# [Traminer-users] pb of memory to compute distance matrix

Mon Feb 11 14:38:09 CET 2013

```Hi Pierre,

I think this is a lack of memory, a 20000x20000 distance matrix requires
a huge amount of memory.  You can try the "full.matrix=FALSE" option so
that only half of the -symmetric- distance matrix is returned by the
seqdist function. Remember also that having other big objects in your
current R environment, like other distance matrices - uses a part of the
available memory.

Regarding weights, these are defined once when creating a sequence
object with seqdef, and used automatically by seqdplot and other plot
and sequence analysis functions. Please see our freely available article
in the journal of statistical software and help(seqdef) for more details.

All the best,
Alexis

Le 11. 02. 13 13:14, Pierre Blavier a écrit :
>
> Hi TramineR-users,
>
> 2 questions :
>
>
> 1) pb of memory computing distance matrix
>
> Everything works perfectly (couts<- seqsubm(seq.seq,
> method="CONSTANT", cval=2) / range(couts) / round(couts, 2) )
>
> Until :
>
> seq.om <http://seq.om><-seqdist(seq.seq, method="OM",indel=1.1, sm=couts)
>
> I obtain :
>
> Erreur : impossible d'allouer un vecteur de taille 1.5 Go
>
> R(351,0xac7312c0) malloc: *** mmap(size=1617408000) failed (error code=12)
>
> *** error: can't allocate region
>
> *** set a breakpoint in malloc_error_break to debug
>
> R(351,0xac7312c0) malloc: *** mmap(size=1617408000) failed (error code=12)
>
> *** error: can't allocate region
>
> *** set a breakpoint in malloc_error_break to debug
>
> My dataset is rather large (43 periods, n=20 000, 6 states) but it is
> rather suprising, how can I solve the problem ? ? (I have a brand-new
> macintosh with 8Go of live memory, so I think this is not the pb).
>
> 2) How can we use the weights in TramineR, for example in order to
> make it take them into account in commands like
>
> > seqdplot(seq.seq, withlegend=T, title="1988", weights="pond")
>
> It does not seem to work...
>
> Thanks a lot and best regards,
>
> Pierre
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