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GA.py
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GA.py
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# -*- coding: utf-8 -*-
"""
Editor de Spyder
Este es un archivo temporal
"""
import matplotlib
matplotlib.use('Agg')
import numpy as np
import random as random
import sys
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import POPULATION as pop
from decimal import Decimal
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt3d
import SYSTEMMODEL as systemmodel
class GA:
def __init__(self, system):
self.system = system
self.populationSize = 200
self.populationPt = pop.POPULATION(self.populationSize)
self.mutationProbability = 0.25
self.rnd = random.Random()
self.scaleLevel='SINGLE' # or OLD
self.reliabilityAwarness = False
self.initialGeneration = 'ADJUSTED' # or RANDOM
self.networkDistanceCalculation = 'MEAN' #or TOTAL
self.thersholdCalculation = 'SINGLE' # or ACCUMULATED
#******************************************************************************************
# MUTATIONS
#******************************************************************************************
def swapMutation_old(self,child,serviceId):
secondServiceId = serviceId
while secondServiceId == serviceId:
secondServiceId = self.rnd.randint(0,len(child)-1)
child[serviceId]['allocationList'],child[secondServiceId]['allocationList'] = child[secondServiceId]['allocationList'],child[serviceId]['allocationList']
def growthMutation_old(self,child,serviceId):
currentLen = len(child[serviceId]['allocationList'])
newElements = [self.rnd.randint(0,self.system.nodenumber-1) for r in xrange(self.rnd.randint(1,currentLen))]
child[serviceId]['allocationList'] += newElements
def shrinkMutation_old(self,child,serviceId):
child[serviceId]['allocationList'] = self.rnd.sample(child[serviceId]['allocationList'],self.rnd.randint(1,len(child[serviceId]['allocationList'])-1))
def mutate_old(self,child):
serviceSelected = self.rnd.randint(0,len(child)-1)
#print "[Offsrping generation]: Mutation of service %s in process**********************" % str(serviceSelected)
numContainers = len(child[serviceSelected]['allocationList'])
mutationOperators = []
mutationOperators.append(self.swapMutation)
mutationOperators.append(self.growthMutation)
if numContainers>1:
mutationOperators.append(self.shrinkMutation)
mutationOperators[self.rnd.randint(0,len(mutationOperators)-1)](child,serviceSelected)
#******************************************************************************************
# END MUTATIONS
#******************************************************************************************
#******************************************************************************************
# MUTATIONS
#******************************************************************************************
def shuffleMutationOLD(self,child):
random.shuffle(child)
def growthMutationOLD(self,child):
for serviceSelected in range(len(child)):
currentLen = len(child[serviceSelected]['allocationList'])
newElements = [self.rnd.randint(0,self.system.nodenumber-1) for r in xrange(self.rnd.randint(1,currentLen))]
child[serviceSelected]['allocationList'] += newElements
def shrinkMutationOLD(self,child):
for serviceSelected in range(len(child)):
if len(child[serviceSelected]['allocationList']) > 1:
child[serviceSelected]['allocationList'] = self.rnd.sample(child[serviceSelected]['allocationList'],self.rnd.randint(1,len(child[serviceSelected]['allocationList'])-1))
def growthMutationSINGLE(self,child):
#aumenta un único elemento lista de allocationList en cada uno de los microservices
for serviceSelected in range(len(child)):
#currentLen = len(child[serviceSelected]['allocationList'])
#newElements = [self.rnd.randint(0,self.system.nodenumber-1) for r in xrange(self.rnd.randint(1,currentLen))]
newElements = [self.rnd.randint(0,self.system.nodenumber-1)]
child[serviceSelected]['allocationList'] += newElements
def shrinkMutationSINGLE(self,child):
#disminuye en uno el número de container que implementa un microservice para cada uno de los microservices
for serviceSelected in range(len(child)):
if len(child[serviceSelected]['allocationList']) > 1:
#child[serviceSelected]['allocationList'] = self.rnd.sample(child[serviceSelected]['allocationList'],self.rnd.randint(1,len(child[serviceSelected]['allocationList'])-1))
child[serviceSelected]['allocationList'] = self.rnd.sample(child[serviceSelected]['allocationList'],len(child[serviceSelected]['allocationList'])-1)
def mutate(self,child):
#print "[Offsrping generation]: Mutation in process**********************"
if (self.scaleLevel=='OLD'):
#las hard son las antiguas, las
mutationOperators = []
mutationOperators.append(self.shuffleMutationOLD)
mutationOperators.append(self.growthMutationOLD)
mutationOperators.append(self.shrinkMutationOLD)
if (self.scaleLevel=='SINGLE'):
mutationOperators = []
mutationOperators.append(self.shuffleMutationOLD)
mutationOperators.append(self.growthMutationSINGLE)
mutationOperators.append(self.shrinkMutationSINGLE)
mutationOperators[self.rnd.randint(0,len(mutationOperators)-1)](child)
#******************************************************************************************
# END MUTATIONS
#******************************************************************************************
#******************************************************************************************
# CROSSOVER
#******************************************************************************************
def crossover(self,f1,f2,offs):
c1 = f1.copy()
c2 = f2.copy()
#crossover of the write/block chromosome
for key,value in c1.iteritems():
allocationF1 = c1[key]['allocationList']
allocationF2 = c2[key]['allocationList']
# print "before"
# print allocationF1
# print allocationF2
crosspoint = self.rnd.randint(0,min(len(allocationF1),len(allocationF2)))
newAllocationCh1 = allocationF1[:crosspoint] + allocationF2[crosspoint:]
newAllocationCh2 = allocationF2[:crosspoint] + allocationF1[crosspoint:]
# print "after"
# print newAllocationCh1
# print newAllocationCh2
# print "*****"
c1[key]['allocationList'] = newAllocationCh1
c2[key]['allocationList'] = newAllocationCh2
offs.append(c1)
#print "[Offsrping generation]: Children 1 added **********************"
offs.append(c2)
#print "[Offsrping generation]: Children 2 added **********************"
#******************************************************************************************
# END CROSSOVER
#******************************************************************************************
#******************************************************************************************
# nodenumber calculation
#******************************************************************************************
def calculateNodeNumber(self,solution):
allNodes = set()
for key in solution:
allNodes = allNodes | set(solution[key]['rnode']+solution[key]['wnode'])
return len(allNodes)
#******************************************************************************************
# END nodenumber calculation
#******************************************************************************************
#******************************************************************************************
# Cluster Balance use calculation
#******************************************************************************************
def calculateClusterBalanceUse(self,nodesLoads):
#nodesLoad.append({"cpuload" : 0.0, "memorysize": 0.0, "memoryload": 0.0, "hdsize": 0.0, "hdload": 0.0})
load = []
for idx,usage in enumerate(nodesLoads):
if usage['computationalResources']>0.0 :
load.append(usage['computationalResources'] / self.system.nodeFeatures[idx]['capacity'] )
return np.std(load)
#******************************************************************************************
# END Cluster Balance use calculation
#******************************************************************************************
#******************************************************************************************
# Failura calculation
#******************************************************************************************
def calculateServiceFailure(self, serviceId, serviceChromosome):
totalFailure = 1.0
allocationList = serviceChromosome['allocationList']
usedNodes = set(allocationList)
serviceFailure = self.system.serviceTupla[serviceId]['failrate']
for node in usedNodes:
failure = serviceFailure * allocationList.count(node)
failure = failure + self.system.nodeFeatures[node]['failrate']
totalFailure = totalFailure * failure
return totalFailure
def calculateFailure(self,solution):
failure = 0.0
for key in solution:
failure = failure + self.calculateServiceFailure(key,solution[key])
return failure
#******************************************************************************************
# END Failura calculation
#******************************************************************************************
#******************************************************************************************
# Container balanced use calculation
#******************************************************************************************
def calculateServiceBalancedUse(self, serviceId, serviceChromosome):
serviceThr = self.system.serviceTupla[serviceId]['threshold']
requestNumber = self.system.requestPerApp[self.system.serviceTupla[serviceId]['application']] * self.system.serviceTupla[serviceId]['requestNumber']
scalabilityLevel = len(serviceChromosome['allocationList'])
resourcesPerRequest = self.system.serviceTupla[serviceId]['computationalResources']
if self.thersholdCalculation=='ACCUMULATED':
return abs( (requestNumber * resourcesPerRequest) - ( serviceThr * scalabilityLevel ) )
else:
return abs( ((requestNumber * resourcesPerRequest)/scalabilityLevel) - serviceThr )
def calculateThreshold(self,solution):
thr = 0.0
for i,service in enumerate(solution):
thr = thr + self.calculateServiceBalancedUse(i,solution[service])
return thr
#******************************************************************************************
# END Container balanced use calculation
#******************************************************************************************
#******************************************************************************************
# NetworkLoad calculation
#******************************************************************************************
def calculateServiceNetwork(self, serviceId, chromosome):
sourceNodes = set(chromosome[serviceId]['allocationList'])
targetNodes = set()
for i in self.system.serviceTupla[serviceId]['consumeServices']:
targetNodes = targetNodes | set(chromosome[i]['allocationList'])
distance = 0.0
for source in sourceNodes:
for target in targetNodes:
distance = distance + self.system.cpdNetwork[source][target]
if self.networkDistanceCalculation == 'MEAN':
if len(sourceNodes)>0 and len(targetNodes)>0:
distance = distance / (len(sourceNodes) * len(targetNodes))
return distance
def calculateNetwork(self,solution):
networkLoad = 0.0
for key in solution:
networkLoad = networkLoad + self.calculateServiceNetwork(key, solution)
return networkLoad
#******************************************************************************************
# END NetworkLoad calculation
#******************************************************************************************
#******************************************************************************************
# Node Workload calculation
#******************************************************************************************
def calculateNodesWorkload(self, chromosome):
nodesLoad = []
for i in range(self.system.nodenumber):
nodesLoad.append({"computationalResources" : 0.0})
for key in chromosome:
requestNumber = self.system.requestPerApp[self.system.serviceTupla[key]['application']]* self.system.serviceTupla[key]['requestNumber']
scalabilityLevel = len(chromosome[key]['allocationList'])
resourcesPerRequest = self.system.serviceTupla[key]['computationalResources']
serviceLoad = requestNumber * resourcesPerRequest / scalabilityLevel
for element in (chromosome[key]['allocationList']):
nodesLoad[element]['computationalResources']= nodesLoad[element]['computationalResources'] + serviceLoad
return nodesLoad
def calculateSolutionsWorkload(self,pop):
for i,citizen in enumerate(pop.population):
pop.nodesUsages[i]=self.calculateNodesWorkload(citizen)
#******************************************************************************************
# END Node Workload calculation
#******************************************************************************************
#******************************************************************************************
# Model constraints
#******************************************************************************************
def resourceUsages(self,nodes):
for idx,v in enumerate(nodes):
if not (v['computationalResources']<self.system.nodeFeatures[idx]['capacity']):
return False
return True
def checkConstraints(self,pop, index):
nodesLoads = pop.nodesUsages[index]
if not self.resourceUsages(nodesLoads):
return False
return True
#******************************************************************************************
# END Model constraints
#******************************************************************************************
#******************************************************************************************
# Objectives and fitness calculation
#******************************************************************************************
def calculateFitnessObjectives(self, pop, index): #TODO
chr_fitness = {}
chr_fitness["index"] = index
#chr_fitness["performance"] = self.rnd.randint(1,100)
chromosome=pop.population[index]
nodeLoads= pop.nodesUsages[index]
if self.checkConstraints(pop,index):
chr_fitness["thresholdDistance"] = self.calculateThreshold(chromosome)
chr_fitness["clusterbalanced"] = self.calculateClusterBalanceUse(nodeLoads)
if self.reliabilityAwarness:
chr_fitness["reliability"] = self.calculateFailure(chromosome)
chr_fitness["networkDistance"] = self.calculateNetwork(chromosome)
else:
chr_fitness["thresholdDistance"] = float('inf')
chr_fitness["clusterbalanced"] = float('inf')
if self.reliabilityAwarness:
chr_fitness["reliability"] = float('inf')
chr_fitness["networkDistance"] = float('inf')
return chr_fitness
def calculatePopulationFitnessObjectives(self,pop):
for index,citizen in enumerate(pop.population):
cit_fitness = self.calculateFitnessObjectives(pop,index)
pop.fitness[index] = cit_fitness
#print "[Fitness calculation]: Calculated **********************"
#******************************************************************************************
# END Objectives and fitness calculation
#******************************************************************************************
#******************************************************************************************
# NSGA-II Algorithm
#******************************************************************************************
def dominates(self,a,b):
#checks if solution a dominates solution b, i.e. all the objectives are better in A than in B
Adominates = True
#### OJOOOOOO Hay un atributo en los dictionarios que no hay que tener en cuenta, el index!!!
for key in a:
if key!="index": #por ese motivo está este if.
if b[key]<=a[key]:
Adominates = False
break
return Adominates
def crowdingDistancesAssigments(self,popT,front):
for i in front:
popT.crowdingDistances[i] = float(0)
frontFitness = [popT.fitness[i] for i in front]
#OJOOOOOO hay un atributo en el listado que es index, que no se tiene que tener en cuenta.
for key in popT.fitness[0]:
if key!="index": #por ese motivo está este if.
orderedList = sorted(frontFitness, key=lambda k: k[key])
popT.crowdingDistances[orderedList[0]["index"]] = float('inf')
minObj = orderedList[0][key]
popT.crowdingDistances[orderedList[len(orderedList)-1]["index"]] = float('inf')
maxObj = orderedList[len(orderedList)-1][key]
normalizedDenominator = float(maxObj-minObj)
if normalizedDenominator==0.0:
normalizedDenominator = float('inf')
for i in range(1, len(orderedList)-1):
popT.crowdingDistances[orderedList[i]["index"]] += (orderedList[i+1][key] - orderedList[i-1][key])/normalizedDenominator
def calculateCrowdingDistances(self,popT):
i=0
while len(popT.fronts[i])!=0:
self.crowdingDistancesAssigments(popT,popT.fronts[i])
i+=1
def calculateDominants(self,popT):
for i in range(len(popT.population)):
popT.dominatedBy[i] = set()
popT.dominatesTo[i] = set()
popT.fronts[i] = set()
for p in range(len(popT.population)):
for q in range(p+1,len(popT.population)):
if self.dominates(popT.fitness[p],popT.fitness[q]):
popT.dominatesTo[p].add(q)
popT.dominatedBy[q].add(p)
if self.dominates(popT.fitness[q],popT.fitness[p]):
popT.dominatedBy[p].add(q)
popT.dominatesTo[q].add(p)
def calculateFronts(self,popT):
addedToFronts = set()
i=0
while len(addedToFronts)<len(popT.population):
popT.fronts[i] = set([index for index,item in enumerate(popT.dominatedBy) if item==set()])
addedToFronts = addedToFronts | popT.fronts[i]
for index,item in enumerate(popT.dominatedBy):
if index in popT.fronts[i]:
popT.dominatedBy[index].add(-1)
else:
popT.dominatedBy[index] = popT.dominatedBy[index] - popT.fronts[i]
i+=1
def fastNonDominatedSort(self,popT):
self.calculateDominants(popT)
self.calculateFronts(popT)
def plotFronts(self,popT):
f = 0
#fig = plt.figure()
colors = iter(cm.rainbow(np.linspace(0, 1, 15)))
while len(popT.fronts[f])!=0:
thisfront = [popT.fitness[i] for i in popT.fronts[f]]
a = [thisfront[i]["thresholdDistance"] for i,v in enumerate(thisfront)]
b = [thisfront[i]["reliability"] for i,v in enumerate(thisfront)]
#ax1 = fig.add_subplot(111)
plt.scatter(a, b, s=10, color=next(colors), marker="o")
#ax1.annotate('a',(a,b))
f +=1
plt.show()
def plot3DFronts(self,popT):
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
f = 0
colors = iter(cm.rainbow(np.linspace(0, 1, 15)))
# For each set of style and range settings, plot n random points in the box
# defined by x in [23, 32], y in [0, 100], z in [zlow, zhigh].
while len(popT.fronts[f])!=0:
thisfront = [popT.fitness[i] for i in popT.fronts[f]]
a = [thisfront[i]["balanceuse"] for i,v in enumerate(thisfront)]
b = [thisfront[i]["network"] for i,v in enumerate(thisfront)]
c = [thisfront[i]["reliability"] for i,v in enumerate(thisfront)]
ax.scatter(a, b, c, color=next(colors), marker="o")
f +=1
ax.set_xlabel('balanceuse')
ax.set_ylabel('network')
ax.set_zlabel('reliability')
plt3d.show()
#******************************************************************************************
# END NSGA-II Algorithm
#******************************************************************************************
#******************************************************************************************
# Evolution based on NSGA-II
#******************************************************************************************
def generatePopulation(self,popT):
for i in range(self.populationSize):
chromosome = {}
for msId in range(0,self.system.numberMicroServices):
if self.initialGeneration == 'RANDOM':
chromosome[msId] = {"allocationList": [self.rnd.randint(0,self.system.nodenumber-1) for r in xrange(self.rnd.randint(1,min(self.system.nodenumber,10)))] }
if self.initialGeneration == 'ADJUSTED':
chromosome[msId] = {"allocationList": [self.rnd.randint(0,self.system.nodenumber-1) for r in xrange(self.system.serviceTupla[msId]['scaleLevel'])] }
popT.population[i]=chromosome
#print "[Citizen generation]: Number %i generated**********************" % i
#chr_fitness = self.calculateFitnessObjectives(chromosome,i)
#popT.fitness[i]=chr_fitness
#print "[Fitness calculation]: Calculated for citizen %i **********************" % i
popT.dominatedBy[i]=set()
popT.dominatesTo[i]=set()
popT.fronts[i]=set()
popT.crowdingDistances[i]=float(0)
self.calculateSolutionsWorkload(popT)
self.calculatePopulationFitnessObjectives(popT)
self.fastNonDominatedSort(popT)
# self.plot3DFronts(popT)
#self.plotFronts(popT)
self.calculateCrowdingDistances(popT)
def tournamentSelection(self,k,popSize):
selected = sys.maxint
for i in range(k):
selected = min(selected,self.rnd.randint(0,popSize-1))
return selected
def fatherSelection(self, orderedFathers): #TODO
i = self.tournamentSelection(2,len(orderedFathers))
return orderedFathers[i]["index"]
def evolveToOffspring(self):
offspring = pop.POPULATION(self.populationSize)
offspring.population = []
orderedFathers = self.crowdedComparisonOrder(self.populationPt)
#offspring generation
while len(offspring.population)<self.populationSize:
father1 = self.fatherSelection(orderedFathers)
father2 = father1
while father1 == father2:
father2 = self.fatherSelection(orderedFathers)
#print "[Father selection]: Father1: %i **********************" % father1
#print "[Father selection]: Father1: %i **********************" % father2
self.crossover(self.populationPt.population[father1],self.populationPt.population[father2],offspring.population)
#offspring mutation
for index,children in enumerate(offspring.population):
if self.rnd.uniform(0,1) < self.mutationProbability:
self.mutate(children)
#print "[Offsrping generation]: Children %i MUTATED **********************" % index
#print "[Offsrping generation]: Population GENERATED **********************"
return offspring
def crowdedComparisonOrder(self,popT):
valuesToOrder=[]
for i,v in enumerate(popT.crowdingDistances):
citizen = {}
citizen["index"] = i
citizen["distance"] = v
citizen["rank"] = 0
valuesToOrder.append(citizen)
f=0
while len(popT.fronts[f])!=0:
for i,v in enumerate(popT.fronts[f]):
valuesToOrder[v]["rank"]=f
f+=1
return sorted(valuesToOrder, key=lambda k: (k["rank"],-k["distance"]))
def evolveNGSA2(self):
offspring = pop.POPULATION(self.populationSize)
offspring.population = []
offspring = self.evolveToOffspring()
self.calculateSolutionsWorkload(offspring)
self.calculatePopulationFitnessObjectives(offspring)
populationRt = offspring.populationUnion(self.populationPt,offspring)
self.fastNonDominatedSort(populationRt)
self.calculateCrowdingDistances(populationRt)
orderedElements = self.crowdedComparisonOrder(populationRt)
finalPopulation = pop.POPULATION(self.populationSize)
for i in range(self.populationSize):
finalPopulation.population[i] = populationRt.population[orderedElements[i]["index"]]
finalPopulation.fitness[i] = populationRt.fitness[orderedElements[i]["index"]]
finalPopulation.nodesUsages[i] = populationRt.nodesUsages[orderedElements[i]["index"]]
for i,v in enumerate(finalPopulation.fitness):
finalPopulation.fitness[i]["index"]=i
#self.populationPt = offspring
self.populationPt = finalPopulation
self.fastNonDominatedSort(self.populationPt)
self.calculateCrowdingDistances(self.populationPt)
#self.plot3DFronts(self.populationPt)
#self.plotFronts(self.populationPt)
#******************************************************************************************
# END Evolution based on NSGA-II
#******************************************************************************************
#blocksPerFilePerMapReduceJobs1 = np.array([[2,3,1],[5,5,0],[3,4,1],[8,3,1]])
#blocksPerFilePerMapReduceJobs = np.array([2,3,1])
#blocksPerFilePerMapReduceJobs = np.vstack((blocksPerFilePerMapReduceJobs,np.array([5,5,0])))
#blocksPerFilePerMapReduceJobs = np.vstack((blocksPerFilePerMapReduceJobs,np.array([3,4,1])))
#blocksPerFilePerMapReduceJobs = np.vstack((blocksPerFilePerMapReduceJobs,np.array([8,3,1])))
#definition of the files for each MapReduce job. 1:1 jobs:files
#nodenumber = 50
#populationSize = 10
#population = []
#
#for i in range(populationSize):
# chromosome = {}
# fileId = 0
# blockId = 0
#
# for (MRjobID,MRjobFileID), value in np.ndenumerate(blocksPerFilePerMapReduceJobs):
# for blockId in range(value): #iteration of the three files of each mapreducejob
# replicationFactor = int(round(np.random.normal(3.0, 0.4))) # mean and standard deviation
# if replicationFactor>nodenumber: #when the block replica is bigger than total node number, is set to the maximum
# replicationFactor=nodenumber
# try:
# allocation=self.rnd.sample(range(1, nodenumber), replicationFactor) #random selection of the node to place the blocks
# #selection of the nodes to be read by the tasks of the mapreduce job
# readallocation=[]
# readnode = self.rnd.choice(allocation)
# allocation.remove(readnode)
# readallocation.append(readnode)
# except ValueError:
# print('Sample size exceeded population size.')
# chromosome[fileId,blockId] = {"filetype": MRjobFileID % 3 , "wnode":allocation,"rnode":readallocation}
# blockId+=1
# fileId+=1
# population.append(chromosome)
#
#
#chromosome
#
#for fileId,totalBlock in enumerate(blocksPerFile):
# for blockId in range(totalBlock):
# chromosome[fileId,b] = {"wnode":[1,2,3],"rnode":[]}