[R] R-1.6.0 crashing on RedHat6.3

[Peter Dalgaard BSA]

Douglas Grove <dgrove at fhcrc.org> writes:

> Hi,
> 
> I'm having what I believe are OS problems with my installation
> of R-1.6.0.  The machine I'm using was previously running R-1.4.0.
> The install seemed fine to me.  I didn't note an error messages
> in 'make' or 'make check'.
> 
> My problem is that I've been running some memory intesive code,
> and the code that ran under 1.4.0 but won't run under R.1.6.0
> (or under 1.5.1).  The code crashes with the message:
> 
>   Error: cannot allocate vector of size 13 Kb
>   Execution halted
> 
> 
> There's nothing special about the code I'm trying to run,
> in fact it's pretty simple (just memory intensive):
> 
>   library(mva)
>   pc.norm <- princomp(D,scores=FALSE)
> 
> D is a matrix of dim 144x5300
>   
> 
> My only guess, based on my very limited knowledge, is the 
> problem stems from some outdated shared library.
> 
> The machine is an two-processor intel-based PC running RedHat6.3.
> I would provide more info, but I'm not really sure what's relevant
> and I'm not very system-savvy.  
> 
> I know the OS should probably be updated, but this isn't feasible
> in the short term due to our sys-admin time constraints.
> Is there is anything I can do short of updating the entire OS?
> 
> BTW, I realize that there isn't much *I* can do, as I'm not the 
> system administrator, but I'm trying to figure out where the
> problem(s) may lie so that I can tell him what to update.

Are you sure that it is 6.3?? To my knowledge, there is nothing
between 6.2 and 7.0. What's in /etc/redhat-release ?

The Fortran in RH6.x was rather badly broken for some packages, but
one would expect that you had run into that before. 1.6.0 has a memory
leak but it generally affects repeated applications of model fits,
rather than big matrices. 

Do you really mean 144x5300 ? (more columns than rows) That's big: The
covariance matrix at 5300x5300 will take more than 200 MB (OK, it
might only be storing upper or lower triangle.) I tried a matrix like
that on a 1.6.1beta system with about 0.75 GB and got an out of memory
error. A 144x2500 problem is currently running in

  PID USER     PRI  NI  SIZE  RSS SHARE STAT %CPU %MEM   TIME COMMAND
16111 pd        17   0  207M 163M 18536 R    99.8 65.8   1:58 R.bin

and seems to be staying there....

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907
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