Re: [R] Problem in executing R on server

From: Erik Iverson <iverson_at_biostat.wisc.edu>
Date: Fri, 06 Jun 2008 08:27:18 -0500

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> <mailto:R-help_at_r-project.org
> <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.
>
>
>
>



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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. Received on Fri 06 Jun 2008 - 16:40:59 GMT

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