Re: [phenixbb] Rosetta refinement fail on Mac

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 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 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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