Memory Allocation Error cannot allocate vector of size 75 1 Mb

Question

In the course of vectorizing some simulation code  I ve run into a memory issue  I m using 32 bit R version 2 15 0  via RStudio version 0 96 122  under Windows XP  My machine has 3 46 GB of RAM    gt  sessionInfo   R version 2 15 0  2012-03-30  Platform  i386-pc-mingw32 i386  32-bit   locale   1  LC COLLATE English United Kingdom 1252  LC CTYPE English United Kingdom 1252     3  LC MONETARY English United Kingdom 1252 LC NUMERIC C                             5  LC TIME English United Kingdom 1252      attached base packages   1  stats     graphics  grDevices utils     datasets  methods   base       other attached packages   1  Matrix 1 0-6   lattice 0 20-6 MASS 7 3-18     loaded via a namespace  and not attached    1  grid 2 15 0  tools 2 15 0   Here is a minimal example of the problem    gt  memory limit 3000   1  3000  gt  rm list   ls     gt  gc             used  Mb  gc trigger   Mb   max used    Mb  Ncells 1069761 28 6    1710298  45 7   1710298   45 7 Vcells  901466  6 9   21692001 165 5 173386187 1322 9  gt  N  lt - 894993  gt  library MASS   gt  sims  lt - mvrnorm n   N  mu   rep 0  11   Sigma   diag nrow   11    gt  sims  lt - mvrnorm n   N   1  mu   rep 0  11   Sigma   diag nrow   11   Error  cannot allocate vector of size 75 1 Mb    In my application the covariance matrix Sigma is not diagonal  but I get the same error either way     I ve spent the afternoon reading about memory allocation issues in R  including here  here and here   From what I ve read  I get the impression that it s not a matter of the available RAM per se  but of the available continuous address space  Still  75 1Mb seems pretty small to me   I d greatly appreciate any thoughts or suggestions that you might have

User · Answer

I had the same warning using the raster package.

> my_mask[my_mask[] != 1] <- NA
Error: cannot allocate vector of size 5.4 Gb

The solution is really simple and consist in increasing the storage capacity of R, here the code line:

##To know the current storage capacity
> memory.limit()
[1] 8103
## To increase the storage capacity
> memory.limit(size=56000)
[1] 56000    
## I did this to increase my storage capacity to 7GB

Hopefully, this will help you to solve the problem Cheers

User · Answer

R has gotten to the point where the OS cannot allocate it another 75 1Mb chunk of RAM  That is the size of memory chunk required to do the next sub-operation  It is not a statement about the amount of contiguous RAM required to complete the entire process  By this point  all your available RAM is exhausted but you need more memory to continue and the OS is unable to make more RAM available to R   Potential solutions to this are manifold  The obvious one is get hold of a 64-bit machine with more RAM  I forget the details but IIRC on 32-bit Windows  any single process can only use a limited amount of RAM  2GB   and regardless Windows will retain a chunk of memory for itself  so the RAM available to R will be somewhat less than the 3 4Gb you have  On 64-bit Windows R will be able to use more RAM and the maximum amount of RAM you can fit install will be increased   If that is not possible  then consider an alternative approach  perhaps do your simulations in batches with the n per batch much smaller than N  That way you can draw a much smaller number of simulations  do whatever you wanted  collect results  then repeat this process until you have done sufficient simulations  You don t show what N is  but I suspect it is big  so try smaller N a number of times to give you N over-all

User · Answer

does R stop no matter the N value you use  try to use small values and see if it s the mvrnorm function that is the issue or you could simply loop it on subsets  Insert the gc   function in the loop to free some RAM continuously

User · Answer

gc   can help  saving data as  RData  closing  re-opening R  and loading the RData can help   see my answer here  https   stackoverflow com a 24754706 190791 for more details

[r] Memory Allocation "Error: cannot allocate vector of size 75.1 Mb"

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