[R] segfault 'memory not mapped', dual core problem?

[Peter Dalgaard]

Benilton Carvalho <bcarvalh at jhsph.edu> writes:

> I had a similar problem, but with the silhouette() function.
> 
> I figured that the function expected that the grouping variable  
> started from 1, ie., if for some reason on my obs I didn't have any  
> observation on group 1, the function would return me random numbers  
> and repeated execution of the code would cause a seg. fault.
> 
> My fix was to remap my group variable so that it would always start  
> from 1.


Ugh! 

You shouldn't "fix" something like that, instead try your very best to
find circumstances where you reproduce the crash as quickly as
possible, prefering using a minimal setup without external data, and
report it (or try debugging it yourself).

 
> Maybe something like this is happening with you?
> 
> cheers,
> b
> 
> On Nov 12, 2006, at 3:05 PM, Barnet Wagman wrote:
> 
> > I encountered a segfault running glm() and wonder if it could have
> > something to do with the way memory is handled in a dual core system
> > (which I just set up).  I'm running R-base-2.4.0-1, installed from the
> > SuSE 10.1 x86_64 rpm (obtained from CRAN).   (My processor is an AMD
> > Athlon 64 x2 4800+).
> >
> > The error and traceback are
> >
> > *** caught segfault ***
> > address 0x8001326f2b, cause 'memory not mapped'
> >
> > Traceback:
> >  1: any(is.na(varmu))
> >  2: glm.fit(x = X, y = Y, weights = weights, start = start, etastart =
> > etastart,     mustart = mustart, offset = offset, family = family,
> > control = control,     intercept = attr(mt, "intercept") > 0)
> >  3: glm(y ~ x, family = binomial("logit"), data = da)
> >  4:  ...
> >
> > Note that this does NOT happen every time I make this call to glm().
> > I'm calling glm() in a loop and it executed correctly many times.
> >
> > The seqfault occurred while I was running two instances of R (in
> > separate Linux processes), so both cores were being utilized.  Free
> > memory exceeded the swap memory in use, so I don't think that there  
> > was
> > a lot of swapping going on.
> >
> > Any thoughts on what might have caused this to happen - and  how to
> > avoid it - would be appreciated.
> >
> > thanks,
> >
> > bw
> >
> > ______________________________________________
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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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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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> 

-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
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