[Bioc-devel] IntAE buffers needs to be freed or not??

[Ge Tan]

Hi Hervé,

Thank you! You always saved my life :-)

Best,
Ge


----------------------------------------
> Date: Mon, 22 Jul 2013 11:47:14 -0700
> From: hpages at fhcrc.org
> To: ge_tan at live.com
> CC: bioc-devel at r-project.org
> Subject: Re: [Bioc-devel] IntAE buffers needs to be freed or not??
>
> Hi Ge,
>
> On 07/22/2013 02:59 AM, Ge Tan wrote:
>> Hi Hervé,
>>
>> Thank you very much!
>> So how about Calloc? Does it run much slower than the direct malloc() too?
>
> Calloc() is just a wrapper to calloc() so it's also user-controlled
> memory (like malloc()). The difference with malloc() is that it sets the
> memory to zero so I expect it to be almost as fast as malloc(), and
> therefore, also much faster than R_alloc().
>
> Note that the auto-extending buffers (like IntAE) in IRanges don't need
> to be set to zero so the choice is really between malloc/realloc (user-
> controlled memory) and R_alloc/S_realloc (transient memory).
>
> Finally I should be a little bit more precise. In addition to malloc()
> being much faster than R_alloc(), realloc() is also much faster than
> S_realloc(). What I observed (last time I checked) was that using
> malloc/realloc was about 10x-20x faster (on my Linux system) than using
> R_alloc/S_realloc for growing a buffer. The reason S_realloc() is much
> slower than realloc() can easily be understood by looking at its
> implementation (<R_home>/src/main/memory.c):
>
> char *S_realloc(char *p, long new, long old, int size)
> {
> size_t nold;
> char *q;
> /* shrinking is a no-op */
> if(new <= old) return p;
> q = R_alloc((size_t)new, size);
> nold = (size_t)old * size;
> memcpy(q, p, nold);
> memset(q + nold, 0, (size_t)new*size - nold);
> return q;
> }
>
> It calls R_alloc(), then copies the data from the old place to the
> new place, and then sets the remaining memory to zero.
>
> OTOH realloc() is system-dependent and my understanding is that,
> on a descent OS, it will try to do an in-place reallocation, thus
> avoiding the need to move the data around.
>
> Cheers,
> H.
>
>>
>> Best,
>> Ge
>>
>> ----------------------------------------
>>> Date: Fri, 19 Jul 2013 17:05:30 -0700
>>> From: hpages at fhcrc.org
>>> To: ge_tan at live.com
>>> CC: bioc-devel at r-project.org
>>> Subject: Re: [Bioc-devel] IntAE buffers needs to be freed or not??
>>>
>>> Hi Ge,
>>>
>>> No you don't. At least not currently, because those buffers use
>>> transient memory which will be freed automatically when .Call()
>>> returns. However, I might change the implementation of the IntAE
>>> buffers to use user-controlled memory at some point (malloc() is
>>> so much faster than R_alloc(), about 10x-20x for me), so when this
>>> happens you will need to do something like
>>>
>>> .Call("AEbufs_free", PACKAGE="IRanges")
>>>
>>> unless you call your .Call entry point with .Call2 (defined in the
>>> IRanges package), which will take care of doing that for you. I highly
>>> recommend you do that if you use the IntAE buffers in your C code or
>>> if you call C functions that use the IntAE buffers (and a lot of C
>>> functions in IRanges and Biostrings use them).
>>>
>>> Cheers,
>>> H.
>>>
>>> On 07/19/2013 03:35 AM, Ge Tan wrote:
>>>> Hi all,
>>>>
>>>> I am using the IntAE buffers (taken from IRanges packages) in my .Call() code.
>>>> Sample code in C:
>>>>
>>>> IntAE width_buf;
>>>> width_buf = new_IntAE(0, 0, 0);
>>>> for(…){
>>>> IntAE_insert_at(&width_buf, IntAE_get_nelt(&width_buf), width);
>>>> }
>>>> PROTECT(width = new_INTEGER_from_IntAE(&width_buf));
>>>> UNPROTECT(1);
>>>> return(width);
>>>>
>>>> So after using .Call(), do I need to run something like ".Call("AEbufs_free", PACKAGE="IRanges")" in R?
>>>> I got this from the IRanges/src/AEbufs.c.
>>>>
>>>> Thanks!
>>>> Ge
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpages at fhcrc.org
>>> Phone: (206) 667-5791
>>> Fax: (206) 667-1319
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319