How to clean up R memory (without the need to restart my PC)?

Question

I am running my code in R (under Windows) which involves a lot of in-memory data. I tried to use rm(list=ls()) to clean up memory, but seems the memory is still

Answer 1

Just adding this for reference in case anybody needs to restart and immediatly run a command.

I'm using this approach just to clear RAM from the system. Make sure you have deleted all objects no longer required. Maybe gc() can also help before hand. But nothing will clear RAM better as restarting the R session.

library(rstudioapi)
restartSession(command = "print('x')")

Answer 2

There is only so much you can do with rm() and gc(). As suggested by Gavin Simpson, even if you free the actual memory in R, Windows often won't reclaim it until you close R or it is needed because all the apparent Windows memory fills up.

This usually isn't a problem. However, if you are running large loops this can sometimes lead to fragmented memory in the long term, such that even if you free the memory and restart R - the fragmented memory may prevent you allocating large chunks of memory. Especially if other applications were allocated fragmented memory while you were running R. rm() and gc() may delay the inevitable, but more RAM is better.

Answer 3

memory.size(max=T) # gives the amount of memory obtained by the OS
[1] 1800
memory.size(max=F) # gives the amount of memory being used
[1] 261.17

Using Paul's example,

m = matrix(runif(10e7), 10000, 1000)

Now

memory.size(max=F)
[1] 1024.18

To clear up the memory

gc()
memory.size(max=F)
[1] 184.86

In other words, the memory should now be clear again. If you loop a code, it is a good idea to add a gc() as the last line of your loop, so that the memory is cleared up before starting the next iteration.

Answer 4

An example under Linux (Fedora 16) shows that memory is freed when R is closed:

$ free -m                                                                                                                                                                                                                                    
             total       used       free     shared    buffers     cached                                                                                                                                                                    
Mem:          3829       2854        974          0        344       1440                                                                                                                                                                    
-/+ buffers/cache:       1069       2759                                                                                                                                                                                                     
Swap:         4095         85       4010     

2854 megabytes is used. Next I open an R session and create a large matrix of random numbers:

m = matrix(runif(10e7), 10000, 1000)

when the matrix is created, 3714 MB is used:

$ free -m                                                                                                                                                                                                                                    
             total       used       free     shared    buffers     cached                                                                                                                                                                    
Mem:          3829       3714        115          0        344       1442                                                                                                                                                                    
-/+ buffers/cache:       1927       1902                                                                                                                                                                                                     
Swap:         4095         85       4010     

After closing the R session, I nicely get back the memory I used (2856 MB free):

$ free -m                                                                                                                                                                                                                                    
             total       used       free     shared    buffers     cached                                                                                                                                                                    
Mem:          3829       2856        972          0        344       1442                                                                                                                                                                    
-/+ buffers/cache:       1069       2759                                                                                                                                                                                                     
Swap:         4095         85       4010   

Ofcourse you use Windows, but you could repeat this excercise in Windows and report how the available memory develops before and after you create this large dataset in R.

Answer 5

I've found it helpful to go into my "tmp" folder and delete all hanging rsession files. This usually frees any memory that seems to be "stuck".

Answer 6

I came under the same problem with R. I dig a bit and come with a solution, that we need to restart R session to fully clean the memory/RAM. For this, you can use a simple code after removing everything from your workspace. the code is as follows :

rm(list = ls())

.rs.restartR()