def launchJob(inp2,k):
"""
Launch Phaser job on cluster and pass back the process job and pid.
"""
Utils.folders(self,k)
#Remove leftover file if rerunning.
if os.path.exists('adf.com'):
os.system('rm -rf adf.com')
queue = Queue()
j = Process(target=RunPhaser,args=(inp2,queue,self.logger))
j.start()
queue.get()#For the log I am not using
if self.output['jobs'] == None:
self.output['jobs'] = {j:k}
self.output['pids'] = {k:queue.get()}
else:
self.output['jobs'].update({j:k})
self.output['pids'].update({k:queue.get()})
#Setup initial results for all running jobs.
self.phaser_results[k] = { 'AutoMR results' : Parse.setPhaserFailed('Still running')}
def Queue(self):
"""
queue system.
"""
if self.verbose:
self.logger.debug('AutoMolRep::Queue')
try:
timed_out = False
timer = 0
jobs = self.output['jobs'].keys()
#set which jobs to watch.
if self.run_before:
jobs = [job for job in jobs if self.output['jobs'][job][-1] == '1']
else:
jobs = [job for job in jobs if self.output['jobs'][job][-1] == '0']
counter = len(jobs)
while counter != 0:
for job in jobs:
if job.is_alive() == False:
jobs.remove(job)
if self.verbose:
self.logger.debug('Finished Phaser on %s'%self.output['jobs'][job])
Utils.folders(self,self.output['jobs'][job])
if self.adf:
if os.path.exists('adf.com'):
del self.output['pids'][self.output['jobs'][job]]
counter -= 1
else:
key = self.output['jobs'].pop(job)
p = self.postprocessPhaser(key)
if p == 'ADF':
#Calculate ADF map.
adf = Process(target=Utils.calcADF,name='ADF%s'%key,args=(self,key))
adf.start()
jobs.append(adf)
self.output['jobs'][adf] = key
else:
counter -= 1
self.postprocess(False)
else:
self.postprocessPhaser(self.output['jobs'][job])
del self.output['pids'][self.output['jobs'][job]]
self.postprocess(False)
counter -= 1
time.sleep(0.2)
timer += 0.2
if self.verbose:
number = round(timer%1,1)
if number in (0.0,1.0):
print 'Waiting for Phaser to finish %s seconds'%timer
if self.phaser_timer:
if timer >= self.phaser_timer:
timed_out = True
break
if timed_out:
self.logger.debug('Phaser timed out.')
print 'Phaser timed out.'
for job in jobs:
self.phaser_results[self.output['jobs'][job]] = {'AutoMR results':Parse.setPhaserFailed('Timed out')}
if self.cluster_use:
#Utils.killChildrenCluster(self,self.output['pids'][self.output['jobs'][job]])
BLspec.killChildrenCluster(self,self.output['pids'][self.output['jobs'][job]])
else:
Utils.killChildren(self,self.output['pids'][self.output['jobs'][job]])
#Check if solution has been found.
if self.run_before == False:
self.checkSolution()
self.logger.debug('Phaser finished.')
except:
self.logger.exception('**ERROR in AutoMolRep.Queue**')