Re: [AMBER] compile errors with AmberTools1.5 + Amber11

From: Jason Swails <jason.swails.gmail.com> Date: Thu, 28 Apr 2011 20:35:17 -0400

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Apr 28, 2011, at 3:52 PM, Robert Wohlhueter <bobwohlhueter.earthlink.net> wrote:
> Trying to build amber11 (patched with current bugfix.all) with 
> AmberTools-1.5 (on an AMD64-bit machine running Ubuntu 10.04) I 
> encounter errors, summarized here, and documented with compilation 
> excerpts copied below.
> 
> 1) Running `./configure gnu` (in $AMBERHOME/AmberTools/src) was 
> apparently successful.
> 2) `make install` reports errors in the Python-2.6.6 module, having to 
> do with unicode syntax.  Two excerpts from `make` output are copied below.
> 3) If I nonetheless proceed with executing AT15_Amber11.py, it fails, 
> due to failures to import "site" and "os" (which probably has nothing to 
> do with the unicode syntax errors.
> 
> Can anyone point the way out of this problem?
> 
> Thanks,
> Bob Wohlhueter
> 
> 
> 
> **********************************************************************************************
> The configuration file, config.h, was successfully created.
> 
> The next step is to type 'make install'
> 
> 
>  NOTE: after installing AmberTools, if you want to compile
>        Amber11 using AmberTools 1.5, you must run the
>        AT15_Amber11.py script first, e.g.:
>        cd /usr/local/lib/amber11; ./AT15_Amber11.py; make serial
>        (See the Amber11 Users' Manual for full instructions,
>        and be sure to have a backup, since the AT15_Amber11.py
>        script will modify your Amber11 files.)
> 
> .
> .
> .
> Compiling 
> /usr/local/lib/amber11/lib/python2.6/json/tests/test_separators.py ...
> Compiling 
> /usr/local/lib/amber11/lib/python2.6/json/tests/test_speedups.py ...
> Compiling 
> /usr/local/lib/amber11/lib/python2.6/json/tests/test_unicode.py ...
> SyntaxError: ("(unicode error) \\N escapes not supported (can't load 
> unicodedata module)", 
> ('/usr/local/lib/amber11/lib/python2.6/json/tests/test_unicode.py', 8, 
> None, "u = u'\\N{GREEK SMALL LETTER ALPHA}\\N{GREEK CAPITAL LETTER 
> OMEGA}'\n"))
> 
> Compiling /usr/local/lib/amber11/lib/python2.6/json/tool.py ...
> Compiling /usr/local/lib/amber11/lib/python2.6/keyword.py ...
> 
> ....
> 
> Compiling /usr/local/lib/amber11/lib/python2.6/test/test_modulefinder.py ...
> Compiling 
> /usr/local/lib/amber11/lib/python2.6/test/test_multibytecodec.py ...
> SyntaxError: ("(unicode error) \\N escapes not supported (can't load 
> unicodedata module)", 
> ('/usr/local/lib/amber11/lib/python2.6/test/test_multibytecodec.py', 
> 229, None, "self.failIf('\\x0e' in u'\\N{SOFT 
> HYPHEN}'.encode('iso-2022-jp-2'))\n"))
> 
> Compiling 
> /usr/local/lib/amber11/lib/python2.6/test/test_multibytecodec_support.py ...
> Compiling /usr/local/lib/amber11/lib/python2.6/test/test_multifile.py ...
> .
> .
> .
> 
> **************************************************************************
> 
> root.winter-linux: ...lib/amber11 (97%)# ./AT15_Amber11.py
> ./AT15_Amber11.py
> 'import site' failed; use -v for traceback
> Traceback (most recent call last):
>   File "./AT15_Amber11.py", line 8, in <module>
>     import os, sys
> ImportError: No module named os
> 
> 
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber