How to save data from Genetic Algorithm in case MATLAB crashes?

Question

Syahmeer How 2019-12-16

1
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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/496955-how-to-save-data-from-genetic-algorithm-in-case-matlab-crashes

评论： Star Strider 2022-11-30

Hi there,

I'm using the GA to find input parameters for my model. My fitness function is computationally expensive and takes about 2 days. In situation if MATLAB unexpectedly crashes, is there a way to save the data?

I have used the 'OutputFcn' option however this seems to save the data once my MATLAB finish the simulation. I purposely stop MATLAB and re-open it but can't seem to access the saved data.

If anyone have any useful tips to save simulation data while the simulation is running so I can access in case it crashes, I would be very grateful.

Many thanks,

How

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Syahmeer How 2019-12-16

编辑：Syahmeer How 2019-12-16

Cheers Stephen for the quick reply. Yup I have read about using the latest population and restarting the simulation again from that population if it stops.

Just wondering though if you could share how to regularly save the population while the GA runs?

Actually I'm using a PSO function which I found from the file exchange but the way it's written was very much like the ga function on matlab, so I wrote ga here for better understanding.

It's the PSO aka (ga) that takes 2 days to calculate. I have written an OutputFcn which saves the population when I can only retrieve the data once the function finished calculating. Just not sure how to write the code in a such a way that if I stop Matlab on purpose, it would give me the output, without waiting for the function to finish calculating. Hope that makes sense.

Cheers

How

Here's my OutputFcn code if it helps and a script which I run the PSO function

OutputFcn code: @gaoutfun

function [state,options,optchanged] = gaoutfun(options,state,flag)

persistent state_record

if isempty(state_record)

state_record = struct('Population', {}, 'xGlobalBest', {}, 'Score', {},'Iteration',{},'SS',{});

end

if nargin == 0

state = state_record;

options = [];

optchanged = [];

else

state_record(end+1) = struct('Population', state.Population, 'xGlobalBest', state.xGlobalBest, 'Score', state.Score,'Iteration',state.Generation,'SS',state.fGlobalBest);

optchanged = false;

end

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

% Script I used to run the pso

tic

clear gaoutfun

options=psooptimset('Generations',200,'PopulationSize',40,'PlotFcns',{@psoplotbestf,@psoplotswarmsurf},'OutputFcns',@gaoutfun);

[ypso,fval,exitflag,output,population,scores]=pso(fitnessfcn,nvars,[],[],[],[],lbound,ubound,[],options);

record = gaoutfun();

toc

gapopulationhistory = vertcat(record.Population);

gabesthistory = vertcat(record.xGlobalBest);

gascorehistory = vertcat(record.Score);

gaiterhistory = vertcat(record.Iteration);

gasshistory = vertcat(record.SS);

save lale.mat

gahistory = [gascorehistory, gabesthistory, gapopulationhistory];

Star Strider 2019-12-16

@Syahmeer How — My pleasure. I have some code that specifically uses ga, so I will experiment with that and will post back here if I have a successful result.

Syahmeer How 2019-12-16

@starstrider Thank you so much :) I look forward to hearing back from you

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Answer 1

Star Strider 2019-12-17

2
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/496955-how-to-save-data-from-genetic-algorithm-in-case-matlab-crashes#answer_406665

在 MATLAB Online 中打开

It took a bit of trial and error, however this appears to work:

    function [state,options,changed] = SaveOut(options,state,flag)
        file_name = 'SaveBest.mat';                                     % Name File
        if strcmp(flag,'iter')
            ibest = state.Best(end);
            ibest = find(state.Score == ibest,1,'last');
            bestx = state.Population(ibest,:);
            previous = load('SaveBest.mat');
            var = [previous.var; bestx];                                % Read Previous Results, Append New Value
            save(file_name, 'var')                                      % Write ‘Best Individual’ To File
        end
        changed = true;                                                 % Necessary For Code, Use  Appropriate Value
    end

It reads the existing saved values of ‘var’, appends the new value to the end of the matrix, then writes the new matrix to the .mat file.

It never occurred to me that this was even possible! I will use it in my longer optimisations from now on.

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Star Strider 2019-12-17

编辑：Star Strider 2019-12-18

在 MATLAB Online 中打开

I ran that code so many times to test it that I did not encounter that problem.

My apologies.

I deleted the file first each time during this test, then ran my optimisation again without problems with slightly edited code.

This works:

    function [state,options,changed,str] = SaveOut(options,state,flag)
        file_name = 'SaveBest.mat';                                     % Name File
        if strcmp(flag,'init')
            Var = state.Population;
            save(file_name, 'Var')                                      % Write ‘Best Individual’ To File
        elseif strcmp(flag,'iter')
            ibest = state.Best(end);
            ibest = find(state.Score == ibest,1,'last');
            bestx = state.Population(ibest,:);
            previous = load('SaveBest.mat');
            Var = [previous.Var; bestx];                                % Read Previous Results, Append New Value
            save(file_name, 'Var')                                      % Write ‘Best Individual’ To File
        end
        changed = true;                                                 % Necessary For Cide, Use  App
    end

If you want to see the last five rows in the .mat file (as I named it):

BestInGen = load('SaveBest.mat')
LastFive = BestInGen.var(end-4:end,:)

EDIT — (18 Dec 2019 at 23:34)

Changed ‘var’ to ‘Var’ to avoid overshadowing the var (variance) function if the file is loaded without output arguments. Code otherwise unchanged.

Manjur Basnet 2022-11-30

Hi Star Strider, I have been trying to use the Saveout function to save best value from each generation but I keep getting this error after 1 generation

"Unrecognized field name "Best".

Error in SaveOut (line 7)

ibest = state.Best(end);

Error in gaoutput (line 51)

[state,optnew,changed] = feval(functions{i},options.OutputPlotFcnOptions,state,flag,args{i}{:});

Error in gamultiobjsolve (line 86)

[state,options] = gaoutput(FitnessFcn,options,state,currentState);

Error in gamultiobj (line 338)

[x,fval,exitFlag,output,population,scores,residuals] = gamultiobjsolve(FitnessFcn,nvars, ...

Error in pareto (line 28)

[x,fval,exitFlag,output] = gamultiobj(fun,5,A,B, Aeq, beq, lb,ub,nlcon, intcon, options);"

Can you help me with this? I tried searching for this kind of error but could find nothing.

Thank you so much.

Star Strider 2022-11-30

@Manjur Basnet — The correct thread for your problem is: Saving population individauls for each generation of GA Multiobjective optimisation.

Unfortunately, Shahrbanoo Shamekhi-Amiri didn’t accept it in spite of my posting a working solution.

See if that Answer solves your problem.

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