error))
# If both values were converted to floats...
if all([type(v) is float for v in val1, val2]):
# Test if they differ by more than a specified
# tolerance.
self.assertAlmostEqual(
val1,
val2,
4,
msg="The values, {} and {}, of the submit_test "
"input files for calcs with prefixes {} and {} "
"are not within the specified number of "
"decimal places."
"".format(val1, val2, prefixes[0], prefix))
# If they weren't floats, then they should have been
# identical, so the test fails.
else:
self.assertEqual(
val1,
val2,
msg="The values, {} and {}, of the submit_test "
"input files for calcs with prefixes {} and {} "
"did not match. They should have been "
"identical!".format(val1, val2, prefixes[0],
prefix))