I have a homology based structure and submitted it to relax protocol. After 24 hours running, it is still work and the terminal always said the following. Should I stop it or still keep it working?
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3975 rotamers at 509 positions.
core.pack.pack_rotamers: IG: 2706856 bytes
core.optimization.LineMinimizer: WARNING: DFPMIN (Armijo) MAX CYCLES 200 EXCEEDED, BUT FUN C NOT CONVERGED!
509 positions is huge; generally we don't recommend running relax on things that big. Relax scales poorly with size, so it will take forever and a day at that size. It's unlikely to be hanging - just slow.
You are using the release version of the executeable, not the debug version, right?
yes, I am using release version. Will there any differece between release version and debug version?
I compiled rosetta by the command "scon"
There should not be differences in the ultimate results. It's just that the debug mode executeable takes 10 times as long to get there because it lacks compiler optimizations, etc.