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    Rosetta compiles.

    The behavior is when the application runs – it will not terminate. The process must be killed if run interactively, or reach the end of walltime if I submit as a batch job, (which makes it impossible for me to estimate walltimes)

    Here’s one that produces output, but the program will not terminate after creating the result (1000 .pdb’s)

    ./rosetta aa prot1 _ -nstruct 1000 -paths /paths.txt

    The predictions (runpsipred_single) and fragments ( have been run previously and are there for rosetta when I run it – I don’t get errors that pieces and parts are missing. It just won’t terminate when it seems to be done processing. If I turn off -silent, as in the example, rosetta will output the 1000 .pdb files, but not terminate after the last one is written. Just sits there, cranking 100% cpu.