[phenixbb] Rosetta refinement fail on Mac

Nigel Moriarty nwmoriarty at lbl.gov
Wed Aug 22 17:47:16 PDT 2018


Aaron

Thanks for the addition email. This answers some of my other questions. I'm
not sure of a timeline but we are just coming to terms with this one.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


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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