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 <maech...@stat.math.ethz.ch>: > >>>>> Dmitriy Selivanov <selivanov.dmit...@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@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Regards Dmitriy Selivanov [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
