[R] How to clear R memory in a for loop

[Uwe Ligges]

On 21.10.2014 19:00, William Dunlap wrote:
> A few minutes with valgrind showed that output_pos was never
> initialized, so the output array was not getting filled correctly.
> The following fixes that problem
>
> diff -ru tuneR/src/readmp3.c /homes/bill/packages/tuneR/src/readmp3.c
> --- tuneR/src/readmp3.c 2014-04-07 04:38:21.000000000 -0700
> +++ /homes/bill/packages/tuneR/src/readmp3.c    2014-10-21
> 09:54:19.351867000 -0700
> @@ -96,6 +96,7 @@
>     state.input = blob;
>     state.input_size = n_blob;
>     state.output_size = 0;
> +  state.output_pos = 0;
>     mad_decoder_init(&decoder, &state,
>              mad_input_cb, mad_header_cb, NULL,
>              NULL, NULL, NULL);


Thanks, Bill!
I haven't found the time to look at it.
Now in the master sources, bugfix release will follow shortly,
Uwe


> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Tue, Oct 21, 2014 at 7:51 AM, Prof Brian Ripley
> <ripley at stats.ox.ac.uk> wrote:
>> On 21/10/2014 15:47, Dimitri Liakhovitski wrote:
>>>
>>> I will try with .wav files and report back.
>>> So far, I am not sure I understood what could be done (if anything) to fix
>>> it...
>>
>>
>> This is nothing to do with my reply!
>>
>> The posting guide asked you to contact the tuneR maintainer *before
>> posting*.  What did he say?
>>
>> Bill Dunlap's reply pointed to a bug in tuneR (or a library it uses).
>>
>>
>>>
>>> On Tue, Oct 21, 2014 at 2:26 AM, Prof Brian Ripley
>>> <ripley at stats.ox.ac.uk> wrote:
>>>>
>>>> On 20/10/2014 17:53, John McKown wrote:
>>>>>
>>>>>
>>>>> On Mon, Oct 20, 2014 at 10:30 AM, Dimitri Liakhovitski <
>>>>> dimitri.liakhovitski at gmail.com> wrote:
>>>>>
>>>>>> Dear Rers,
>>>>>>
>>>>>> I am trying to run a for-loop in R.
>>>>>> During each iteration I read in an mp3 file and do some basic
>>>>>> processing.
>>>>>> If I do what I need to do for each file one by one - it works fine.
>>>>>> But once I start running a loop, it soon runs out of memory and says:
>>>>>> can't
>>>>>> allocate a vector of size...
>>>>>> In each iteration of my loop I always overwrite the previously created
>>>>>> object and do gc().
>>>>>>
>>>>>> Any hints on how to fight this?
>>>>>>
>>>>>> Thanks a lot!
>>>>>>
>>>>>>
>>>>>>
>>>>> Please don't use HTML for messages.
>>>>>
>>>>> What occurs to me, from reading the other replies, is that perhaps
>>>>> within
>>>>> the loop you are causing other objects to be allocated. And that can be
>>>>> done just by doing a simple assignment, so it may not be obvious. What
>>>>> this
>>>>> can do is cause what we called a "sand bar" in the old days. That's
>>>>> where
>>>>> you allocate a big chunk of memory for an object. Say this take up 1/2
>>>>> of
>>>>> your available space. You now create a small object. This object is
>>>>> _probably_ right next to the large object. You now release the large
>>>>> object. Your apparent free space is now almost what it was at the
>>>>> beginning. But when you try to allocate another large object which is,
>>>>> say,
>>>>> 2/3 of the maximum space, you can't because that small object is sitting
>>>>> right in the middle of our memory space. So you _can_ allocate 2 large
>>>>> objects which are 1/3 your free space size, but not 1 object which is
>>>>> 2/3
>>>>> of the free space size. Which can lead to your type of situation.
>>>>>
>>>>> This is just a SWAG based on some experience in other systems. Most
>>>>> "garbage collection" do _not_ do memory consolidation. I don't know
>>>>> about
>>>>> R.
>>>>>
>>>>>
>>>> That is true of R (except for the early days which did have a moving
>>>> garbage
>>>> collector).
>>>>
>>>> However 'your available space' is not the amount of RAM you have but the
>>>> process address space.  The latter is enormous on any 64-bit OS, so
>>>> 'memory
>>>> fragmentation' (as this is termed) is a thing of the past except for
>>>> those
>>>> limited to many-years-old OSes.
>>>>
>>>>
>>>> --
>>>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>>>> Emeritus Professor of Applied Statistics, University of Oxford
>>>> 1 South Parks Road, Oxford OX1 3TG, UK
>>
>>
>>
>>
>> --
>> Brian D. Ripley,                  ripley at stats.ox.ac.uk
>> Emeritus Professor of Applied Statistics, University of Oxford
>> 1 South Parks Road, Oxford OX1 3TG, UK
>>
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