issue with Multithreading in MATLAB?

Hello,

I have very long for loops i.e.

for i=1:109771
    % Many steps
    % STEP FOR APPENDING A MATRIX INTO A gif
end

Each step in for loop takes about 3 seconds. Is there a way to do this in parallel processing?

Can you please help me with an example. On how to modify this above code to get it working in a High Performance Computing environment.

On how many cores can I run this code?

Sincere Regards,

Sanchit

Answer 1

[Walter Roberson]

pool_cluster = 'myCluster';

numframes = 109771;
frame_rows = 512;   %adjust as appropriate
frame_cols = 768;   %adjust as appropriate
frame_panes = 3;    %1 for grayscale or pseudocolor
cmap = [];          %256 x 3 for pseudocolor
gif_frame_rate = 22; %fps
gif_delay = 1/gif_frame_rate;

gif_array = zeros(frame_rows, frame_cols, frame_panes, numframes, 'uint8');

myCluster = parcluster(pool_cluster);

parfor (frameidx = 1 : numframes, myCluster)
    %many steps
    thisframe = something_appropriate;  %that is frame_rows x frame_cols x frame_panes
    gif_array(:, :, :, frameidx) = thisframe;
end

if frame_panes == 1    %only valid for grayscale or pseudocolor
    imwrite(gif_array, cmap, 'YourGifFileName.gif', 'DelayTime', gif_delay);
else %rgb has to be appended a frame at a time
    imwrite(gif_array(:,:,:,1), cmap, 'YourGifFileName.gif', 'DelayTime', gif_delay, 'WriteMode', 'overwrite');
    for frameidx = 2 : numframes
        imwrite(gif_array(:,:,:,frameidx), cmap, 'YourGifFileName.gif', 'DelayTime', gif_delay, 'WriteMode', 'append');
    end
end

"On how many cores can I run this code?"

The above code is for the case where you have a Distributed Computing license and a cluster named myCluster has been configured. The number of cores that would be used would depend upon what was specified in the cluster profile. It is common for the number of cores configured in a profile is the number of physical cores on the cluster, but other numbers could be configured for economic or policy reasons.

[Sanchit Sharma]

Hello,

Many thanks for your response, I tried implementying your code, but am unsuccessfull.

here is my code. Can you please recommend me something:

cd ("C:\Users\sanchitsharma\Desktop\MATLABscripts\NeutronCSV\");
Z=zeros(256,256);
Gamma=2065;
Neutron=109771;
h = figure;
axis tight manual % this ensures that getframe() returns a consistent size
filename = 'PerFrame_neutron_clusters.gif';
for i=1:Neutron
    fileName = sprintf('NFrame%d.csv',i);
    Gamma=csvread(fileName);
    Z=Gamma+Z;
    figure(1);
    imagesc( Gamma' );
    % pick a colormap and show "zero" (approx. A(X,Y)<1) as white
    mymap = colormap( parula(1e5) );
    mymap(1,:)=1;
    colormap( mymap )
    colorbar    
    xlabel('X - Pixels');
    ylabel('Y - Pixels');
    title('Charge Deposit (0.0253 eV monoenergetic neutron)');
    % flip the YAxis
    ax = gca;
    ax.YAxis.Direction = 'normal'; 
    drawnow
    
      % Capture the plot as an image 
      frame = getframe(h); 
      im = frame2im(frame); 
      [imind,cm] = rgb2ind(im,256); 
      % Write to the GIF File 
      if i == 1 
          imwrite(imind,cm,filename,'gif','DelayTime',0, 'Loopcount',inf); 
      else 
          imwrite(imind,cm,filename,'gif','DelayTime',0, 'WriteMode','append'); 
      end  
end

[Walter Roberson]

What problem are you observing with that code? Or is that the code to be made parallel?

[Walter Roberson]

In that code the frames cannot be calculated in parallel. You effectively have a cumulative sum of csv files, so the calculations are not independent.

[Sanchit Sharma]

Hello,

The code is fine its just that I need to parallize it. Even if this code runs in parallel without the cumulative sum of CSV files it will work for me. I.e. if we can parallize the below code:

Also, I have a Distributed Computing license i.e. it is installed on a high performance computing system, but I do not know if a cluster has been configured.

cd ("C:\Users\sanchitsharma\Desktop\MATLABscripts\NeutronCSV\");
Z=zeros(256,256);
Gamma=2065;
Neutron=109771;
h = figure;
axis tight manual % this ensures that getframe() returns a consistent size
filename = 'PerFrame_neutron_clusters.gif';
for i=1:Neutron
    fileName = sprintf('NFrame%d.csv',i);
    Gamma=csvread(fileName);
    figure(1);
    imagesc( Gamma' );
    % pick a colormap and show "zero" (approx. A(X,Y)<1) as white
    mymap = colormap( parula(1e5) );
    mymap(1,:)=1;
    colormap( mymap )
    colorbar    
    xlabel('X - Pixels');
    ylabel('Y - Pixels');
    title('Charge Deposit (0.0253 eV monoenergetic neutron)');
    % flip the YAxis
    ax = gca;
    ax.YAxis.Direction = 'normal'; 
    drawnow
    
      % Capture the plot as an image 
      frame = getframe(h); 
      im = frame2im(frame); 
      [imind,cm] = rgb2ind(im,256); 
      % Write to the GIF File 
      if i == 1 
          imwrite(imind,cm,filename,'gif','DelayTime',0, 'Loopcount',inf); 
      else 
          imwrite(imind,cm,filename,'gif','DelayTime',0, 'WriteMode','append'); 
      end  
end 

[Walter Roberson]

The writing of the file cannot be within the parfor, but you can save all of the imind, cm as you generate them.

Caution: getframe does not always return the same size output unless you pass it the size to capture. Axes frame sizes turn out to vary slightly depending on titles and tick text and axes labels