[phenixbb] Phenix.rosetta build Ubuntu 16.04

[Joseph Brock]

Dear all,


I just wanted to post the solution to this incase anybody else runs into a similar problem. I just needed to compile the latest phenix (phenix-1.13-299) from source and now it works with my rosetta installation just fine. After downloading the source installer I changed into the install directory and ran:


sudo ./install --prefix=/usr/local/stow --nproc=4 --try-unsupported --source --debug --rosetta --without-pymol (installed in non-standard location so as not to overwrite my binary installation)


added source statement to .bashrc as instructed:

source /usr/local/stow/phenix-1.13-2998/phenix_env.sh



Since I had already compiled rosetta 3.7 (2016.32.58837) using scons as described:
https://www.phenix-online.org/documentation/reference/rosetta_install.html
https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation

I then ran:

rosetta.build_phenix_interface_1.13-2998 nproc=4
rosetta.run_tests



Cheers,

Joseph.

Joseph S. Brock | PhD
Researcher
Drew Lab
Department of Biochemistry and Biophysics
Stockholm University
________________________________
From: Joseph Brock
Sent: Wednesday, 25 April 2018 10:38 PM
To: phenixbb at phenix-online.org
Subject: Phenix.rosetta build Ubuntu 16.04


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:

https://www.phenix-online.org/documentation/reference/rosetta_install.html

https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation


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:

http://www.phenix-online.org/pipermail/phenixbb/2013-October/020274.html


Any suggestions on how to move forward greatly appreciated!


Cheers,

Joseph.


_________________________________________________________________________________________________________



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):
                    BOOST_ADAPTBX_FPE_DEFAULT
                    BOOST_ADAPTBX_SIGNALS_DEFAULT
                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
    debug=params.output.debug)
  File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__
    self.run_jobs()
  File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs
    check_result(result)
  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
Researcher
Drew Lab
Department of Biochemistry and Biophysics
Stockholm University
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