From: Ardid, Salva <address@hidden>
Sent: Tuesday, March 10, 2020 4:22 PM
To: Ian McCallion <address@hidden>; Rory Conolly <address@hidden>
Cc: Kai Torben Ohlhus <address@hidden>; Octave Help <address@hidden>
Subject: Re: CPU time, Octave vs MATLAB On Tue, 10 Mar 2020 at 14:31, Rory Conolly <address@hidden> wrote:
>
>
>
> On Tue, Mar 10, 2020 at 10:08 AM Kai Torben Ohlhus <address@hidden> wrote:
>>
>> On 3/10/20 9:39 PM, Rory Conolly wrote:
>> > I have a program that describes biological mechanisms of cancer. Running
>> > the code in MATLAB takes 112 minutes. The almost identical code in
>> > Octave takes about 10 hr, so about 5 times slower. Is this an expected
>> > difference between Octave and MATLAB or more likely due to something in
>> > my code? Code is hundreds of lines over several files.
>> >
>> > - Rory
>> >
>>
>> Dear Rory,
>>
>> Unless you present (a meaningful portion of) your code, it is fortune
>> telling and blind guessing what could be wrong. Most likely your code
>> is not properly vectorized [1] and uses lots of nested loops, e.g.
>>
>> for k = 1:P
>> for i = 1:M
>> for j = 1:N
>> A(i,j) = A(i,j) + B(i,j);
>> endfor
>> endfor
>> endfor
>>
>> You can make use of profiling [2] to find the bottlenecks.
>>
>> HTH,
>> Kai
>>
>> [1] https://nam05.safelinks.protection.outlook.com/?url="">
>> [2] https://nam05.safelinks.protection.outlook.com/?url="">
>
>
>
> Kai, thanks for your input. My question is more about the relative speed of Octave vs MATLAB. My code was originally developed in MATLAB and is vectorized. The code reads parameter values from an Excel file. The Octave call to Excel requires the file extension while the MATLAB call does not. So that’s the only modification of the code running in Octave. So the two codes are pretty much identical, but the Octave code runs much more slowly. Happy to provide the code but it’s in several files and probably a thousand or more lines.
> Octave generally is nothing like 5 times slower than Matlab. My own
> code for example runs at about the same speed. However I believe
> Matlab has worked hard to improve nested loop performance in
> particular. Hence Kai's suggestions.
> Vectorisation also improves quality and readability. Go for it!
> Cheers... Ian
Hi Rory,
To be a bit more specific on this Matlab has worked hard to improve nested loop performance
The difference between Matlab and Octave here is related to the JIT compiler. Vectorisation also improves quality and readability. Go for it!
In some cases, I have seen Matlab unvectorized loops working faster than vectorized expressions, so even if you can and further vectorize your code in Octave, you may still see a time difference wrt Matlab.
Moreover, not all nested loops can be avoided, unfortunately. If that would be your case, there's not much you can do about it.
In any case, you may want to check the profilers and see where the bottleneck is. Salva I find that Octave can be 10 – 20 % slower than ML. One significant exception I found to be the svd. The default processing in Octave is rather slower than ML, especially when the matrix gets large. There is a thread about this not that long ago. Henk Borsje |