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Re: CPU time, Octave vs MATLAB

From: Kai Torben Ohlhus
Subject: Re: CPU time, Octave vs MATLAB
Date: Tue, 10 Mar 2020 23:08:44 +0900
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.5.0

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);

You can make use of profiling [2] to find the bottlenecks.



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