[phenixbb] Phenix Rosetta install

Nathaniel Echols nechols at lbl.gov
Fri Dec 19 10:25:31 PST 2014


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 at 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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