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 ~ ↳ 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 <bbolker@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
>
> ______________________________________________
> 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.
>

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