For loops are too slow

43 views (last 30 days)
Joseph
Joseph on 5 Aug 2013
I have some MATLAB code that was given to me by a coworker. This code contains a three layered for loop. So the code has the basic structure:
for
for
for
The code works but it takes an incredibly long time to execute as the three layered for loop is performing operations on a 40000x4 matrix. I need a way to either bypass the for loops or make them run faster. Someone mentioned to me that I could call Perl in MATLAB to do this but I am unsure how this works. Dose anyone have any ideas. Thank you.
  3 Comments
Matt Kindig
Matt Kindig on 7 Aug 2013
I think the pre-allocating xmsd would help streamline the code, while still retaining the for loops. Something like this:
xmsd = NaN(nmax, 3);
for i = 1:1:N
for j = 1:1:norigin
jstart = (j-1)*N + i;
for k = nmin:1:nmax
kend = jstart + k*N;
xmsd(k,1:3) = xmsd(k,1:3) + (md_msd(kend,1:3) - md_msd(jstart,1:3) ).^2;
end
end
end

Sign in to comment.

Accepted Answer

dpb
dpb on 7 Aug 2013
Edited: dpb on 8 Aug 2013
for i = 1:1:N
for j = 1:1:norigin
jstart = (j-1)*N + i;
for k = nmin:1:nmax
kend = jstart + k*N;
xmsd(k,1:3) = xmsd(k,1:3) + (md_msd(kend,1:3)-md_msd(jstart,1:3)).^2;
end
end
end
Start in the inner loop...first off
md_msd(jstart,1:3)
is invariant w/ k so replace the indexed expression w/ the equivalent
...
for j = 1:1:norigin
jstart = (j-1)*N + i;
mdj=md_msd(jstart,1:3);
for k = nmin:nmax
kend = jstart + k*N;
xmsd(k,1:3) = xmsd(k,1:3) + (md_msd(kend,1:3)-mdj).^2;
end
end
Then, kend takes on values of jstart+N, jstart+2N, jstart+3N, ... so define an index vector as
kdx=jstart+N:N:jstart+nmax*N;
and then the loop on k can be written as
xmsd(nmin:nmax,1:3) = xmsd(nmin:nmax,1:3) + (md_msd(kdx,1:3)-mdj).^2;
So, after the first loop reduction you're left with
for i = 1:1:N
for j = 1:1:norigin
jstart = (j-1)*N + i;
kdx=jstart+nmin*N:N:jstart+nmax*N;
mdj=md_msd(jstart,1:3);
xmsd(nmin:nmax,1:3) = xmsd(nmin:nmax,1:3) + (md_msd(kdx,1:3)-mdj).^2;
end
end
Now, see what you can do from here... :)
ADDENDUM: Forgot to add -- xmsd IS preallocated, correct????
ERRATUM: "Then, kend takes on values of jstart+N, jstart+2N, jstart+3N, ..."
Actually, the first value is jstart+nmin*N not jstart+N. The increment is N, however, so only the lower bound needs must be corrected.
  1 Comment
Joseph
Joseph on 7 Aug 2013
Thank you very much this helped!

Sign in to comment.

More Answers (0)

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by