Error messages like "ImportError: No module named site" usually indicate that a Python installation is seriously broken.  The intent was to use the Python distributed with Phenix but it looks like Rosetta's build system makes additional Python calls that may use a different interpreter.  What is the output of these commands?

which python
python -c "import socket"

-Nat

On Thu, Dec 18, 2014 at 4:36 AM, Felipe Trajtenberg <felipet@pasteur.edu.uy> wrote:
Dear all,

I am trying to build the hybrid installation between Rosetta and Phenix using the rosetta.build_phenix_interface command

Phenix version: phenix-1.9-1692
Rosetta version: rosetta_2014.35.57232

I have no problem in compiling rosetta alone but when I try to build the hybrid system I get the following error:

False
scons: Reading SConscript files ...
Running versioning script ... Done. (0.0 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 "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/SConstruct", line 172:
    main()
  File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/SConstruct", line 163:
    SConscript("SConscript", "build")
  File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614:
    return method(*args, **kw)
  File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551:
    return _SConscript(self.fs, *files, **subst_kw)
  File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260:
    exec _file_ in call_stack[-1].globals
  File "/home/Xtal/Rosetta_phenix/rosetta_2014.35.57232_bundle/main/source/SConscript", line 28:
    subprocess.check_call(["./update_options.sh"])
  File "/home/Xtal/Phenix/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 540:
    raise CalledProcessError(retcode, cmd)

thanks in advance

Felipe
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