[AMBER-Developers] Python build error

From: Brent Krueger <kruegerb.hope.edu>
Date: Fri, 18 Mar 2016 16:55:56 -0400

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
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Received on Fri Mar 18 2016 - 14:00:04 PDT
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