Systems and methods for utilizing a defect map to configure an automata processor in order to avoid defects when configuring the automata processor. A system includes automata processor having a state machine lattice. The system also includes a non-volatile memory having a defect map stored thereon and indicating logical defects found on the automata processor. By including the defect map, a compiler may access the defect map to map out defects in the automata processor during configuring to avoid such defects.