[Rd] Help to create bugzilla account
selivanov.dmitriy at gmail.com
Fri Aug 11 16:28:49 CEST 2017
Thanks Martin, I've received invitation and will create ticket soon.
Regarding issue - basically the problem is that on operating systems which
use glibc memory is not freed (R releases it, but system doesn't trim it).
Setting corresponding environment variable (MALLOC_TRIM_THRESHOLD_) doesn't
help, but manual call to `*malloc_trim*` does.
Implication is following - for long-running jobs linux OOM killer can kill
R process because highly-fragmented pieces of memory never returned back to
OS. Very simple example:
1. I have 2gb of RAM on the machine.
2. I create large list of small objects which occupies 1.5 gig.
3. I remove it (even can manually call gc()) - "top" still shows 1.5 gig
occupied. If I decide to recreate similar 1.5gig list - ram will be reused.
4. However if after removal of the list I will decide to create normal
continuous integer/double vector of size 500+ mb - R will report that it
can't allocate vector of such size.
Hope this helped.
2017-08-11 18:00 GMT+04:00 Martin Maechler <maechler at stat.math.ethz.ch>:
> >>>>> Dmitriy Selivanov <selivanov.dmitriy at gmail.com>
> >>>>> on Fri, 11 Aug 2017 17:33:31 +0400 writes:
> > Hi mailing list and R-core. Could someone from R-core please help me
> > create account in bugzilla? I would like to submit issue related to
> gc() to
> > wishlist.
> I will create one.
> Your previous e-mails left me pretty clueless about what the
> problem is that you want to solve ... but maybe others
> understand better what you mean.
> Note that in the case of such a relatively sophisticated wish
> without a clear sign of a problem (in my view)
> chances are not high that anything will change, unless someone
> provides a (small footprint) patch towards the (R-devel aka
> "trunk") sources *and* reproducible R code that depicts the
> Still: Thank you for trying to make R better by contributing with
> careful bug reports !
> > Related context is here -
> > https://stat.ethz.ch/pipermail/r-devel/2017-July/074715.html
> > --
> > Regards
> > Dmitriy Selivanov
> > [[alternative HTML version deleted]]
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
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