[phenixbb] Rosetta refine compilation issue Centos 7

Paul Adams pdadams at lbl.gov
Wed Sep 23 14:09:08 PDT 2015


Hi Ludovic,

  the problems seem to occur when scons is called to compile Rosetta. I notice that the scons.py file uses the python that appears first in your path (#! /usr/bin/env python). Is it possible that this is a python that is broken in some way? 

  Cheers,
	Paul

> On Sep 23, 2015, at 9:11 AM, ludovic Pecqueur <ludovic.pecqueur at college-de-france.fr> wrote:
> 
> Dear Developers, 
> 
> I have a fresh Centos 7 system and after installing Phenix I wanted to compile the Rosetta.refine module. (Rosetta from source version 2015.31.58019)
> 
> I have succesfully compiled Rosetta but when I try to build the dedicated Rosetta for Rosetta_refine with rosetta.build_phenix_interface after setting up PHENIX_ROSETTA_PATH and ROSETTA3_DB I get the following error message: 
> 
> [XXX at ...]$ rosetta.build_phenix_interface nproc=6
> False
> scons: Reading SConscript files ...
> Running versioning script ... Done. (0.1 seconds)
> Could not find platform independent libraries <prefix>
> Could not find platform dependent libraries <exec_prefix>
> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
> ImportError: No module named site
> CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1:
>  File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 172:
>    main()
>  File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 163:
>    SConscript("SConscript", "build")
>  File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614:
>    return method(*args, **kw)
>  File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551:
>    return _SConscript(self.fs, *files, **subst_kw)
>  File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260:
>    exec _file_ in call_stack[-1].globals
>  File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConscript", line 28:
>    subprocess.check_call(["./update_options.sh"])
>  File "/usr/local/PROGRAMS/XTAL/PHENIX/phenix-1.10-2155/base/lib/python2.7/subprocess.py", line 540:
>    raise CalledProcessError(retcode, cmd).
> 
> If you have any idea of what could cause the problem, I would welcome any suggestions.
> I updated Phenix and I could compile phenix.rosetta_refine without problems on Centos 6.7.
> 
> Thank you very much for your time and help. 
> 
> Kind regards, 
> 
> Ludovic.
> 
> 
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-- 
Paul Adams
Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

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