Hi Marcelo,
If I use this command:
vi /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11
I get NOTHING!
This is my /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py
file:
""Don't add these to the __all__ variable though
"""
from __future__ import division, absolute_import, print_function
import warnings
from numpy import *
_msg = "The oldnumeric module will be dropped in Numpy 1.9"
warnings.warn(_msg, ModuleDeprecationWarning)
def _move_axis_to_0(a, axis):
if axis == 0:
return a
n = len(a.shape)
if axis < 0:
axis += n
axes = list(range(1, axis+1)) + [0,] + list(range(axis+1, n))
return transpose(a, axes)
# Add these
from .compat import *
from .functions import *
from .precision import *
from .ufuncs import *
from .misc import *
from . import compat
from . import precision
from . import functions
from . import misc
from . import ufuncs
import numpy
__version__ = numpy.__version__
del numpy
__all__ = ['__version__']
__all__ += compat.__all__
__all__ += precision.__all__
__all__ += functions.__all__
__all__ += ufuncs.__all__
__all__ += misc.__all__
del compat
del functions
del precision
del ufuncs
del misc
from numpy.testing import Tester
test = Tester().test
bench = Tester().bench
On Wed, Feb 24, 2016 at 4:05 PM, Marcelo Andrade Chagas <
andrade.mchagas.gmail.com> wrote:
> Hi Elisa
>
> u walk this way
>
> vi /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11
>
> open the file and see the lines that the program shows 256 and 289
>
> in my case I was missing libraries
>
> show here a print of your file in this part for me to see and compare with
> my
> installation
>
> researching his error I found the following link
>
>
> http://stackoverflow.com/questions/17557190/python-nameerror-global-name-is-not-defined
>
> maybe you can help
>
> Best regards
>
> Marcelo
>
> Marcelo Andrade Chagas, MSc
> (PhD student)
> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> * http://lqcmm.qui.ufmg.br/
> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> Tel:(31)3409-5776
>
> 2016-02-24 10:15 GMT-03:00 Elisa Pieri <elisa.pieri90.gmail.com>:
>
> > Jason: I tried compiling Amber in serial, but I got exactly the same
> error.
> >
> > Marcelo: I did what you suggested, my amber.sh file looks exactly as
> yours,
> > but I still have the same problem.
> >
> > Anyway I have this problem with cpinutil.py only using the -op flag;
> > without it, it works.
> >
> > Other ideas?
> > Elisa
> >
> > On Wed, Feb 24, 2016 at 4:26 AM, Marcelo Andrade Chagas <
> > andrade.mchagas.gmail.com> wrote:
> >
> > > Hi
> > >
> > > I had a similar problem in python2.7 respectively scripts for
> > > MCPB.py and parmed.py
> > >
> > > managed to solve AmberTools15 reinstalling as follows:
> > >
> > > First installed libraries missing:
> > >
> > > http://www.scipy.org/install.html
> > >
> > > sudo apt-get install python-numpy python-scipy python-matplotlib
> ipython
> > > ipython-notebook python-pandas python-SymPy python-nose
> > >
> > > open your file and look for the error line I think it should be
> something
> > > like
> > >
> > > vi /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11
> > >
> > > do this before installing
> > >
> > > tar jxvf Amber14.tar.bz2
> > >
> > > export AMBERHOME=`pwd`
> > >
> > > ./configure --with-python /usr/bin/python2.7
> > >
> > > source amber.sh
> > >
> > > make install
> > >
> > > make test
> > >
> > > The following command to install in parallel (requires first install
> mpi
> > > with the same compiler gnu)
> > >
> > > ./configure --with-python /usr/bin/python2.7 -mpi gnu
> > >
> > > make install
> > >
> > > then it was just to set the bash file contents amber.sh
> > >
> > > In my case:
> > >
> > > export AMBERHOME = "/ home / Marcelo / PROGRAMS / AMBER-NEW / amber14"
> > > export PATH = "$ {AMBERHOME} / bin: $ {PATH}"
> > >
> > > # Add location of Amber Python modules to default Python search path
> > > if [-z "$ PYTHONPATH ']; Then
> > > export PYTHONPATH = "$ {} AMBERHOME /lib/python2.7/site-packages"
> > > else
> > > export PYTHONPATH = "$ {} AMBERHOME /lib/python2.7/site-packages: $
> > > {PYTHONPATH}"
> > > fi
> > > if [-z "$ {LD_LIBRARY_PATH}"]; Then
> > > export LD_LIBRARY_PATH = "$ {AMBERHOME} /lib"
> > > else
> > > export LD_LIBRARY_PATH = "$ {AMBERHOME} /lib: $ {LD_LIBRARY_PATH}"
> > > fi
> > >
> > >
> > > The problem in my case it was because they lacked python files and to
> set
> > > needed which seek python2.7
> > >
> > > Best regards
> > >
> > > Marcelo
> > >
> > >
> > > Marcelo Andrade Chagas, MSc
> > > (PhD student)
> > > Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> > > * http://lqcmm.qui.ufmg.br/
> > > Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> > > Tel:(31)3409-5776
> > >
> > > 2016-02-23 12:39 GMT-03:00 Elisa Pieri <elisa.pieri90.gmail.com>:
> > >
> > > > Hi everybody,
> > > >
> > > > I have Amber14, but when I use the command
> > > >
> > > > cpinutil.py -p crys.solv10.parm7 -igb 2 -o crys.solv10.cpin -op
> > > > crys.solv10.modO.parm7 -resnames AS4 GL4 HIP
> > > >
> > > > I get this error:
> > > >
> > > > /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11:
> > > > ModuleDeprecationWarning: The oldnumeric module will be dropped in
> > Numpy
> > > > 1.9
> > > > warnings.warn(_msg, ModuleDeprecationWarning)
> > > > Traceback (most recent call last):
> > > > File "/home/elisa/amber14/bin/cpinutil.py", line 289, in <module>
> > > > main(opt)
> > > > File "/home/elisa/amber14/bin/cpinutil.py", line 256, in main
> > > > changeradii(parm, 'mbondi2').execute()
> > > > NameError: global name 'changeradii' is not defined
> > > >
> > > > and OC crys.solv10.modO.parm7 is not produced. What's happening?
> > > >
> > > > Elisa
> > > > _______________________________________________
> > > > 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
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
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Received on Wed Feb 24 2016 - 07:30:04 PST
