[R] Problem in executing R on server

[Erik Iverson]

Run the sessionInfo() command in R, as the posting guide requests!

Jason Lee wrote:
> Hi,
> 
> I am not too sure its what you meant :-
> Below is the closest data for each session from "top"
>  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
> 26792 jason     25   0 283m 199m 2620 R 100 0.6 0:00.38 R
>  
> The numbers changed as the processes are running. I am actually sharing 
> the server with other few people. I dont think this is a problem.
> 
> And, for my own pc,
>  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
>  6192 jason     25   0  157m 148m 2888 R  100 14.8   1081:21 R
>     
> On Fri, Jun 6, 2008 at 12:46 PM, Erik Iverson <iverson at biostat.wisc.edu 
> <mailto:iverson at biostat.wisc.edu>> wrote:
> 
>     And what is your sessionInfo() in each case!
> 
>     Jason Lee wrote:
> 
>         Hi,
> 
>         I query free -m,
> 
>         On my server it is,
> 
>                     total       used       free     shared    buffers  
>           cached
>         Mem:         32190       8758      23431          0        742  
>             2156
> 
>         And on my pc,
> 
>                     total       used       free     shared    buffers  
>           cached
>         Mem:          1002        986         16          0        132  
>              255
> 
> 
>         On the server, the above figure is after I exited the R.
>         It seems that there are still alot free MB available if I am not
>         wrong.
> 
>         On Fri, Jun 6, 2008 at 12:29 PM, Erik Iverson
>         <iverson at biostat.wisc.edu <mailto:iverson at biostat.wisc.edu>
>         <mailto:iverson at biostat.wisc.edu
>         <mailto:iverson at biostat.wisc.edu>>> wrote:
> 
>            How much RAM is installed in your Sun Solaris server?  How
>         much RAM
>            is installed on your PC?
> 
>            Jason Lee wrote:
> 
>                Hi,
> 
>                I am actually trying to do some matrix multiplications of
>         large
>                datasets of 3000 columns and 150 rows.
> 
>                And I am running R version 2.7.0. <http://2.7.0.>
>         <http://2.7.0.> <http://2.7.0.>
> 
> 
> 
>                I tried setting  R --min-vsize=10M --max-vsize=100M
>                --min-nsize=500k --max-nsize=1000M
> 
>                Yet I still get:-
> 
>                Error: cannot allocate vector of size 17.7 Mb
> 
>                I am running on Sun Solaris server.
> 
>                Please advise.
>                Thanks.
>                On Fri, Jun 6, 2008 at 11:50 AM, Erik Iverson
>                <iverson at biostat.wisc.edu
>         <mailto:iverson at biostat.wisc.edu>
>         <mailto:iverson at biostat.wisc.edu <mailto:iverson at biostat.wisc.edu>>
>                <mailto:iverson at biostat.wisc.edu
>         <mailto:iverson at biostat.wisc.edu>
>                <mailto:iverson at biostat.wisc.edu
>         <mailto:iverson at biostat.wisc.edu>>>> wrote:
> 
> 
> 
>                   Jason Lee wrote:
> 
>                       Hi R-listers,
> 
>                       I have problem in executing my R on server. It
>         returns me
> 
>                       Error: cannot allocate vector of size 15.8 Mb
> 
>                       each time when i execute R on the server. But it
>         doesnt
>                give me
>                       any problem
>                       when i try executing on my own Pc (except it runs
>                extremely slow).
> 
>                       Any pointers to this? I tried to read the FAQ on
>         this issue
>                       before in the
>                       archive but it seems there is no one solution to this.
> 
> 
>                   And that is because there is no one cause to this
>         issue.  I might
>                   guess your 'server' has less memory than your 'PC',
>         but you
>                didn't
>                   say anything your respective setups, or what you are even
>                trying to
>                   do with R.
> 
> 
>                    I tried to
> 
>                       simplified my code but it seems the problem is
>         still the
>                same.
> 
> 
> 
>                       Please advise. Thanks.
> 
>                              [[alternative HTML version deleted]]
> 
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>         <mailto:R-help at r-project.org>>>
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> 
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>                       PLEASE do read the posting guide
>                       http://www.R-project.org/posting-guide.html
>                       and provide commented, minimal, self-contained,
>                reproducible code.
> 
> 
> 
>