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 Code, Computer
from aiida.common.folders import SandboxFolder
from aiida.common.exceptions import (InputValidationError)
from aiida.orm.data.remote import RemoteData
from aiida.utils.logger 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)
computer = calc.get_computer()
with SandboxFolder() as folder:
calcinfo, script_filename = calc._presubmit(
folder, use_unstored_links=False)
codes_info = calcinfo.codes_info
input_codes = [
load_node(_.code_uuid, parent_class=Code) for _ in codes_info
]
for code in input_codes:
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))
# 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()
# 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.
for code in input_codes:
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',
link_type=LinkType.CREATE)
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()
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.utils.logger 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 = list(
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="******", 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
## 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
