[phenixbb] Rosetta refinement fail on Mac

Aaron Oakley aarono at uow.edu.au
Wed Aug 22 15:11:43 PDT 2018

System: macOS 10.13.6
Phenix version: phenix-1.14rc1-3177
Rosetta version: 3.9 (rosetta_src_2018.09.60072_bundle)

So I rebuilt rosetta 3.9 as root and can now run "Rosetta refinement". However...Rosetta refinement ran for 2 hours, slowly gobbling memory up to a maximum of 25GB before failing (error below).
Also gobbled up disk space, creating a 78 GB file “outtmp.map”.

A memory leak issue?



RuntimeError : File 'None' not found.
  File "/Applications/phenix-1.14rc1-3177/modules/cctbx_project/libtbx/runtime_utils.py", line 179, in run
    return_value = self.target()

  File "/Applications/phenix-1.14rc1-3177/modules/cctbx_project/libtbx/runtime_utils.py", line 74, in __call__
    result = self.run()

  File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/command_line/rosetta_refine.py", line 304, in run
    return run(args=list(self.args))

  File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run

  File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__

  File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs

  File "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py", line 383, in check_result
    raise RuntimeError("File '%s' not found." % result.file_name)

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