[Rd] Help to create bugzilla account

[luke-tierney at uiowa.edu]

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
>>
>>
>>
>
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>
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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
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