def _parse_joblist_output(self, retval, stdout, stderr):
import xml.dom.minidom
if retval != 0:
self.logger.error("Error in _parse_joblist_output: retval={}; "
"stdout={}; stderr={}".format(
retval, stdout, stderr))
raise SchedulerError("Error during joblist retrieval, retval={}".\
format(retval))
if stderr.strip():
self.logger.warning("in _parse_joblist_output for {}: "
"there was some text in stderr: {}".format(
str(self.transport), stderr))
if stdout:
try:
xmldata = xml.dom.minidom.parseString(stdout)
except xml.parsers.expat.ExpatError:
self.logger.error("in sge._parse_joblist_output: "
"xml parsing of stdout failed:"
"{}".format(stdout))
raise SchedulerParsingError("Error during joblist retrieval,"
"xml parsing of stdout failed")
else:
self.logger.error("Error in sge._parse_joblist_output: retval={}; "
"stdout={}; stderr={}".format(
retval, stdout, 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 not 'queue_info' in tag_names_sec:
self.logger.error("Error in sge._parse_joblist_output: "
"no queue_info: {}".\
format(stdout))
raise SchedulerError
if not 'job_info' in tag_names_sec:
self.logger.error("Error in sge._parse_joblist_output: "
"no job_info: {}".\
format(stdout))
raise SchedulerError
except SchedulerError:
self.logger.error("Error in sge._parse_joblist_output: stdout={}"\
.format(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("Error in sge._parse_joblist_output: stdout={}"\
.format(stdout))
raise SchedulerError("Error during xml processing, of stdout")
jobs = [i for i in 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("Error in sge._parse_joblist_output:"
"no job id is given, stdout={}"\
.format(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 = job_states.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 = job_states.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("No 'job_owner' field for job "
"id {}".format(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("No 'title' field for job "
"id {}".format(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 == job_states.RUNNING:
self.logger.warning("No 'queue_name' field for job "
"id {}".format(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("Error parsing 'JB_submission_time' "
"for job id {} ('{}')".format(
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("Error parsing 'JAT_start_time'"
"for job id {} ('{}')".format(
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 == job_states.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("No 'slots' field for job "
"id {}".format(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:
#self.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():
self.logger.warning("Warning in _parse_joblist_output, non-empty "
"(filtered) stderr='{}'".format(filtered_stderr))
if retval != 0:
raise SchedulerError(
"Error during qstat parsing (_parse_joblist_output function)")
jobdata_raw = [] # will contain raw data parsed from qstat output
# Get raw data and split in lines
for line_num, l 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 l.startswith('Job Id:'):
jobdata_raw.append(
{'id': l.split(':', 1)[1].strip(),
'lines': [], 'warning_lines_idx': []})
# warning_lines_idx: lines that do not start either with
# tab or space
else:
if l.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")
#self.logger.warning("I found some text before the "
#"first job: {}".format(l))
else:
if l.startswith(' '):
# If it starts with a space, it is a new field
jobdata_raw[-1]['lines'].append(l)
elif l.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, l))
jobdata_raw[-1]['lines'][-1] += l[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(l)
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?
self.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:
self.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
#self.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:
self.logger.warning("Unrecognized job_state '{}' for job "
"id {}".format(job_state_string,
this_job.job_id))
this_job.job_state = job_states.UNDETERMINED
except KeyError:
self.logger.debug("No 'job_state' field for job id {}".format(
this_job.job_id))
this_job.job_state = job_states.UNDETERMINED
try:
this_job.job_substate = raw_data['substate']
except KeyError:
self.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 e:
self.logger.debug("Problem parsing the node names, I "
"got Exception {} with message {}; "
"exec_hosts was {}".format(
str(type(e)), e.message, 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:
self.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:
self.logger.debug("No 'resource_list.ncpus' field for job id "
"{}".format(this_job.job_id))
except ValueError:
self.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:
self.logger.debug("No 'resource_list.mpiprocs' field for job id "
"{}".format(this_job.job_id))
except ValueError:
self.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:
self.logger.debug("No 'resource_list.nodect' field for job id "
"{}".format(this_job.job_id))
except ValueError:
self.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(this_job.allocated_machines) != this_job.num_machines:
self.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:
self.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:
self.logger.debug("No 'resource_list.walltime' field for "
"job id {}".format(this_job.job_id))
except ValueError:
self.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:
self.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:
self.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:
self.logger.debug("No 'ctime' field for job id "
"{}".format(this_job.job_id))
except ValueError:
self.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:
self.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
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,
that is here implemented as a list of lines, one for each
job, with _field_separator as separator. The order is described
in the _get_joblist_command function.
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.
"""
num_fields = len(self.fields)
# 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:
#self.logger.warning("Error in _parse_joblist_output: retval={}; "
# "stdout={}; stderr={}".format(retval, stdout, stderr))
# issue a warning if there is any stderr output and
# there is no line containing "Invalid job id specified", that happens
# when I ask for specific calculations, and they are all finished
if stderr.strip() and "Invalid job id specified" not in stderr:
self.logger.warning("Warning in _parse_joblist_output, non-empty "
"stderr='{}'".format(stderr.strip()))
if retval != 0:
raise SchedulerError(
"Error during squeue parsing (_parse_joblist_output function)"
)
# will contain raw data parsed from output: only lines with the
# separator, and already split in fields
# I put num_fields, because in this way
# if the symbol _field_separator appears in the title (that is
# the last field), I don't split the title.
# This assumes that _field_separator never
# appears in any previous field.
jobdata_raw = [
l.split(_field_separator, num_fields) for l in stdout.splitlines()
if _field_separator in l
]
# Create dictionary and parse specific fields
job_list = []
for job in jobdata_raw:
thisjob_dict = {k[1]: v for k, v in zip(self.fields, job)}
this_job = JobInfo()
try:
this_job.job_id = thisjob_dict['job_id']
this_job.annotation = thisjob_dict['annotation']
job_state_raw = thisjob_dict['state_raw']
except KeyError:
# I skip this calculation if I couldn't find this basic info
# (I don't append anything to job_list before continuing)
self.logger.error("Wrong line length in squeue output! '{}'"
"".format(job))
continue
try:
job_state_string = _map_status_slurm[job_state_raw]
except KeyError:
self.logger.warning("Unrecognized job_state '{}' for job "
"id {}".format(job_state_raw,
this_job.job_id))
job_state_string = job_states.UNDETERMINED
# QUEUED_HELD states are not specific states in SLURM;
# they are instead set with state QUEUED, and then the
# annotation tells if the job is held.
# I check for 'Dependency', 'JobHeldUser',
# 'JobHeldAdmin', 'BeginTime'.
# Other states should not bring the job in QUEUED_HELD, I believe
# (the man page of slurm seems to be incomplete, for instance
# JobHeld* are not reported there; I also checked at the source code
# of slurm 2.6 on github (https://github.com/SchedMD/slurm),
# file slurm/src/common/slurm_protocol_defs.c,
# and these seem all the states to be taken into account for the
# QUEUED_HELD status).
# There are actually a few others, like possible
# failures, or partition-related reasons, but for the moment I
# leave them in the QUEUED state.
if (job_state_string == job_states.QUEUED
and this_job.annotation in [
'Dependency', 'JobHeldUser', 'JobHeldAdmin',
'BeginTime'
]):
job_state_string = job_states.QUEUED_HELD
this_job.job_state = job_state_string
####
# Up to here, I just made sure that there were at least three
# fields, to set the most important fields for a job.
# I now check if the length is equal to the number of fields
if len(job) < num_fields:
# I store this job only with the information
# gathered up to now, and continue to the next job
# Also print a warning
self.logger.warning("Wrong line length in squeue output!"
"Skipping optional fields. Line: '{}'"
"".format(jobdata_raw))
# I append this job before continuing
job_list.append(this_job)
continue
# TODO: store executing_host?
this_job.job_owner = thisjob_dict['username']
try:
this_job.num_machines = int(thisjob_dict['number_nodes'])
except ValueError:
self.logger.warning("The number of allocated nodes is not "
"an integer ({}) for job id {}!".format(
thisjob_dict['number_nodes'],
this_job.job_id))
try:
this_job.num_mpiprocs = int(thisjob_dict['number_cpus'])
except ValueError:
self.logger.warning("The number of allocated cores is not "
"an integer ({}) for job id {}!".format(
thisjob_dict['number_cpus'],
this_job.job_id))
# ALLOCATED NODES HERE
# string may be in the format
# nid00[684-685,722-723,748-749,958-959]
# therefore it requires some parsing, that is unnecessary now.
# I just store is as a raw string for the moment, and I leave
# this_job.allocated_machines undefined
if this_job.job_state == job_states.RUNNING:
this_job.allocated_machines_raw = thisjob_dict[
'allocated_machines']
this_job.queue_name = thisjob_dict['partition']
try:
this_job.requested_wallclock_time_seconds = (
self._convert_time(thisjob_dict['time_limit']))
except ValueError:
self.logger.warning("Error parsing the time limit "
"for job id {}".format(this_job.job_id))
# Only if it is RUNNING; otherwise it is not meaningful,
# and may be not set (in my test, it is set to zero)
if this_job.job_state == job_states.RUNNING:
try:
this_job.wallclock_time_seconds = (self._convert_time(
thisjob_dict['time_used']))
except ValueError:
self.logger.warning("Error parsing time_used "
"for job id {}".format(
this_job.job_id))
try:
this_job.dispatch_time = self._parse_time_string(
thisjob_dict['dispatch_time'])
except ValueError:
self.logger.warning("Error parsing dispatch_time for job "
"id {}".format(this_job.job_id))
try:
this_job.submission_time = self._parse_time_string(
thisjob_dict['submission_time'])
except ValueError:
self.logger.warning("Error parsing submission_time for job "
"id {}".format(this_job.job_id))
this_job.title = thisjob_dict['job_name']
# Everything goes here anyway for debugging purposes
this_job.raw_data = job
# Double check of redundant info
# Not really useful now, allocated_machines in this
# version of the plugin is never set
if (this_job.allocated_machines is not None
and this_job.num_machines is not None):
if len(this_job.allocated_machines) != this_job.num_machines:
self.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))
# I append to the list of jobs to return
job_list.append(this_job)
return job_list
