###############################################################################################
#copy exec sources and inputs to remote resource
log("#"*80)
log("Preparing to copy application signature calculator,\n app. kernel input files and \n HPCC,IMB,IOR and Graph500 source code to remote resource\n\n")
str_io=cStringIO.StringIO()
try:
#sys.stdout = sys.stderr = str_io
akrr.sshCommand(rsh,"cd %s"%resource['appKerDir'])
out=akrr.sshCommand(rsh,"ls "+resource['appKerDir'])
files_in_appKerDir=out.strip().split()
if not ("inputs" in files_in_appKerDir or "inputs/" in files_in_appKerDir):
log("Copying app. kernel input tarball to %s"%resource['appKerDir'])
akrr.scpToResource(resource,curdir+"/../../appker_repo/inputs.tar.gz",resource['appKerDir'],logfile=str_io)
log("Unpacking app. kernel input files to %s/inputs"%resource['appKerDir'])
print >>str_io, akrr.sshCommand(rsh,"tar xvfz %s/inputs.tar.gz"%resource['appKerDir'])
out=akrr.sshCommand(rsh,"df -h %s/inputs"%resource['appKerDir'])
if out.count("No such file or directory")==0:
log("App. kernel input files are in %s/inputs\n"%resource['appKerDir'],highlight="ok")
else:
print >>str_io, out
raise Exception("files are not copied!")
else:
log("WARNING %d: App. kernel inputs directory %s/inputs is present, assume they are correct.\n"%(warningCount+1,resource['appKerDir']),highlight='warning')
warningCount+=1
str_io=cStringIO.StringIO()
def CreateBatchJobScriptAndSubmitIt(self):
self.JobScriptName=self.appName+".job"
print "### Creating batch job script and submitting it to remote machine"
#as a current bypass will create a job script remotely and copy it here
#get ssh to remote resource
sh=None
try:
sh=akrr.sshResource(self.resource)
#Create remote directories if needed
def CheckAndCreateDir(self,sh,d):
cmd="if [ ! -d \"%s\" ]\n then mkdir \"%s\"\n fi"%(d,d)
akrr.sshCommand(sh,cmd)
cmd="if [ -d \"%s\" ]\n then \necho EXIST\n else echo DOESNOTEXIST\n fi"%(d)
msg=akrr.sshCommand(sh,cmd)
if msg.find("DOESNOTEXIST")>=0:
raise akrr.akrrError(akrr.ERROR_REMOTE_FILES,"Can not create directory %s on %s."%(d,self.resource['name']))
#akrrdata
CheckAndCreateDir(self,sh,self.resource['akrrdata'])
#dir for app
CheckAndCreateDir(self,sh,os.path.join(self.resource['akrrdata'],self.appName))
#dir for task
CheckAndCreateDir(self,sh,self.remoteTaskDir)
#CheckAndCreateDir(self,sh,os.path.join(self.remoteTaskDir,"batchJob_pl"))
#cd to remoteTaskDir
akrr.sshCommand(sh,"cd %s"%(self.remoteTaskDir))
#get walltime from DB
dbdefaults={}
try:
db,cur=akrr.getDB()
cur.execute('''SELECT resource,app,resource_param,app_param FROM ACTIVETASKS
WHERE task_id=%s ;''',(self.task_id,))
raw=cur.fetchall()
(resource,app,resource_param,app_param)=raw[0]
cur.execute("""SELECT walllimit
FROM akrr_default_walllimit
WHERE resource=%s AND app=%s AND resource_param=%s AND app_param=%s """,(resource,app,resource_param,app_param))
raw=cur.fetchall()
if len(raw)>0:
dbdefaults['walllimit']=raw[0][0]
#db.commit()
cur.close()
del db
except Exception as e:
pass
#create job-script
batchvars={}
#print "#"*80
for di in [self.resource,self.app,dbdefaults,self.resourceParam, self.appParam]:
batchvars.update(di)
#stack the subtasks
subTaskInfo=self.GetSubTaskInfo()
if batchvars['shuffleSubtasks']:
random.shuffle(subTaskInfo)
subTasksExecution=""
for subtask_id,subtask_status,subtask_datetimestamp,subtask_resource,subtask_app,subtask_task_param in subTaskInfo:
remoteSubTaskDir=self.GetRemoteTaskDir(self.resource['akrrdata'],subtask_app,subtask_datetimestamp)
SubTaskJobScriptName=self.GetJobScriptName(subtask_app)
SubTaskJobScriptPath=os.path.join(remoteSubTaskDir,SubTaskJobScriptName)
subTasksExecution+="cd "+remoteSubTaskDir+"\n"
#subTasksExecution+="cp "+os.path.join(self.remoteTaskDir,"job.id ")+"./\n"
subTasksExecution+="echo Starting "+subtask_app+"\n"
subTasksExecution+=self.resource['shell']+" "+SubTaskJobScriptPath+" > stdout 2> stderr\n"
subTasksExecution+="echo Done with "+subtask_app+"\n"+"\n"
batchvars['subTasksExecution']=subTasksExecution
#calculate NNodes and NCores
tmpNNodes=None
tmpNCores=None
if batchvars.has_key('nnodes'):
tmpNNodes=batchvars['nnodes']
tmpNCores=tmpNNodes*batchvars['ppn']
else:
tmpNCores=batchvars['ncores']
if tmpNCores%batchvars['ppn']==0:
tmpNNodes=tmpNCores/batchvars['ppn']
else:
tmpNNodes=(tmpNCores/batchvars['ppn'])+1
batchvars['akrrNCores']=tmpNCores
batchvars['akrrNNodes']=tmpNNodes
#Set batchvars remaps
batchvars['akrrPPN']=batchvars['ppn']
batchvars['akrrNCoresToBorder']=batchvars['akrrPPN']*batchvars['akrrNNodes']
batchvars['akrrTaskWorkingDir']=self.remoteTaskDir
batchvars['akrrWallTimeLimit']="%02d:%02d:00"%(int(batchvars['walllimit'])/60,int(batchvars['walllimit'])%60)
batchvars['localPATH']=akrr.sshCommand(sh,"echo $PATH").strip()
batchvars['akrrAppKerName']=self.app['name']
batchvars['akrrResourceName']=self.resource['name']
batchvars['akrrTimeStamp']= self.timeStamp
if batchvars['akrrNNodes']==1: batchvars['akrrPPN4NodesOrCores4OneNode']=batchvars['akrrNCores']
else: batchvars['akrrPPN4NodesOrCores4OneNode']=batchvars['akrrPPN']
if 'nodeListSetterTemplate' not in batchvars:
batchvars['nodeListSetterTemplate']=batchvars['nodeListSetter'][batchvars['batchScheduler']]
#set AppKerLauncher
#if self.resource['name'] in batchvars['runScript']:
# batchvars['akrrStartAppKer']=akrr.formatRecursively(batchvars['runScript'][self.resource['name']],batchvars,keepDoubleBrakets=True)
#else:
# batchvars['akrrStartAppKer']=akrr.formatRecursively(batchvars['runScript']['default'],batchvars,keepDoubleBrakets=True)
#process templates
batchvars['akrrCommonCommands']=akrr.formatRecursively(batchvars['akrrCommonCommandsTemplate'],batchvars,keepDoubleBrakets=True)
#batchvars['akrrCommonTests']=akrr.formatRecursively(batchvars['akrrCommonTestsTemplate'],batchvars,keepDoubleBrakets=True)
#batchvars['akrrStartAppKer']=batchvars['akrrStartAppKerTemplate'].format(**batchvars)
batchvars['akrrCommonCleanup']=akrr.formatRecursively(batchvars['akrrCommonCleanupTemplate'],batchvars,keepDoubleBrakets=True)
#do parameters adjustment
if 'process_params' in batchvars:
batchvars['process_params'](batchvars)
#generate job script
jobScript=akrr.formatRecursively(self.resource["batchJobTemplate"],batchvars)
fout=open(os.path.join(self.taskDir,"jobfiles",self.JobScriptName),"w")
fout.write(jobScript)
fout.close()
msg=akrr.scpToResource(self.resource,os.path.join(self.taskDir,"jobfiles",self.JobScriptName),os.path.join(self.remoteTaskDir))
##akrr.sshCommandNoReturn(sh,"cat > %s << EOF1234567\n%s\nEOF1234567\n"%(self.JobScriptName,jobScript))
akrr.sshCommand(sh,"cat %s "%(self.JobScriptName))
#send to queue
from string import Template
sendToQueue=Template(submitCommands[self.resource['batchScheduler']]).substitute(scriptPath=self.JobScriptName)
msg=akrr.sshCommand(sh,sendToQueue)
matchObj=re.search(jidExtractPatterns[self.resource['batchScheduler']],msg,re.M|re.S)
JobID=None
if matchObj:
try:
JobID=int(matchObj.group(1))
except:
raise akrr.akrrError(akrr.ERROR_REMOTE_JOB,"Can't get job id. "+msg)
else:
raise akrr.akrrError(akrr.ERROR_REMOTE_JOB,"Can't get job id. "+msg)
akrr.sshCommand(sh,"echo %d > job.id"%(JobID))
#cp job id to subtasks
for subtask_id,subtask_status,subtask_datetimestamp,subtask_resource,subtask_app,subtask_task_param in subTaskInfo:
remoteSubTaskDir=self.GetRemoteTaskDir(self.resource['akrrdata'],subtask_app,subtask_datetimestamp)
akrr.sshCommand(sh,"cp job.id %s"%(remoteSubTaskDir))
self.RemoteJobID=JobID
self.TimeJobSubmetedToRemoteQueue=datetime.datetime.today()
sh.sendline("exit")
sh.close(force=True)
del sh
sh=None
print "\nRemoteJobID=",self.RemoteJobID
print "copying files from remote machine"
msg=akrr.scpFromResource(self.resource,os.path.join(self.remoteTaskDir,"*"),os.path.join(self.taskDir,"jobfiles"),"-r")
#update DB time_submitted_to_queue
db,cur=akrr.getDB()
cur.execute('''UPDATE ACTIVETASKS
SET time_submitted_to_queue=%s
WHERE task_id=%s ;''',(datetime.datetime.today().strftime("%Y-%m-%d %H:%M:%S"),self.task_id))
cur.close()
del db
self.status="Created batch job script and have submitted it to remote queue."
self.statusinfo="Remote job ID is %d"%(self.RemoteJobID)
self.ToDoNextString="CheckTheJobOnRemoteMachine"
#check first time in 1 minute
return datetime.timedelta(days=0, hours=0, minutes=1)
except Exception as e:
if sh!=None:
sh.sendline("exit")
sh.close(force=True)
del sh
self.status="ERROR Can not created batch job script and submit it to remote queue"
self.statusinfo=traceback.format_exc()
if akrr.max_fails_to_submit_to_the_queue>=0:
if hasattr(self, "FailsToSubmitToTheQueue"):
self.FailsToSubmitToTheQueue+=1
if self.FailsToSubmitToTheQueue>akrr.max_fails_to_submit_to_the_queue:
#Stop execution of the task and submit results to db
self.ToDoNextString="PushToDB"
resultFile=os.path.join(self.taskDir,"result.xml")
self.WriteErrorXML(resultFile)
return datetime.timedelta(seconds=3)
else:
self.FailsToSubmitToTheQueue=1
else:
self.FatalErrorsCount+=1
akrr.printException(self.status)
return akrr.RepeateAfterFailsToSubmitToTheQueue
def CreateBatchJobScriptAndSubmitIt(self,doNotSubmitToQueue=False):
self.JobScriptName=self.GetJobScriptName(self.appName)
print "### Creating batch job script and submitting it to remote machine"
#as a current bypass will create a job script remotely and copy it here
#get ssh to remote resource
sh=None
try:
sh=akrr.sshResource(self.resource)
#Create remote directories if needed
def CheckAndCreateDir(self,sh,d):
cmd="if [ ! -d \"%s\" ]\n then mkdir \"%s\"\n fi"%(d,d)
akrr.sshCommand(sh,cmd)
cmd="if [ -d \"%s\" ]\n then \necho EXIST\n else echo DOESNOTEXIST\n fi"%(d)
msg=akrr.sshCommand(sh,cmd)
if msg.find("DOESNOTEXIST")>=0:
raise akrr.akrrError(akrr.ERROR_REMOTE_FILES,"Can not create directory %s on %s."%(d,self.resource['name']))
#akrrdata
CheckAndCreateDir(self,sh,self.resource['akrrdata'])
#dir for app
CheckAndCreateDir(self,sh,os.path.join(self.resource['akrrdata'],self.appName))
#dir for task
CheckAndCreateDir(self,sh,self.remoteTaskDir)
#CheckAndCreateDir(self,sh,os.path.join(self.remoteTaskDir,"batchJob_pl"))
#cd to remoteTaskDir
akrr.sshCommand(sh,"cd %s"%(self.remoteTaskDir))
#GenerateBatchJobScript
self.GenerateBatchJobScript()
msg=akrr.scpToResource(self.resource,os.path.join(self.taskDir,"jobfiles",self.JobScriptName),os.path.join(self.remoteTaskDir))
if doNotSubmitToQueue:
return
##akrr.sshCommandNoReturn(sh,"cat > %s << EOF1234567\n%s\nEOF1234567\n"%(self.JobScriptName,jobScript))
akrr.sshCommand(sh,"cat %s "%(self.JobScriptName))
#send to queue
from string import Template
JobID=0
if not 'masterTaskID' in self.taskParam:
#i.e. submit to queue only if task is independent
sendToQueue=Template(submitCommands[self.resource['batchScheduler']]).substitute(scriptPath=self.JobScriptName)
msg=akrr.sshCommand(sh,sendToQueue)
matchObj=re.search(jidExtractPatterns[self.resource['batchScheduler']],msg,re.M|re.S)
if matchObj:
try:
JobID=int(matchObj.group(1))
except:
raise akrr.akrrError(akrr.ERROR_REMOTE_JOB,"Can't get job id:\n"+msg)
else:
raise akrr.akrrError(akrr.ERROR_REMOTE_JOB,"Can't get job id:\n"+msg)
akrr.sshCommand(sh,"echo %d > job.id"%(JobID))
self.RemoteJobID=JobID
self.TimeJobSubmetedToRemoteQueue=datetime.datetime.today()
sh.sendline("exit")
sh.close(force=True)
del sh
sh=None
print "\nRemoteJobID=",self.RemoteJobID
print "copying files from remote machine"
msg=akrr.scpFromResource(self.resource,os.path.join(self.remoteTaskDir,"*"),os.path.join(self.taskDir,"jobfiles"),"-r")
#update DB time_submitted_to_queue
db,cur=akrr.getDB()
cur.execute('''UPDATE ACTIVETASKS
SET time_submitted_to_queue=%s
WHERE task_id=%s ;''',(datetime.datetime.today().strftime("%Y-%m-%d %H:%M:%S"),self.task_id))
cur.close()
del db
if not 'masterTaskID' in self.taskParam:
#i.e. idepentent task
self.status="Created batch job script and have submitted it to remote queue."
self.statusinfo="Remote job ID is %d"%(self.RemoteJobID)
self.ToDoNextString="CheckTheJobOnRemoteMachine"
#check first time in 1 minute
return datetime.timedelta(days=0, hours=0, minutes=1)
else:
#i.e. this is subtask
#i.e. idepentent task
self.status="Created batch job script."
self.statusinfo="Created batch job script. Waiting for master task to execute it."
self.ToDoNextString="CheckTheJobOnRemoteMachine"
#master task will update the time when it will finish task execution
return datetime.timedelta(days=111*365)
except Exception as e:
if sh!=None:
sh.sendline("exit")
sh.close(force=True)
del sh
self.status="ERROR Can not created batch job script and submit it to remote queue"
self.statusinfo=traceback.format_exc()
if akrr.max_fails_to_submit_to_the_queue>=0:
if hasattr(self, "FailsToSubmitToTheQueue"):
self.FailsToSubmitToTheQueue+=1
if (self.FailsToSubmitToTheQueue>akrr.max_fails_to_submit_to_the_queue or
(self.taskParam['test_run']==True and self.FailsToSubmitToTheQueue>=2)):
#Stop execution of the task and submit results to db
self.ToDoNextString="PushToDB"
resultFile=os.path.join(self.taskDir,"result.xml")
self.WriteErrorXML(resultFile)
return datetime.timedelta(seconds=3)
else:
self.FailsToSubmitToTheQueue=1
else:
self.FatalErrorsCount+=1
akrr.printException(self.status)
return akrr.repeat_after_fails_to_submit_to_the_queue
