I have only 2 core CPU so logically I want to set only two parallel threads/clusters for jags.parallel. unfortunatelly, when I try it and the number of chains is 3 or 4, jags fails with an error:
Error in res[[ch]] : subscript out of bounds
Is lower number of threads (than chains) not allowed?
I have not encountered such statement in the documentation. Anyway, it doesn't make sense to run 4 chains in 4 threads/clusters, when your CPU only has 2 cores! Threads will fight for CPU, caches won't be used optimally and the result will be much slower than using 2 threads only.
Full code:
set.seed(123) ### 14.1.2. Data generation n.site <- 10 x <- gl(n = 2, k = n.site, labels = c("grassland", "arable")) eps <- rnorm(2*n.site, mean = 0, sd = 0.5)# Normal random effect lambda.OD <- exp(0.69 +(0.92*(as.numeric(x)-1) + eps) ) lambda.Poisson <- exp(0.69 +(0.92*(as.numeric(x)-1)) ) # For comparison C.OD <- rpois(n = 2*n.site, lambda = lambda.OD) C.Poisson <- rpois(n = 2*n.site, lambda = lambda.Poisson) ### 14.1.4. Analysis using WinBUGS # Define model sink("Poisson.OD.t.test.txt") cat(" model { # Priors alpha ~ dnorm(0,0.001) beta ~ dnorm(0,0.001) sigma ~ dunif(0, 10) tau <- 1 / (sigma * sigma) maybe_overdisp <- mean(exp_eps[]) # Likelihood for (i in 1:n) { C.OD[i] ~ dpois(lambda[i]) log(lambda[i]) <- alpha + beta *x[i] #+ eps[i] eps[i] ~ dnorm(0, tau) exp_eps[i] <- exp(eps[i]) } } ",fill=TRUE) sink() # Bundle data x = as.numeric(x)-1 n = length(x) win.data <- list(C.OD = C.OD, x = as.numeric(x)-1, n = length(x)) # Inits function inits <- function(){ list(alpha=rlnorm(1), beta=rlnorm(1), sigma = rlnorm(1))} # Parameters to estimate params <- c("lambda","alpha", "beta", "sigma", "maybe_overdisp") # MCMC settings nc <- 3 # Number of chains ni <- 3000 # Number of draws from posterior per chain nb <- 1000 # Number of draws to discard as burn-in nt <- 5 # Thinning rate require(R2jags) # THIS WORKS FINE out <- R2jags::jags(win.data, inits, params, "Poisson.OD.t.test.txt", nc, ni, nb, nt); # THIS PRODUCES ERROR out <- do.call(jags.parallel, list(names(win.data), inits, params, "Poisson.OD.t.test.txt", nc, ni, nb, nt, n.cluster = 2));