[BioC] startup options

[Martin Morgan]

Also in R-devel under ?Memory there is

      How much time R spends in the garbage collector will depend on
      these initial settings and on the trade-off the memory manager
      makes, when memory fills up, between collecting garbage to free up
      unused memory and growing these areas.  The strategy used for
      growth can be specified by setting the environment variable
      'R_GC_MEM_GROW' to an integer value between 0 and 3. This variable
      is read at start-up. Higher values grow the heap more
      aggressively, thus reducing garbage collection time but using more
      memory.

and I would be interested in experiences with adjustments to this value in real 
work flows.

Martin

On 03/13/2013 08:07 AM, Nicolas Delhomme wrote:
> Hej Kasper, Benilton!
>
> This is from a previous post from Martin (titled SummarizedExperiments from September 5 2012):
>
> As a miscellaneous 'tip', when working with large data I find it useful to start R with --min-vsize=2048M --min-nsize=20M. These are documented in RShowDoc("R-intro") as 'for expert use only' and influence how much memory R allocates for vectors ('vsize'; vsize can be very large) and for S-expressions ('nsize' 50000000) and help get up to large memory allocations without innumerable garbage collections. Of course having big memory is of primary importance.
>
> These are not OS specific as far as I know.
>
> Cheers,
>
> Nico
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> Genome Biology Computational Support
>
> European Molecular Biology Laboratory
>
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>
>
>
> On Mar 13, 2013, at 3:35 PM, Benilton Carvalho wrote:
>
>> --max-mem-size and --max-vsize are the only items that I can
>> remember... but, AFAIR, they're Windows-exclusive...
>>
>> 2013/3/13 Kasper Daniel Hansen <kasperdanielhansen at gmail.com>:
>>> When we load say IRanges, it takes a while.  I seem to recall it has
>>> something to do with memory allocation or something, and that there is
>>> (or used to be) a startup option to R where you could increase the
>>> relevant memory and thereby decrease startup time (including loading
>>> of "standard" packages).  I seem to recall Martin Morgan posting about
>>> it.
>>>
>>> Does this ring any bells?
>>>
>>> Best,
>>> Kasper
>>>
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>>
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