Unexpected speedup when running script in barebones matlab

I have a function I've been running for the last several months, which typically takes around 2 hours to run. In order to run it on our cluster I'm now calling the same function in a headless matlab, using the following command from a terminal:

matlab -nosplash -nojvm -singleCompThread -nodesktop -r "myFunc(1,20)"

where I would otherwise use this command from within matlab:

myFunc(1,20)

While I expected this to run slightly faster (~10%) due to removing the overhead of the matlab GUI, the code is now running in under 15 minutes, about 8x faster than normal. This speedup is consistent accross several computers, including the linux cluster and two windows desktops.

My question is: are there any known reasons the same code should run this much faster, and is can I be confident that the results from running the code this way are the same as before?

For a little more detail, my function is effectively shuffling a 2d matrix of 1's and 0's, attempting to match particular distribution requirements. Most of the runtime is spent in Matlabs conv2 function, followed by find and randi.

[per isakson]

I cannot reproduce your result. The only reason for an 8x increase in performance that I can think of is the extra memory available to the Matlab process. Did your process run low on memory when started in the Matlab GUI?

[Nelis]

Sorry for the late reply. It's not a memory issue, as the process requires at most 2GB of RAM, out of 16GB available. I've since done some more testing of the results, by running the function both ways (headless and normal) with the same random seed - the results are identical.

The overall function is far from trivial, so it may be difficult to reproduce the result. If theres any more interest I'll try and come up with a minimal working example.

[Titus Edelhofer]

Interesting observation... Have you tried to run your desktop MATLAB with singleCompThread flag as well?

[Nelis]

I haven't tried running the desktop with any of those flags, only the exact command above both in a unix terminal, and cmd on my windows desktop, with similair results. I think I've just had the same effect in an entirely different program (also with a lot of calls to conv2), I'll try and build a minimal working example from that and try a few different scenarios.