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Re: dynamic allocation of cell arrays is sloooow

From: Juan Pablo Carbajal
Subject: Re: dynamic allocation of cell arrays is sloooow
Date: Wed, 16 Mar 2016 13:52:15 +0100

On Wed, Mar 16, 2016 at 12:17 PM, Francesco Potortì <address@hidden> wrote:
> Dynamic allocation of array-like data structures is inherently
> inefficient, but sometimes it vastly simplifies coding, especially when
> the total size of the data structure is unknown in advance.
> Octave does a good job at doing dynamic allocation of arrays, but is
> apparently very inefficient when cell arrays or struct arrays are
> involved.  Here is a simple benchmark:
>>> version
> ans = 4.0.0
>>> a=[]; for esp=1:6; tic; for i=1:10^esp; a(i)=i; end; toc; end
> Elapsed time is 0.000110149 seconds.
> Elapsed time is 0.000464916 seconds.
> Elapsed time is 0.00417209 seconds.
> Elapsed time is 0.040483 seconds.
> Elapsed time is 0.417366 seconds.
> Elapsed time is 5.72097 seconds.
>>> a={}; for esp=1:6; tic; for i=1:10^esp; a{i}=i; end; toc; end
> Elapsed time is 0.000128031 seconds.
> Elapsed time is 0.000672817 seconds.
> Elapsed time is 0.00595999 seconds.
> Elapsed time is 0.063189 seconds.
> Elapsed time is 1.49592 seconds.
> Elapsed time is 145.996 seconds.
>>> a=struct("a",{}); for esp=1:6; tic; for i=1:10^esp; a(i).a=i; end; toc; end
> Elapsed time is 0.00019598 seconds.
> Elapsed time is 0.140211 seconds.
> Elapsed time is 0.0078249 seconds.
> Elapsed time is 0.0820489 seconds.
> Elapsed time is 1.82587 seconds.
> Elapsed time is 158.164 seconds.
> I find myself in the latter case: a struct array with around a million
> entries.  The only reasonable way I found is to do excess initial
> allocation and then delete the excess entries at the end.  Is this the
> recommended way?
> --
> Francesco Potortì (ricercatore)        Voice:  +39.050.621.3058
> ISTI - Area della ricerca CNR          Mobile: +39.348.8283.107
> via G. Moruzzi 1, I-56124 Pisa         Skype:  wnlabisti
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Assuming you are forced to use cells, that is, shape/type of element
sis inhomogeneous. I do not think there is a solution. Check the
functions with names starting with "cell", maybe some of those help
Your next chance would be to code some C++, but I am unsure what would
be the benefit. it would be nice to see a benchmark.
I am currently thinking to write a sort of acumcell function, but wont
have time till end of April to actually do serious work there. Maybe
that is also of your interest.

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