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The size of .vec file is about 3200. Sizes are different, most of them are 60x60.

That is actually not possible. Once you use the create samples interface, you need to specify -w and -h parameter and thus all samples are rescaled to that resolution, to ensure that all training data is equal. I am guessing you choose 60x60 pixels there also?

The program kind of stuck at stage 12 since it hasn't updated any information for more than 2 days

If you are using the latest OpenCV 2.4 or master branch then it should not get stuck. It either has a hard time solving the next stage or you still have an old buggy version. Keep in mind that if you take a basic HAAR based classifier that some models train for longer than a week! So no progress in 2 days is perfectly possible. Keep a look at the data collection (and see if that increases, even if it is single samples an hour).

I tried to kill the program and generate a XML file with the existing 12 stages(0-11). However, the program just got killed after it displayed: Stages 0-11 are loaded.

That is the expected behaviour. Normally your cascade folder should now show you a cascade.xml file which is the previous stages combined. If that did not work, it was still busy with the 11th stage and running the command with -numStages=11 should fix your problem!