Re: CPU time, Octave vs MATLAB

[Rory Conolly]

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://octave.org/doc/v5.2.0/Basic-Vectorization.html
[2] https://octave.org/doc/v5.2.0/Profiling.html

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.