I'm happy to try to debug this but since I don't ordinarily go through the Rosetta refinement protocol -- that's the protein side, which Frank is expert in -- I will probably need to know what Rosetta command line is generated by the above.

On Wed, Aug 22, 2018 at 5:51 PM Billy Poon <BKPoon@lbl.gov> wrote:
Hi Aaron,

This looks like a High Sierra issue since this excessive amount of memory usage is not seen on 10.12. We are tracking this down and will be contacting the Rosetta developers. It looks like any version of Rosetta will cause this problem (I tested back to Rosetta 3.7).

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909


On Wed, Aug 22, 2018 at 4:53 PM Aaron Oakley <aarono@uow.edu.au> wrote:
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?

Thanks,

a++



RuntimeError : File 'None' not found.
Traceback:
  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
    debug=params.output.debug)

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

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

  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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