def _parse_submit_output(self, retval, stdout, stderr):
"""
Parse the output of the submit command, as returned by executing the
command returned by _get_submit_command command.
To be implemented by the plugin.
Return a string with the JobID.
"""
if retval != 0:
self.logger.error('Error in _parse_submit_output: retval={}; '
'stdout={}; stderr={}'.format(
retval, stdout, stderr))
raise SchedulerError('Error during submission, retval={}\n'
'stdout={}\nstderr={}'.format(
retval, stdout, stderr))
try:
transport_string = ' for {}'.format(self.transport)
except SchedulerError:
transport_string = ''
if stderr.strip():
self.logger.warning('in _parse_submit_output{}: '
'there was some text in stderr: {}'.format(
transport_string, stderr))
try:
return stdout.strip().split('Job <')[1].split('>')[0]
except IndexError:
raise SchedulerParsingError(
'Cannot parse submission output: {}'.format(stdout))
def _parse_submit_output(self, retval, stdout, stderr):
"""
Parse the output of the submit command, as returned by executing the
command returned by _get_submit_command command.
To be implemented by the plugin.
Return a string with the JobID.
"""
if retval != 0:
self.logger.error(f'Error in _parse_submit_output: retval={retval}; stdout={stdout}; stderr={stderr}')
raise SchedulerError(f'Error during submission, retval={retval}\nstdout={stdout}\nstderr={stderr}')
try:
transport_string = f' for {self.transport}'
except SchedulerError:
transport_string = ''
if stderr.strip():
self.logger.warning(f'in _parse_submit_output{transport_string}: there was some text in stderr: {stderr}')
try:
return stdout.strip().split('Job <')[1].split('>')[0]
except IndexError as exc:
raise SchedulerParsingError(f'Cannot parse submission output: `{stdout}`') from exc
def parse_sge_script(local_script_path):
"""
Parse the SGE script
:returns: A dictionary of the options for constructing AiiDAJobFirework
"""
with open(local_script_path) as handle:
lines = handle.readlines()
options = {
'stdout_fname': '_scheduler-stdout.txt',
'stderr_fname': '_scheduler-stderr.txt',
'priority':
100, # Base priority of AiiDA jobs in the FW system, hard coded to 100 for now
}
for line in lines:
if '#$ -N' in line:
options['job_name'] = line.split()[-1] # Name of the job
if '#$ -o' in line:
options['stdout_fname'] = line.replace("#$ -o", "").strip()
if '#$ -e' in line:
options['stderr_fname'] = line.replace("#$ -e", "").strip()
if '#$ -pe' in line:
options['mpinp'] = int(line.split()[-1])
if 'h_rt' in line:
timestring = line.split('=')[1].strip()
hours, minutes, seconds = timestring.split(':')
seconds = int(seconds) + int(minutes) * 60 + int(hours) * 3600
options['walltime'] = int(seconds)
if '#$ -p ' in line:
options['priority'] += int(line.split()[-1])
required_fields = ['job_name', 'mpinp', 'walltime']
missing = [field for field in required_fields if field not in options]
if missing:
raise SchedulerParsingError(
f"Missing fields: {missing} while parsing the job script")
return options
def _parse_joblist_output(self, retval, stdout, stderr):
# pylint: disable=too-many-statements,too-many-branches
if retval != 0:
self.logger.error(
f'Error in _parse_joblist_output: retval={retval}; stdout={stdout}; stderr={stderr}'
)
raise SchedulerError(
f'Error during joblist retrieval, retval={retval}')
if stderr.strip():
self.logger.warning(
f'in _parse_joblist_output for {str(self.transport)}: there was some text in stderr: {stderr}'
)
if stdout:
try:
xmldata = xml.dom.minidom.parseString(stdout)
except xml.parsers.expat.ExpatError:
self.logger.error(
f'in sge._parse_joblist_output: xml parsing of stdout failed: {stdout}'
)
raise SchedulerParsingError(
'Error during joblist retrieval, xml parsing of stdout failed'
)
else:
self.logger.error(
f'Error in sge._parse_joblist_output: retval={retval}; stdout={stdout}; stderr={stderr}'
)
raise SchedulerError(
'Error during joblist retrieval, no stdout produced')
try:
first_child = xmldata.firstChild
second_childs = first_child.childNodes
tag_names_sec = [elem.tagName for elem in second_childs \
if elem.nodeType == 1]
if 'queue_info' not in tag_names_sec:
self.logger.error(
f'Error in sge._parse_joblist_output: no queue_info: {stdout}'
)
raise SchedulerError
if 'job_info' not in tag_names_sec:
self.logger.error(
f'Error in sge._parse_joblist_output: no job_info: {stdout}'
)
raise SchedulerError
except SchedulerError:
self.logger.error(
f'Error in sge._parse_joblist_output: stdout={stdout}')
raise SchedulerError('Error during xml processing, of stdout:'
"There is no 'job_info' or no 'queue_info'"
'element or there are no jobs!')
# If something weird happens while firstChild, pop, etc:
except Exception:
self.logger.error(
f'Error in sge._parse_joblist_output: stdout={stdout}')
raise SchedulerError('Error during xml processing, of stdout')
jobs = list(first_child.getElementsByTagName('job_list'))
# jobs = [i for i in jobinfo.getElementsByTagName('job_list')]
# print [i[0].childNodes[0].data for i in job_numbers if i]
joblist = []
for job in jobs:
this_job = JobInfo()
# In case the user needs more information the xml-data for
# each job is stored:
this_job.raw_data = job.toxml()
try:
job_element = job.getElementsByTagName('JB_job_number').pop(0)
element_child = job_element.childNodes.pop(0)
this_job.job_id = str(element_child.data).strip()
if not this_job.job_id:
raise SchedulerError
except SchedulerError:
self.logger.error(
f'Error in sge._parse_joblist_output:no job id is given, stdout={stdout}'
)
raise SchedulerError(
'Error in sge._parse_joblist_output: no job id is given')
except IndexError:
self.logger.error("No 'job_number' given for job index {} in "
'job list, stdout={}'.format(jobs.index(job) \
, stdout))
raise IndexError(
'Error in sge._parse_joblist_output: no job id is given')
try:
job_element = job.getElementsByTagName('state').pop(0)
element_child = job_element.childNodes.pop(0)
job_state_string = str(element_child.data).strip()
try:
this_job.job_state = _MAP_STATUS_SGE[job_state_string]
except KeyError:
self.logger.warning("Unrecognized job_state '{}' for job "
'id {}'.format(job_state_string,
this_job.job_id))
this_job.job_state = JobState.UNDETERMINED
except IndexError:
self.logger.warning("No 'job_state' field for job id {} in"
'stdout={}'.format(this_job.job_id,
stdout))
this_job.job_state = JobState.UNDETERMINED
try:
job_element = job.getElementsByTagName('JB_owner').pop(0)
element_child = job_element.childNodes.pop(0)
this_job.job_owner = str(element_child.data).strip()
except IndexError:
self.logger.warning(
f"No 'job_owner' field for job id {this_job.job_id}")
try:
job_element = job.getElementsByTagName('JB_name').pop(0)
element_child = job_element.childNodes.pop(0)
this_job.title = str(element_child.data).strip()
except IndexError:
self.logger.warning(
f"No 'title' field for job id {this_job.job_id}")
try:
job_element = job.getElementsByTagName('queue_name').pop(0)
element_child = job_element.childNodes.pop(0)
this_job.queue_name = str(element_child.data).strip()
except IndexError:
if this_job.job_state == JobState.RUNNING:
self.logger.warning(
f"No 'queue_name' field for job id {this_job.job_id}")
try:
job_element = job.getElementsByTagName(
'JB_submission_time').pop(0)
element_child = job_element.childNodes.pop(0)
time_string = str(element_child.data).strip()
try:
this_job.submission_time = self._parse_time_string(
time_string)
except ValueError:
self.logger.warning(
f"Error parsing 'JB_submission_time' for job id {this_job.job_id} ('{time_string}')"
)
except IndexError:
try:
job_element = job.getElementsByTagName(
'JAT_start_time').pop(0)
element_child = job_element.childNodes.pop(0)
time_string = str(element_child.data).strip()
try:
this_job.dispatch_time = self._parse_time_string(
time_string)
except ValueError:
self.logger.warning(
f"Error parsing 'JAT_start_time'for job id {this_job.job_id} ('{time_string}')"
)
except IndexError:
self.logger.warning("No 'JB_submission_time' and no "
"'JAT_start_time' field for job "
'id {}'.format(this_job.job_id))
# There is also cpu_usage, mem_usage, io_usage information available:
if this_job.job_state == JobState.RUNNING:
try:
job_element = job.getElementsByTagName('slots').pop(0)
element_child = job_element.childNodes.pop(0)
this_job.num_mpiprocs = str(element_child.data).strip()
except IndexError:
self.logger.warning(
f"No 'slots' field for job id {this_job.job_id}")
joblist.append(this_job)
# self.logger.debug("joblist final: {}".format(joblist))
return joblist
def _parse_joblist_output(self, retval, stdout, stderr):
"""
Parse the queue output string, as returned by executing the
command returned by _get_joblist_command command (qstat -f).
Return a list of JobInfo objects, one of each job,
each relevant parameters implemented.
Note: depending on the scheduler configuration, finished jobs may
either appear here, or not.
This function will only return one element for each job find
in the qstat output; missing jobs (for whatever reason) simply
will not appear here.
"""
# I don't raise because if I pass a list of jobs, I get a non-zero status
# if one of the job is not in the list anymore
# retval should be zero
# if retval != 0:
# _LOGGER.warning("Error in _parse_joblist_output: retval={}; "
# "stdout={}; stderr={}".format(retval, stdout, stderr))
# issue a warning if there is any stderr output
# but I strip lines containing "Unknown Job Id", that happens
# also when I ask for a calculation that has finished
#
# I also strip for "Job has finished" because this happens for
# those schedulers configured to leave the job in the output
# of qstat for some time after job completion.
filtered_stderr = '\n'.join(
l for l in stderr.split('\n')
if 'Unknown Job Id' not in l and 'Job has finished' not in l)
if filtered_stderr.strip():
_LOGGER.warning('Warning in _parse_joblist_output, non-empty '
"(filtered) stderr='{}'".format(filtered_stderr))
if retval != 0:
raise SchedulerError('Error during qstat parsing, retval={}\n'
'stdout={}\nstderr={}'.format(
retval, stdout, stderr))
jobdata_raw = [] # will contain raw data parsed from qstat output
# Get raw data and split in lines
for line_num, line in enumerate(stdout.split('\n'), start=1):
# Each new job stanza starts with the string 'Job Id:': I
# create a new item in the jobdata_raw list
if line.startswith('Job Id:'):
jobdata_raw.append({
'id': line.split(':', 1)[1].strip(),
'lines': [],
'warning_lines_idx': []
})
# warning_lines_idx: lines that do not start either with
# tab or space
else:
if line.strip():
# This is a non-empty line, therefore it is an attribute
# of the last job found
if not jobdata_raw:
# The list is still empty! (This means that I found a
# non-empty line, before finding the first 'Job Id:'
# string: it is an error. However this may happen
# only before the first job.
raise SchedulerParsingError(
'I did not find the header for the first job')
# _LOGGER.warning("I found some text before the "
# "first job: {}".format(l))
else:
if line.startswith(' '):
# If it starts with a space, it is a new field
jobdata_raw[-1]['lines'].append(line)
elif line.startswith('\t'):
# If a line starts with a TAB,
# I append to the previous string
# stripping the TAB
if not jobdata_raw[-1]['lines']:
raise SchedulerParsingError(
'Line {} is the first line of the job, but it '
'starts with a TAB! ({})'.format(
line_num, line))
jobdata_raw[-1]['lines'][-1] += line[1:]
else:
# raise SchedulerParsingError(
# "Wrong starting character at line {}! ({})"
# "".format(line_num, l))
## For some reasons, the output of 'comment' and
## 'Variable_List', for instance, can have
## newlines if they are included... # I do a
## workaround
jobdata_raw[-1]['lines'][-1] += '\n{}'.format(line)
jobdata_raw[-1]['warning_lines_idx'].append(
len(jobdata_raw[-1]['lines']) - 1)
# Create dictionary and parse specific fields
job_list = []
for job in jobdata_raw:
this_job = JobInfo()
this_job.job_id = job['id']
lines_without_equals_sign = [
i for i in job['lines'] if '=' not in i
]
# There are lines without equals sign: this is bad
if lines_without_equals_sign:
# Should I only warn?
_LOGGER.error('There are lines without equals sign! {}'.format(
lines_without_equals_sign))
raise SchedulerParsingError(
'There are lines without equals sign.')
raw_data = {
i.split('=', 1)[0].strip().lower(): i.split('=',
1)[1].lstrip()
for i in job['lines'] if '=' in i
}
## I ignore the errors for the time being - this seems to be
## a problem if there are \n in the content of some variables?
## I consider this a workaround...
# for line_with_warning in set(job['warning_lines_idx']):
# if job['lines'][line_with_warning].split(
# '=',1)[0].strip().lower() != "comment":
# raise SchedulerParsingError(
# "Wrong starting character in one of the lines "
# "of job {}, and it's not a comment! ({})"
# "".format(this_job.job_id,
# job['lines'][line_with_warning]))
problematic_fields = []
for line_with_warning in set(job['warning_lines_idx']):
problematic_fields.append(
job['lines'][line_with_warning].split(
'=', 1)[0].strip().lower())
if problematic_fields:
# These are the fields that contain unexpected newlines
raw_data['warning_fields_with_newlines'] = problematic_fields
# I believe that exit_status and terminating_signal cannot be
# retrieved from the qstat -f output.
# I wrap calls in try-except clauses to avoid errors if a field
# is missing
try:
this_job.title = raw_data['job_name']
except KeyError:
_LOGGER.debug("No 'job_name' field for job id {}".format(
this_job.job_id))
try:
this_job.annotation = raw_data['comment']
except KeyError:
# Many jobs do not have a comment; I do not complain about it.
pass
# _LOGGER.debug("No 'comment' field for job id {}".format(
# this_job.job_id))
try:
job_state_string = raw_data['job_state']
try:
this_job.job_state = self._map_status[job_state_string]
except KeyError:
_LOGGER.warning("Unrecognized job_state '{}' for job "
'id {}'.format(job_state_string,
this_job.job_id))
this_job.job_state = JobState.UNDETERMINED
except KeyError:
_LOGGER.debug("No 'job_state' field for job id {}".format(
this_job.job_id))
this_job.job_state = JobState.UNDETERMINED
try:
this_job.job_substate = raw_data['substate']
except KeyError:
_LOGGER.debug("No 'substate' field for job id {}".format(
this_job.job_id))
try:
exec_hosts = raw_data['exec_host'].split('+')
except KeyError:
# No exec_host information found (it may be ok, if the job
# is not running)
pass
else:
# parse each host; syntax, from the man page:
# hosta/J1+hostb/J2*P+...
# where J1 and J2 are an index of the job
# on the named host and P is the number of
# processors allocated from that host to this job.
# P does not appear if it is 1.
try:
exec_host_list = []
for exec_host in exec_hosts:
node = MachineInfo()
node.name, data = exec_host.split('/')
data = data.split('*')
if len(data) == 1:
node.jobIndex = int(data[0])
node.num_cpus = 1
elif len(data) == 2:
node.jobIndex = int(data[0])
node.num_cpus = int(data[1])
else:
raise ValueError(
'Wrong number of pieces: {} '
'instead of 1 or 2 in exec_hosts: '
'{}'.format(len(data), exec_hosts))
exec_host_list.append(node)
this_job.allocated_machines = exec_host_list
except Exception as exc:
_LOGGER.debug('Problem parsing the node names, I '
'got Exception {} with message {}; '
'exec_hosts was {}'.format(
str(type(exc)), exc, exec_hosts))
try:
# I strip the part after the @: is this always ok?
this_job.job_owner = raw_data['job_owner'].split('@')[0]
except KeyError:
_LOGGER.debug("No 'job_owner' field for job id {}".format(
this_job.job_id))
try:
this_job.num_cpus = int(raw_data['resource_list.ncpus'])
# TODO: understand if this is the correct field also for
# multithreaded (OpenMP) jobs.
except KeyError:
_LOGGER.debug(
"No 'resource_list.ncpus' field for job id {}".format(
this_job.job_id))
except ValueError:
_LOGGER.warning("'resource_list.ncpus' is not an integer "
'({}) for job id {}!'.format(
raw_data['resource_list.ncpus'],
this_job.job_id))
try:
this_job.num_mpiprocs = int(raw_data['resource_list.mpiprocs'])
# TODO: understand if this is the correct field also for
# multithreaded (OpenMP) jobs.
except KeyError:
_LOGGER.debug(
"No 'resource_list.mpiprocs' field for job id {}".format(
this_job.job_id))
except ValueError:
_LOGGER.warning("'resource_list.mpiprocs' is not an integer "
'({}) for job id {}!'.format(
raw_data['resource_list.mpiprocs'],
this_job.job_id))
try:
this_job.num_machines = int(raw_data['resource_list.nodect'])
except KeyError:
_LOGGER.debug(
"No 'resource_list.nodect' field for job id {}".format(
this_job.job_id))
except ValueError:
_LOGGER.warning("'resource_list.nodect' is not an integer "
'({}) for job id {}!'.format(
raw_data['resource_list.nodect'],
this_job.job_id))
# Double check of redundant info
if (this_job.allocated_machines is not None
and this_job.num_machines is not None):
if len(
set(machine.name for machine in this_job.
allocated_machines)) != this_job.num_machines:
_LOGGER.error('The length of the list of allocated '
'nodes ({}) is different from the '
'expected number of nodes ({})!'.format(
len(this_job.allocated_machines),
this_job.num_machines))
try:
this_job.queue_name = raw_data['queue']
except KeyError:
_LOGGER.debug("No 'queue' field for job id {}".format(
this_job.job_id))
try:
this_job.RequestedWallclockTime = (self._convert_time(
raw_data['resource_list.walltime']))
except KeyError:
_LOGGER.debug(
"No 'resource_list.walltime' field for job id {}".format(
this_job.job_id))
except ValueError:
_LOGGER.warning(
"Error parsing 'resource_list.walltime' for job id {}".
format(this_job.job_id))
try:
this_job.wallclock_time_seconds = (self._convert_time(
raw_data['resources_used.walltime']))
except KeyError:
# May not have started yet
pass
except ValueError:
_LOGGER.warning(
"Error parsing 'resources_used.walltime' for job id {}".
format(this_job.job_id))
try:
this_job.cpu_time = (self._convert_time(
raw_data['resources_used.cput']))
except KeyError:
# May not have started yet
pass
except ValueError:
_LOGGER.warning(
"Error parsing 'resources_used.cput' for job id {}".format(
this_job.job_id))
#
# ctime: The time that the job was created
# mtime: The time that the job was last modified, changed state,
# or changed locations.
# qtime: The time that the job entered the current queue
# stime: The time when the job started execution.
# etime: The time that the job became eligible to run, i.e. in a
# queued state while residing in an execution queue.
try:
this_job.submission_time = self._parse_time_string(
raw_data['ctime'])
except KeyError:
_LOGGER.debug("No 'ctime' field for job id {}".format(
this_job.job_id))
except ValueError:
_LOGGER.warning("Error parsing 'ctime' for job id {}".format(
this_job.job_id))
try:
this_job.dispatch_time = self._parse_time_string(
raw_data['stime'])
except KeyError:
# The job may not have been started yet
pass
except ValueError:
_LOGGER.warning("Error parsing 'stime' for job id {}".format(
this_job.job_id))
# TODO: see if we want to set also finish_time for finished jobs,
# if there are any
# Everything goes here anyway for debugging purposes
this_job.raw_data = raw_data
# I append to the list of jobs to return
job_list.append(this_job)
return job_list