[phenixbb] Phenix Rosetta install

Felipe Trajtenberg felipet at pasteur.edu.uy
Mon Dec 22 05:41:10 PST 2014


Dear Nat

Indeed the python is not the one distributed with Phenix!

which python

/usr/bin/python

python -c "import socket"

no output at all!

I change the python and now is installed!

thanks!

felipe


On 12/19/2014 04:25 PM, Nathaniel Echols wrote:
> 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 <mailto: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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>     phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
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>

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