def __condor_evaluate(self,candidates,args):
"""
Run simulations on grid and analyse data locally
WARNING: (???I'm quite confused here...there is a mistake somewhere
as the name doesn't match the description - which method is which?)
Once each generation has finished, all data is pulled to local
workstation in form of sqlite databases (1 database per job)
and these are analysed and the fitness estimated sequentially
the fitness array is then returned.
"""
import time
import ssh_utils
self.CandidateData_list=[]
self.__build_condor_files(candidates) #Build submit and runx.sh files, exp_id now corresponds to position in chromosome and fitness arrays
messagehost=ssh_utils.host(optimizer_params.host,optimizer_params.username,optimizer_params.password,optimizer_params.port)
self.__delete_remote_files__(messagehost)#delete everything in thssh_utilse directory you're about to put files in
filelist=os.listdir(self.tmpdir)
self.__put_multiple_files(messagehost,filelist,localdir=self.tmpdir,remotedir=optimizer_params.remotedir)#copy local files over
filelist=os.listdir(self.portableswdir)
self.__put_multiple_files(messagehost,filelist,localdir=self.portableswdir,remotedir=optimizer_params.remotedir)#copy local files over
ssh_utils.issue_command(messagehost,'export PATH=/opt/Condor/release/bin:$PATH\ncondor_submit submitfile.submit')
self.jobdbnames=[]
for job_num in range(self.num_jobs): #make a list of the databases we need:
jobdbname='outputdb'+str(job_num)+'.sqlite'
self.jobdbnames.append(jobdbname)
#wait till you know file exists:
dbs_created=False
pulled_dbs=[] # list of databases which have been extracted from remote server
while (dbs_created==False):
print 'waiting..'
time.sleep(20)
print 'checking if dbs created:'
command='ls'
remote_filelist=ssh_utils.issue_command(messagehost, command)
for jobdbname in self.jobdbnames:
db_exists=jobdbname+'\n' in remote_filelist
if (db_exists==False):
print jobdbname,' has not been generated'
dbs_created=False
elif db_exists==True and jobdbname not in pulled_dbs:
print jobdbname,' has been generated'
remotefile=optimizer_params.remotedir+jobdbname
localpath=os.path.join(self.datadir,str(self.generation)+jobdbname)
ssh_utils.get_file(messagehost,remotefile,localpath)
pulled_dbs.append(jobdbname) #so that it is not extracted more than once
#here pop-in the fitness evaluation
if len(pulled_dbs)==len(self.jobdbnames):
dbs_created=True
fitness=[]
for CandidateData in self.CandidateData_list:
job_num = CandidateData.job_num
dbname=str(self.generation)+'outputdb'+str(job_num)+'.sqlite'
dbpath=os.path.join(self.datadir,dbname)
exp_id=CandidateData.exp_id
connection=sqldbutils.db_connect(dbpath) #establish a database connection
query='SELECT numerical_value\
FROM output_params WHERE experiment_id=\
'+str(exp_id)+' AND parameter="fitness"'
exp_fitness=sqldbutils.execute_query(connection,query)
exp_fitness=exp_fitness.fetchall()
exp_fitness=exp_fitness[0][0]
print 'fitness:'
print exp_fitness
fitness.append(exp_fitness)
self.generation+=1
return fitness
def __condor_run(self, candidates, parameters):
"""
Run simulations on grid and analyse data locally (???I'm quite confused here...there is a mistake somewhere as the name doesn't match the description - which method is which?)
Once each generation has finished, all data is pulled to local
workstation in form of sqlite databases (1 database per job)
and these are analysed and the fitness estimated sequentially
the fitness array is then returned.
"""
import time
import ssh_utils
#Build submit and runx.sh files, exp_id now corresponds
#to position in chromosome and fitness arrays
self.context.__build_condor_files(candidates,
parameters,
candidates_per_job=self.cpj)
#This is a file handling block..
#delete everything in the ssh_utilse directory you're about to put files in
self.__delete_remote_files__()
filelist = os.listdir(self.tmpdir)
#copy local files over, some stuff is missing here as it needs to be an attribute in the condor context
self.__put_multiple_files(filelist, localdir=self.tmpdir)
filelist = os.listdir(self.portableswdir)
#copy portable software files over:
self.__put_multiple_files(filelist, localdir=self.portableswdir)
#issue a command to the message host to issue commands to the grid:
ssh_utils.issue_command(
context.messagehost,
'export PATH=/opt/Condor/release/bin:$PATH\ncondor_submit submitfile.submit'
)
#make a list of the database files we need:
self.jobdbnames = []
for job_num in range(self.num_jobs):
jobdbname = 'outputdb' + str(job_num) + '.sqlite'
self.jobdbnames.append(jobdbname)
#wait till we know file exists:
dbs_created = False
pulled_dbs = [
] # list of databases which have been extracted from remote server
while (dbs_created == False):
print('waiting..')
time.sleep(20)
print('checking if dbs created:')
command = 'ls'
remote_filelist = ssh_utils.issue_command(self.messagehost,
command)
for jobdbname in self.jobdbnames:
db_exists = jobdbname + '\n' in remote_filelist
if (db_exists == False):
print(jobdbname + ' has not been generated')
dbs_created = False
elif db_exists == True and jobdbname not in pulled_dbs:
print(jobdbname + ' has been generated')
remotefile = optimizer_params.remotedir + jobdbname
localpath = os.path.join(self.datadir,
str(self.generation) + jobdbname)
ssh_utils.get_file(self.messagehost, remotefile, localpath)
pulled_dbs.append(
jobdbname) #so that it is not extracted more than once
#here pop-in the fitness evaluation
if len(pulled_dbs) == len(self.jobdbnames):
dbs_created = True
#this block can be simplified, it need simply return exp_data containers
fitness = []
for CandidateData in self.CandidateData_list:
job_num = CandidateData.job_num
dbname = str(
self.generation) + 'outputdb' + str(job_num) + '.sqlite'
dbpath = os.path.join(self.datadir, dbname)
exp_id = CandidateData.exp_id
connection = sqldbutils.db_connect(
dbpath) #establish a database connection
query = 'SELECT numerical_value\
FROM output_params WHERE experiment_id=\
' + str(exp_id) + ' AND parameter="fitness"'
exp_fitness = sqldbutils.execute_query(connection, query)
exp_fitness = exp_fitness.fetchall()
exp_fitness = exp_fitness[0][0]
print('Fitness:')
print(exp_fitness)
fitness.append(exp_fitness)
self.generation += 1
return fitness
def __delete_remote_files(self,host):
import ssh_utils
command='rm -rf ./*'
ssh_utils.issue_command(host, command)
def __delete_remote_files(self, host):
import ssh_utils
command = 'rm -rf ./*'
ssh_utils.issue_command(host, command)