On 23.11.2010 09:26, derek eder wrote:
Hello,
I am facing the dreaded "Error: cannot allocate vector of size x Gb" and
don't understand
enough about R (or operating system) memory management to diagnose and
solve the problem
-- despite studying previous posts and relevant R help -- e.g.:
"Error messages beginning cannot allocate vector of size indicate a
failure to obtain memory,
either because the size exceeded the address-space limit for a process
or, more likely,
because the system was unable to provide the memory.
[...] On all builds of R, the maximum length (number of elements)
of a vector is 2^31 - 1 ~ 2*10^9, as lengths are stored as signed integers.
In addition, the storage space cannot exceed the address limit."
- from Memory-limits {Base}
Simple question: Given 64-bit R (AMD64 Linux) with a ulimit of
"unlimited", can the size of an R object exceed the amount of availlable
RAM
memory?
Empirically my system with 4Gb RAM and ample Swap, is failing:
> x <- integer(10^9)
> object.size(x)
4000000040 bytes
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 121195 6.5 350000 18.7 350000 18.7
Vcells 500124024 3815.7 606849099 4629.9 550124408 4197.2
> matrix(x, ncol=16)
Error: cannot allocate vector of size 3.7 Gb
I don't understand how this operation violates the limits detailed in
the Memory-limit help (above).
Why? If you have a limit of 4Gb, 4Gb are already used and you try to
work with a 4Gb objeczt in the matrix function which makes a copy and
creates another copy (with dim attributed), so 8Gb additionally. You
will need at least 12 of your 4Gb. Probably R does not get a sufficient
amount of non-fragmented memory from the OS or your swap space is not
"ample".
To make the above more efficient, just use:
dim(x) <- c(10^8/16, 16)
and you won't get any copies.
Uwe
Thank you!
Derek Eder
-------------------------------------------------------------------------------------------------
> version
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 11.1
year 2010
month 05
day 31
svn rev 52157
language R
version.string R version 2.11.1 (2010-05-31)
de...@papanca:~$ top
top - 09:10:18 up 51 min, 4 users, load average: 0.51, 0.51, 0.45
Tasks: 160 total, 2 running, 158 sleeping, 0 stopped, 0 zombie
Cpu(s): 0.0%us, 25.0%sy, 0.0%ni, 75.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st
Mem: 3796484k total, 3764852k used, 31632k free, 14204k buffers
Swap: 2929660k total, 834240k used, 2095420k free, 94800k cached
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
2854 derek 20 0 239m 9260 5448 S 6 0.2 0:05.53 gnome-terminal
1164 root 20 0 218m 31m 10m S 4 0.8 1:29.71 Xorg
3331 derek 20 0 19276 1324 944 R 1 0.0 0:00.6 top
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