[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] import errors

Mauricio Carrillo Tripp wrote:
> It seems you're on the right track, but still I have no clue why
> modpy.sh /usr/bin/python is using /usr/lib64/python2.3/lib-dynload/math.so
> if all env variables seem to be pointing to the modeller install only,
> or is that even the problem? (I added echoes to modpy.sh):

No, that's what it's supposed to be doing. Modeller isn't supposed to
"break" your regular Python (it just adds its own Python modules to the
search path by setting PYTHONPATH), so you should be loading
/usr/lib64/python2.3/lib-dynload/math.so in both cases.

> PYTHONHOME: Undefined variable.

That's good. You should generally *not* set PYTHONHOME, because that
also changes the location where Python looks for standard packages. So
changing that will often break all sorts of things.

>> /usr/bin/python
> Python 2.3.4 (#1, Oct 13 2006, 15:53:00)
> [GCC 3.3.4 (pre 3.3.5 20040809)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import math

Hmm, so it works fine, but simply adding the Modeller modules to the
path breaks it. That's very odd, and I can't explain why it only happens
here and not with the 'mod9v5' script. But every hit I can find
regarding this problem says that it's a Python 2.2/2.3 issue, so one
possible solution would be to upgrade Python on your machine. Modeller
will also work with the newer Python 2.4 or 2.5.

>>modpy.sh /usr/bin/python
> LD_LIBRARY_PATH /gremlin/people/trippm/modeller9v5/lib/x86_64-intel8
> DYLD_LIBRARY_PATH  /gremlin/people/trippm/modeller9v5/lib/x86_64-intel8
> /gremlin/people/trippm/modeller9v5/lib/x86_64-intel8:/gremlin/people/trippm/modeller9v5/modlib
> LIBPATH /gremlin/people/trippm/modeller9v5/lib/x86_64-intel8

Right, these look fine. The modpy.sh script simply adds the Modeller
Python libraries to PYTHONPATH (binary files in the lib/x86_64-intel8/
directory; pure Python code in modlib/) and the underlying low-level
dynamic libraries to the search path (LD_LIBRARY_PATH). (It also sets
DYLD_LIBRARY_PATH and LIBPATH to the same thing so that it also works on
Macs and AIX.)

	Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage