[phenixbb] Rosetta refinement fail on Mac

Andy Watkins andy.watkins2 at gmail.com
Wed Aug 22 17:53:17 PDT 2018


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 at 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
> 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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