R help - Sep 2008 - Memory allocation problem (during kmeans)

Dear all,

I am trying to apply kmeans clusterring on a data file (size is about 300
Mb)

I read this file using

x=read.table('file path' , sep=" ")

then i do kmeans(x,25)

but the process stops after two minutes with an error :

Error: cannot allocate vector of size 907.3 Mb

when i read the archive i notice that the best solution is to use a 64bit
OS.

"Error messages beginning cannot allocate vector of size indicate a failure
to obtain memory, either because the size exceeded the address-space limit
for a process or, more likely, because the system was unable to provide the
memory. Note that on a 32-bit OS there may well be enough free memory
available, but not a large enough contiguous block of address space into
which to map it. "

the problem that I have two machines with two OS (32bit and 64bit) and when
i used the 64bit OS the same error remains.

Thank you if you have any suggestions to me and excuse me because i am a
newbie.

Here the default information for the 64bit os:
> sessionInfo()
R version 2.7.1 (2008-06-23)
x86_64-redhat-linux-gnu
> gc()
         used (Mb) gc trigger (Mb) max used (Mb)
Ncells 137955  7.4     350000 18.7   350000 18.7
Vcells 141455  1.1     786432  6.0   601347  4.6

I tried also to start R using the options to control the available memory
and the result still the same. or maybe i don't assign the correct values.


Thank you in advance.

-- 
Rami BATAL

	[[alternative HTML version deleted]]

rami batal skrev:
> Dear all,
>
> I am trying to apply kmeans clusterring on a data file (size is about 300
> Mb)
>
> I read this file using
>
> x=read.table('file path' , sep=" ")
>
> then i do kmeans(x,25)
>
> but the process stops after two minutes with an error :
>
> Error: cannot allocate vector of size 907.3 Mb
>
> when i read the archive i notice that the best solution is to use a 64bit
> OS.
>
> "Error messages beginning cannot allocate vector of size indicate a
failure
> to obtain memory, either because the size exceeded the address-space limit
> for a process or, more likely, because the system was unable to provide the
> memory. Note that on a 32-bit OS there may well be enough free memory
> available, but not a large enough contiguous block of address space into
> which to map it. "
>
> the problem that I have two machines with two OS (32bit and 64bit) and when
> i used the 64bit OS the same error remains.
>
> Thank you if you have any suggestions to me and excuse me because i am a
> newbie.
>
> Here the default information for the 64bit os:
>
>   
>> sessionInfo()
>>     
> R version 2.7.1 (2008-06-23)
> x86_64-redhat-linux-gnu
>
>   
>> gc()
>>     
>          used (Mb) gc trigger (Mb) max used (Mb)
> Ncells 137955  7.4     350000 18.7   350000 18.7
> Vcells 141455  1.1     786432  6.0   601347  4.6
>
> I tried also to start R using the options to control the available memory
> and the result still the same. or maybe i don't assign the correct
values.
>
>   
It might be a good idea first to work out what the actual memory
requirements are. 64 bits does not help if you are running out of RAM
(+swap).

-- 
   O__  ---- Peter Dalgaard             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark      Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)              FAX: (+45) 35327907