Top and Free are rather useless for "where does my memory go".
They show you "how much is left" which generally should be zero as the system 
fills up all that is left with caches and it is good that it does so.

Therefore Top/Free are really not the tools to look for memory
consumption.

It always depends how deep you want to go, take a look here and pick whatever 
suits you.
https://share.confex.com/share/123/webprogram/Handout/Session15754/Tools-V6-ShareDesign.pdf
So many years and still mostly applies :-)

The two recommendations of /proc/meminfo and smem are a good entry point
for you I'd think.

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https://bugs.launchpad.net/bugs/1892648

Title:
  VM eating twice the memory allocated

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