VMD-L Mailing List

From: Oliver Beckstein (oliver_at_biop.ox.ac.uk)
Date: Tue Feb 04 2003 - 09:45:46 CST

Hello,

I am running VMD 1.8 (December 9, 2002) on a Linux RedHat 8.0 system
with python 2.2. Apparently, the built-in python interpreter does not
find Numeric which is installed in
/usr/lib/python2.2/site-packages/Numeric and has a proper Numeric.pth
file in site-packages. This is a bit odd, given that the path seems to
be ok:

>>> import sys
>>> sys.path
['', '/usr/local/lib/vmd/scripts/python', '/usr/local/lib/vmd/plugins/LINUX/python', '/usr/local/lib/vmd/plugins/noarch/python', '/usr/lib/python2.2', '/usr/lib/python2.2/plat-linux2', '/usr/lib/python2.2/lib-tk', '/usr/lib/python2.2/lib-dynload', '/usr/lib/python2.2/site-packages']

However, importing fails:
>>> import Numeric
Traceback (most recent call last):
  File "VMD", line 1, in ?
ImportError: No module named Numeric

I tried to run the 'magic' site-import facility manually (I think,
for 2.2 it really works automagically):

>>> import site
>>> sys.path
['', '/usr/local/lib/vmd/scripts/python', '/usr/local/lib/vmd/plugins/LINUX/python', '/usr/local/lib/vmd/plugins/noarch/python', '/usr/lib/python2.2', '/usr/lib/python2.2/plat-linux2', '/usr/lib/python2.2/lib-tk', '/usr/lib/python2.2/lib-dynload', '/usr/lib/python2.2/site-packages']

but as you can see, /usr/lib/python2.2/site-packages/Numeric is not
added.

However, if I run the whole session in my system's python interpreter
everything works.

I think I traced it down to a call in site.py where a list of all the
*.pth files is generated:

names = os.listdir(sitedir)

It seems that os.listdir() generates garbage when run from within
vmd. Consider an example test directory with contents

> ls
bar boing foo

>From python (external):

> python
Python 2.2.1 (#1, Aug 30 2002, 12:15:30)
[GCC 3.2 20020822 (Red Hat Linux Rawhide 3.2-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import os
>>> os.listdir('.')
['bar', 'boing', 'foo']

>From vmd:
> vmd -python
>>> import os
>>> os.listdir('.')
['', '', '', 'g', '']

This list cannot be parsed succesfully by site.py and hence no
additional modules are found.

In general, I am slightly worried because I don't know where similar
bugs might come up; in particular I'd like to use the python
interpreter in vmd with different additional modules.

Has anyone got an idea where this might come from, or have I got to
set some special environment variables? Could it be some
incompatibility between vmd's python and mine? I should add that there
is also a small directory /usr/lib/python1.5 which, however, does not
seem to be in the path or otherwise directly used.

Thanks for any help,
Oliver 

-- 
Oliver Beckstein * oliver_at_bioch.ox.ac.uk
 http://indigo1.biop.ox.ac.uk/oliver/