Improve Topology construction and fix MPI/NBX bug #1212

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Treating cmake as a formula. For the cask, use homebrew/cask/cmake or specify the `--cask` flag. To silence this message, use the `--formula` flag.

cmake 3.31.0 is already installed and up-to-date. To reinstall 3.31.0, run: brew reinstall cmake

pkg-config 0.29.2_3 is already installed and up-to-date. To reinstall 0.29.2_3, run: brew reinstall pkg-config

gcc 14.2.0_1 is already installed and up-to-date. To reinstall 14.2.0_1, run: brew reinstall gcc