[phenixbb] Rosetta refinement fail on Mac

Billy Poon BKPoon at lbl.gov
Wed Aug 22 17:49:56 PDT 2018


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
Web: https://phenix-online.org


On Wed, Aug 22, 2018 at 4:53 PM Aaron Oakley <aarono at 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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