Re: Paralleling in Octave

[Benson Muite]

On Thu, Apr 23, 2020, at 1:12 PM, Maria Jose Casas Serrano wrote:

Hi!

Oh, yes, of course! I hoped for a theoretical answer so, that’s why my code proposal was more pseudocode than an executable one. 

I hope that the attached files are more helpful now.

Parallelisation_test.m file is the main program. evaluationParallel_test.m is the piece of code that I’m interested on parallelise, keeping LsystemGeneratorNP_test.m and getAspectRatioNP_test.m files as sequential execution. `outputparam1` and `outputparam2` ought to be the same size of P.  Would it be possible? 

This is the output I’m getting: 

evaluationParallel: individual G++GG[G]

evaluationParallel: inputparam2 GG—G      <——— Error 1: Here there is the first error because this value ought to be a float defined in parallelisation_test.m file (targetaspectratio) instead of the second element of P set.

evaluationParallel: inputparam3 GG[G[GG]G[GG]G]    <——— Error 2: The same mistake as Error 1. This value ought to be a float defined in parallelisation_test.m file (branchingweight) instead of the third element of P set.

evaluationParallel: Building the phenotype of the individual G++GG[G]

candidate = +

height =  16

width =  10

branchesnumber =  5

evaluationParallel: Calculating the aspect ratio of the individual G++GG[G]

getAspectRatio_test: height 16.000000

getAspectRatio_test: width 10.000000

getAspectRatio_test: branchesnumber 5.000000

getAspectRatio_test: targetaspectratio GG—G

getAspectRatio_test: branchingweight GG[G[GG]G[GG]G]

error: getAspectRatio_test: operator /: nonconformant arguments (op1 is 1x1, op2 is 1x15). <———— As `targetaspectratio` and `branchingweight` parameters are received as strings instead of float elements, the operation gives an error. 

parallelisation_test: Elapsed time 0.664954

Please, let me know if something else is needed of me. 

Thanks for your time!!!

Cheers

Maria J.

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On 23 Apr 2020, at 09:49, Kai Torben Ohlhus <address@hidden> wrote:

On 4/21/20 2:46 AM, Maria Jose Casas Serrano wrote:

Hi,

It’s the first time I’m trying to parallelise some code and I’m stuck in

a basic concept that I hope someone could help me with.

 

First, I’ll try to explain what my code is about. I’m doing Evolutionary

Computation and I have a large population of elements that represent the

genomes of modelled plants. This population should be evaluated by a

fitness function and then, some of the elements will evolve depending on

the probabilities of some genetic operators.

The bottleneck happens when evaluating them so, I thought that I could

parallelise that part of the code. 

[...]

However in the “inputparam2” and “inputparam3” parameters, the

evaluationParallel function is receinving the second and third elements

of the population.

Do you know what I am doing wrong? Perhaps I misunderstood the

parallelisation concept but I thought I could apply it in a piece of

code meanwhile there weren’t dependencies with the rest of the process.

Thanks in advance

Cheers

Maria J

Unfortunately, I have some trouble running your code.  It requires

octave-slf4o [1].  It would be nice to reduce it to simple "fprintf"

statements to avoid potential helpers to install dependencies

unnecessary for the problem.  Additionally, can you attach your code as

fully self-contained m-files, rather than pasting it into the email.

The code for generating "P" would also be nicer than a display of the

cell array.  Otherwise, I have to do the work to construct that cell

array myself.

HTH,

Kai

[1] https://github.com/apjanke/octave-slf4o

Attachments:

• parallelisation_test.m
  
• evaluationParallel_test.m
  
• LsystemGeneratorNP_test.m
  
• getAspectRatioNP_test.m
  

If there is nothing proprietary, you may want to put your code online somewhere, eg.

* gist [1]

* pastebin [2]

or for longer lived projects Gitlab, Github or similar. Will you also run your code run on a cluster?

[1] https://gist.github.com

[2] https://pastebin.com/