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Monitor.py
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Monitor.py
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import atexit
import time
import os
import commands
import json
import re
import sys
import pUtil
import signal
import traceback
import Node
import Job
from shutil import copy, copy2
from random import shuffle
from glob import glob
from JobRecovery import JobRecovery
from processes import killProcesses, checkProcesses, killOrphans, getMaxMemoryUsageFromCGroups, get_current_cpu_consumption_time, findProcessesInGroup
from PilotErrors import PilotErrors
from FileStateClient import createFileStates, dumpFileStates, getFileState
from WatchDog import WatchDog
from PilotTCPServer import PilotTCPServer
from UpdateHandler import UpdateHandler
from RunJobFactory import RunJobFactory
from FileHandling import updatePilotErrorReport, getDirSize, storeWorkDirSize, getOsTimesTuple, readFile, get_files, tail, find_latest_modified_file
import inspect
def lineno():
""" Returns the current line number in our program """
return inspect.currentframe().f_back.f_lineno
globalSite = None
class Monitor:
__skip = False
__localsizelimit_stdout = 2*1024**2 # size limit of payload stdout size during running. unit is in kB
def __init__(self, env):
self.__error = PilotErrors()
self.__env = env
#self.__env['pilot_startup'] = None
self.__env['create_softlink'] = True
self.__env['return_code'] = None
self.__env['curtime_sp'] = int(time.time())
self.__env['curtime_pr'] = int(time.time())
self.__env['lastTimeFilesWereModified'] = {}
self.__wdog = WatchDog()
self.__runJob = None # Remember the RunJob instance
# using thread pool
self.__threadpool = None
self.__jobs_added_to_threadpool = []
self.__jobs_cleaned_up = []
# register cleanup function
atexit.register(pUtil.cleanup, self.__wdog, self.__env['pilot_initdir'], self.__env['wrapperFlag'], self.__env['rmwkdir'])
signal.signal(signal.SIGTERM, pUtil.sig2exc)
signal.signal(signal.SIGQUIT, pUtil.sig2exc)
signal.signal(signal.SIGSEGV, pUtil.sig2exc)
signal.signal(signal.SIGXCPU, pUtil.sig2exc)
signal.signal(signal.SIGBUS, pUtil.sig2exc)
signal.signal(signal.SIGUSR1, pUtil.sig2exc)
def __allowLoopingJobKiller(self):
""" Should the looping job killer be run? """
# This decision is not on an Experiment level but is relevant only for the type of subprocess that is requested
# E.g. the looping job killer should normally be run for a normal ATLAS job, but not on an HPC. Therefore, the
# decision is made inside the subprocess class (RunJob, RunJobHPC, ..)
allow = True
# Which RunJob class do we need to ask?
if not self.__runJob:
# First get an Experiment object, which will tell us which subprocess to ask
thisExperiment = pUtil.getExperiment(self.__env['experiment'])
subprocessName = thisExperiment.getSubprocessName(self.__env['jobDic']["prod"][1].eventService)
pUtil.tolog("subprocessName = %s" % (subprocessName))
# Now get an instance of the corresponding class from the RunJobFactory
factory = RunJobFactory()
_rJ = factory.newRunJob(subprocessName)
self.__runJob = _rJ()
if self.__runJob:
# Is the looping job killer allowed by the subprocess?
allow = self.__runJob.allowLoopingJobKiller()
name = os.path.splitext(self.__runJob.getRunJobFileName())[0]
if allow:
pUtil.tolog("Looping job killer is allowed by subprocess %s" % (name))
else:
pUtil.tolog("Looping job killer is not allowed by subprocess %s" % (name))
else:
pUtil.tolog("!!WARNING!!2121!! Could not get an instance of a RunJob* class (cannot decide about looping job killer)")
allow = False
return allow
def __checkPayloadStdout(self):
""" Check the size of the payload stdout """
# loop over all parallel jobs
# (after multitasking was removed from the pilot, there is actually only one job)
for k in self.__env['jobDic'].keys():
# get list of log files
fileList = glob("%s/log.*" % (self.__env['jobDic'][k][1].workdir))
# is this a multi-trf job?
nJobs = self.__env['jobDic'][k][1].jobPars.count("\n") + 1
for _i in range(nJobs):
# get name of payload stdout file created by the pilot
_stdout = self.__env['jobDic'][k][1].stdout
if nJobs > 1:
_stdout = _stdout.replace(".txt", "_%d.txt" % (_i + 1))
filename = "%s/%s" % (self.__env['jobDic'][k][1].workdir, _stdout)
# add the primary stdout file to the fileList
fileList.append(filename)
# now loop over all files and check each individually (any large enough file will fail the job)
for filename in fileList:
if "job.log.tgz" in filename:
pUtil.tolog("(Skipping file size check of file (%s) since it is a special log file)" % (filename))
continue
if os.path.exists(filename):
try:
# get file size in bytes
fsize = os.path.getsize(filename)
except Exception, e:
pUtil.tolog("!!WARNING!!1999!! Could not read file size of %s: %s" % (filename, str(e)))
else:
# is the file too big?
if fsize > self.__env['localsizelimit_stdout'] * 1024: # convert to bytes
pilotErrorDiag = "Payload stdout file too big: %d B (larger than limit %d B)" % (fsize, self.__env['localsizelimit_stdout'] * 1024)
pUtil.tolog("!!FAILED!!1999!! %s" % (pilotErrorDiag))
# kill the job
#pUtil.tolog("Going to kill pid %d" %lineno())
pUtil.createLockFile(True, self.__env['jobDic'][k][1].workdir, lockfile="JOBWILLBEKILLED")
killProcesses(self.__env['jobDic'][k][0], self.__env['jobDic'][k][1].pgrp)
self.__env['jobDic'][k][1].result[0] = "failed"
self.__env['jobDic'][k][1].currentState = self.__env['jobDic'][k][1].result[0]
self.__env['jobDic'][k][1].result[2] = self.__error.ERR_STDOUTTOOBIG
self.__env['jobDic'][k][1].pilotErrorDiag = pilotErrorDiag
self.__skip = True
# store the error info
updatePilotErrorReport(self.__env['jobDic'][k][1].result[2], pilotErrorDiag, "1", self.__env['jobDic'][k][1].jobId, self.__env['pilot_initdir'])
# remove the payload stdout file after the log extracts have been created
# remove any lingering input files from the work dir
if self.__env['jobDic'][k][1].inFiles:
if len(self.__env['jobDic'][k][1].inFiles) > 0:
ec = pUtil.removeFiles(self.__env['jobDic'][k][1].workdir, self.__env['jobDic'][k][1].inFiles)
else:
pUtil.tolog("Payload stdout (%s) within allowed size limit (%d B): %d B" % (_stdout, self.__env['localsizelimit_stdout']*1024, fsize))
else:
pUtil.tolog("(Skipping file size check of payload stdout file (%s) since it has not been created yet)" % (_stdout))
def __getMaxAllowedWorkDirSize(self):
"""
Return the maximum allowed size of the work directory
"""
try:
maxwdirsize = int(pUtil.readpar('maxwdir'))*1024**2 # from MB to B, e.g. 16336 MB -> 17,129,537,536 B
except:
maxInputSize = pUtil.getMaxInputSize()
maxwdirsize = maxInputSize + self.__env['localsizelimit_stdout']*1024
pUtil.tolog("Work directory size check will use %d B as a max limit (maxinputsize [%d B] + local size limit for stdout [%d B])" %\
(maxwdirsize, maxInputSize, self.__env['localsizelimit_stdout']*1024))
else:
pUtil.tolog("Work directory size check will use %d B as a max limit (maxwdirsize)" % (maxwdirsize))
return maxwdirsize
def __checkWorkDir(self):
"""
Check the size of the work directory
"""
# get the limit of the workdir
maxwdirsize = self.__getMaxAllowedWorkDirSize()
# add grace margin of 10%
maxwdirsize = int(maxwdirsize * 1.10)
pUtil.tolog('Added a 10%% grace margin to maxwdir: %d B' % maxwdirsize)
# after multitasking was removed from the pilot, there is actually only one job
for k in self.__env['jobDic'].keys():
# get size of workDir
workDir = self.__env['jobDic'][k][1].workdir
if os.path.exists(workDir):
size = getDirSize(workDir)
if size > 0:
# is user dir within allowed size limit?
if size > maxwdirsize:
pilotErrorDiag = "Work directory (%s) too large: %d B (must be < %d B)" %\
(workDir, size, maxwdirsize)
pUtil.tolog("!!FAILED!!1999!! %s" % (pilotErrorDiag))
cmd = 'ls -altrR %s' % workDir
pUtil.tolog("%s: %s" % (cmd + '\n', commands.getoutput(cmd)))
# kill the job
pUtil.createLockFile(True, self.__env['jobDic'][k][1].workdir, lockfile="JOBWILLBEKILLED")
killProcesses(self.__env['jobDic'][k][0], self.__env['jobDic'][k][1].pgrp)
self.__env['jobDic'][k][1].result[0] = "failed"
self.__env['jobDic'][k][1].currentState = self.__env['jobDic'][k][1].result[0]
self.__env['jobDic'][k][1].result[2] = self.__error.ERR_USERDIRTOOLARGE
self.__env['jobDic'][k][1].pilotErrorDiag = pilotErrorDiag
self.__skip = True
# store the error info
updatePilotErrorReport(self.__env['jobDic'][k][1].result[2], pilotErrorDiag, "1", self.__env['jobDic'][k][1].jobId, self.__env['pilot_initdir'])
# remove any lingering input files from the work dir
if self.__env['jobDic'][k][1].inFiles:
if len(self.__env['jobDic'][k][1].inFiles) > 0:
ec = pUtil.removeFiles(self.__env['jobDic'][k][1].workdir, self.__env['jobDic'][k][1].inFiles)
# remeasure the size of the workdir at this point since the value is stored below
size = getDirSize(workDir)
else:
pUtil.tolog("Size of work directory %s: %d B (within %d B limit)" % (workDir, size, maxwdirsize))
# Store the measured disk space (the max value will later be sent with the job metrics)
status = storeWorkDirSize(size, self.__env['pilot_initdir'], self.__env['jobDic'][k][1])
else:
pUtil.tolog("Skipping size of of workDir since it could not be measured")
else:
pUtil.tolog("(Skipping size check of workDir since it has not been created yet)")
def __checkLocalSpace(self, disk):
""" Check the remaining local disk space during running """
spaceleft = int(disk)*1024**2 # B (node.disk is in MB)
_localspacelimit = self.__env['localspacelimit'] * 1024 # B
# do we have enough local disk space to continue running the job?
if spaceleft < _localspacelimit:
pilotErrorDiag = "Too little space left on local disk to run job: %d B (need > %d B)" % (spaceleft, _localspacelimit)
pUtil.tolog("!!FAILED!!1999!! %s" % (pilotErrorDiag))
for k in self.__env['jobDic'].keys():
# kill the job
#pUtil.tolog("Going to kill pid %d" %lineno())
pUtil.createLockFile(True, self.__env['jobDic'][k][1].workdir, lockfile="JOBWILLBEKILLED")
killProcesses(self.__env['jobDic'][k][0], self.__env['jobDic'][k][1].pgrp)
self.__env['jobDic'][k][1].result[0] = "failed"
self.__env['jobDic'][k][1].currentState = self.__env['jobDic'][k][1].result[0]
self.__env['jobDic'][k][1].result[2] = self.__error.ERR_NOLOCALSPACE
self.__env['jobDic'][k][1].pilotErrorDiag = pilotErrorDiag
self.__skip = True
# Store the exit code so that it is reported when the pilot finishes
pUtil.writeToFile(os.path.join(self.__env['thisSite'].workdir, "EXITCODE"), str(self.__error.ERR_NOLOCALSPACE))
# store the error info
updatePilotErrorReport(self.__env['jobDic'][k][1].result[2], pilotErrorDiag, "1", self.__env['jobDic'][k][1].jobId, self.__env['pilot_initdir'])
# remove any lingering input files from the work dir
if self.__env['jobDic'][k][1].inFiles:
if len(self.__env['jobDic'][k][1].inFiles) > 0:
ec = pUtil.removeFiles(self.__env['jobDic'][k][1].workdir, self.__env['jobDic'][k][1].inFiles)
else:
pUtil.tolog("Remaining local disk space: %d B" % (spaceleft))
def __check_remaining_proxy(self):
"""
Every five minutes, check the remaining proxy life time
"""
if (int(time.time()) - self.__env['curtime_pr']) > 5*60:
pUtil.tolog("Verifying proxy life time (should have at least ten minutes left)")
thisExperiment = pUtil.getExperiment(self.__env['experiment'])
ec, pilotErrorDiag = thisExperiment.verifyProxy(envsetup="", limit=10./60.) # limit is in hours
if ec != 0:
pilotErrorDiag = "Proxy has less than ten minutes left - aborting job"
pUtil.tolog("!!FAILED!!1999!! %s" % (pilotErrorDiag))
for k in self.__env['jobDic'].keys():
# kill the job
pUtil.createLockFile(True, self.__env['jobDic'][k][1].workdir, lockfile="JOBWILLBEKILLED")
killProcesses(self.__env['jobDic'][k][0], self.__env['jobDic'][k][1].pgrp)
self.__env['jobDic'][k][1].result[0] = "failed"
self.__env['jobDic'][k][1].currentState = self.__env['jobDic'][k][1].result[0]
self.__env['jobDic'][k][1].result[2] = self.__error.ERR_NOPROXY
self.__env['jobDic'][k][1].pilotErrorDiag = pilotErrorDiag
self.__skip = True
# store the error info
updatePilotErrorReport(self.__env['jobDic'][k][1].result[2], pilotErrorDiag, "1", self.__env['jobDic'][k][1].jobId, self.__env['pilot_initdir'])
# remove any lingering input files from the work dir
if self.__env['jobDic'][k][1].inFiles:
if len(self.__env['jobDic'][k][1].inFiles) > 0:
ec = pUtil.removeFiles(self.__env['jobDic'][k][1].workdir, self.__env['jobDic'][k][1].inFiles)
# update the time for checking the proxy
self.__env['curtime_pr'] = int(time.time())
def __check_memory_usage(self):
"""
Every minute check the memory usage of the payload
Note: requires that the memory monitoring tool is executed (as specified in Experiment::shouldExecuteUtility())
"""
if (int(time.time()) - self.__env['curtime_mem']) > 60:
# Check the memory from the utility every minute
# get the experiment object and check if the memory utility should be used
thisExperiment = pUtil.getExperiment(self.__env['experiment'])
if thisExperiment.shouldExecuteUtility():
for k in self.__env['jobDic'].keys():
# Get the maxPSS value from the memory monitor
summary_dictionary = thisExperiment.getMemoryValues(self.__env['jobDic'][k][1].workdir, self.__env['pilot_initdir'])
try:
maxPSS_int = summary_dictionary['Max']['maxPSS']
except Exception, e:
if summary_dictionary != {}:
pUtil.tolog("!!WARNING!!3434!! Could not extract maxPSS value from: %s" % str(summary_dictionary))
else:
# Normally this means that the memory output file has not been produced yet, so skip it
pass
maxPSS_int = -1
# Only proceed if values are set
if maxPSS_int != -1:
maxRSS = pUtil.readpar('maxrss') # string
if maxRSS:
# correction for SCORE/4CORE/nCORE jobs on UCORE queues
try:
pUtil.tolog('job.coreCount=%f' % float(self.__env['jobDic'][k][1].coreCount))
pUtil.tolog('schedconfig.corecount=%f' % float(pUtil.readpar('corecount')))
scale = float(self.__env['jobDic'][k][1].coreCount) / float(pUtil.readpar('corecount'))
pUtil.tolog('scale=%f' % scale)
except Exception as e:
pUtil.tolog('!!WARNING!!9910!! Exception caught: %s' % e)
scale = 1
try:
maxRSS_int = 2 * int(maxRSS * scale) * 1024 # Convert to int and kB
except Exception, e:
pUtil.tolog("!!WARNING!!9900!! Unexpected value for maxRSS: %s" % e)
else:
# Compare the maxRSS with the maxPSS from memory monitor
if maxRSS_int > 0:
if maxPSS_int > 0:
if maxPSS_int > maxRSS_int:
pilotErrorDiag = "Job has exceeded the memory limit %d kB > %d kB (2*schedconfig.maxrss)" % (maxPSS_int, maxRSS_int)
pUtil.tolog("!!WARNING!!9902!! %s" % (pilotErrorDiag))
# Create a lockfile to let RunJob know that it should not restart the memory monitor after it has been killed
pUtil.createLockFile(False, self.__env['jobDic'][k][1].workdir, lockfile="MEMORYEXCEEDED")
# Kill the job
killProcesses(self.__env['jobDic'][k][0], self.__env['jobDic'][k][1].pgrp)
self.__env['jobDic'][k][1].result[0] = "failed"
self.__env['jobDic'][k][1].currentState = self.__env['job'].result[0]
self.__env['jobDic'][k][1].result[2] = self.__error.ERR_PAYLOADEXCEEDMAXMEM
self.__env['jobDic'][k][1].pilotErrorDiag = pilotErrorDiag
else:
pUtil.tolog("Max memory (maxPSS) used by the payload is within the allowed limit: %d kB (2*maxRSS=%d kB, scale=%f)" % (maxPSS_int, maxRSS_int, scale))
else:
pUtil.tolog("!!WARNING!!9903!! Unexpected MemoryMonitor maxPSS value: %d" % (maxPSS_int))
else:
if maxRSS == 0 or maxRSS == "0":
pUtil.tolog("schedconfig.maxrss set to 0 (no memory checks will be done)")
else:
pUtil.tolog("!!WARNING!!9904!! schedconfig.maxrss is not set")
# update the time for checking memory
self.__env['curtime_mem'] = int(time.time())
def __check_remaining_space(self):
"""
Every ten minutes, check the remaining disk space, the size of the workdir
and the size of the payload stdout file
"""
if (int(time.time()) - self.__env['curtime_sp']) > self.__env['update_freq_space']:
# check the size of the payload stdout
self.__skip = self.__checkPayloadStdout()
# update the worker node info (i.e. get the remaining disk space)
self.__env['workerNode'].collectWNInfo(self.__env['thisSite'].workdir)
self.__skip = self.__checkLocalSpace(self.__env['workerNode'].disk)
# check the size of the workdir
self.__skip = self.__checkWorkDir()
# update the time for checking disk space
self.__env['curtime_sp'] = int(time.time())
def __createSoftLink(self):
""" create a soft link to the athena stdout in the site work dir """
# create_softlink is mutable
# will only point to the first stdout file currently
for k in self.__env['jobDic'].keys():
# is this a multi-trf job?
nJobs = self.__env['jobDic'][k][1].jobPars.count("\n") + 1
for _i in range(nJobs):
_stdout = self.__env['jobDic'][k][1].stdout
if nJobs > 1:
_stdout = _stdout.replace(".txt", "_%d.txt" % (_i + 1))
filename = os.path.join(self.__env['jobDic'][k][1].workdir, _stdout)
# create the soft link only if the stdout has been created
if os.path.exists(filename):
lnfilename = os.path.join(self.__env['thisSite'].workdir, _stdout)
# only create the soft link once..
if not os.path.exists(lnfilename):
# ..and only if the size of stdout is > 0
if os.path.getsize(filename) > 0:
ec, rs = commands.getstatusoutput("ln -s %s %s" % (filename, lnfilename))
if ec == 0:
pUtil.tolog("Created soft link to %s in sitedir: %s" % (_stdout, lnfilename))
else:
pUtil.tolog("!!WARNING!!1999!! Could not create soft link: %d, %s" % (ec, rs))
self.__env['create_softlink'] = False
else:
self.__env['create_softlink'] = False
else:
pUtil.tolog("(%s has not been created yet)" % (_stdout))
def create_softlink(self):
"""
create a soft link in the site workdir to the payload stdout
"""
if self.__env['create_softlink']:
try:
self.__createSoftLink()
except Exception, e:
pUtil.tolog("!!WARNING!!1999!! Caught an exception during soft link creation: %s" % str(e))
self.__env['create_softlink'] = False
def __failMaxTimeJob(self):
"""
Reached maximum batch system time limit, fail the job
"""
pUtil.tolog("!!WARNING!!1999!! The pilot has decided to kill the job since there is less than 10 minutes of the allowed batch system running time")
pilotErrorDiag = "Reached maximum batch system time limit"
pUtil.tolog("!!FAILED!!1999!! %s" % (pilotErrorDiag))
# after multitasking was removed from the pilot, there is actually only one job
for k in self.__env['jobDic'].keys():
if self.__env['jobDic'][k][1].eventService:
pUtil.createLockFile(True, self.__env['jobDic'][k][1].workdir, lockfile="SOFTKILL")
else:
# kill the job
#pUtil.tolog("Going to kill pid %d" %lineno())
pUtil.createLockFile(True, self.__env['jobDic'][k][1].workdir, lockfile="JOBWILLBEKILLED")
killProcesses(self.__env['jobDic'][k][0], self.__env['jobDic'][k][1].pgrp)
self.__env['jobDic'][k][1].result[0] = "failed"
self.__env['jobDic'][k][1].currentState = self.__env['jobDic'][k][1].result[0]
self.__env['jobDic'][k][1].result[2] = self.__error.ERR_REACHEDMAXTIME
self.__env['jobDic'][k][1].pilotErrorDiag = pilotErrorDiag
# store the error info
updatePilotErrorReport(self.__env['jobDic'][k][1].result[2], pilotErrorDiag, "1", self.__env['jobDic'][k][1].jobId, self.__env['pilot_initdir'])
def __monitor_processes(self):
# monitor the number of running processes and the pilot running time
if (int(time.time()) - self.__env['curtime_proc']) > self.__env['update_freq_proc']:
# check the number of running processes
nProc = checkProcesses(self.__env['jobDic']["prod"][0])
if nProc > self.__env['maxNProc']:
self.__env['maxNProc'] = nProc
# monitor the pilot running time (once every five minutes = update_freq_proc)
time_passed_since_pilot_startup = int(time.time()) - self.__env['pilot_startup']
pUtil.tolog("Time passed since pilot startup = %d s (maximum allowed batch system time = %d s)"
% (time_passed_since_pilot_startup, self.__env['maxtime']))
if (self.__env['maxtime'] - time_passed_since_pilot_startup) < 10*60 and not self.__env['stageout']:
# reached maximum batch system time limit
if not "NO_PILOT_TIME_LIMIT_KILL" in pUtil.readpar('catchall'):
self.__failMaxTimeJob()
self.__skip = True
else:
pUtil.tolog("Max allowed batch system time passed (%d s) - but pilot will not kill job since NO_PILOT_TIME_LIMIT_KILL is present in catchall field" % (time_passed_since_pilot_startup))
# update the time for checking processes
self.__env['curtime_proc'] = int(time.time())
def __verifyOutputFileSizes(self):
""" Verify output file sizes """
pilotErrorDiag = ""
job_index = 0
rc = 0
pUtil.tolog("Verifying output file sizes")
for k in self.__env['jobDic'].keys():
if len(self.__env['jobDic'][k][1].outFiles) > 0:
for file_name in self.__env['jobDic'][k][1].outFiles:
findFlag = False
# locate the file first
out = commands.getoutput("find %s -name %s" % (self.__env['jobDic'][k][1].workdir, file_name))
if out != "":
for line in out.split('\n'):
try:
file_size = os.path.getsize(line)
findFlag = True
if file_size > self.__env['outputlimit']:
pilotErrorDiag = 'File: \"%s\" is too large %d > %d B)' % (line, file_size, self.__env['outputlimit'])
pUtil.tolog('!!WARNING!!2999!!%s' % (pilotErrorDiag))
job_index = k
rc = self.__error.ERR_OUTPUTFILETOOLARGE
else:
pUtil.tolog('File: \"%s\" currently has size %d < %d B)' % (line, file_size, self.__env['outputlimit']))
except:
pass
if not findFlag and file_name != self.__env['jobDic'][k][1].logFile:
pUtil.tolog("Could not access file %s: %s" % (file_name, out))
return rc, pilotErrorDiag, job_index
def __checkOutputFileSizes(self):
""" check that the output file sizes are within the limit """
# return True for too large files, to skip looping test and normal server update
# verify the file sizes
rc, pilotErrorDiag, job_index = self.__verifyOutputFileSizes()
if rc == 0:
pUtil.tolog("Completed output file size verification")
else:
# found too large output file, stop the job
self.__env['jobDic'][job_index][1].result[0] = "failed"
self.__env['jobDic'][job_index][1].currentState = self.__env['jobDic'][job_index][1].result[0]
self.__env['jobDic'][job_index][1].result[2] = rc
self.__env['jobDic'][job_index][1].pilotErrorDiag = pilotErrorDiag
self.__skip = True
# store the error info
updatePilotErrorReport(self.__env['jobDic'][job_index][1].result[2], pilotErrorDiag, "1", self.__env['jobDic'][k][1].jobId, self.__env['pilot_initdir'])
def __verify_output_sizes(self):
# verify output file sizes every ten minutes
if (int(time.time()) - self.__env['curtime_of']) > self.__env['update_freq_space']:
# check the output file sizes
self.__skip = self.__checkOutputFileSizes()
# update the time for checking output file sizes
self.__env['curtime_of'] = int(time.time())
# FOR TESTING ONLY
# def __verify_memory_limits(self):
# if (int(time.time()) - self.__env['curtime_mem']) > 1*60: #self.__env['update_freq_mem']:
# # check the CGROUPS memory
# max_memory = getMaxMemoryUsageFromCGroups()
# if max_memory:
# pUtil.tolog("cgroups max_memory = %s" % (max_memory))
# else:
# pUtil.tolog("cgroups max_memory not defined")
#
# # update the time for checking memory
# self.__env['curtime_mem'] = int(time.time())
def __killLoopingJob(self, job, pid, setStageout=False):
""" kill the looping job """
# the child process is looping, kill it
pilotErrorDiag = "Pilot has decided to kill looping job %s at %s" %\
(job.jobId, pUtil.timeStamp())
pUtil.tolog("!!FAILED!!1999!! %s" % (pilotErrorDiag))
cmd = 'ps -fwu %s' % (commands.getoutput("whoami"))
pUtil.tolog("%s: %s" % (cmd + '\n', commands.getoutput(cmd)))
cmd = 'ls -ltr %s' % (job.workdir)
pUtil.tolog("%s: %s" % (cmd + '\n', commands.getoutput(cmd)))
cmd = 'ps -o pid,ppid,sid,pgid,tpgid,stat,comm -u %s' % (commands.getoutput("whoami"))
pUtil.tolog("%s: %s" % (cmd + '\n', commands.getoutput(cmd)))
pUtil.createLockFile(True, job.workdir, lockfile="JOBWILLBEKILLED")
killProcesses(pid, job.pgrp)
if self.__env['stagein']:
pilotErrorDiag += " (Job stuck in stage-in state)"
pUtil.tolog("!!FAILED!!1999!! Job stuck in stage-in state: file copy time-out")
job.result[2] = self.__error.ERR_GETTIMEOUT
elif setStageout:
pilotErrorDiag += " (Job stuck in stage-out state)"
pUtil.tolog("!!FAILED!!1999!! Job stuck in stage-out state: file copy time-out")
job.result[2] = self.__error.ERR_PUTTIMEOUT
job.result[0] = "failed"
job.currentState = job.result[0]
else:
job.result[2] = self.__error.ERR_LOOPINGJOB
job.result[0] = "failed"
job.currentState = job.result[0]
job.pilotErrorDiag = pilotErrorDiag
# store the error info
updatePilotErrorReport(job.result[2], pilotErrorDiag, "1", job.jobId, self.__env['pilot_initdir'])
# remove any lingering input files from the work dir
if job.inFiles:
if len(job.inFiles) > 0:
ec = pUtil.removeFiles(job.workdir, job.inFiles)
return job
def __updateJobs(self, onlyUpdateStateChangedJobs=False):
""" Send a heartbeat """
# get the stdout tails
stdout_dictionary = pUtil.getStdoutDictionary(self.__env['jobDic'])
# loop over all parallel jobs, update server, kill job if necessary
# (after multitasking was removed from the pilot, there is actually only one job)
for k in self.__env['jobDic'].keys():
pUtil.tolog("onlyUpdateStateChangedJobs: %s, lastState: %s, currentState: %s" % (onlyUpdateStateChangedJobs, self.__env['jobDic'][k][1].lastState, self.__env['jobDic'][k][1].currentState))
if onlyUpdateStateChangedJobs and self.__env['jobDic'][k][1].lastState == self.__env['jobDic'][k][1].currentState:
continue
self.__env['jobDic'][k][1].lastState = self.__env['jobDic'][k][1].currentState
# update the CPU consumption time
t0 = getOsTimesTuple(self.__env['jobDic'][k][1].workdir)
if t0 and self.__env['jobDic'][k][1].currentState == 'running':
path = os.path.join(self.__env['jobDic'][k][1].workdir, 'cpid.txt')
cpid = readFile(path)
if cpid:
try:
_cpid = int(cpid)
except Exception as e:
pUtil.tolog('failed to convert %s to int: %s' % (cpid, e))
else:
cpuconsumptiontime = get_current_cpu_consumption_time(_cpid)
#cpuconsumptiontime = get_instant_cpu_consumption_time(_cpid)
#cpuconsumptiontime = get_instant_cpu_consumption_time(self.__env['jobDic']["prod"][0])
self.__env['jobDic'][k][1].cpuConsumptionTime = int(cpuconsumptiontime)
self.__env['jobDic'][k][1].cpuConsumptionUnit = 's'
self.__env['jobDic'][k][1].cpuConversionFactor = 1.0
pUtil.tolog("Job CPU usage: %d" % (self.__env['jobDic'][k][1].cpuConsumptionTime))
tmp = self.__env['jobDic'][k][1].result[0]
if tmp != "finished" and tmp != "failed" and tmp != "holding":
# get the tail if possible
if self.__env['jobDic'][k][1].debug:
try:
# find the latest updated log file
list_of_files = get_files(pattern="*.log")
if not list_of_files: # some TRFs produce logs with different naming scheme
list_of_files = get_files(pattern="log.*")
latest_file = max(list_of_files, key=os.path.getmtime)
pUtil.tolog('tail of file %s will be added to heartbeat' % latest_file)
# now get the tail of the found log file
_tail = latest_file + "\n" + tail(latest_file)
self.__env['stdout_tail'] = _tail # stdout_dictionary[self.__env['jobDic'][k][1].jobId]
index = "path-%s" % (self.__env['jobDic'][k][1].jobId)
self.__env['stdout_path'] = stdout_dictionary[index]
except Exception, e:
pUtil.tolog("!!WARNING!!4545!! Failed to get stdout tail: %s" % e)
self.__env['stdout_tail'] = "(stdout tail not available)"
self.__env['stdout_path'] = ""
# update the panda server
try:
self.__env['jobDic'][k][1].updatingPandaServer = True
ret, retNode = pUtil.updatePandaServer(self.__env['jobDic'][k][1], stdout_tail = self.__env['stdout_tail'], stdout_path = self.__env['stdout_path'])
self.__env['jobDic'][k][1].updatingPandaServer = False
except Exception, e:
self.__env['jobDic'][k][1].updatingPandaServer = False
raise e
if ret == 0:
pUtil.tolog("Successfully updated panda server at %s" % pUtil.timeStamp())
else:
pUtil.tolog("!!WARNING!!1999!! updatePandaServer returned a %d" % (ret))
# kill a job if signaled from panda server
if "tobekilled" in self.__env['jobDic'][k][1].action:
pilotErrorDiag = "Pilot received a panda server signal to kill job %s at %s" %\
(self.__env['jobDic'][k][1].jobId, pUtil.timeStamp())
pUtil.tolog("!!FAILED!!1999!! %s" % (pilotErrorDiag))
if not self.processCanBeKilled(self.__env['jobDic'][k][0]):
pUtil.tolog("Process %s cannot be killed. It's shared by other panda job" % self.__env['jobDic'][k][0])
continue
if self.__env['jobrec']:
self.__env['jobrec'] = False
pUtil.tolog("Switching off job recovery")
# kill the real job process(es)
#pUtil.tolog("Going to kill pid %d" %lineno())
pUtil.createLockFile(True, self.__env['jobDic'][k][1].workdir, lockfile="JOBWILLBEKILLED")
killProcesses(self.__env['jobDic'][k][0], self.__env['jobDic'][k][1].pgrp)
self.__env['jobDic'][k][1].result[0] = "failed"
self.__env['jobDic'][k][1].subStatus = "pilot_killed"
self.__env['jobDic'][k][1].currentState = self.__env['jobDic'][k][1].result[0]
self.__env['jobDic'][k][1].result[2] = self.__error.ERR_PANDAKILL
self.__env['jobDic'][k][1].pilotErrorDiag = pilotErrorDiag
# store the error info
updatePilotErrorReport(self.__env['jobDic'][k][1].result[2], pilotErrorDiag, "1", self.__env['jobDic'][k][1].jobId, self.__env['pilot_initdir'])
if "softkill" in self.__env['jobDic'][k][1].action:
pilotErrorDiag = "Pilot received a panda server softkill signal to kill job %s at %s" %\
(self.__env['jobDic'][k][1].jobId, pUtil.timeStamp())
pUtil.createLockFile(True, self.__env['jobDic'][k][1].workdir, lockfile="SOFTKILL")
# did we receive a command to turn on debug mode?
if "debug" in self.__env['jobDic'][k][1].action.lower():
pUtil.tolog("Pilot received a command to turn on debug mode from the server")
self.__env['update_freq_server'] = 5*60
pUtil.tolog("Server update frequency lowered to %d s" % (self.__env['update_freq_server']))
self.__env['jobDic'][k][1].debug = True
# did we receive a command to turn off debug mode?
if "debugoff" in self.__env['jobDic'][k][1].action.lower():
pUtil.tolog("Pilot received a command to turn off debug mode from the server")
self.__env['update_freq_server'] = 30*60
pUtil.tolog("Server update frequency increased to %d s" % (self.__env['update_freq_server']))
self.__env['jobDic'][k][1].debug = False
def __loopingJobKiller(self):
""" Look for looping job """
pUtil.tolog("Checking for looping job")
for k in self.__env['jobDic'].keys():
# if current run state is "stageout", just make sure that the stage out copy command is not hanging
if self.__env['stageout']:
pUtil.tolog("Making sure that the stage out copy command is not hanging")
if not self.__env['stageoutStartTime']:
pUtil.tolog("!!WARNING!!1700!! Stage-out start time not set")
else:
# how much time has passed since stage-out began?
time_passed = int(time.time()) - self.__env['stageoutStartTime']
# max time-out as defined in movers/base
timeout = 5 + 3*3600
pUtil.tolog("Stage-out with %s site mover began at %s (%d s ago, site mover time-out: %d s)"
%(pUtil.readpar('copytool'), time.strftime("%H:%M:%S", time.gmtime(self.__env['stageoutStartTime'])), time_passed, timeout))
grace_time = 5*60
if time_passed > timeout:
pUtil.tolog("Adding a grace time of %d s in case copy command has been aborted but file removal is not complete" % (grace_time))
if time_passed > timeout + grace_time:
self.__env['jobDic'][k][1] = self.__killLoopingJob(self.__env['jobDic'][k][1], self.__env['jobDic'][k][0], setStageout = True)
elif len(self.__env['jobDic'][k][1].outFiles) > 0: # only check for looping job for jobs with output files
# loop over all job output files and find the one with the latest modification time
# note that some files might not have been created at this point (e.g. RDO built from HITS)
# locate all files that were modified the last N minutes
cmd = "find %s -mmin -%d" % (self.__env['jobDic'][k][1].workdir, int(self.__env['loopingLimit']/60))
pUtil.tolog("Executing command: %s" % (cmd))
out = commands.getoutput(cmd)
if out != "":
files = out.split("\n")
if len(files) > 0:
# remove unwanted list items (*.py, *.pyc, workdir, ...)
_files = []
for _file in files:
if not (self.__env['jobDic'][k][1].workdir == _file or
".lib.tgz" in _file or
".py" in _file or
"PoolFileCatalog" in _file or
"setup.sh" in _file or
"jobState" in _file or
"pandaJob" in _file or
"runjob" in _file or
"matched_replicas" in _file or
"memory_" in _file or
"mem." in _file or
"DBRelease-" in _file):
_files.append(_file)
if _files != []:
pUtil.tolog("Found %d files that were recently updated" % len(_files))
# now get the mod times for these files, and identify the most recently update file
# try protection against file system problems
try:
latest_modified_file, mtime = find_latest_modified_file(_files)
except Exception as e:
pUtil.tolog("!!WARNING!!2332!! Exception caught (file system problem?): %s" % e)
mtime = None
if mtime:
pUtil.tolog("File %s is the most recently updated file (at time=%d)" % (latest_modified_file, mtime))
# set lastTimeFilesWereModified to the mod time of the most recently updated file
self.__env['lastTimeFilesWereModified'][k] = mtime
else:
pUtil.tolog("WARNING: found no recently updated files!")
else:
pUtil.tolog("WARNING: found no recently updated files")
else:
pUtil.tolog("WARNING: Found no recently updated files")
# check if the last modification time happened long ago
# (process is considered to be looping if it's files have not been modified within loopingLimit time)
pUtil.tolog("int(time.time())=%d"%int(time.time()))
pUtil.tolog("lastTimeFilesWereModified=%d"%self.__env['lastTimeFilesWereModified'][k])
pUtil.tolog("loopingLimit=%d"%self.__env['loopingLimit'])
if (int(time.time()) - self.__env['lastTimeFilesWereModified'][k]) > self.__env['loopingLimit']:
self.__env['jobDic'][k][1] = self.__killLoopingJob(self.__env['jobDic'][k][1], self.__env['jobDic'][k][0])
def __check_looping_jobs(self):
# every 30 minutes, look for looping jobs
if (int(time.time()) - self.__env['curtime']) > self.__env['update_freq_server'] and not self.__skip: # 30 minutes
# check when the workdir files were last updated or that the stageout command is not hanging
if self.__allowLoopingJobKiller():
self.__loopingJobKiller()
# make final server update for all ended jobs
self.__updateJobs()
# update the time for checking looping jobs
self.__env['curtime'] = int(time.time())
self.__updateJobs(onlyUpdateStateChangedJobs=True)
def __set_outputs(self):
# all output will be written to the pilot log as well as to stdout [with the pUtil.tolog() function]
pUtil.setPilotlogFilename("%s/pilotlog.txt" % (self.__env['thisSite'].workdir))
# redirect stderr
pUtil.setPilotstderrFilename("%s/pilot.stderr" % (self.__env['thisSite'].workdir))
sys.stderr = open(pUtil.getPilotstderrFilename(), 'w')
def __verify_permissions(self):
# verify permissions
cmd = "stat %s" % (self.__env['thisSite'].workdir)
pUtil.tolog("(1b) Executing command: %s" % (cmd))
rc, rs = commands.getstatusoutput(cmd)
pUtil.tolog("\n%s" % (rs))
def __getsetWNMem(self):
""" Get the memory limit from queuedata or from the -k pilot option and set it """
wn_mem = 0
# Get the memory limit primarily from queuedata
_maxrss = pUtil.readpar('maxrss')
if _maxrss != "":
try:
maxrss = int(_maxrss) # Should already be an int
except Exception, e:
pUtil.tolog("Could not convert maxrss to an int: %s" % (e))
maxrss = -1
else:
pUtil.tolog("Got max memory limit: %d MB (from queuedata)" % (maxrss))
else:
maxrss = -1
# Get the max memory limit from the -k pilot option if specified
if maxrss == -1 and self.__env['memory']:
try:
maxrss = int(self.__env['memory'])
except Exception, e:
pUtil.tolog("Could not convert memory to an int: %s" % (e))
maxrss = -1
else:
pUtil.tolog("Got max memory limit: %d MB (from pilot option -k)" % (maxrss))
# Set the memory limit
if maxrss > 0:
# Convert MB to Bytes for the setrlimit function
_maxrss = maxrss*1024**2
max_memory = getMaxMemoryUsageFromCGroups()
if max_memory:
pUtil.tolog("cgroups max_memory = %s" % (max_memory))
else:
pUtil.tolog("cgroups max_memory not defined")
cmd = "ulimit -a"
pUtil.tolog("Executing command: %s" % (cmd))
out = commands.getoutput(cmd)
pUtil.tolog("\n%s" % (out))
else:
pUtil.tolog("Max memory will not be set")
return maxrss
def __checkLocalDiskSpace(self, disk):
""" Do we have enough local disk space left to run the job? """
ec = 0
# convert local space to B and compare with the space limit
spaceleft = int(disk)*1024**2 # B (node.disk is in MB)
_localspacelimit = self.__env['localspacelimit0'] * 1024 # B
pUtil.tolog("Local space limit: %d B" % (_localspacelimit))
if spaceleft < _localspacelimit:
pUtil.tolog("!!FAILED!!1999!! Too little space left on local disk to run job: %d B (need > %d B)" % (spaceleft, _localspacelimit))
ec = self.__error.ERR_NOLOCALSPACE
else:
pUtil.tolog("Remaining local disk space: %d B" % (spaceleft))
return ec
def __getLoopingLimit(self, maxCpuCount, jobPars, analyJob):
""" Get the looping time limit for the current job (in seconds) """
# start with the default looping time limit, use maxCpuCount if necessary
if analyJob:
loopingLimit = self.__env['loopingLimitDefaultUser']
else:
loopingLimit = self.__env['loopingLimitDefaultProd']
if maxCpuCount >= self.__env['loopingLimitMinDefault']:
_loopingLimit = max(self.__env['loopingLimitMinDefault'], maxCpuCount)
else:
_loopingLimit = max(loopingLimit, maxCpuCount)
if _loopingLimit != loopingLimit:
pUtil.tolog("Task request: Updated looping job limit from %d s to %d s using maxCpuCount" % \
(loopingLimit, _loopingLimit))
loopingLimit = _loopingLimit
else:
# increase the looping job limit for multi-trf jobs
if jobPars.find("\n") >= 0:
pUtil.tolog("Multi-trf job encountered: will double the looping job limit")
loopingLimit = 2*loopingLimit
pUtil.tolog("Using looping job limit: %d s" % (loopingLimit))
pUtil.tolog("maxCpuCount: %d s" % (maxCpuCount))
return loopingLimit
def __storePilotInitdir(self, targetdir, pilot_initdir):
""" Store the pilot launch directory in a file used by environment.py """
# This function is used to store the location of the init directory in the init directory itself as well as in the
# site work directory. The location file is used by environment.py to set the global env['pilot_initdir'] used
# by the pilot and the Monitor
# This function must be called before the global env variable is instantiated in the pilot
path = os.path.join(targetdir, "PILOT_INITDIR")
pUtil.tolog("Creating file %s with content %s" % (path, pilot_initdir))
pUtil.writeToFile(path, pilot_initdir)
# def __copyPilotVersion(self):
# """ Copy the PILOTVERSION file into the jobs' work directory """
def __createJobWorkdir(self, job, stderr):
""" Attempt to create the job workdir """
ec, errorText = job.mkJobWorkdir(self.__env['thisSite'].workdir)
if ec != 0:
job.setState(["failed", 0, self.__error.ERR_MKDIRWORKDIR])
ret, retNode = pUtil.updatePandaServer(job)
if ret == 0:
pUtil.tolog("Successfully updated panda server at %s" % pUtil.timeStamp())
else:
pUtil.tolog("!!WARNING!!1999!! updatePandaServer returned a %d" % (ret))
# send to stderr
print >> stderr, errorText
# remove the site workdir before exiting
pUtil.writeToFile(os.path.join(self.__env['thisSite'].workdir, "EXITCODE"), str(self.__error.ERR_GENERALERROR))
else:
pUtil.tolog("Created job workdir at %s" % (job.workdir))
# copy the job def file into job workdir
copy("%s/Job_%s.py" % (os.getcwd(), job.jobId), "%s/newJobDef.py" % job.workdir)
# also copy the time stamp file if it exists
_path = os.path.join(self.__env['pilot_initdir'], 'START_TIME_%s' % (job.jobId))
if os.path.exists(_path):
copy(_path, job.workdir)
pUtil.tolog("File %s copied to workdir" % (_path))
self.__storePilotInitdir(self.__env['job'].workdir, self.__env['pilot_initdir'])
return ec, job
def __throttleJob(self):
""" short delay requested by the server """
# dictionary for throttling job startup (setting running state)
throttleDic = {'CA':6, 'CERN':1.33, 'DE':6, 'ES':6, 'FR':6, 'IT':6, 'ND':0, 'NDGF':0, 'NL':6, 'TW':6, 'UK':6, 'US':6}
if self.__env['nSent'] > 0:
try:
_M = throttleDic[pUtil.readpar('cloud')]
except Exception, e:
pUtil.tolog("Warning: %s (using default value 6 as multiplier for throttling)" % str(e))
_M = 6
if os.environ.has_key('Nordugrid_pilot'):
pUtil.tolog("Nordugrid, using multiplier 0 for throttling")
_M = 0
_t = (self.__env['nSent'] + 1)*_M
# protect for potential unreasonably high sleeping times
max_sleep = 60
if _t > max_sleep:
_t = max_sleep
pUtil.tolog("!!WARNING!!1111!! Throttle time out of bounds, reset to %d s (nSent = %d)" % (max_sleep, self.__env['nSent']))
pUtil.tolog("Throttle sleep: %d s" % (_t))