func Run(conf Config) error {
rand.Seed(time.Now().UTC().UnixNano())
fmt.Println("Loading proteins...")
id, start, end, err := db.GetProteins(conf.DB)
if err != nil {
panic(err)
}
fmt.Println("Initializing probabilities...")
r, _ := rules.Create(conf.CA.InitStates, conf.CA.TransStates, conf.CA.HasJoker, conf.CA.R)
probs := NewProbs(r.Prm)
var pop Population
pop.rule = make([]*rules.Rule, conf.Design.Population)
pop.fitness = make([]float64, conf.Design.Population)
pop.rule[0], _ = rules.Create(conf.CA.InitStates, conf.CA.TransStates, conf.CA.HasJoker, conf.CA.R)
cellauto, _ := ca.Create1D(id, start, end, pop.rule[0], conf.CA.Steps, conf.CA.Consensus)
pop.fitness[0] = Fitness(cellauto)
for i := 1; i < conf.Design.Population; i++ {
pop.rule[i] = probs.GenRule()
cellauto.SetRule(pop.rule[i])
pop.fitness[i] = Fitness(cellauto)
}
pop.save("")
return nil
}
// func Run(selby string, fnrulein string, fnruleout string, fnprobout string, gen int, pop int, steps int, ca *ca.CellAuto1D, prm rules.Params) error {
func Run(conf Config) error {
rand.Seed(time.Now().UTC().UnixNano())
fmt.Println("Loading proteins...")
id, start, end, err := db.GetProteins(conf.DB)
if err != nil {
panic(err)
}
fmt.Println("Initializing probabilities...")
rule, _ := rules.Create(conf.CA.InitStates, conf.CA.TransStates, conf.CA.HasJoker, conf.CA.R)
probs := NewProbs(rule.Prm)
fmt.Println(probs)
var calist []*ca.CellAuto1D
calist = make([]*ca.CellAuto1D, conf.CGA.Selection)
for i := 0; i < len(calist); i++ {
r := probs.GenRule()
calist[i], _ = ca.Create1D(id, start, end, r, conf.CA.Steps, conf.CA.Consensus)
}
var wg1 sync.WaitGroup
for i := 0; i < conf.CGA.Generations; i++ {
fmt.Println("Generation", i)
fmt.Println("Adjusting probabilities...")
probs.AdjustByRanking(calist, 1.0/float64(conf.CGA.Population))
fmt.Println("OK")
if probs.Converged() {
fmt.Println("Probabilities converged\nDONE")
break
}
for i := 0; i < len(calist); i++ {
wg1.Add(1)
go func(i int) {
defer wg1.Done()
calist[i].SetRule(probs.GenRule())
}(i)
// calist[i], _ = ca.Create1D(id, start, end, r, conf.CA.Steps)
}
fmt.Printf("Waiting ")
wg1.Wait()
fmt.Println("OK")
}
err = ioutil.WriteFile(conf.CGA.OutputProbs, []byte(probs.String()), 0644)
if err != nil {
fmt.Println("Erro gravar as probabilidades")
fmt.Println(probs)
}
return nil
}
func Run(conf Config) error {
rand.Seed(time.Now().UTC().UnixNano())
fmt.Println("Loading proteins...")
id, start, end, err := proteindb.GetProteins(conf.ProteinDB)
if err != nil {
panic(err)
}
fmt.Println("Initializing simulated annealing")
rule, _ := rules.Create(conf.CA.InitStates, conf.CA.TransStates, conf.CA.HasJoker, conf.CA.R)
cellauto, _ := ca.Create1D(id, start, end, rule, conf.CA.Steps, conf.CA.Consensus)
solution := &Solution{rule, Fitness(cellauto)}
solution_new := &Solution{rule, Fitness(cellauto)}
solution_best := &Solution{rule, Fitness(cellauto)}
alpha := math.Pow((conf.SA.Tfinal / conf.SA.Tini), 1.0/float64(conf.SA.OuterLoop))
temp := conf.SA.Tini
for outer := 0; outer < conf.SA.OuterLoop; outer++ {
fmt.Println("@ Temperature", temp)
for inner := 0; inner < conf.SA.InnerLoop; inner++ {
solution_new.Neighbor(solution)
cellauto.SetRule(solution_new.rule)
solution_new.fitness = Fitness(cellauto)
if solution_new.fitness >= solution.fitness {
fmt.Println("Update", solution.fitness, "->", solution_new.fitness)
solution.rule = solution_new.rule
solution.fitness = solution_new.fitness
//fmt.Println("Check update", solution.fitness, "=", solution_new.fitness)
if solution.fitness > solution_best.fitness {
fmt.Println("Update BEST", solution_best.fitness, "->", solution.fitness)
solution_best.rule = solution.rule
solution_best.fitness = solution.fitness
}
} else if math.Exp(solution_new.fitness-solution.fitness/temp) > rand.Float64() {
fmt.Println("*Update", solution.fitness, "->", solution_new.fitness)
solution.rule = solution_new.rule
solution.fitness = solution_new.fitness
//fmt.Println("*Check update", solution.fitness, "=", solution_new.fitness)
}
}
temp = alpha * temp
}
err = ioutil.WriteFile(conf.Rules.Output, []byte(solution_best.rule.String()), 0644)
if err != nil {
fmt.Println("Erro gravar a melhor regra")
fmt.Println(solution_best.rule)
}
fmt.Println("Melhor regra", solution_best.fitness)
return nil
}
func RunSlave(conf Config) {
// Cria o receptor que recebe a probabilidade emitida pelo master na porta A
receiver, _ := zmq.NewSocket(zmq.PULL)
defer receiver.Close()
receiver.Connect("tcp://" + conf.Dist.MasterURL + ":" + conf.Dist.PortA)
// Cria o emissor que envia o individuo vencedor do torneio na rede pela
// porta B
sender, _ := zmq.NewSocket(zmq.PUSH)
defer sender.Close()
sender.Connect("tcp://" + conf.Dist.MasterURL + ":" + conf.Dist.PortB)
// semente randomica
rand.Seed(time.Now().UTC().UnixNano())
// Le os dados das proteinas no DB
fmt.Println("Loading proteins...")
id, start, end, err := db.GetProteins(conf.DB)
if err != nil {
fmt.Println("Erro no banco de DADOS")
panic(err)
}
fmt.Println("Done")
// ? Ha vantagem em enviar um sinal de Ok (proteinas lidas) para o master?
var prob Probabilities
var tourn Tournament
tourn = make([]Individual, conf.EDA.Tournament)
// tourn.rule = make([]*rules.Rule, conf.EDA.Tournament)
// tourn.fitness = make([]float64, conf.EDA.Tournament)
r, _ := rules.Create(conf.CA.InitStates, conf.CA.TransStates, conf.CA.HasJoker, conf.CA.R)
// probabilidade temporaria para ser substituida pelas recebidas
p_tmp := NewProbs(r.Prm)
cellAuto := make([]*ca.CellAuto1D, conf.EDA.Tournament)
for i := 0; i < conf.EDA.Tournament; i++ {
// tourn.rule[i] = p_tmp.GenRule()
tourn[i].Rule = p_tmp.GenRule()
// cellAuto[i], _ = ca.Create1D(id, start, end, tourn.rule[i], conf.CA.Steps, conf.CA.Consensus)
cellAuto[i], _ = ca.Create1D(id, start, end, tourn[i].Rule, conf.CA.Steps, conf.CA.Consensus)
}
// Individuo vencedor do torneio
var (
ind Individual
b []byte
m string
conerr error
)
for {
// m é a mensagem com as probabilidades
m, conerr = receiver.Recv(0)
// m, err := conn.Request(conf.Dist.TopicFromMaster, []byte("get"), 2*time.Second)
if conerr == nil {
// para cada individuo no torneio
// gera uma regra de acordo com a probabilidade atual
// roda o automato celular
// calcula o fitness
// seleciona o vencedor do torneio
// retorna sua regra e seu fitness)
// converte a probabilidade recebida em JSON para uma estrutura
json.Unmarshal([]byte(m), &prob)
fmt.Printf("PID: %d, Geracacao: %d\n", prob.PID, prob.Generation)
// for i := 0; i < len(tourn.rule); i++ {
for i := 0; i < len(tourn); i++ {
// copia a probabilidade recebida para a probabilidade dos individuos
copy(p_tmp.probs, prob.Data)
// gera a regra e atribui ao membro do torneio
tourn[i].Rule = p_tmp.GenRule()
// define a regra do automato como sendo a nova regra
cellAuto[i].SetRule(tourn[i].Rule)
// retorna o fitness e outras medidas de desempenho do autômato
tourn[i].Fitness, tourn[i].Q3 = FitnessAndQ3(cellAuto[i])
// fmt.Println("Individuo", i, "Fitness", tourn.fitness[i])
fmt.Println("Individuo", i, "Fitness", tourn[i].Fitness)
}
// Ordena os individuos do torneio de acordo com o fitness (maior primeiro)
sort.Sort(sort.Reverse(tourn))
// ind.PID, ind.Generation, ind.Rule, ind.Fitness = prob.PID, prob.Generation, tourn.rule[0], tourn.fitness[0]
ind.PID, ind.Generation, ind.Rule, ind.Fitness, ind.Q3 = prob.PID, prob.Generation, tourn[0].Rule, tourn[0].Fitness, tourn[0].Q3
// Codifica o individuo vencedor em JSON e envia para o master
b, _ = json.Marshal(ind)
fmt.Println("Fitness selecionado", tourn[0].Fitness)
sender.Send(string(b), 0)
} else {
// Erro na conexão
fmt.Println(err)
}
}
}
func Run(conf Config) error {
rand.Seed(time.Now().UTC().UnixNano())
fmt.Println("Loading proteins...")
id, start, end, err := proteindb.GetProteins(conf.ProteinDB)
if err != nil {
panic(err)
}
fmt.Println("Initializing probabilities...")
r, _ := rules.Create(conf.CA.InitStates, conf.CA.TransStates, conf.CA.HasJoker, conf.CA.R)
probs := NewProbs(r.Prm)
// fmt.Println(probs)
var pop Population
pop.rule = make([]*rules.Rule, conf.EDA.Population)
pop.fitness = make([]float64, conf.EDA.Population)
cellAuto := make([]*ca.CellAuto1D, conf.EDA.Population)
var wg1 sync.WaitGroup
// tmp := 0
for i := 0; i < conf.EDA.Population; i++ {
wg1.Add(1)
go func(pop *Population, i int) {
defer wg1.Done()
pop.rule[i] = probs.GenRule()
// ca, _ := ca.Create1D(id, start, end, pop.rule[i], conf.CA.Steps, conf.CA.Consensus)
cellAuto[i], _ = ca.Create1D(id, start, end, pop.rule[i], conf.CA.Steps, conf.CA.Consensus)
pop.fitness[i] = Fitness(cellAuto[i])
}(&pop, i) //preciso definir o que por aqui
if i%48 == 0 && i > 0 {
fmt.Println("Waiting", i)
wg1.Wait()
}
}
wg1.Wait()
fmt.Println("População inicial = ", conf.EDA.Population, "OK")
// tmp := make([]float64, len(pop.fitness))
// for j := range tmp {
// tmp[j] = pop.fitness[j] * 1.1
// }
var wg2 sync.WaitGroup
for i := 0; i < conf.EDA.Generations; i++ {
fmt.Println("Generation", i+1)
fmt.Println("Adjusting probabilities...")
probs.AdjustProbs(pop, conf.EDA.Selection, conf.EDA.Tournament)
fmt.Println("OK")
if probs.Converged() {
fmt.Println("Probabilities converged\nDONE")
break
}
if (i+1)%conf.EDA.SaveSteps == 0 {
ioutil.WriteFile(fmt.Sprintf("%s_%d", conf.EDA.OutputProbs, i+1), []byte(probs.String()), 0644)
}
for j := 0; j < len(pop.rule); j++ {
wg2.Add(1)
go func(pop *Population, j int) {
defer wg2.Done()
pop.rule[j] = probs.GenRule()
// ca, _ := ca.Create1D(id, start, end, pop.rule[j], conf.CA.Steps, conf.CA.Consensus)
cellAuto[j].SetRule(pop.rule[j])
pop.fitness[j] = Fitness(cellAuto[j])
}(&pop, j)
if j%24 == 0 && j > 0 {
fmt.Println("Waiting", j)
wg2.Wait()
}
}
fmt.Printf("Wait - Setting new rule")
wg2.Wait()
fmt.Println("OK")
//Este é o melhor lugar para criar o grafico? pop
plot.Histogram(pop.fitness, nil, i)
}
err = ioutil.WriteFile(conf.EDA.OutputProbs, []byte(probs.String()), 0644)
if err != nil {
fmt.Println("Erro gravar as probabilidades")
fmt.Println(probs)
}
return nil
}
func Run(conf Config) error {
rand.Seed(time.Now().UTC().UnixNano())
fmt.Println("Loading proteins...")
id, start, end, err := proteindb.GetProteins(conf.ProteinDB)
if err != nil {
panic(err)
}
var pop Population
pop.rule = make([]*rules.Rule, conf.GA.Population)
pop.fitness = make([]float64, conf.GA.Population)
var wg1 sync.WaitGroup
// tmp := 0
for i := 0; i < conf.GA.Population; i++ {
wg1.Add(1)
go func(pop *Population, i int) {
defer wg1.Done()
pop.rule[i], _ = rules.Create(conf.CA.InitStates, conf.CA.TransStates, conf.CA.HasJoker, conf.CA.R)
ca, _ := ca.Create1D(id, start, end, pop.rule[i], conf.CA.Steps, conf.CA.Consensus)
pop.fitness[i] = Fitness(ca)
}(&pop, i) //preciso definir o que por aqui
if i%100 == 0 && i > 0 {
fmt.Println("Waiting", i)
wg1.Wait()
}
}
wg1.Wait()
var selection Selection
selection.rule = make([]*rules.Rule, conf.GA.Selection)
selection.fitness = make([]float64, conf.GA.Selection)
// var tournament Tournament
// tournament.rule = make([]*rules.Rule, conf.GA.Tournament)
// tournament.fitness = make([]float64, conf.GA.Tournament)
var wg2 sync.WaitGroup
for i := 0; i < conf.GA.Generations; i++ {
fmt.Println("Gen", i)
sort.Sort(sort.Reverse(pop))
for j := 0; j < conf.GA.Selection; j++ {
winner := len(pop.rule)
for k := 0; k < conf.GA.Tournament; k++ {
x := rand.Intn(len(pop.rule))
if x < winner {
winner = x
}
}
//sort.Sort(sort.Reverse(tournament))
selection.rule[j] = pop.rule[winner]
selection.fitness[j] = pop.fitness[winner]
}
fmt.Println("Selection OK")
plot.Histogram(pop.fitness, selection.fitness, i)
fmt.Println("Plot", i, "ok")
for p := 0; p < len(pop.rule); p++ {
wg2.Add(1)
go func(pop *Population, p int) {
defer wg2.Done()
s := rand.Intn(len(selection.rule))
Mutate(selection.rule[s], conf.GA.Mutation)
pop.rule[p] = selection.rule[s]
ca, _ := ca.Create1D(id, start, end, pop.rule[p], conf.CA.Steps, conf.CA.Consensus)
pop.fitness[p] = Fitness(ca)
}(&pop, p)
if p%10 == 0 && p > 0 {
fmt.Println("Waiting", p)
wg2.Wait()
}
}
fmt.Println("New pop OK")
}
return nil
}