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
