script running for 13 hours. should I be worried?

I have a function going through 9 excel files with about 1.7mil cells. It imports them, puts everything into one column then goes through and removes all the 0's and saves the output of about 300k cells. Its been running for about 13 hours of so now and I'm concerned that I may have messed up the code so I was hoping someone would help me out a fresh set of eyes.

it does look like its working, maybe? the output files look with theyve been edited, but I can't really be sure. this is the code i'm using at the moment.

function [ m ] = combine( input_args )

source = 'C:\Users\aoneil\Desktop\ODEN\trimmed'; %input the directory to choose the source folder

dest_dir = 'C:\Users\aoneil\Desktop\ODEN\graphs'; %choose where to output the resulting file

files = dir(fullfile(source, '*.CSV'));

for j = 1:length(files)  %loops through all the file in the directory folder

    a = xlsread(fullfile(source, files(j).name));

    for  x = 1 : size(a,1)  %steps through the matrix

            d((1+((x-1)*size(a,2))):(size(a,2)*x), 1) = a(x,1:end); %saves all the values of original to matrix "d" 

    end

    n=1;
    for y=1:size(d,1)

       if d(y,1) > 0 

           m(n,1) = d(y,1)

           n=n+1;

       end

    end

 csvwrite(fullfile(dest_dir, files(j).name), m); %outputs matrix "d" to the file name/directory chosen
  end

end

Answer 1

[Jan]

You urgently require a "pre-allocation". Letting arrays grow iteratively is extremely expensive. Example:

x = [];
for k = 1:1e5
  x[k] = rand;
end

Now in each iteration a completely new vector x is created and the older values are copied. This means, that the OS has to reserve sum(1:1e5) * 8 bytes in total and copy almost the same amount of data in addition.

A vectorization solves the pre-allocation implicitly:

n=1;
for y=1:size(d,1)
  if d(y,1) > 0 
     m(n,1) = d(y,1)
     n=n+1;
  end
end

Better without loop and IF:

m = d(d > 0);

Answer 2

[Alessandro Masullo]

You can use a task manager to check if matlab is still using the CPU. If not, it probably got stuck.