The Atom package for GDB integration does not work out-of-the-box with newer versions of the editor (likely Atom 1.39.0 and up). This is because one of its pre-compiled modules (pty) is not compatible with newer versions of Electron (a core dependency of Atom).
Judging from these directory entries after installing the package, it appears the last compatible version of Atom is 1.38.x (the last release to use Electron 2, and thus Node JS ABI v57 according to the ABI registry):
$ ls ~/.atom/packages/atom-ide-debugger-native-gdb/node_modules/nuclide-prebuilt-libs/pty/build
pty-electron-v1.7-darwin-x64
pty-electron-v1.7-linux-x64