On Fri, Apr 29, 2011 at 4:06 PM, Robert Wohlhueter <
bobwohlhueter.earthlink.net> wrote:
> 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
>
Ooh, I would not do this as root. In several places, I think, the Amber
install references files in $AMBERHOME/bin. If AMBERHOME is blank, this
will just be parsed as /bin/, which is one of the last places you want to
mess around in (especially if it's *not* your scripts, so you don't know
what it's doing).
./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
>
Not good... Either you didn't start from a clean tree and it's still trying
to use the broken python from $AMBERHOME/bin, or your system python is
busted (very not good). The first means just get rid of the whole
AmberTools 1.5 directory and start over. If it's the second one, and you're
using Ubuntu, then something is seriously wrong (I use Ubuntu all the time
and have never seen this...).
> ****************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
>
I don't know why this is happening, but I can reproduce it. If you just
delete the last 2 lines it goes away... but not sure what'll happen when we
add another patch.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 29 2011 - 13:00:04 PDT
