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Fix problem with prematurely erased sandbox folder retrieved_temporary_folder #1168

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merged 2 commits into from
Feb 21, 2018
Merged

Fix problem with prematurely erased sandbox folder retrieved_temporary_folder #1168

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6927957
Fix problem with prematurely erased sandbox folder retrieved_temporar…
sphuber Feb 20, 2018
c9b3095
Move dummy TemplatereplacerDoublerParser to more consistent filename
sphuber Feb 20, 2018
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2 changes: 1 addition & 1 deletion .travis-data/test_daemon.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,7 +127,7 @@ def create_calculation(code, counter, inputval, use_cache=False):
calc.set_max_wallclock_seconds(5 * 60) # 5 min
calc.set_resources({"num_machines": 1})
calc.set_withmpi(False)
calc.set_parser_name('simpleplugins.templatereplacer.test.doubler')
calc.set_parser_name('simpleplugins.templatereplacer.doubler')

calc.use_parameters(parameters)
calc.use_template(template)
Expand Down
92 changes: 42 additions & 50 deletions aiida/daemon/execmanager.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,9 @@
the routines make reference to the suitable plugins for all
plugin-specific operations.
"""
import os
from backports import tempfile

from aiida.backends.utils import get_authinfo
from aiida.common.datastructures import calc_states
from aiida.scheduler.datastructures import job_states
Expand All @@ -28,13 +31,9 @@
from aiida.orm import DataFactory
from aiida.orm.data.folder import FolderData
from aiida.common.log import get_dblogger_extra
import os


# Until we fix the broken daemon logger https://github.com/aiidateam/aiida_core/issues/943
# execlogger = aiidalogger.getChild('execmanager')
import logging
execlogger = logging.getLogger('execmanager')
execlogger = aiidalogger.getChild('execmanager')


def update_running_calcs_status(authinfo):
Expand Down Expand Up @@ -694,42 +693,44 @@ def retrieve_and_parse(calc, transport=None):
logger_extra = get_dblogger_extra(calc)
transport._set_logger_extra(logger_extra)

try:
retrieved_temporary_folder = retrieve_all(calc, transport, logger_extra)
except Exception:
import traceback
with tempfile.TemporaryDirectory() as retrieved_temporary_folder:

tb = traceback.format_exc()
newextradict = logger_extra.copy()
newextradict['full_traceback'] = tb
try:
retrieve_all(calc, transport, retrieved_temporary_folder, logger_extra)
except Exception:
import traceback

execlogger.error(
"Error retrieving calc {}. Traceback: {}".format(calc.pk, tb),
extra=newextradict
)
_set_state_noraise(calc, calc_states.RETRIEVALFAILED)
return False
tb = traceback.format_exc()
newextradict = logger_extra.copy()
newextradict['full_traceback'] = tb

try:
parse_results(calc, retrieved_temporary_folder, logger_extra)
except Exception:
import traceback
execlogger.error(
"Error retrieving calc {}. Traceback: {}".format(calc.pk, tb),
extra=newextradict
)
_set_state_noraise(calc, calc_states.RETRIEVALFAILED)
return False

tb = traceback.format_exc()
newextradict = logger_extra.copy()
newextradict['full_traceback'] = tb
execlogger.error(
"Error parsing calc {}. Traceback: {}".format(calc.pk, tb),
extra=newextradict
)
# TODO: add a 'comment' to the calculation
_set_state_noraise(calc, calc_states.PARSINGFAILED)
return False
try:
parse_results(calc, retrieved_temporary_folder, logger_extra)
except Exception:
import traceback

tb = traceback.format_exc()
newextradict = logger_extra.copy()
newextradict['full_traceback'] = tb
execlogger.error(
"Error parsing calc {}. Traceback: {}".format(calc.pk, tb),
extra=newextradict
)
# TODO: add a 'comment' to the calculation
_set_state_noraise(calc, calc_states.PARSINGFAILED)
return False

return True


def retrieve_all(job, transport, logger_extra=None):
def retrieve_all(job, transport, retrieved_temporary_folder, logger_extra=None):
try:
job._set_state(calc_states.RETRIEVING)
except ModificationNotAllowed:
Expand Down Expand Up @@ -764,28 +765,23 @@ def retrieve_all(job, transport, logger_extra=None):
retrieve_singlefile_list = job._get_retrieve_singlefile_list()

with SandboxFolder() as folder:
retrieve_files_from_list(job, transport, folder, retrieve_list)
retrieve_files_from_list(job, transport, folder.abspath, retrieve_list)
# Here I retrieved everything; now I store them inside the calculation
retrieved_files.replace_with_folder(folder.abspath, overwrite=True)

# Second, retrieve the singlefiles
with SandboxFolder() as folder:
_retrieve_singlefiles(job, transport, folder, retrieve_singlefile_list, logger_extra)

# Retrieve the temporary files in a separate temporary folder if any files were
# Retrieve the temporary files in the retrieved_temporary_folder if any files were
# specified in the 'retrieve_temporary_list' key
if retrieve_temporary_list:
retrieved_temporary_folder = FolderData()
with SandboxFolder() as folder:
retrieve_files_from_list(job, transport, folder, retrieve_temporary_list)
retrieved_temporary_folder.replace_with_folder(folder.abspath, overwrite=True)
retrieve_files_from_list(job, transport, retrieved_temporary_folder, retrieve_temporary_list)

# Log the files that were retrieved in the temporary folder
for entry in retrieved_temporary_folder.get_folder_list():
for filename in os.listdir(retrieved_temporary_folder):
execlogger.debug("[retrieval of calc {}] Retrieved temporary file or folder '{}'".format(
job.pk, entry), extra=logger_extra)
else:
retrieved_temporary_folder = None
job.pk, filename), extra=logger_extra)

# Store everything
execlogger.debug(
Expand All @@ -794,8 +790,6 @@ def retrieve_all(job, transport, logger_extra=None):
extra=logger_extra)
retrieved_files.store()

return retrieved_temporary_folder


def parse_results(job, retrieved_temporary_folder=None, logger_extra=None):
job._set_state(calc_states.PARSING)
Expand Down Expand Up @@ -957,11 +951,9 @@ def retrieve_files_from_list(calculation, transport, folder, retrieve_list):
upto what level of the original remotepath nesting the files will be copied.

:param transport: the Transport instance
:param folder: a local Folder instance for the transport to store files into
:param folder: an absolute path to a folder to copy files in
:param retrieve_list: the list of files to retrieve
"""
import os

for item in retrieve_list:
if isinstance(item, list):
tmp_rname, tmp_lname, depth = item
Expand All @@ -979,7 +971,7 @@ def retrieve_files_from_list(calculation, transport, folder, retrieve_list):
if depth > 1: # create directories in the folder, if needed
for this_local_file in local_names:
new_folder = os.path.join(
folder.abspath,
folder,
os.path.split(this_local_file)[0])
if not os.path.exists(new_folder):
os.makedirs(new_folder)
Expand All @@ -993,4 +985,4 @@ def retrieve_files_from_list(calculation, transport, folder, retrieve_list):

for rem, loc in zip(remote_names, local_names):
transport.logger.debug("[retrieval of calc {}] Trying to retrieve remote item '{}'".format(calculation.pk, rem))
transport.get(rem, os.path.join(folder.abspath, loc), ignore_nonexisting=True)
transport.get(rem, os.path.join(folder, loc), ignore_nonexisting=True)
17 changes: 13 additions & 4 deletions ...rs/simpleplugins/templatereplacer/test.py → ...simpleplugins/templatereplacer/doubler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,8 @@ def parse_with_retrieved(self, retrieved):

:param retrieved: a dictionary of retrieved nodes
"""
import os

output_nodes = []

try:
Expand Down Expand Up @@ -65,18 +67,25 @@ def parse_with_retrieved(self, retrieved):
# FolderData node in the 'retrieved' arguments
if retrieve_temporary_files is not None:
try:
temporary_folder = retrieved[self.retrieved_temporary_folder_key]
retrieved_temporary_folder = retrieved[self.retrieved_temporary_folder_key]
except KeyError:
self.logger.error('the {} was not passed as an argument'.format(self.retrieved_temporary_folder_key))
return False, ()

for retrieved_file in retrieve_temporary_files:
if retrieved_file not in temporary_folder.get_folder_list():
self.logger.error('the file {} was not found in the temporary retrieved folder'.format(retrieved_file))

file_path = os.path.join(retrieved_temporary_folder, retrieved_file)

if not os.path.isfile(file_path):
self.logger.error('the file {} was not found in the temporary retrieved folder {}'
.format(retrieved_file, retrieved_temporary_folder))
return False, ()

with open(file_path, 'r') as handle:
parsed_value = handle.read().strip()

# We always strip the content of the file from whitespace to simplify testing for expected output
output_dict['retrieved_temporary_files'].append((retrieved_file, temporary_folder.get_file_content(retrieved_file).strip()))
output_dict['retrieved_temporary_files'].append((retrieved_file, parsed_value))

output_parameters = ParameterData(dict=output_dict)
output_nodes.append((self.get_linkname_outparams(), output_parameters))
Expand Down
2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@
],
'aiida.cmdline': [],
'aiida.parsers': [
'simpleplugins.templatereplacer.test.doubler = aiida.parsers.simpleplugins.templatereplacer.test:TemplatereplacerDoublerParser',
'simpleplugins.templatereplacer.doubler = aiida.parsers.simpleplugins.templatereplacer.doubler:TemplatereplacerDoublerParser',
],
'aiida.schedulers': [
'direct = aiida.scheduler.plugins.direct:DirectScheduler',
Expand Down