# -*- coding: utf-8 -*-
"""
This file contains the main routines to submit, check and retrieve calculation
results. These are general and contain only the main logic; where appropriate,
the routines make reference to the suitable plugins for all
plugin-specific operations.
"""
from django.core.exceptions import ObjectDoesNotExist, MultipleObjectsReturned
from aiida.common.datastructures import calc_states
from aiida.scheduler.datastructures import job_states
from aiida.common.exceptions import (
AuthenticationError,
ConfigurationError,
ModificationNotAllowed,
)
from aiida.common import aiidalogger
__copyright__ = u"Copyright (c), 2015, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland and ROBERT BOSCH LLC, USA. All rights reserved."
__license__ = "MIT license, see LICENSE.txt file"
__version__ = "0.4.1"
__contributors__ = "Andrea Cepellotti, Giovanni Pizzi, Marco Dorigo, Marco Gibertini, Nicolas Mounet, Riccardo Sabatini"
execlogger = aiidalogger.getChild('execmanager')
[docs]def update_running_calcs_status(authinfo):
"""
Update the states of calculations in WITHSCHEDULER status belonging
to user and machine as defined in the 'dbauthinfo' table.
"""
from aiida.orm import JobCalculation, Computer
from aiida.scheduler.datastructures import JobInfo
from aiida.djsite.utils import get_dblogger_extra
if not authinfo.enabled:
return
execlogger.debug("Updating running calc status for user {} "
"and machine {}".format(
authinfo.aiidauser.email, authinfo.dbcomputer.name))
# This returns an iterator over aiida JobCalculation objects
calcs_to_inquire = JobCalculation._get_all_with_state(
state=calc_states.WITHSCHEDULER,
computer=authinfo.dbcomputer,
user=authinfo.aiidauser)
# NOTE: no further check is done that machine and
# aiidauser are correct for each calc in calcs
s = Computer(dbcomputer=authinfo.dbcomputer).get_scheduler()
t = authinfo.get_transport()
computed = []
# I avoid to open an ssh connection if there are
# no calcs with state WITHSCHEDULER
if len(calcs_to_inquire):
jobids_to_inquire = [str(c.get_job_id()) for c in calcs_to_inquire]
# Open connection
with t:
s.set_transport(t)
# TODO: Check if we are ok with filtering by job (to make this work,
# I had to remove the check on the retval for getJobs,
# because if the job has computed and is not in the output of
# qstat, it gives a nonzero retval)
# TODO: catch SchedulerError exception and do something
# sensible (at least, skip this computer but continue with
# following ones, and set a counter; set calculations to
# UNKNOWN after a while?
if s.get_feature('can_query_by_user'):
found_jobs = s.getJobs(user="$USER", as_dict = True)
else:
found_jobs = s.getJobs(jobs=jobids_to_inquire, as_dict = True)
# I update the status of jobs
for c in calcs_to_inquire:
try:
logger_extra = get_dblogger_extra(c)
t._set_logger_extra(logger_extra)
jobid = c.get_job_id()
if jobid is None:
execlogger.error("JobCalculation {} is WITHSCHEDULER "
"but no job id was found!".format(
c.pk), extra=logger_extra)
continue
# I check if the calculation to be checked (c)
# is in the output of qstat
if jobid in found_jobs:
# jobinfo: the information returned by
# qstat for this job
jobinfo = found_jobs[jobid]
execlogger.debug("Inquirying calculation {} (jobid "
"{}): it has job_state={}".format(
c.pk, jobid, jobinfo.job_state), extra=logger_extra)
# For the moment, FAILED is not defined
if jobinfo.job_state in [job_states.DONE]: #, job_states.FAILED]:
computed.append(c)
try:
c._set_state(calc_states.COMPUTED)
except ModificationNotAllowed:
# Someone already set it, just skip
pass
elif jobinfo.job_state == job_states.UNDETERMINED:
#try:
# c._set_state(calc_states.UNDETERMINED)
#except ModificationNotAllowed:
# # Someone already set it, just skip
# pass
#execlogger.error("There is an undetermined calc "
# "with pk {}".format(
# c.pk), extra=logger_extra)
## Do not do anything! If it changes back to a
## valid state, that the state ordering would not
## work, and moreover it risks to go back to a
## valid WITHSCHEDULER STATE.
pass
## Do not set the WITHSCHEDULER state multiple times,
## this would raise a ModificationNotAllowed
#else:
# c._set_state(calc_states.WITHSCHEDULER)
c._set_scheduler_state(jobinfo.job_state)
c._set_last_jobinfo(jobinfo)
else:
execlogger.debug("Inquirying calculation {} (jobid "
"{}): not found, assuming "
"job_state={}".format(
c.pk, jobid, job_states.DONE), extra=logger_extra)
# calculation c is not found in the output of qstat
computed.append(c)
c._set_scheduler_state(job_states.DONE)
except Exception as e:
# TODO: implement a counter, after N retrials
# set it to a status that
# requires the user intervention
execlogger.warning("There was an exception for "
"calculation {} ({}): {}".format(
c.pk, e.__class__.__name__, e.message),
extra=logger_extra)
continue
for c in computed:
try:
logger_extra = get_dblogger_extra(c)
try:
detailed_jobinfo = s.get_detailed_jobinfo(
jobid=c.get_job_id())
except NotImplementedError:
detailed_jobinfo = (
u"AiiDA MESSAGE: This scheduler does not implement "
u"the routine get_detailed_jobinfo to retrieve "
u"the information on "
u"a job after it has finished.")
last_jobinfo = c._get_last_jobinfo()
if last_jobinfo is None:
last_jobinfo = JobInfo()
last_jobinfo.job_id = c.get_job_id()
last_jobinfo.job_state = job_states.DONE
last_jobinfo.detailedJobinfo = detailed_jobinfo
c._set_last_jobinfo(last_jobinfo)
except Exception as e:
execlogger.warning("There was an exception while "
"retrieving the detailed jobinfo "
"for calculation {} ({}): {}".format(
c.pk, e.__class__.__name__, e.message),
extra=logger_extra)
continue
finally:
# Set the state to COMPUTED as the very last thing
# of this routine; no further change should be done after
# this, so that in general the retriever can just
# poll for this state, if we want to.
try:
c._set_state(calc_states.COMPUTED)
except ModificationNotAllowed:
# Someone already set it, just skip
pass
return computed
[docs]def get_authinfo(computer, aiidauser):
from aiida.djsite.db.models import DbComputer, DbAuthInfo
try:
authinfo = DbAuthInfo.objects.get(
# converts from name, Computer or DbComputer instance to
# a DbComputer instance
dbcomputer=DbComputer.get_dbcomputer(computer),
aiidauser=aiidauser)
except ObjectDoesNotExist:
raise AuthenticationError(
"The aiida user {} is not configured to use computer {}".format(
aiidauser.email, computer.name))
except MultipleObjectsReturned:
raise ConfigurationError(
"The aiida user {} is configured more than once to use "
"computer {}! Only one configuration is allowed".format(
aiidauser.email, computer.name))
return authinfo
[docs]def retrieve_jobs():
from aiida.orm import JobCalculation, Computer
from aiida.djsite.db.models import DbComputer, DbUser
# I create a unique set of pairs (computer, aiidauser)
computers_users_to_check = set(
JobCalculation._get_all_with_state(
state=calc_states.COMPUTED,
only_computer_user_pairs = True)
)
for dbcomputer_id, aiidauser_id in computers_users_to_check:
dbcomputer = DbComputer.objects.get(id=dbcomputer_id)
if not Computer(dbcomputer=dbcomputer).is_enabled():
continue
aiidauser = DbUser.objects.get(id=aiidauser_id)
execlogger.debug("({},{}) pair to check".format(
aiidauser.email, dbcomputer.name))
try:
authinfo = get_authinfo(dbcomputer, aiidauser)
retrieve_computed_for_authinfo(authinfo)
except Exception as e:
msg = ("Error while retrieving calculation status for "
"aiidauser={} on computer={}, "
"error type is {}, error message: {}".format(
aiidauser.email,
dbcomputer.name,
e.__class__.__name__, e.message))
execlogger.error(msg)
# Continue with next computer
continue
# in daemon
[docs]def update_jobs():
"""
calls an update for each set of pairs (machine, aiidauser)
"""
from aiida.orm import JobCalculation, Computer
from aiida.djsite.db.models import DbComputer, DbUser
# I create a unique set of pairs (computer, aiidauser)
computers_users_to_check = set(
JobCalculation._get_all_with_state(
state=calc_states.WITHSCHEDULER,
only_computer_user_pairs = True)
)
for dbcomputer_id, aiidauser_id in computers_users_to_check:
dbcomputer = DbComputer.objects.get(id=dbcomputer_id)
if not Computer(dbcomputer=dbcomputer).is_enabled():
continue
aiidauser = DbUser.objects.get(id=aiidauser_id)
execlogger.debug("({},{}) pair to check".format(
aiidauser.email, dbcomputer.name))
try:
authinfo = get_authinfo(dbcomputer, aiidauser)
computed_calcs = update_running_calcs_status(authinfo)
except Exception as e:
msg = ("Error while updating calculation status "
"for aiidauser={} on computer={}, "
"error type is {}, error message: {}".format(
aiidauser.email,
dbcomputer.name,
e.__class__.__name__, e.message))
execlogger.error(msg)
# Continue with next computer
continue
[docs]def submit_jobs():
"""
Submit all jobs in the TOSUBMIT state.
"""
from aiida.orm import JobCalculation, Computer
from aiida.djsite.db.models import DbComputer, DbUser
from aiida.djsite.utils import get_dblogger_extra
# I create a unique set of pairs (computer, aiidauser)
computers_users_to_check = set(
JobCalculation._get_all_with_state(
state=calc_states.TOSUBMIT,
only_computer_user_pairs = True)
)
for dbcomputer_id, aiidauser_id in computers_users_to_check:
dbcomputer = DbComputer.objects.get(id=dbcomputer_id)
if not Computer(dbcomputer=dbcomputer).is_enabled():
continue
aiidauser = DbUser.objects.get(id=aiidauser_id)
execlogger.debug("({},{}) pair to submit".format(
aiidauser.email, dbcomputer.name))
try:
try:
authinfo = get_authinfo(dbcomputer, aiidauser)
except AuthenticationError:
# Put each calculation in the SUBMISSIONFAILED state because
# I do not have AuthInfo to submit them
calcs_to_inquire = JobCalculation._get_all_with_state(
state=calc_states.TOSUBMIT,
computer=dbcomputer,
user=aiidauser)
for calc in calcs_to_inquire:
try:
calc._set_state(calc_states.SUBMISSIONFAILED)
except ModificationNotAllowed:
# Someone already set it, just skip
pass
logger_extra = get_dblogger_extra(calc)
execlogger.error("Submission of calc {} failed, "
"computer pk= {} ({}) is not configured "
"for aiidauser {}".format(
calc.pk, dbcomputer.pk,
dbcomputer.name, aiidauser.email),
extra=logger_extra)
# Go to the next (dbcomputer,aiidauser) pair
continue
submitted_calcs = submit_jobs_with_authinfo(authinfo)
except Exception as e:
import traceback
msg = ("Error while submitting jobs "
"for aiidauser={} on computer={}, "
"error type is {}, traceback: {}".format(
aiidauser.email,
dbcomputer.name,
e.__class__.__name__, traceback.format_exc()))
execlogger.error(msg)
# Continue with next computer
continue
[docs]def submit_jobs_with_authinfo(authinfo):
"""
Submit jobs in TOSUBMIT status belonging
to user and machine as defined in the 'dbauthinfo' table.
"""
from aiida.orm import JobCalculation, Computer
from aiida.scheduler.datastructures import JobInfo
from aiida.djsite.utils import get_dblogger_extra
if not authinfo.enabled:
return
execlogger.debug("Submitting jobs for user {} "
"and machine {}".format(
authinfo.aiidauser.email, authinfo.dbcomputer.name))
# This returns an iterator over aiida JobCalculation objects
calcs_to_inquire = JobCalculation._get_all_with_state(
state=calc_states.TOSUBMIT,
computer=authinfo.dbcomputer,
user=authinfo.aiidauser)
# I do it here so that the transport is opened only once per computer
t = authinfo.get_transport()
# I avoid to open an ssh connection if there are
# no calcs with state WITHSCHEDULER
if len(calcs_to_inquire):
# Open connection
try:
with t:
for c in calcs_to_inquire:
logger_extra = get_dblogger_extra(c)
t._set_logger_extra(logger_extra)
try:
submit_calc(calc=c, authinfo=authinfo, transport=t)
except Exception as e:
# TODO: implement a counter, after N retrials
# set it to a status that
# requires the user intervention
execlogger.warning("There was an exception for "
"calculation {} ({}): {}".format(
c.pk, e.__class__.__name__, e.message))
# I just proceed to the next calculation
continue
# Catch exceptions also at this lavel (this happens only if there is
# a problem opening the transport in the 'with t' statement,
# because any other exception is catched and skipped above
except Exception as e:
import traceback
from aiida.djsite.utils import get_dblogger_extra
for calc in calcs_to_inquire:
logger_extra = get_dblogger_extra(calc)
try:
calc._set_state(calc_states.SUBMISSIONFAILED)
except ModificationNotAllowed:
# Someone already set it, just skip
pass
execlogger.error("Submission of calc {} failed, check also the "
"log file! Traceback: {}".format(calc.pk,
traceback.format_exc()),
extra=logger_extra)
raise
[docs]def submit_calc(calc, authinfo, transport=None):
"""
Submit a calculation
:note: if no transport is passed, a new transport is opened and then
closed within this function. If you want to use an already opened
transport, pass it as further parameter. In this case, the transport
has to be already open, and must coincide with the transport of the
the computer defined by the authinfo.
:param calc: the calculation to submit
(an instance of the aiida.orm.JobCalculation class)
:param authinfo: the authinfo for this calculation.
:param transport: if passed, must be an already opened transport. No checks
are done on the consistency of the given transport with the transport
of the computer defined in the authinfo.
"""
from aiida.orm import JobCalculation, Code, Computer
from aiida.common.folders import SandboxFolder
from aiida.common.exceptions import (
FeatureDisabled, InputValidationError)
from aiida.orm.data.remote import RemoteData
from aiida.djsite.utils import get_dblogger_extra
if not authinfo.enabled:
return
logger_extra = get_dblogger_extra(calc)
if transport is None:
t = authinfo.get_transport()
must_open_t = True
else:
t = transport
must_open_t = False
t._set_logger_extra(logger_extra)
if calc._has_cached_links():
raise ValueError("Cannot submit calculation {} because it has "
"cached input links! If you "
"just want to test the submission, use the "
"test_submit() method, otherwise store all links"
"first".format(calc.pk))
# Double check, in the case the calculation was 'killed' (and therefore
# put in the 'FAILED' state) in the meantime
# Do it as near as possible to the state change below (it would be
# even better to do it with some sort of transaction)
if calc.get_state() != calc_states.TOSUBMIT:
raise ValueError("Can only submit calculations with state=TOSUBMIT! "
"(state of calc {} is {} instead)".format(
calc.pk, calc.get_state()))
# I start to submit the calculation: I set the state
try:
calc._set_state(calc_states.SUBMITTING)
except ModificationNotAllowed:
raise ValueError("The calculation has already been submitted by "
"someone else!")
try:
if must_open_t:
t.open()
s = Computer(dbcomputer=authinfo.dbcomputer).get_scheduler()
s.set_transport(t)
input_codes = calc.get_inputs(type=Code)
if len(input_codes) != 1:
raise InputValidationError("JobCalculation {} must have "
"one and only one input code".format(calc.pk))
code = input_codes[0]
computer = calc.get_computer()
if not code.can_run_on(computer):
raise InputValidationError("The selected code {} for calculation "
"{} cannot run on computer {}".format(
code.pk, calc.pk, computer.name))
with SandboxFolder() as folder:
calcinfo, script_filename = calc._presubmit(folder,
use_unstored_links=False)
# After this call, no modifications to the folder should be done
calc._store_raw_input_folder(folder.abspath)
# NOTE: some logic is partially replicated in the 'test_submit'
# method of JobCalculation. If major logic changes are done
# here, make sure to update also the test_submit routine
remote_user = t.whoami()
computer = calc.get_computer()
# TODO Doc: {username} field
# TODO: if something is changed here, fix also 'verdi computer test'
remote_working_directory = authinfo.get_workdir().format(
username=remote_user)
if not remote_working_directory.strip():
raise ConfigurationError("[submission of calc {}] "
"No remote_working_directory configured for computer "
"'{}'".format(calc.pk, computer.name))
# If it already exists, no exception is raised
try:
t.chdir(remote_working_directory)
except IOError:
execlogger.debug("[submission of calc {}] "
"Unable to chdir in {}, trying to create it".format(
calc.pk, remote_working_directory),
extra=logger_extra)
try:
t.makedirs(remote_working_directory)
t.chdir(remote_working_directory)
except (IOError, OSError) as e:
raise ConfigurationError("[submission of calc {}] "
"Unable to create the remote directory {} on "
"computer '{}': {}".format(calc.pk,
remote_working_directory, computer.name,
e.message))
# Store remotely with sharding (here is where we choose
# the folder structure of remote jobs; then I store this
# in the calculation properties using _set_remote_dir
# and I do not have to know the logic, but I just need to
# read the absolute path from the calculation properties.
t.mkdir(calcinfo.uuid[:2],ignore_existing=True)
t.chdir(calcinfo.uuid[:2])
t.mkdir(calcinfo.uuid[2:4], ignore_existing=True)
t.chdir(calcinfo.uuid[2:4])
t.mkdir(calcinfo.uuid[4:])
t.chdir(calcinfo.uuid[4:])
workdir = t.getcwd()
# I store the workdir of the calculation for later file
# retrieval
calc._set_remote_workdir(workdir)
# I first create the code files, so that the code can put
# default files to be overwritten by the plugin itself.
# Still, beware! The code file itself could be overwritten...
# But I checked for this earlier.
if code.is_local():
# Note: this will possibly overwrite files
for f in code.get_folder_list():
t.put(code.get_abs_path(f), f)
t.chmod(code.get_local_executable(), 0755) # rwxr-xr-x
# copy all files, recursively with folders
for f in folder.get_content_list():
execlogger.debug("[submission of calc {}] "
"copying file/folder {}...".format(calc.pk,f),
extra=logger_extra)
t.put(folder.get_abs_path(f), f)
# local_copy_list is a list of tuples,
# each with (src_abs_path, dest_rel_path)
# NOTE: validation of these lists are done
# inside calc._presubmit()
local_copy_list = calcinfo.local_copy_list
remote_copy_list = calcinfo.remote_copy_list
remote_symlink_list = calcinfo.remote_symlink_list
if local_copy_list is not None:
for src_abs_path, dest_rel_path in local_copy_list:
execlogger.debug("[submission of calc {}] "
"copying local file/folder to {}".format(
calc.pk, dest_rel_path),
extra=logger_extra)
t.put(src_abs_path, dest_rel_path)
if remote_copy_list is not None:
for (remote_computer_uuid, remote_abs_path,
dest_rel_path) in remote_copy_list:
if remote_computer_uuid == computer.uuid:
execlogger.debug("[submission of calc {}] "
"copying {} remotely, directly on the machine "
"{}".format(calc.pk, dest_rel_path, computer.name))
try:
t.copy(remote_abs_path, dest_rel_path)
except (IOError,OSError):
execlogger.warning("[submission of calc {}] "
"Unable to copy remote resource from {} to {}! "
"Stopping.".format(calc.pk,
remote_abs_path,dest_rel_path),
extra=logger_extra)
raise
else:
# TODO: implement copy between two different
# machines!
raise NotImplementedError(
"[presubmission of calc {}] "
"Remote copy between two different machines is "
"not implemented yet".format(calc.pk))
if remote_symlink_list is not None:
for (remote_computer_uuid, remote_abs_path,
dest_rel_path) in remote_symlink_list:
if remote_computer_uuid == computer.uuid:
execlogger.debug("[submission of calc {}] "
"copying {} remotely, directly on the machine "
"{}".format(calc.pk, dest_rel_path, computer.name))
try:
t.symlink(remote_abs_path, dest_rel_path)
except (IOError,OSError):
execlogger.warning("[submission of calc {}] "
"Unable to create remote symlink from {} to {}! "
"Stopping.".format(calc.pk,
remote_abs_path,dest_rel_path),
extra=logger_extra)
raise
else:
raise IOError("It is not possible to create a symlink "
"between two different machines for "
"calculation {}".format(calc.pk))
remotedata = RemoteData(computer = computer,
remote_path = workdir)
remotedata._add_link_from(calc, label='remote_folder')
remotedata.store()
job_id = s.submit_from_script(t.getcwd(),script_filename)
calc._set_job_id(job_id)
# This should always be possible, because we should be
# the only ones submitting this calculations,
# so I do not check the ModificationNotAllowed
calc._set_state(calc_states.WITHSCHEDULER)
## I do not set the state to queued; in this way, if the
## daemon is down, the user sees '(unknown)' as last state
## and understands that the daemon is not running.
#if job_tmpl.submit_as_hold:
# calc._set_scheduler_state(job_states.QUEUED_HELD)
#else:
# calc._set_scheduler_state(job_states.QUEUED)
execlogger.debug("submitted calculation {} on {} with "
"jobid {}".format(calc.pk, computer.name, job_id),
extra=logger_extra)
except Exception as e:
import traceback
try:
calc._set_state(calc_states.SUBMISSIONFAILED)
except ModificationNotAllowed:
# Someone already set it, just skip
pass
execlogger.error("Submission of calc {} failed, check also the "
"log file! Traceback: {}".format(
calc.pk,
traceback.format_exc()),
extra=logger_extra)
raise
finally:
# close the transport, but only if it was opened within this function
if must_open_t:
t.close()
[docs]def retrieve_computed_for_authinfo(authinfo):
from aiida.orm import JobCalculation
from aiida.common.folders import SandboxFolder
from aiida.orm.data.folder import FolderData
from aiida.djsite.utils import get_dblogger_extra
from aiida.orm import DataFactory
from aiida.orm.data.singlefile import SinglefileData
import os
if not authinfo.enabled:
return
calcs_to_retrieve = JobCalculation._get_all_with_state(
state=calc_states.COMPUTED,
computer=authinfo.dbcomputer,
user=authinfo.aiidauser)
retrieved = []
# I avoid to open an ssh connection if there are no
# calcs with state not COMPUTED
if len(calcs_to_retrieve):
# Open connection
with authinfo.get_transport() as t:
for calc in calcs_to_retrieve:
logger_extra = get_dblogger_extra(calc)
t._set_logger_extra(logger_extra)
try:
calc._set_state(calc_states.RETRIEVING)
except ModificationNotAllowed:
# Someone else has already started to retrieve it,
# just log and continue
execlogger.debug("Attempting to retrieve more than once "
"calculation {}: skipping!".format(calc.pk),
extra=logger_extra)
continue # with the next calculation to retrieve
try:
execlogger.debug("Retrieving calc {}".format(calc.pk),
extra=logger_extra)
workdir = calc._get_remote_workdir()
retrieve_list = calc._get_retrieve_list()
retrieve_singlefile_list=calc._get_retrieve_singlefile_list()
execlogger.debug("[retrieval of calc {}] "
"chdir {}".format(calc.pk, workdir),
extra=logger_extra)
t.chdir(workdir)
retrieved_files = FolderData()
retrieved_files._add_link_from(calc,
label=calc._get_linkname_retrieved())
# First, retrieve the files of folderdata
with SandboxFolder() as folder:
for item in retrieve_list:
# I have two possibilities:
# * item is a string
# * or is a list
# then I have other two possibilities:
# * there are file patterns
# * or not
# First decide the name of the files
if isinstance(item,list):
tmp_rname,tmp_lname,depth = item
# if there are more than one file I do something differently
if t.has_magic(tmp_rname):
remote_names = t.glob(tmp_rname)
local_names = []
for rem in remote_names:
to_append = rem.split(os.path.sep)[-depth:] if depth>0 else []
local_names.append( os.path.sep.join([tmp_lname]+to_append) )
else:
remote_names = [tmp_rname]
to_append = remote_names.split(os.path.sep)[-depth:] if depth>0 else []
local_names = [os.path.sep.join([tmp_lname]+to_append)]
if depth>1: # create directories in the folder, if needed
for this_local_file in local_names:
new_folder = os.path.join(
folder.abspath,
os.path.split(this_local_file)[0])
if not os.path.exists(new_folder):
os.makedirs(new_folder)
else: # it is a string
if t.has_magic(item):
remote_names = t.glob(item)
local_names = [ os.path.split(rem)[1] for rem in remote_names ]
else:
remote_names = [item]
local_names = [ os.path.split(item)[1] ]
for rem,loc in zip(remote_names,local_names):
execlogger.debug("[retrieval of calc {}] "
"Trying to retrieve remote item '{}'".format(
calc.pk, rem),
extra=logger_extra)
t.get(rem,
os.path.join(folder.abspath,loc),
ignore_nonexisting=True)
# 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:
singlefile_list = []
for (linkname,subclassname,filename) in retrieve_singlefile_list:
execlogger.debug("[retrieval of calc {}] Trying "
"to retrieve remote singlefile '{}'".format(
calc.pk, filename),
extra=logger_extra)
localfilename = os.path.join(
folder.abspath,os.path.split(filename)[1])
t.get(filename, localfilename,
ignore_nonexisting=True)
singlefile_list.append((linkname,subclassname,
localfilename))
# ignore files that have not been retrieved
singlefile_list = [ i for i in singlefile_list if
os.path.exists(i[2]) ]
#after retrieving from the cluster, I create the objects
singlefiles = []
for (linkname,subclassname,filename) in singlefile_list:
SinglefileSubclass = DataFactory(subclassname)
singlefile = SinglefileSubclass()
singlefile.set_file(filename)
singlefile._add_link_from(calc,label=linkname)
singlefiles.append(singlefile)
# Finally, store
execlogger.debug("[retrieval of calc {}] "
"Storing retrieved_files={}".format(
calc.pk, retrieved_files.dbnode.pk),
extra=logger_extra)
retrieved_files.store()
for fil in singlefiles:
execlogger.debug("[retrieval of calc {}] "
"Storing retrieved_singlefile={}".format(
calc.pk, fil.dbnode.pk),
extra=logger_extra)
fil.store()
# If I was the one retrieving, I should also be the only
# one parsing! I do not check
calc._set_state(calc_states.PARSING)
Parser = calc.get_parserclass()
# If no parser is set, the calculation is successful
successful = True
if Parser is not None:
# TODO: parse here
parser = Parser(calc)
successful,new_nodes_tuple = parser.parse_from_calc()
for label,n in new_nodes_tuple:
n._add_link_from(calc,label=label)
n.store()
if successful:
try:
calc._set_state(calc_states.FINISHED)
except ModificationNotAllowed:
# I should have been the only one to set it, but
# in order to avoid unuseful error messages, I
# just ignore
pass
else:
try:
calc._set_state(calc_states.FAILED)
except ModificationNotAllowed:
# I should have been the only one to set it, but
# in order to avoid unuseful error messages, I
# just ignore
pass
execlogger.error("[parsing of calc {}] "
"The parser returned an error, but it should have "
"created an output node with some partial results "
"and warnings. Check there for more information on "
"the problem".format(calc.pk), extra=logger_extra)
retrieved.append(calc)
except Exception:
import traceback
tb = traceback.format_exc()
newextradict = logger_extra.copy()
newextradict['full_traceback'] = tb
if calc.get_state() == calc_states.PARSING:
execlogger.error("Error parsing calc {}. "
"Traceback: {}".format(calc.pk, tb),
extra=newextradict)
# TODO: add a 'comment' to the calculation
try:
calc._set_state(calc_states.PARSINGFAILED)
except ModificationNotAllowed:
pass
else:
execlogger.error("Error retrieving calc {}. "
"Traceback: {}".format(calc.pk, tb),
extra=newextradict)
try:
calc._set_state(calc_states.RETRIEVALFAILED)
except ModificationNotAllowed:
pass
raise
return retrieved