yea -- already solved :)
On Fri, Mar 18, 2016 at 4:37 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> Can you try to rename or delete the "/home/krieg/.local/lib/python2.7"
> version?
>
> In your case, amber.python was used ($AMBERHOME/miniconda/) but you had a
> folder in .local/python2.7. Probably that (in .local folder) version was
> not compatible with amber.python
>
> Hai
>
> On Fri, Mar 18, 2016 at 1:55 PM, Brent Krueger <kruegerb.hope.edu> wrote:
>
> > I've been having a consistent problem building amber16 -- just related to
> > the python stuff.
> >
> > If I build with:
> > ./configure --skip-python intel
> > then everything works just fine on my system.
> >
> >
> > But if I include python by doing the basic ./confingure intel I get the
> > following from stdout:
> >
> > ~~~~~~~~~~~~~~~
> > make[2]: Leaving directory
> > `/home/krieg/source/amber_git/amber/AmberTools/src/quick'
> > (if [ "no" = "no" ]; then \
> > make python_serial ;\
> > fi;\
> > )
> > make[2]: Entering directory
> > `/home/krieg/source/amber_git/amber/AmberTools/src'
> > (cd parmed && /home/krieg/source/amber_git/amber/bin/amber.python
> setup.py
> > install --no-setuptools -f --prefix=/home/krieg/source/amber_git/amber
> > --install-scripts=/home/krieg/source/amber_git/amber/bin)
> > ~~~~~~~~~~~~~~~
> >
> > and then it dies.
> >
> > stderr contains:
> >
> > ~~~~~~~~~~~~~~~
> > ar: creating quick_lib.a
> > Traceback (most recent call last):
> > File "setup.py", line 57, in <module>
> > import parmed
> > File
> >
> >
> "/home/krieg/source/amber_git/amber/AmberTools/src/parmed/parmed/__init__.py",
> > line 21, in <module>
> > from parmed.structure import Structure, StructureView
> > File
> >
> >
> "/home/krieg/source/amber_git/amber/AmberTools/src/parmed/parmed/structure.py",
> > line 29, in <module>
> > import numpy as np
> > File
> "/home/krieg/.local/lib/python2.7/site-packages/numpy/__init__.py",
> > line 137, in <module>
> > import add_newdocs
> > File
> > "/home/krieg/.local/lib/python2.7/site-packages/numpy/add_newdocs.py",
> line
> > 9, in <module>
> > from numpy.lib import add_newdoc
> > File
> > "/home/krieg/.local/lib/python2.7/site-packages/numpy/lib/__init__.py",
> > line 4, in <module>
> > from type_check import *
> > File
> > "/home/krieg/.local/lib/python2.7/site-packages/numpy/lib/type_check.py",
> > line 8, in <module>
> > import numpy.core.numeric as _nx
> > File
> > "/home/krieg/.local/lib/python2.7/site-packages/numpy/core/__init__.py",
> > line 5, in <module>
> > import multiarray
> > ImportError:
> > /home/krieg/.local/lib/python2.7/site-packages/numpy/core/multiarray.so:
> > undefined symbol: PyUnicodeUCS2_AsUnicodeEscapeString
> > make[2]: *** [parmed] Error 1
> > make[1]: *** [serial] Error 2
> > make: *** [install] Error 2
> > ~~~~~~~~~~~~~~~
> >
> > So the installation of Python 2.7 is not working properly.
> >
> > This system is my old one that I've mentioned before: CentOS 5.6 in
> which
> > the native python is 2.4.3
> >
> > I can send the full configure and install stdout/stderr files if desired.
> >
> >
> > Cheers,
> > Brent
> >
> >
> > --
> > _______________________________________________
> > Brent P. Krueger.....................phone: 616 395 7629
> > Professor.................................fax: 616 395 7118
> > Hope College..........................Schaap Hall 2120
> > Department of Chemistry
> > Holland, MI 49423
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> _______________________________________________
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>
--
Jason M. Swails
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Received on Fri Mar 18 2016 - 17:00:06 PDT
