Re: CPU time, Octave vs MATLAB

[Kai Torben Ohlhus]

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