Is that code in a function? (It should be.) Also, one of your variable
names changed to `counter1s`. Suspect a type instability.
On Mar 12, 2016 4:12 AM, "Tim Loderhose" <[email protected]> wrote:
> I tried around with that a bit, but then it gets much worse: From ~1s to
> ~6s, allocation as shown:
>
> 153710487 mat = Array{Complex64}(dims...)
> 4722450 file = Mmap.mmap(filename, Array{Complex64,2},
> (dims[2],length(counter1)))
> 9568 for i = 1:dims[2]
> 4000 for j = 1:length(counter1)
> 1690462534 mat[counter1s[j],i,counter2[j]] = file[i,j]
> - end
>
> I swapped the for loops around here, but that didn't matter. I can gain a
> little bit by indexing i into the first dimension of mat, but it still lags
> far behind.
> Any other ideas?
>
> On Saturday, 12 March 2016 03:15:33 UTC+1, Greg Plowman wrote:
>>
>> I think array slices (on right hand side of assignment) create new
>> arrays, hence the allocation.
>> Try writing an explicit loop instead, something like:
>>
>> for j = 1:length(counter1)
>> for i = 1:size(file,1)
>> mat[counter1[j],i,counter2[j]] = file[i,j]
>> end
>> end
>>
>>
>> On Saturday, March 12, 2016 at 12:25:00 PM UTC+11, Tim Loderhose wrote:
>>
>>> Hi,
>>>
>>> I have a question regarding some allocation in my code I would like to
>>> get rid of.
>>> I am memory mapping a file (which could be very large) which is part of
>>> a complex 3D matrix, and then put its contents into the preallocated matrix
>>> along the second dimension. I need the counters because the contents of
>>> file are only a subset of the full matrix.
>>>
>>> Here's a profiled snippet, where the file which is loaded has 120619520
>>> bytes.
>>>
>>> 153705063 mat = Array{Complex64}(dims...)
>>> 4721282 file = Mmap.mmap(filename, Array{Complex64,2},
>>> (dims[2],length(counter1)))
>>> 16 for i = 1:length(counter1)
>>> 148179531 mat[counter1[i],:,counter2[i]] = file[:,i]
>>> - end
>>>
>>> Why does the code allocate so much memory inside the for-loop (even more
>>> bytes than the contents of file)?
>>> It seems like this is a trivial matter, right now I just can't get my
>>> head around it, any help is appreciated :)
>>>
>>> Thanks,
>>> Tim
>>>
>>
