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In my Linux machine I have boost libraries (libboost*.so files) in all of the above directories. I am wondering what is the difference between them. Can I remove the duplicate so files?

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The differences : man hier

It displays short and to the point information about almost every file/folder in the Linux File System Hierarchy. And for the files/folders you want to know, It says :

/usr/lib
          Object libraries, including dynamic libraries, plus some executables which
          usually are not invoked directly. More complicated programs may have whole
          subdirectories there.

/usr/local/lib
          Files associated with locally installed programs.

And for the file/folder /usr/lib/x86_64-linux-gnu, I (am not sure, but) think this :

/usr/lib/x86_64-linux-gnu
          Files associated with locally installed programs for 64-bit architecture`

Can I remove the duplicate so files ?

I'm not sure what exactly consequences may be of removing the duplicates but would advise not do so. Read this.

 /usr    This directory is usually mounted from a separate partition.
          It should hold only shareable, read-only data, so that it can
          be mounted by various machines running Linux.

Hope you noticed read-only data and shareable.

Feel free to add in more details.

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