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