# coding: utf-8
"""
Objects and methods to contact the resource manager to get info on the status of the job and useful statistics.
Note that this is not a wrapper for the C API but a collection of simple wrappers around the shell commands
provided by the resource manager (qsub, qdel and qstat for PBS, sinfo, squeue... for Slurm).
The main goal indeed is providing a simplified common interface for different resource managers without
having to rely on external libraries.
"""
import shlex
from collections import OrderedDict, defaultdict
from subprocess import Popen, PIPE
from monty.collections import AttrDict
from monty.inspect import all_subclasses
import logging
logger = logging.getLogger(__name__)
[docs]class JobStatus(int):
"""
This object is an integer representing the status of a :class:`QueueJob`.
Slurm API, see `man squeue`.
JOB STATE CODES
Jobs typically pass through several states in the course of their execution. The typical states are
PENDING, RUNNING, SUSPENDED, COMPLETING, and COMPLETED. An explanation of each state follows::
BF BOOT_FAIL Job terminated due to launch failure, typically due to a hardware failure (e.g.
unable to boot the node or block and the job can not be requeued).
CA CANCELLED Job was explicitly cancelled by the user or system administrator.
The job may or may not have been initiated.
CD COMPLETED Job has terminated all processes on all nodes.
CF CONFIGURING Job has been allocated resources, but are waiting for them to become ready for use (e.g. booting).
CG COMPLETING Job is in the process of completing. Some processes on some nodes may still be active.
F FAILED Job terminated with non-zero exit code or other failure condition.
NF NODE_FAIL Job terminated due to failure of one or more allocated nodes.
PD PENDING Job is awaiting resource allocation.
PR PREEMPTED Job terminated due to preemption.
R RUNNING Job currently has an allocation.
S SUSPENDED Job has an allocation, but execution has been suspended.
TO TIMEOUT Job terminated upon reaching its time limit.
SE SPECIAL_EXIT The job was requeued in a special state. This state can be set by users, typically
in EpilogSlurmctld, if the job has terminated with a particular exit value.
"""
_STATUS_TABLE = OrderedDict([
(-1, "UNKNOWN"),
(0, "PENDING"),
(1, "RUNNING"),
(2, "RESIZING"),
(3, "SUSPENDED"),
(4, "COMPLETED"),
(5, "CANCELLED"),
(6, "FAILED"),
(7, "TIMEOUT"),
(8, "PREEMPTED"),
(9, "NODEFAIL"),
])
def __repr__(self):
return "<%s: %s, at %s>" % (self.__class__.__name__, str(self), id(self))
def __str__(self):
"""String representation."""
return self._STATUS_TABLE[self]
[docs] @classmethod
def from_string(cls, s):
"""Return a :class:`JobStatus` instance from its string representation."""
for num, text in cls._STATUS_TABLE.items():
if text == s: return cls(num)
else:
#raise ValueError("Wrong string %s" % s)
logger.warning("Got unknown status: %s" % s)
return cls.from_string("UNKNOWN")
[docs]class QueueJob(object):
"""
This object provides methods to contact the resource manager to get info on the status
of the job and useful statistics. This is an abstract class.
"""
QTYPE = None
# Used to handle other resource managers.
S_UNKNOWN = JobStatus.from_string("UNKNOWN")
# Slurm status
S_PENDING = JobStatus.from_string("PENDING")
S_RUNNING = JobStatus.from_string("RUNNING")
S_RESIZING = JobStatus.from_string("RESIZING")
S_SUSPENDED = JobStatus.from_string("SUSPENDED")
S_COMPLETED = JobStatus.from_string("COMPLETED")
S_CANCELLED = JobStatus.from_string("CANCELLED")
S_FAILED = JobStatus.from_string("FAILED")
S_TIMEOUT = JobStatus.from_string("TIMEOUT")
S_PREEMPTED = JobStatus.from_string("PREEMPTED")
S_NODEFAIL = JobStatus.from_string("NODEFAIL")
[docs] @staticmethod
def from_qtype_and_id(qtype, queue_id, qname=None):
"""
Return a new istance of the appropriate subclass.
Args:
qtype: String specifying the Resource manager type.
queue_id: Job identifier.
qname: Name of the queue (optional).
"""
for cls in all_subclasses(QueueJob):
if cls.QTYPE == qtype: break
else:
logger.critical("Cannot find QueueJob subclass registered for qtype %s" % qtype)
cls = QueueJob
return cls(queue_id, qname=qname)
def __init__(self, queue_id, qname="UnknownQueue"):
"""
Args:
queue_id: Job identifier.
qname: Name of the queue (optional).
"""
self.qid, self.qname = queue_id, qname
# Initialize properties.
self.status, self.exitcode, self.signal = None, None, None
def __repr__(self):
return "<%s, qid=%s, status=%s, exit_code=%s>" % (
self.__class__.__name__, self.qid, self.status, self.exitcode)
def __bool__(self):
return self.qid is not None
__nonzero__ = __bool__
#In many cases, we only need to know if job is terminated or not
#def is_terminated()
@property
def is_completed(self):
return self.status == self.S_COMPLETED
@property
def is_running(self):
return self.status == self.S_RUNNING
@property
def is_failed(self):
return self.status == self.S_FAILED
@property
def timeout(self):
return self.status == self.S_TIMEOUT
@property
def has_node_failures(self):
return self.status == self.S_NODEFAIL
@property
def unknown_status(self):
return self.status == self.S_UNKNOWN
[docs] def set_status_exitcode_signal(self, status, exitcode, signal):
self.status, self.exitcode, self.signal = status, exitcode, signal
[docs] def likely_code_error(self):
"""
See <http://man7.org/linux/man-pages/man7/signal.7.html>
========= ========= ======= ========================================================================
SIGHUP 1 Term Hangup detected on controlling terminal or death of controlling process
SIGINT 2 Term Interrupt from keyboard
SIGQUIT 3 Core Quit from keyboard
SIGILL 4 Core Illegal Instruction
SIGABRT 6 Core Abort signal from abort(3)
SIGFPE 8 Core Floating point exception
SIGKILL 9 Term Kill signal
SIGSEGV 11 Core Invalid memory reference
SIGPIPE 13 Term Broken pipe: write to pipe with no readers
SIGALRM 14 Term Timer signal from alarm(2)
SIGTERM 15 Term Termination signal
SIGUSR1 30,10,16 Term User-defined signal 1
SIGUSR2 31,12,17 Term User-defined signal 2
SIGCHLD 20,17,18 Ign Child stopped or terminated
SIGCONT 19,18,25 Cont Continue if stopped
SIGSTOP 17,19,23 Stop Stop process
SIGTSTP 18,20,24 Stop Stop typed at terminal
SIGTTIN 21,21,26 Stop Terminal input for background process
SIGTTOU 22,22,27 Stop Terminal output for background process
========= ========= ======= ========================================================================
The signals SIGKILL and SIGSTOP cannot be caught, blocked, or ignored.
Next the signals not in the POSIX.1-1990 standard but described in SUSv2 and POSIX.1-2001.
========== ========= ======== ========================================
Signal Value Action Comment
SIGBUS 10,7,10 Core Bus error (bad memory access)
SIGPOLL Term Pollable event (Sys V).
Synonym for SIGIO
SIGPROF 27,27,29 Term Profiling timer expired
SIGSYS 12,31,12 Core Bad argument to routine (SVr4)
SIGTRAP 5 Core Trace/breakpoint trap
SIGURG 16,23,21 Ign Urgent condition on socket (4.2BSD)
SIGVTALRM 26,26,28 Term Virtual alarm clock (4.2BSD)
SIGXCPU 24,24,30 Core CPU time limit exceeded (4.2BSD)
SIGXFSZ 25,25,31 Core File size limit exceeded (4.2BSD)
========== ========= ======== ========================================
"""
for sig_name in ("SIGFPE",):
if self.received_signal(sig_name): return sig_name
return False
[docs] def received_signal(self, sig_name):
if self.signal is None: return False
# Get the numeric value from signal and compare it with self.signal
import signal
try:
return self.signal == getattr(signal, sig_name)
except AttributeError:
# invalid sig_name or sig_name not available on this OS.
return False
[docs] def estimated_start_time(self):
"""Return date with estimated start time. None if it cannot be detected"""
return None
[docs] def get_info(self, **kwargs):
return None
[docs] def get_nodes(self, **kwargs):
return None
[docs] def get_stats(self, **kwargs):
return None
[docs]class ShellJob(QueueJob):
"""Handler for Shell jobs."""
QTYPE = "shell"
[docs]class SlurmJob(QueueJob):
"""Handler for Slurm jobs."""
QTYPE = "slurm"
[docs] def estimated_start_time(self):
#squeue --start -j 116791
# JOBID PARTITION NAME USER ST START_TIME NODES NODELIST(REASON)
# 116791 defq gs6q2wop username PD 2014-11-04T09:27:15 16 (QOSResourceLimit)
cmd = "squeue" "--start", "--job %d" % self.qid
process = Popen(shlex.split(cmd), stdout=PIPE, stderr=PIPE)
out, err = process.communicate()
if process.returncode != 0:
logger.critical(err)
return None
lines = out.splitlines()
if len(lines) <= 2: return None
from datetime import datetime
for line in lines:
tokens = line.split()
if int(tokens[0]) == self.qid:
date_string = tokens[5]
if date_string == "N/A": return None
return datetime.strptime(date_string, "%Y-%m-%dT%H:%M:%S")
return None
[docs] def get_info(self, **kwargs):
# See https://computing.llnl.gov/linux/slurm/sacct.html
#If SLURM job ids are reset, some job numbers will
#probably appear more than once refering to different jobs.
#Without this option only the most recent jobs will be displayed.
#state Displays the job status, or state.
#Output can be RUNNING, RESIZING, SUSPENDED, COMPLETED, CANCELLED, FAILED, TIMEOUT,
#PREEMPTED or NODE_FAIL. If more information is available on the job state than will fit
#into the current field width (for example, the uid that CANCELLED a job) the state will be followed by a "+".
#gmatteo@master2:~
#sacct --job 112367 --format=jobid,exitcode,state --allocations --parsable2
#JobID|ExitCode|State
#112367|0:0|RUNNING
#scontrol show job 800197 --oneliner
# For more info
#login1$ scontrol show job 1676354
#cmd = "sacct --job %i --format=jobid,exitcode,state --allocations --parsable2" % self.qid
cmd = "scontrol show job %i --oneliner" % self.qid
process = Popen(shlex.split(cmd), stdout=PIPE, stderr=PIPE)
out, err = process.communicate()
if process.returncode != 0:
logger.critical(err)
return None
tokens = out.splitlines()
info = AttrDict()
for line in tokens:
#print(line)
k, v = line.split("=")
info[k] = v
#print(info)
qid = int(info.JobId)
assert qid == self.qid
exitcode = info.ExitCode
status = info.JobState
if ":" in exitcode:
exitcode, signal = map(int, exitcode.split(":"))
else:
exitcode, signal = int(exitcode), None
i = status.find("+")
if i != -1: status = status[:i]
self.set_status_exitcode_signal(JobStatus.from_string(status), exitcode, signal)
return AttrDict(exitcode=exitcode, signal=signal, status=status)
[docs] def get_stats(self, **kwargs):
cmd = "sacct --long --job %s --parsable2" % self.qid
process = Popen(shlex.split(cmd), stdout=PIPE, stderr=PIPE)
out, err = process.communicate()
if process.returncode != 0:
logger.critical(err)
return {}
lines = out.splitlines()
keys = lines[0].strip().split("|")
values = lines[1].strip().split("|")
#print("lines0", lines[0])
return dict(zip(keys, values))
[docs]class PbsProJob(QueueJob):
"""
Handler for PbsPro Jobs.
See also https://github.com/plediii/pbs_util for a similar project.
"""
QTYPE = "pbspro"
# Mapping PrbPro --> Slurm. From `man qstat`
#
# S The job’s state:
# B Array job has at least one subjob running.
# E Job is exiting after having run.
# F Job is finished.
# H Job is held.
# M Job was moved to another server.
# Q Job is queued.
# R Job is running.
# S Job is suspended.
# T Job is being moved to new location.
# U Cycle-harvesting job is suspended due to keyboard activity.
# W Job is waiting for its submitter-assigned start time to be reached.
# X Subjob has completed execution or has been deleted.
PBSSTAT_TO_SLURM = defaultdict(lambda x: QueueJob.S_UNKNOWN, [
("E", QueueJob.S_FAILED),
("F", QueueJob.S_COMPLETED),
("Q", QueueJob.S_PENDING),
("R", QueueJob.S_RUNNING),
("S", QueueJob.S_SUSPENDED),
])
[docs] def estimated_start_time(self):
# qstat -T - Shows the estimated start time for all jobs in the queue.
# Est
# Req'd Req'd Start
#Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
#--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
#5669001.frontal username large gs.Pt -- 96 96 -- 03:00 Q --
cmd = "qstat %s -T" % self.qid
process = Popen(shlex.split(cmd), stdout=PIPE, stderr=PIPE)
out, err = process.communicate()
if process.returncode != 0:
logger.critical(err)
return None
line = out.splitlines()[-1]
sdate = line.split()[-1]
if sdate in ("--", "?"):
return None
# TODO One should convert to datetime
return sdate
[docs] def get_info(self, **kwargs):
# See also qstat -f
#http://sc.tamu.edu/help/origins/batch.shtml#qstat
#$> qstat 5666289
#frontal1:
# Req'd Req'd Elap
#Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
#--------------- -------- -------- ---------- ------ --- --- ------ ----- - -----
#5666289.frontal username main_ivy MorfeoTChk 57546 1 4 -- 08:00 R 00:17
cmd = "qstat %d" % self.qid
process = Popen(shlex.split(cmd), stdout=PIPE, stderr=PIPE)
out, err = process.communicate()
if process.returncode != 0:
# qstat: 5904257.frontal1 Job has finished, use -x or -H to obtain historical job information\n
cmd = "qstat %d -x" % self.qid
process = Popen(shlex.split(cmd), stdout=PIPE, stderr=PIPE)
out, err = process.communicate()
if process.returncode != 0:
logger.critical(out)
logger.critical(err)
return None
# Here I don't know what's happeing but I get an output that differs from the one obtained in the terminal.
# Job id Name User Time Use S Queue
# ---------------- ---------------- ---------------- -------- - -----
# 5905011.frontal1 t0 gmatteo 01:37:08 F main_wes
#print(out)
line = out.splitlines()[-1]
#print(line.split())
status = self.PBSSTAT_TO_SLURM[line.split()[4]]
# Exit code and signal are not available.
# Once could use tracejob....
# See also http://docs.adaptivecomputing.com/torque/3-0-5/a.gprologueepilogue.php
self.set_status_exitcode_signal(status, None, None)
#################################
# Unsupported resource managers #
#################################
[docs]class TorqueJob(QueueJob):
"""Not supported"""
QTYPE = "torque"
[docs]class SgeJob(QueueJob):
"""Not supported"""
QTYPE = "sge"
[docs]class MoabJob(QueueJob):
"""Not supported"""
QTYPE = "moab"
[docs]class BlueGeneJob(QueueJob):
"""Not supported"""
QTYPE = "bluegene"