Internal Error: Sub-system: SSYN, File: /quartus/synth/ssyn/ssyn_env.cpp, Line: 304m_atom_node_vector[atom_node->get_id()] == 0

Due to a problem in the Quartus® II software version 12.0 SP2 and earlier, you may see this internal error during Analysis & Synthesis if your project has Physical Synthesis options turned on.

To work around this problem, on the Assignments menu, click on Settings. In the Settings dialog box, click on Physical Synthesis Optimizations under the Compilation Process Settings category. Turn off the following two options under the Optimize for performance (physical synthesis) heading.

• Perform physical synthesis for combinational logic
• Perform register retiming

This issue is scheduled to be fixed in a future release of the Quartus II software.