The message from 'ar' is harmless and can be ignored. I was able to build a non-parallel version w/ o problems on an Ubuntu system; I got the same message about ar, but the build completed.

ar: `u' modifier ignored since `D' is the default (see `U')
ar: `u' modifier ignored since `D' is the default (see `U')> CHARMM Installation is completed.
              The CHARMM executable is /u/rvenable/Charmm/c42b2/exec/gnu/charmm.> Phase 3 completed.
Sun May 10 15:51:23 EDT 2020

I cannot test the parallel build easily, as we use CentOS for our compute nodes, and all of our MPI libraries have been built on those machines, and there are some subtle differences between Debian-based Linux (like Ubuntu) and RedHat-based Linux (such as CentOS). I don't see any errors here.

Note that with the gnu compiler, any MPI library used must be built with the same compiler version used to build CHARMM.

Rick Venable
computational chemist