What is the origin of friction on the atomic (sub-atomic) scale?
Start by googling for "origin friction", then come back with some more specific questions after you've read some of what you find. You will get better and more helpful answers that way.
I am just asking what causes friction?
Do you mean:
"Why is the frictional force opposite in direction to the direction of travel?"
Here's the Tomlinson's model on the orgin of friction:
Please note that this is a very specific example. Your question is actually rather vague, because not only are there different proposed mechanisms for static and kinetic friction, but there are also different models for solid-liquid friction, liquid-liquid friction, etc. It is why Nugatory suggested that you do a bit of homework on your own first and figure out exactly how to ask your question in a more informed manner.
Separate names with a comma.