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
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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