From selivanov.dmitriy at gmail.com  Fri Aug 11 16:28:49 2017
From: selivanov.dmitriy at gmail.com (Dmitriy Selivanov)
Date: Fri, 11 Aug 2017 18:28:49 +0400
Subject: [Rd] Help to create bugzilla account
In-Reply-To: <22925.47256.496267.20679@stat.math.ethz.ch>
References: <CAJdZCv3oUhwiqJUTwKy0ZvwkcB=qdA5WcBdfMsdAcJED9f356w@mail.gmail.com>
 <22925.47256.496267.20679@stat.math.ethz.ch>
Message-ID: <CAJdZCv1WtaHP-EZy6sEA5BCKzdOu0h1ntF=RsNmiiQMMsxV2NA@mail.gmail.com>

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
> to
>     > 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
> problem.
>
> Still: Thank you for trying to make R better by contributing with
> careful bug reports !
>
> Best,
> Martin
>
>
>     > 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
>



-- 
Regards
Dmitriy Selivanov

	[[alternative HTML version deleted]]



[Rd] Help to create bugzilla account
Dmitriy Selivanov