Hi Paul, Nigel, Thank you for the suggestion. I tried to set PYTHONHOME with export PYTHONHOME=/usr/bin/python or export PYTHONHOME=to PHENIX's python or 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? Cheers, Ludovic. On Sep 23, 2015, at 11:09 PM, Paul Adams 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?

Cheers, Paul

...

On Sep 23, 2015, at 9:11 AM, ludovic Pecqueur 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@...]$ 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 Consider setting $PYTHONHOME to <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.

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- 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

Building 33, Room 347 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA.

Executive Assistant: Louise Benvenue [ [email protected] ][ 1-510-495-2506 ] --