What is the difference between gc() and rm()

Question

I am periodically cleaning the memory in R using a call to rm(list=ls()).
Do I need to call the garbage collector gc() after that?

What is the difference between these 2 functions? Does gc() call rm() for certain variables?

Answer 1

First, it is important to note that the two are very different in that gc does not delete any variables that you are still using- it only frees up the memory for ones that you no longer have access to (whether removed using rm() or, say, created in a function that has since returned). Running gc() will never make you lose variables.

The question of whether you should call gc() after calling rm(), though, is a good one. The documentation for gc helpfully notes:

A call of gc causes a garbage collection to take place. This will also take place automatically without user intervention, and the primary purpose of calling gc is for the report on memory usage.

However, it can be useful to call gc after a large object has been removed, as this may prompt R to return memory to the operating system.

So the answer is that it can be good to call gc() (and at the very least, can't hurt), even though it would likely be triggered anyway (if not right away, then soon).

Answer 2

Personally I like to include the gc() in loops to free up some RAM when the loops start filling up the available space. Something like

for(i in 1:1000){
res[[i]] = some operation
gc()
}

Answer 3

Re ThankGoat's comment on gc penalty, while this is true, one could of course decide to call gc every N iterations in a loop (where N can be parameterised in a number of ways). For loops where number of iterations is large, but resource usage within a given iteration is more modest, it may well not be necessary to do GC each and every iteration in order to regain desired performance.

Of course, if you're looping with a very large number of very high usage iterations, it's a different story, but at that stage it may well the case that the code simply needs to be vectorised and / or maybe even written in another language.