https://gcc.gnu.org/bugzilla/show_bug.cgi?id=69393 --- Comment #2 from Martin Michlmayr <tbm at cyrius dot com> --- Ok, I can reproduce this issue like this: g++-6 -o STAR -flto -flto -g -O2 -fopenmp STAR.ii Genome.ii Stats.ii genomeGenerate.ii I've attached the preprocessed source.