Re: [R] Error: cannot allocate vector of size x Gb (64-bit ... yet again)
On Tue, 23 Nov 2010, 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)
400040 bytes
gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells1211956.5 35 18.735 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).
It doesn't, and that example works on my (32GB RAM) 64-bit system
gc()
used (Mb) gc trigger(Mb) max used(Mb)
Ncells 1340547.2 3518.7 3518.7
Vcells 1000131158 7630.4 1575382823 12019.3 1500131550 11445.1
So maybe you don't have 'ample swap' and/or have a VM limit set.
Note that
dim(x) - c(length(x)/16, 16)
is much more efficient use of memory.
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
day31
svn rev52157
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 %MEMTIME+ COMMAND
2854 derek 20 0 239m 9260 5448 S6 0.2 0:05.53 gnome-terminal
1164 root 20 0 218m 31m 10m S4 0.8 1:29.71 Xorg
3331 derek 20 0 19276 1324 944 R1 0.0 0:00.6 top
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
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[R] Error: cannot allocate vector of size x Gb (64-bit ... yet again)
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)
400040 bytes
gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells1211956.5 35 18.735 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).
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
day31
svn rev52157
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 %MEMTIME+ COMMAND
2854 derek 20 0 239m 9260 5448 S6 0.2 0:05.53
gnome-terminal
1164 root 20 0 218m 31m 10m S4 0.8 1:29.71 Xorg
3331 derek 20 0 19276 1324 944 R1 0.0 0:00.6 top
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error: cannot allocate vector of size x Gb (64-bit ... yet again)
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)
400040 bytes
gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 121195 6.5 35 18.7 35 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
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
