[Rd] Help to create bugzilla account

Sun Aug 13 20:22:00 CEST 2017

FWIW if we are talking about alternative allocators, tcmalloc is another candidate that we are using for our projects where we care about allocations and performance (another upshot is that it's very flexible so you can do a lot of cool things if you care). However I didn't try it with R - I'll have a look if it can address the issue we're talking about.

> On Aug 12, 2017, at 4:10 PM, luke-tierney at uiowa.edu wrote:
> 
> On Sat, 12 Aug 2017, Dmitriy Selivanov wrote:
> 
>> Strange because in my all my experiments calling malloc.trim always helped
>> - memory reported by top decreased to the level it supposed to be. Do you
>> have in mind case when calling malloc.trim won't do anything? Also
>> shouldn't MALLOC_TRIM_THRESHOLD_ env variable has impact on malloc.trim
>> calls? At the moment seems any value is ignored...
> 
> This is a question for glibc developers. For that matter, this entire
> thread is really about tuning of the malloc in glibc and should
> ideally be addressed upstream.
> 
> There has been some discussion of this in other contexts, e.g. Python at
> 
> https://nuald.blogspot.com/2013/06/memory-reclaiming-in-python.html
> 
> and emacs at
> 
> http://notes.secretsauce.net/notes/2016/04/08_glibc-malloc-inefficiency.html
> 
> As the Python posts poitns out, it is possible to use alternate malloc
> implementations, either rebuilding R to use them or using LD_PRELOAD.
> On Ubuntu for example, you can have R use jemalloc with
> 
> sudo apt-get install libjemalloc1
> env LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libjemalloc.so.1 R
> 
> This does not seem to hold onto memory to the same degree, but I don't
> know about any other aspect of its performance.
> 
> The emacs post suggests that calling malloc_trim may have more of an
> effect in some cases: the post describes callign it via gdb on all
> running processes and sees a substantial memory footprint drop for
> emacs, Xorg and opera. I tried the same experiment on my system with
> emacs, Xorg and firefox and didn't see what that post saw -- maybe 1
> few percent recovery.
> 
> At this point I'm not sure we have enough data to show that adding
> malloc_trim calls at the end of each GC, say, would warrant the
> nusance of having to add configure checks. It would also be necessary
> to make sure that adding this doesn't significantly ompact malloc
> performance.
> 
> I don't know if this issue exists on Windows as well; it might as the
> basic malloc we use there is the same as used in glibc (Dog Lea's
> malloc).
> 
> Best,
> 
> luke
> 
> 
>> 
>> 12 авг. 2017 г. 6:09 ПП пользователь "Simon Urbanek" <
>> simon.urbanek at r-project.org> написал:
>> 
>>> 
>>> > On Aug 11, 2017, at 12:57 PM, Iñaki Úcar <i.ucar86 at gmail.com> wrote:
>>> >
>>> > 2017-08-11 16:00 GMT+02:00 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.
>>> >
>>> > How to reproduce it:
>>> >
>>> > a <- replicate(2e6, new.env()) # ~ 1.4 GB of memory
>>> > rm(a)
>>> > gc() # the R process still has the memory assigned
>>> >
>>> 
>>> Right, but that's unavoidable because of the way Linux allocates memory -
>>> see FAQ 7.42
>>> The memory is free, Linux just keeps it for future allocations.
>>> 
>>> Running malloc.trim doesn't help, because the issue is fragmentation due
>>> to the linear design of the pool - you likely will have another object on
>>> top so in most practical cases malloc.trim() doesn't actually do anything.
>>> You can always call malloc.trim() yourself is you think it helps, but it
>>> doesn't in the general case. The only way to address that would be to move
>>> allocated objects from top of the pool down, but that's not something R can
>>> allow, because it cannot know which code still has SEXP pointers referring
>>> to that object.
>>> 
>>> Cheers,
>>> Simon
>>> 
>>> 
>>> 
>> 
>> 	[[alternative HTML version deleted]]
>> 
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> 
> -- 
> Luke Tierney
> Ralph E. Wareham Professor of Mathematical Sciences
> University of Iowa                  Phone:             319-335-3386
> Department of Statistics and        Fax:               319-335-3017
>   Actuarial Science
> 241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
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