Re: [ccp4bb] problem about BALBES

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: problem about BALBES
From: Xiang Liu pku06a15 {- at -} YAHOO {- dot -} COM {- dot -} CN
Date: 2009-01-05

Next message:
Subject: Postdoctoral position at the University of Queensland, Brisbane, Australia
From: Bostjan Kobe b {- dot -} kobe {- at -} UQ {- dot -} EDU {- dot -} AU
Date: 2009-01-05

Subject: Re: problem about BALBES
From: "Dr {- dot -} F Long" fei {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-01-05

Hi Xiang Liu,

I have been trying to repeat your problem. It looks the python lib
file "pyexpat.so" under pymol directory has at least a
incompatibility issue when you run a python of different version
(Peter Zwart also pointed out that earlier) . This file comes along
with python libs within the software suite pymol. I downloaded the
pymol package and tried to repeat the error. The following shows what
goes wrong.

$ python
Python 2.5.2 (r252:60911, Sep 30 2008, 15:41:38)
[GCC 4.3.2 20080917 (Red Hat 4.3.2-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import os, sys
>>> sys.path
['', '/usr/lib/python25.zip', '/usr/lib/python2.5',
'/usr/lib/python2.5/plat-linux2', '/usr/lib/python2.5/lib-tk',
'/usr/lib/python2.5/lib-dynload', '/usr/lib/python2.5/site-packages',
'/usr/lib/python2.5/site-packages/Numeric',
'/usr/lib/python2.5/site-packages/PIL',
'/usr/lib/python2.5/site-packages/gst-0.10',
'/usr/lib/python2.5/site-packages/gtk-2.0',
'/usr/lib/python2.5/site-packages/scim-0.1']

This show my current python lib-dynload is under
'/usr/lib/python2.5/lib-dynload'. Now I change it to the one under
pymol

>>> sys.path[5] = '/work/fei/pymol/ext/lib/python2.4/lib-dynload'
>>> sys.path
['', '/usr/lib/python25.zip', '/usr/lib/python2.5',
'/usr/lib/python2.5/plat-linux2', '/usr/lib/python2.5/lib-tk',
'/work/fei/pymol/ext/lib/python2.4/lib-dynload',
'/usr/lib/python2.5/site-packages',
'/usr/lib/python2.5/site-packages/Numeric',
'/usr/lib/python2.5/site-packages/PIL',
'/usr/lib/python2.5/site-packages/gst-0.10',
'/usr/lib/python2.5/site-packages/gtk-2.0',
'/usr/lib/python2.5/site-packages/scim-0.1']

It has been changed. Now I run 'import expat'

>>> from xml.parsers import expat
Traceback (most recent call last):
File "", line 1, in
File "/usr/lib/python2.5/xml/parsers/expat.py", line 4, in
from pyexpat import *
ImportError: /work/fei/pymol/ext/lib/python2.4/lib-dynload/pyexpat.so:
undefined symbol: PyUnicodeUCS2_DecodeUTF8

which is exactly the error showed on your log. Now I change the lib
file back to the orignal one.

>>> sys.path[5] = '/usr/lib/python2.5/lib-dynload'
>>> sys.path
['', '/usr/lib/python25.zip', '/usr/lib/python2.5',
'/usr/lib/python2.5/plat-linux2', '/usr/lib/python2.5/lib-tk',
'/usr/lib/python2.5/lib-dynload', '/usr/lib/python2.5/site-packages',
'/usr/lib/python2.5/site-packages/Numeric',
'/usr/lib/python2.5/site-packages/PIL',
'/usr/lib/python2.5/site-packages/gst-0.10',
'/usr/lib/python2.5/site-packages/gtk-2.0',
'/usr/lib/python2.5/site-packages/scim-0.1']

then run 'import expat' again,
>>> from xml.parsers import expat
>>>
Things are fine after the lib file is changed back.

The problem may be that you run balbes using a version of python and
then somehow on your machine, the python dynamical loaded lib file is
set to be the one under pymol directory which is incompatible with the
python you run.

I suggest that you check how come the python lib-dynload directory is
set to be fixed on the one uder pymol, and if possible, unset it and
use the default one come with your os or get the new version of python
runing. This could be serious when you update your OS in the
futrue(like some later version of linux with new python) but still use
the lib files under pymol. It may then cause problems when you run any
python based programs using pyexpat.so (which is used very
frequently).

If you have urgent jobs and want to run BALBES before you fix the
problem. Please try BALBES on our web server
http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp

Thanks

Fei

2009/1/5 Xiang Liu :
> Dear all,
>
> I have pasted all the message as following.
> Could it do some help for me?
>
> python 2.4.5 (#1, Sep 18 2008, 14:53:26)
> [GCC 3.2 20020903 (Red Hat Linux 8.0 3.2-7)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import pyexpat
>>>> pyexpat
>
> '/software/exe/Xtal/pymol/ext/lib/python2.4/lib-dynload/pyexpat.so'>
>>>> from pyexpat import *
>>>>
>
> Thank you for your help and patience.
>
> Xiang Liu
> the fourth year Ph.D candidate
> lab of structural biology, college of life science
> Peking University, Beijing, P.R.China
> 100871
> Tel:86-10-62755714
>
>
> --- 09Äê1ÔÂ5ÈÕ£¬ÖÜÒ», Dr. F Long Ð´µÀ£º
>
> ·¢¼þÈË: Dr. F Long
> Ö÷Ìâ: Re: [ccp4bb] problem about BALBES
> ÊÕ¼þÈË: CCP4BB@JISCMAIL.AC.UK
> ÈÕÆÚ: 2009,15,ÖÜÒ»,3:09ÉÏÎç
>
> Dear Xiang Liu,
>
> From the log file, it looks you use a version of Python that comes
> with CCP4 and the lib file 'pyexpat.so' in it may have a problem (or
> this file does not work properly in your machine). Please could you do
> the following to help us find what kind of problem it is.
> In one of your directories (anyone):
> 1) type python
> 2) it will show something like
> Python 2.4.3 (#1, Oct 23 2006, 14:19:45)
> [GCC 4.1.1 20060525 (Red Hat 4.1.1-1)] on linux2
> Type "help", "copyright",
> "credits" or
> "license" for more information.
>>>>
> 3)type from pyexpat import *
> i.e >>> from pyexpat import *
>
> Please let me know what shows in your screen. This problem may be due
> to a python lib file problem we did not see here, not be related
> particularly to BALBES.
>
> Thanks,
>
> Fei
>
> 2009/1/4 Xiang Liu :
>> I just installized the CCP4-6.10 and tried to use BALBES for MR. But I
> have
>> only got the error log file as following:
>>
> "/software/exe/Xtal/CCP4/CCP4_6.10/ccp4-6.1.0/share/balbes/BALBES_0.0.1/bin_py/balbes",
>> line 37, in ? import PyExpat File
>>
> "/software/exe/Xtal/CCP4/CCP4_6.10/ccp4-6.1.0/share/balbes/BALBES_0.0.1/PyXML-0.8.4/xml/dom/ext/reader/PyExpat.py",
>> line 35, in ? from xml.parsers import expat File
>>
> "/software/exe/Xtal/pymol/ext/lib/python2.4/xml/parsers/expat.py",
> line 4,
>> in
> ? from pyexpat import *
>> ImportError:
>> /software/exe/Xtal/pymol/ext/lib/python2.4/lib-dynload/pyexpat.so:
> undefined
>> symbol: PyUnicodeUCS2_DecodeUTF8"
>>
>> I google the error message "undefined symbol:
> PyUnicodeUCS2_DecodeUTF8" and
>> cannot get some useful help. So I wonder if someone here had met similar
>> situation yet and how to solve it.
>>
>> Thank you for your attention.
>>
>>
>> Xiang Liu
>> the fourth year Ph.D candidate
>> lab of structural biology, college of life science
>> Peking University, Beijing, P.R.China
>> 100871
>> Tel:86-10-62755714
>>
>> ________________________________
>> ºÃÍæºØ¿¨µÈÄã·¢£¬ÓÊÏäºØ¿¨È«ÐÂÉÏÏß£¡
>
> ________________________________
> ºÃÍæºØ¿¨µÈÄã·¢£¬ÓÊÏäºØ¿¨È«ÐÂÉÏÏß£¡

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: problem about BALBES
From: Xiang Liu pku06a15 {- at -} YAHOO {- dot -} COM {- dot -} CN
Date: 2009-01-05

Next message:
Subject: Postdoctoral position at the University of Queensland, Brisbane, Australia
From: Bostjan Kobe b {- dot -} kobe {- at -} UQ {- dot -} EDU {- dot -} AU
Date: 2009-01-05