[R] problem with generalized singular value decomposition using LAPACK

[Altuna Akalin]

Quoting elw at stderr.org:

> 
> > I'm trying to run generalized singular value decomposition (GSVD) 
> > function from LAPACK library. Basically my problem is that I can not run 
> > it for large matrices, I get a memory error. I'm using R 2.5.1.  I tried 
> > this on intel centos5 machines with 2 GB memory and 8 GB memory. I have 
> > unlimited max memory,cpu time and virtual memory.
> >
> >>  res=GSVD( matrix(1:35000,5000,6), matrix(1:35000,5000,6)  ) #runs 
> >> without
> > problems
> >>  res=GSVD( matrix(1:36000,6000,6), matrix(1:36000,6000,6)  )
> > Error: cannot allocate vector of size 274.7 Mb
> 
> 
> Did you examine R's internal memory limits, e.g. ?memory for help...
> 
> that should help.  [You should, most likely, be able to allocate a ~274MB 
> vector on a 2GB machine... but you might have to coerce R into taking that 
> much memory from the system, rather than trying to be conservative.]
> 
> --elijah
> 

Hi Elijah,
Thanks for your reply. I checked internal memory limits and it seems there is no
maxima set for consecutive cells or vector heap so i guess only limit is machine
resources. Also I set the "--max-ppsize" to the maximum value allowed with the
hope that it might help, it didn't change, still can not allocate memory. Below
I pasted ulimit -a output, maybe it helps for diagnostics. Further more, I
changed the stack size to "unlimited", that didn't help either.

core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
max nice                        (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 32759
max locked memory       (kbytes, -l) 32
max memory size         (kbytes, -m) unlimited
open files                      (-n) 1024
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
max rt priority                 (-r) 0
stack size              (kbytes, -s) 10240
cpu time               (seconds, -t) unlimited
max user processes              (-u) 32759
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

cheers
altuna