Memory allocation fails in R 2.2.1 and R 2.3.0 on SGI Irix, while plenty of memory available (PR#8861)
On Mon, 15 May 2006, m.vroonhoven at erasmusmc.nl wrote:
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.
You can tell if you have a 64bit build of R by looking at .Machine$sizeof.pointer in R, which should be 8. If not, then you need to set whatever C and Fortran compilation flags give a 64bit system. It doesn't look to me as if R's configure script has any special handling for C compiler flags on SGI. If you have a 64bit build then something strange is happening. The message you quote happens only when malloc() returns NULL, so it is hard to see how R could be causing it, though. -thomas Thomas Lumley Assoc. Professor, Biostatistics tlumley at u.washington.edu University of Washington, Seattle