# ssh -X -Y -l aliaksah abel.uio.no
# scp -r /usit/abel/u1/aliaksah/simulations/scenario1 aliaksah@pittheus.uio.no://mn/sarpanitu/ansatte-u2/aliaksah/Desktop/package/simulations
# cat slurm-16078690.out
# squeue -u aliaksah
#
#source("https://raw.githubusercontent.com/aliaksah/EMJMCMC2016/master/R/the_mode_jumping_package4.r")
library(inline)
includes <- '#include <sys/wait.h>'
code <- 'int wstat; while (waitpid(-1, &wstat, WNOHANG) > 0) {};'
wait <- cfunction(body=code, includes=includes, convention='.C')
estimate.gamma.cpen <- function(formula, data,r = 1.0/223.0,logn=log(223.0),relat=c("cosi","sigmoid","tanh","atan","sini","troot","m("))
{
fparam<-NULL
fmla.proc<-as.character(formula)[2:3]
fobserved <- fmla.proc[1]
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = " ",replacement = "")
fmla.proc[2]<-stri_replace_all(str = fmla.proc[2],fixed = "\n",replacement = "")
fparam <-stri_split_fixed(str = fmla.proc[2],pattern = "+I",omit_empty = F)[[1]]
sj<-(stri_count_fixed(str = fparam, pattern = "("))
sj<-sj+(stri_count_fixed(str = fparam, pattern = "+"))
for(rel in relat)
sj<-sj+(stri_count_fixed(str = fparam, pattern = rel))
sj<-sj+1
tryCatch(capture.output({
out <- glm(formula = formula,data = data, family = gaussian)
# 1 for aic, 2 bic prior, else g.prior
mlik = (-(out$deviance -2*log(r)*sum(sj)))/2
waic = -(out$deviance + 2*out$rank)
dic = -(out$deviance + logn*out$rank)
summary.fixed =list(mean = coefficients(out))
}, error = function(err) {
print(err)
mlik = -10000
waic = 10000
dic = 10000
summary.fixed =list(mean = array(0,dim=length(fparam)))
}))
return(list(mlik = mlik,waic = waic , dic = dic,summary.fixed =summary.fixed))
}
parall.gmj <<- mclapply
simplifyposteriors<-function(X,posteriors,th=0.0001,thf=0.3)
{
posteriors<-posteriors[-which(posteriors[,2]<th),]
rhash<-hash()
for(i in 1:length(posteriors[,1]))
{
expr<-posteriors[i,1]
print(expr)
res<-model.matrix(data=X,object = as.formula(paste0("RadiusJpt~",expr)))
res[,1]<-res[,1]-res[,2]
ress<-c(stri_flatten(res[,1],collapse = ""),stri_flatten(res[,2],collapse = ""),posteriors[i,2],expr)
if(!((ress[2] %in% values(rhash))))
rhash[[ress[1]]]<-ress
else
{
if(ress[1] %in% keys(rhash))
{
rhash[[ress[1]]][3]<- (as.numeric(rhash[[ress[1]]][3]) + as.numeric(ress[3]))
if(stri_length(rhash[[ress[1]]][4])>stri_length(expr))
rhash[[ress[1]]][4]<-expr
}
else
{
rhash[[ress[2]]][3]<- (as.numeric(rhash[[ress[2]]][3]) + as.numeric(ress[3]))
if(stri_length(rhash[[ress[2]]][4])>stri_length(expr))
rhash[[ress[2]]][4]<-expr
}
}
}
res<-as.data.frame(t(values(rhash)[c(3,4),]))
res$V1<-as.numeric(as.character(res$V1))
res<-res[which(res$V1>thf),]
res<-res[order(res$V1, decreasing = T),]
clear(rhash)
rm(rhash)
res[which(res[,1]>1),1]<-1
colnames(res)<-c("posterior","tree")
return(res)
}
cosi<-function(x)cos(x/180*pi)
sini<-function(x)sin(x/180*pi)
expi<-function(x)
{
r<-exp(x)
if(r==Inf)
return(10000000)
else
return(r)
}
InvX<-function(x)
{
if(x==0)
return(10000000)
else
return(1/x)
}
troot<-function(x)abs(x)^(1/3)
MM = 100
M = 4
NM= 1000
compmax = 16
th<-(10)^(-5)
thf<-0.05
paral<-function(X,FUN)
{
return(mclapply(X = X,FUN = FUN,mc.preschedule = F, mc.cores = 32))
}
runpar<-function(vect)
{
set.seed(as.integer(vect[22]))
do.call(runemjmcmc, vect[1:21])
vals<-values(hashStat)
fparam<-mySearch$fparam
cterm<-max(vals[1,],na.rm = T)
ppp<-mySearch$post_proceed_results_hash(hashStat = hashStat)
post.populi<-sum(exp(values(hashStat)[1,][1:NM]-cterm),na.rm = T)
clear(hashStat)
rm(hashStat)
rm(vals)
gc()
return(list(post.populi = post.populi, p.post = ppp$p.post, cterm = cterm, fparam = fparam))
}
for(j in 1:1)
{
tryCatch({
set.seed(j)
X<-read.csv("/mn/sarpanitu/ansatte-u2/aliaksah/Desktop/package/EMJMCMC/examples/exaplanets/exa1.csv")
formula1 = as.formula(paste(colnames(X)[5],"~ 1 +",paste0(colnames(X)[-5],collapse = "+")))
data.example = as.data.frame(X)
print(formula1)
#wait()
vect<-list(formula = formula1,data = data.example,estimator =estimate.gamma.cpen,estimator.args = list(data = data.example),recalc_margin = 249, save.beta = F,interact = T,outgraphs=F,relations=c("cosi","sigmoid","tanh","atan","sini","troot"),relations.prob =c(0.1,0.1,0.1,0.1,0.1,0.1),interact.param=list(allow_offsprings=4,mutation_rate = 250,last.mutation=10500, max.tree.size = 5, Nvars.max =15,p.allow.replace=0.9,p.allow.tree=0.01,p.nor=0.9,p.and = 0.9),n.models = 10000,unique =T,max.cpu = 4,max.cpu.glob = 4,create.table = F,create.hash = T,pseudo.paral = T,burn.in = 100,print.freq = 100,advanced.param = list(
max.N.glob=as.integer(10),
min.N.glob=as.integer(5),
max.N=as.integer(3),
min.N=as.integer(1),
printable = F))
aaa=do.call(runemjmcmc,vect[1:21])
aaa$p.post
params <- list(vect)[rep(1,M)]
for(i in 1:M)
{
params[[i]]$cpu<-i*j
params[[i]]$simul<-"scenario_JM_"
params[[i]]$simid<-j
}
gc()
print(paste0("begin simulation ",j))
results<-parall.gmj(X = params,FUN = runpar,mc.preschedule = F, mc.cores = M)
#print(results)
wait()
resa<-array(data = 0,dim = c(compmax,M*3))
post.popul <- array(0,M)
max.popul <- array(0,M)
nulls<-NULL
not.null<-1
for(k in 1:M)
{
if(length(results[[k]])==0)
{
nulls<-c(nulls,k)
next
}
else
{
not.null <- k
}
}
for(k in 1:M)
{
if(k %in% nulls)
{
results[[k]]<-results[[not.null]]
}
max.popul[k]<-results[[k]]$cterm
post.popul[k]<-results[[k]]$post.populi
resa[,k*3-2]<-c(results[[k]]$fparam,"Post.Gen.Max")
resa[,k*3-1]<-c(results[[k]]$p.post,results[[k]]$cterm)
resa[,k*3]<-rep(post.popul[k],length(results[[k]]$p.post)+1)
}
gc()
rm(results)
ml.max<-max(max.popul)
post.popul<-post.popul*exp(-ml.max+max.popul)
p.gen.post<-post.popul/sum(post.popul)
hfinal<-hash()
for(ii in 1:M)
{
resa[,ii*3]<-p.gen.post[ii]*as.numeric(resa[,ii*3-1])
resa[length(resa[,ii*3]),ii*3]<-p.gen.post[ii]
if(p.gen.post[ii]>0)
{
for(jj in 1:(length(resa[,ii*3])-1))
{
if(resa[jj,ii*3]>0)
{
#print(paste0(ii," and ",jj))
if(as.integer(has.key(hash = hfinal,key =resa[jj,ii*3-2]))==0)
hfinal[[resa[jj,ii*3-2]]]<-as.numeric(resa[jj,ii*3])
else
hfinal[[resa[jj,ii*3-2]]]<-hfinal[[resa[jj,ii*3-2]]]+as.numeric(resa[jj,ii*3])
}
}
}
}
posteriors<-values(hfinal)
#print(posteriors)
clear(hfinal)
rm(hfinal)
rm(resa)
rm(post.popul)
rm(max.popul)
posteriors<-as.data.frame(posteriors)
posteriors<-data.frame(X=row.names(posteriors),x=posteriors$posteriors)
posteriors$X<-as.character(posteriors$X)
tryCatch({
res1<-simplifyposteriors(X = X,posteriors = posteriors, th,thf)
write.csv(x =res1,row.names = F,file = paste0("postJA32_",j,".csv"))
},error = function(err){
print("error")
write.csv(x =posteriors,row.names = F,file = paste0("posteriorsJA32_",j,".csv"))
},finally = {
print(paste0("end simulation ",j))
})
rm(X)
#rm(data.example)
#rm(vect)
#rm(params)
gc()
print(paste0("end simulation ",j))
},error = function(err){
print("error")
j=j-1
print(paste0("repeat simulation ",j))
},finally = {
print(paste0("end simulation ",j))
#rm(X)
rm(data.example)
rm(vect)
rm(params)
gc()
})
}
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