Release memory in R

Question

I use some variables, but when it is used, I never need it again, so I need to remove it and release the memory, but the function rm() seems not help:

memory.size() 30.69 tmp=matrix(rnorm(6e5*20),6e5,20) memory.size() 207.64 rm(tmp) memory.size() 207.64 

Does it mean that I remove the tmp but the memory is not released?

Answer 1

I use gc() to free up RAM between operations. Below is example of how I use it in a loop, but see here for a more detailed discussion of gc() and here for more on memory management during an R session.

# load library library(topicmodels)  # get data data("AssociatedPress"))  # set number of topics to start with k <- 20  # set model options control_LDA_VEM <- list(estimate.alpha = TRUE, alpha = 50/k, estimate.beta = TRUE, verbose = 0, prefix = tempfile(), save = 0, keep = 0, seed = as.integer(100), nstart = 1, best = TRUE, var = list(iter.max = 10, tol = 10^-6), em = list(iter.max = 10, tol = 10^-4), initialize = "random")   # create the sequence that stores the number of topics to  # iterate over sequ <- seq(20, 300, by = 20)  # basic loop to iterate over different topic numbers with gc # after each run to empty out RAM lda <- vector(mode='list', length = length(sequ)) for(k in sequ) {   lda[[k]] <- LDA(AssociatedPress[1:20,], k, method= "VEM", control = control_LDA_VEM)   gc() # here's where I put the garbage collection to free up memory before the next round of the loop }  # convert list output to dataframe (suggestions for a simpler method are welcome!) best.model.logLik <- data.frame(logLik = as.matrix(lapply(lda[sequ], logLik)), ntopic = sequ)  # plot with(best.model.logLik, plot(ntopic, logLik, type = 'l', xlab="Number of topics", ylab="Log likelihood")) 

# print ordered dataframe to see which number of topics has the highest log likelihood (best.model.logLik.sort <- best.model.logLik[order(-as.numeric(best.model.logLik$logLik)), ])      logLik       ntopic 2  -17904.12     40 3  -18105.48     60 1  -18181.84     20 4   -18569.7     80 5  -19736.94    100 6   -21919.6    120 7  -23785.08    140 8  -24914.23    160 9  -25493.76    180 10 -25837.64    200 11 -25964.23    220 12 -26061.01    240 13 -26117.92    260 14 -26149.44    280 15 -26168.91    300