Hi Jason,
Well, configuring (a clean slate) with -nopython flag circumvented the
weird python errors, but brought me other troubles (see below):
apparently my local python installation is not up to snuff. On a long
shot, I tried the `AT15_Amber11.py` script again anyway, but got the
same errors as previously (can't import "site", "os").
Not to muddy the waters, but I also tried a clean build with the latest
(half an hour ago) bugfix.all for AT 1.5. You might be interested that
it gives a "malformed patch" error (see below), but didn't affect my
python problem.
Bob Wohlhueter
*****************************************************************
cpp -traditional -P -DBINTRAJ lapack.f > _lapack.f
gfortran -c -O0 -o lapack.o _lapack.f
cpp -traditional -P -DBINTRAJ resp.f > _resp.f
gfortran -c -O0 -o resp.o _resp.f
gfortran \
lapack.o resp.o -o resp
gfortran -o calcpka calcpka.f90
./py_setup.sh
Using system python
Error importing cpinutil.py python modules! cpinutil will not work.
make[1]: *** [python] Error 1
make[1]: Leaving directory `/usr/local/lib/amber11/AmberTools/src/etc'
make: *** [serial] Error 2
root.winter-linux: ...lib/amber11 (25%)# ./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
****************bugfix.all patch
error*************************************************
patching file AmberTools/src/cpptraj/src/AmberNetcdf.cpp
patching file AmberTools/src/mmpbsa_py/MMPBSA_mods/alamdcrd.py
patching file AmberTools/src/mmpbsa_py/setup.sh
patch: **** malformed patch at line 3176: Workarounds: none
On 4/28/11 8:35 PM, Jason Swails wrote:
> Hmm.. Weird. I don't see those issues. Reconfigure with -nopython, starting from a clean tree.
>
> HTH,
> Jason
>
> --
> 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
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Received on Fri Apr 29 2011 - 07:30:03 PDT
