[phenixbb] Rosetta refine compilation issue Centos 7
ludovic.pecqueur at college-de-france.fr
Thu Sep 24 07:43:40 PDT 2015
Hi Paul, Nigel,
Thank you for the suggestion.
I tried to set PYTHONHOME with
export PYTHONHOME=to PHENIX's python
export PYTHONHOME=to a local python compiled from source that I use to compile programs like Pymol
to no avail, I get the same error message.
As I can compile Rosetta without phenix using : ./scons.py -j6 mode=release bin, do you think the problem could reside in the way rosetta.build_phenix_interface works?
On Sep 23, 2015, at 11:09 PM, Paul Adams <pdadams at lbl.gov> wrote:
> 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?
>> 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
>> 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:
>> 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:
>> 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,
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> Unsubscribe: phenixbb-leave at phenix-online.org
> Paul Adams
> Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
> Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
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> Vice President for Technology, the Joint BioEnergy Institute
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