def kill(self): """ Kill the job """ cmdlist = [self.cmds['scancel'], str(self.pid)] try: cmd.run(cmdlist) except (OSError, subprocess.CalledProcessError): # pragma: no cover pass
def submit(self): """ Submit the job @returns: The `utils.cmd.Cmd` instance """ # run self as a script c = cmd.run([sys.executable, path.realpath(__file__), self.script], bg = True) c.rc = 0 return c
def submit (self): """ Try to submit the job """ c = cmd.run([ sys.executable, path.realpath(__file__), self.script[-1] if isinstance(self.script, list) else self.script ], bg = True) c.rc = 0 return c
def alive(self): """ Tell if the job is alive @returns: `True` if it is else `False` """ if self.pid is None: return False cmdlist = [self.cmds['qstat'], '-j', str(self.pid)] try: r = cmd.run(cmdlist) return r.rc == 0 except (OSError, subprocess.CalledProcessError): return False
def alive(self): """ Tell if the job is alive @returns: `True` if it is else `False` """ if self.pid is None: return False cmdlist = [self.cmds['squeue'], '-j', str(self.pid)] try: r = cmd.run(cmdlist) if r.rc != 0: return False return r.stdout.splitlines()[1].split()[0] == str(self.pid) except (OSError, subprocess.CalledProcessError): return False
def submit(self): """ Submit the job @returns: The `utils.cmd.Cmd` instance if succeed else a `Box` object with stderr as the exception and rc as 1 """ cmdlist = [self.cmds['sbatch'], self.script] try: r = cmd.run(cmdlist) # sbatch: Submitted batch job 99999999 m = re.search(r'\s(\d+)$', r.stdout) if not m: # pragma: no cover r.rc = 1 else: self.pid = m.group(1) return r except (OSError, subprocess.CalledProcessError) as ex: # pragma: no cover r = Box() r.stderr = str(ex) r.rc = 1 return r
def submit(self):
"""
Submit the job
@returns:
The `utils.cmd.Cmd` instance if succeed
else a `Box` object with stderr as the exception and rc as 1
"""
cmdlist = [self.cmds['qsub'], self.script]
try:
r = cmd.run(cmdlist)
# Your job 6556149 ("pSort.notag.3omQ6NdZ.0") has been submitted
m = re.search(r'\s(\d+)\s', r.stdout)
if not m:
r.rc = 1
else:
self.pid = m.group(1)
return r
except (OSError, subprocess.CalledProcessError) as ex:
r = Box()
r.stderr = str(ex)
r.rc = 1
return r