Hi again and thank you all for the answers
i need to add that im a relatively R neewb so i apologize in advance
i started R with the --vanilla option and ran gc()
this is the output i get:
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 182236 9.8 407500 21.8 350000 18.7
Vcells 277896 2.2 786432 6.0 785897 6.0
also this is the memory.profile()
> memory.profile()
NULL symbol pairlist closure environment promise
1 5611 86695 2277 314 4175
language special builtin char logical integer
21636 44 637 6361 4574 11089
double complex character ... any list
782 1 20934 0 0 8023
expression bytecode externalptr weakref raw S4
1 6271 1272 364 365 831
>
im running on linux (arch linux) and 'free' shows this:
zeltak@zuni ~ â³ free -h
total used free shared buffers cached
Mem: 251G 99G 152G 66G 249M 84G
-/+ buffers/cache: 14G 237G
Swap: 0B 0B 0B
im not running any parrallel stuff at all
milan: how does one know if the memory is fragmented?
thank you all again i really appreciate the help
best
Z
On Thu, Jan 2, 2014 at 10:35 PM, Ben Bolker <bbol...@gmail.com> wrote:
> Xebar Saram <zeltakc <at> gmail.com> writes:
>
> >
> > Hi All,
> >
> > I have a terrible issue i cant seem to debug which is halting my work
> > completely. I have R 3.02 installed on a linux machine (arch
> linux-latest)
> > which I built specifically for running high memory use models. the system
> > is a 16 core, 256 GB RAM machine. it worked well at the start but in the
> > recent days i keep getting errors and crashes regarding memory use, such
> as
> > "cannot create vector size of XXX, not enough memory" etc
> >
> > when looking at top (linux system monitor) i see i barley scrape the 60
> GB
> > of ram (out of 256GB)
> >
> > i really don't know how to debug this and my whole work is halted due to
> > this so any help would be greatly appreciated
>
> I'm very sympathetic, but it will be almost impossible to debug
> this sort of a problem remotely, without a reproducible example.
> The only guess that I can make, if you *really* are running *exactly*
> the same code as you previously ran successfully, is that you might
> have some very large objects hidden away in a saved workspace in a
> .RData file that's being loaded automatically ...
>
> I would check whether gc(), memory.profile(), etc. give sensible results
> in a clean R session (R --vanilla).
>
> Ben Bolker
>
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