[Numpy-discussion] Array concatenation performance

Christopher Barker Chris.Barker@noaa....
Fri Jul 16 14:33:44 CDT 2010


Sturla Molden wrote:
> Christopher Barker skrev:
>> However, Python lists hold python objects, so it's bit inefficient, at 
>> least in terms of memory use.
>>
> I guess that is mainly in terms of memory use, as the Python (scalar) 
> objects must be created for the call to append. np.array([]) can also be 
> inefficient, as Anne explained yesterday, but an appendable ndarray 
> would not have that problem. But I don't know how important it is to 
> save a few milliseconds worth of cpu time for this.

not very.

> At least not enough 
> to convince me to spend my time on it. The memory issue is more 
> important though.

I agree.

> But arrays with O(1) amortized append are memory 
> inefficient on their own.

well, yes, but by the amount that you buffer them -- I've seen reference 
to methods that allocate twice as much memory as needed on each 
expansion, so that would be a maximum of a 2X hit.

In poking around the python code, it looks like lists and array.arrays 
over allocate by 1/16 (once the arrays are large, anyway). In my code, 
It defaults to over allocating by 1/4. In my very limited testing, I 
didn't see a performance gain by allocating more than that. So it's a 
maximum of 25% memory hit -- and it's user configurable.

> So it might make more sence to save a list of 
> equally long short buffers (e.g. ndarrays), and flatten to a contigous 
> buffer when needed.

I did that in a C extension I wrote a while back for reading big text 
files. I found that the size of the buffer hardly mattered to performance.

In my newer code, I found it a lot easier to over-allocate, and even if 
you over allocate by 1/10 or 1/16, performance is still pretty good.

> Personally I am not convinced about an appendable array, neither speed 
> nor memory wise, I just wanted to hear what other people think.

I still think it's a good idea -- though clearly not important enough 
for me to have gone further with my code (though I am using it now).

For me, the reasons are memory and the ability to deal natively with 
numpy data types that don't map directly to Python types. I think there 
could be a real benefit to loadtxt() for instance.

> there is one more thing that makes me sceptical: We cannot use realloc() 
> to grow an appendable array. That is because it would segfault if there 
> are array views in use (the views might suddenly get a dangling data 
> pointer). And prohibiting realloc(), the performance of an appendable 
> array might not be fantastic

I used ndarray.resize, which I'm pretty sure uses realloc(). And that's 
why I didn't subclass ndarray, but rather have an ndarray as the buffer, 
which never gets a view on it. When slicing, a copy is returned.

But  you're right this limits the utility, as it's not a first class 
citizen of numpy -- you still use it like you do list -- accumulate in 
it, then convert to a regular numpy array for further processing.

I'd love to see someone with more C chops than me pick this up -- but 
Sturla's right -- it's hard to find the motivation for the relatively 
small gains.

-Chris


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Christopher Barker, Ph.D.
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