[phenixbb] Phenix.rosetta build Ubuntu 16.04

Joseph Brock joseph.brock at dbb.su.se
Wed Apr 25 13:38:35 PDT 2018

Dear phenix community,

I am trying to get phenix to run with rosetta on my Ubuntu 16.04 station.

I am running the latest official phenix version (phenix-1.13-2998) and and compiled rosetta 3.7 (2016.32.58837) using scons as described:



Then ran rosetta.build_phenix_interface.

All went without error but running rosetta.run_tests then gave the segmentation fault below. Defining variables as suggested did not help.

I found a similar question  in the phenixbb archives but no resolution:


Any suggestions on how to move forward greatly appreciated!




Segmentation fault (Python and libc call stacks above)
                This crash may be due to a problem in any imported
                Python module, including modules which are not part
                of the cctbx project. To disable the traps leading
                to this message, define these environment variables
                (e.g. assign the value 1):
                This will NOT solve the problem, just mask it, but
                may allow you to proceed in case it is not critical.
Traceback (most recent call last):
  File "/usr/local/phenix-1.13-2998/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 305, in <module>
    run(sys.argv[1:], create_dir=True)
  File "/usr/local/phenix-1.13-2998/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run
  File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__
  File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs
  File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result
    raise RuntimeError("Aborted due to error in job %d." % result.job_id)
RuntimeError: Aborted due to error in job 1.

Joseph S. Brock | PhD
Drew Lab
Department of Biochemistry and Biophysics
Stockholm University
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