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
>
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Fri Mar 18 2016 - 17:00:05 PDT
