Dear R developers,
We have a big SGI Origin computation server with 32 cpu's and 64 Gb of
RAM. In R 2.0.0 we could run large jobs, allocating 8 Gb of RAM was not
a problem, for example by running:
> v1 <- seq(1,2^29)
> v2 <- seq(1,2^29)
> v3 <- seq(1,2^29)
> v4 <- seq(1,2^29)
This yields an R process, consuming about 8 Gb of RAM:
PID PGRP USERNAME PRI SIZE RES STATE TIME WCPU% CPU% COMMAND
177484 177484 mirjam 20 8225M 8217M sleep 1:18 29.3 0.00 R
After upgrading from R 2.0.0 to R 2.2.1, we cannot allocate more than
about 1300 M of memory, as shown below:
> v1 <- seq(1,2^29)
Error: cannot allocate vector of size 2097152 Kb
> v1 <- seq(1,2^28)
> v2 <- seq(1,2^27)
Error: cannot allocate vector of size 524288 Kb
> v2 <- seq(1,2^25)
> v3 <- seq(1,2^24)
> v4 <- seq(1,2^23)
> v5 <- seq(1,2^22)
Error: cannot allocate vector of size 16384 Kb
> v5 <- seq(1,2^21)
> v6 <- seq(1,2^20)
> v7 <- seq(1,2^19)
> v8 <- seq(1,2^18)
> q()
Save workspace image? [y/n/c]: n
Upgrading to R 2.3.0 yields the same results.
This yields an R executable taking 1284M of RAM, refusing to allocate
more RAM, with about 30Gb free on the machine.
Is there any special configuration option I should turn on to make it
possible to use more memory? The OS memory limits (ulimit -a) are set
appropriately:
data seg size (kbytes, -d) unlimited
max memory size (kbytes, -m) 63385824
stack size (kbytes, -s) 65536
virtual memory (kbytes, -v) unlimited
If it is not some special (compile time) option that I should have set,
I think this is a bug.....
With kind regards,
Mirjam van Vroonhoven
--
Dr. Mirjam van Vroonhoven
system administrator/programmer, dept. of Bioinformatics
Erasmus Medical Center, Rotterdam, The Netherlands
Room Number Ee 15.32, phone +31-10-463 81 11
Web: http://www.erasmusmc.nl/bioinformatics/
E-mail: [EMAIL PROTECTED]
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