def runjob(self):
param=self.param[0]
couchinfo('job {0}'.format(set(param.keys())))
envparam=submitformkey.intersection(set(param.keys()))
runjobparam=runjobkey.intersection(set(param.keys()))
resourceparam=resources.intersection(set(param.keys()))
#moduleparam=set(param['module'])
#generate batch script for PBS standard
#resources
resl=['{0}={1}'.format(k,param[k]) for k in resourceparam]
lbuf='#PBS -l '
while len(resl)>0: lbuf=lbuf+resl.pop()+':'
lla=['']
lla.append(lbuf[:-1])
lla.append('#PBS -l walltime={0}'.format(param['walltime']))
#account
lla.append('#PBS -A {0}'.format(param['account']))
#environment
lla.append('#PBS -N {0}'.format(param['job_name']))
#variables
#lla.append('#PBS -d {0}'.format(param['initialdir']))
#mail
lla.append('#PBS -m {0}'.format(param['notification']))
lla.append('#PBS -M {0}'.format(param['mail']))
#stdio
lla.append('#PBS -o {0}'.format(param['initialdir']))
lla.append('#PBS -e {0}'.format(param['initialdir']))
#other
rja=['-{0} {1}'.format(k,param[k]) for k in runjobparam]
buffer='#!/bin/bash\n'
while len(lla)>0: buffer=buffer+lla.pop()+'\n'
#buffer=buffer+'#@ queue\n'
if param.has_key('modules'):
for m in param['modules']:
buffer=buffer+'module load '+m+'\n'
#buffer=buffer+'module load args\n'
# insert runjob for computation node execute
#buffer=buffer+'nrniv '
buffer=buffer+param['engine']+' '
# insert dll for mech selection
while len(rja)>0: buffer=buffer+rja.pop()+' '
buffer=buffer+param['exe']+' '
if param.has_key('args'):
for arg in param['args']: buffer=buffer+' '+arg+' '
buffer=buffer+'\n'
with open('web.job','w') as file: file.write(buffer)
submit=self.subprocess.Popen(['qsub','web.job'],stdout=self.subprocess.PIPE)
result=submit.communicate()[0]
#send to couchdb jobid or error to display
couchinfo('qsub response:{0}'.format(result))
##res=requests.post('{0}/users/_design/jobs/_update/batch/{1}'.format(AGENTSERVER,user),data=@open('web.job','r'))
res=requests.post('{0}/users/_design/jobs/_update/submit/{1}'.format(AGENTSERVER,user),data=result)
return
def fullstat(self):
#qselect=self.subprocess.Popen(['qselect','-xu','{0}'.format(me)],stdout=self.subprocess.PIPE)
couchinfo('fullstat for '+self.param[0])
qstat=self.subprocess.Popen(['qstat','-x','-f',self.param[0]],stdout=self.subprocess.PIPE)
result=qstat.communicate()[0]
couchinfo('qstat response:{0}'.format(result))
res=requests.post('{0}/users/_design/jobs/_update/fullstat/{1}'.format(AGENTSERVER,user),data=result)
return
def do(self,linein):
couchinfo('do it')
for p in self.param: linein+='{0} '.format(p)
try:
#maybe shell in crashed
self.shell.stdin.writelines(unicode(linein+'\n'))
except Exception as e:
self.printexception("do",e)
self.killme()
self.updateresp=self.requests.post('{0}/commands/_design/schedule/_update/next/{1}'.format(AGENTSERVER,self.sessionid),data=None)
def route(self,recv,*args,**kwargs):
try:
couchinfo(recv)
buffer=recv.content
if (len(buffer)<2): return
couchinfo('xmlrpc: {0} '.format(buffer))
self.param,self.method=self.xmlrpclib.loads(buffer)
func=getattr(self,self.method,self.domethod)
func()
except Exception as e:
self.printexception("route exception",e)
def runagent():
pid=os.getpid()
couchinfo('start agent services')
while True:
requests.post('{0}/agents/_design/heartbeat/_update/agent/{1}'.format(AGENTSERVER,agentname),hooks=dict(response=createprocess))
qstat=subprocess.Popen(['qstat','-T','-x','-u','{0}'.format(user)],stdout=subprocess.PIPE)
result=qstat.communicate()[0]
res=requests.post('{0}/users/_design/jobs/_update/jobqueue/{1}'.format(AGENTSERVER,user),data=result)
localdir=os.listdir(config.DEFAULTFOLDER)
res=requests.get('{0}/folders/{1}'.format(AGENTSERVER,'webfolder'))
obj=res.content.replace('true','True').replace('false','False')
stats=eval(obj)['stats']
remotedir=[file for file in stats]
diff=[file for file in localdir if file not in remotedir]
for file in diff:
if 'user.author' not in xattr.listxattr('{0}/{1}'.format(config.DEFAULTFOLDER,file)):
with open ('{0}/{1}'.format(config.DEFAULTFOLDER,file),'a'):
os.utime('{0}/{1}'.format(config.DEFAULTFOLDER,file),None)
else:
os.unlink('{0}/{1}'.format(config.DEFAULTFOLDER,file))
time.sleep(6)
def createprocess(resp,*arg,**kwarg):
json=eval(resp.content)
couchinfo(json)
res=0
for key in json.get('sessions'):
if not key in proc:
proc[key]=Process(target=createthread,args=(key,))
proc[key].start()
else:
if proc[key].is_alive():
couchinfo("process {0} is alive".format(key))
else:
couchinfo("process {0} is dead".format(key))
res+=proc[key].is_alive()
if(res==0):
couchinfo('no active sessions: suicide!')
os.system("kill -9 {0}".format(os.getpid()))
def createthread(sessionid):
ch,masterfd=pty.fork()
if ch==0:
couchinfo("create shell process")
os.execl(SHELL,'Morg@{0}'.format(sessionid))
elif ch==-1:
couchinfo("Error on fork shell child!")
else:
couchinfo("create thread for id {0}".format(sessionid))
winsz=fctnl.ioctl(masterfd,termios.TIOCGWINSZ,'00000000')
th=th_popandexec(0,sessionid,masterfd)
th.start()
th.join()
def printexception(self,msg,e):
couchinfo("popandexec exception:{0} {1}".format(msg,e))
def getagentvars(self,res,*arg,**kwargs): couchinfo(res)
def __dir__(self):
res=[a for a in dir(self) if not a.startswith('__')]
couchinfo(res)
def killme(self):
self.pid=self.os.getpid()
couchinfo('kill myself pid:{0}'.format(self.pid))
self.os.system("kill -9 {0}".format(self.pid))
def signal(self):
couchinfo('send singnal to shell')
return
def restart(self):
couchinfo('execute restart from main thread')
return
def domethod(self):
couchinfo('domethod')
line='{0} '.format(self.method)
return self.do(line)
def execute(self):
couchinfo('execute')
line=''
return self.do(line)