hi
as far as I know, AmberTools 15 does not support python3 yet (we will try
make all python packages compat with both 2 and 3 version in future). You
don't need to use "ln" stuff. I highly recommend to install anaconda
http://continuum.io/downloads, which bundles with many popular python
packages (numpy, scipy, pandas, ...) and it have really nice package
management, named "conda"
http://conda.pydata.org/docs/install/install.html
You don't need to be root to install, the default folder is
/home/your_user_name/anaconda
To create a python2 environment, just `conda create -n your_whatever_name
python=2 numpy scipy matplotlib pandas`
and then switch to python2 env by `source activate your_whatever_name`.
To change back to your normal env, just `source deactivate`.
Try to google about `conda` and I think you will really like it.
good luck
Hai
On Mon, Jun 15, 2015 at 4:45 AM, Jean-Patrick Francoia <
jeanpatrick.francoia.gmail.com> wrote:
> Yes sir :)
>
> - which python: /usr/bin/python
> - which -a python: /usr/bin/python
>
> - env python:
> Python 3.4.3 (default, Mar 25 2015, 17:13:50)
> [GCC 4.9.2 20150304 (prerelease)] on linux
>
> I got your point, the default version of python on Archlinux is version
> 3. So I had to change it:
>
> cd /usr/bin
> ln -sf python2 python
>
> To reverse it:
> ln -sf python3 python
>
> Thank you for your suggestion. However, it's a drastic solution to do
> that, and I think it can cause many problems for linux distributions
> which use python 3. If you have a better solution, I take it.
>
> But thank you anyway :)
>
>
> Le 14/06/2015 22:40, Gerald Monard a écrit :
> > Hello,
> >
> > Can you output the results of the following commands?
> > - which python
> > - which -a python
> > - env python
> >
> > and after adding "set -x" at line 2 of test_at_serial.sh (in
> > $AMBERHOME/AmberTools/test):
> > - make test
> >
> > Thanks,
> >
> > Gerald.
> >
> > On 06/14/2015 07:44 PM, Jean-Patrick Francoia wrote:
> >> Hi,
> >>
> >> I'm trying to install amber from the AmberTools free package available
> >> on the website. I downloaded it yesterday, so it should be up-to-date.
> >>
> >> The configure gnu and make install commands went smoothly. However, when
> >> I try to run the tests with "make test", as mentionned in the
> >> installation guide, I get the following exception from python:
> >>
> >> (cd AmberTools/test && make test)
> >> make[1] : on entre dans le répertoire
> >> « /home/djipey/SOFT/amber14/AmberTools/test »
> >> ./test_at_serial.sh
> >> Traceback (most recent call last):
> >> File "<stdin>", line 18, in <module>
> >> File
> >>
> "/home/djipey/SOFT/amber14/lib/python2.7/site-packages/chemistry/__init__.py",
> >> line 10, in <module>
> >> from chemistry.structure import Structure
> >> File
> >>
> "/home/djipey/SOFT/amber14/lib/python2.7/site-packages/chemistry/structure.py",
> >> line 36, in <module>
> >> from chemistry.topologyobjects import (AtomList, ResidueList,
> >> TrackedList,
> >> File
> >>
> "/home/djipey/SOFT/amber14/lib/python2.7/site-packages/chemistry/topologyobjects.py",
> >> line 14, in <module>
> >> from compat24 import all, property
> >> File
> >> "/home/djipey/SOFT/amber14/lib/python2.7/site-packages/compat24.py",
> >> line 68, in <module>
> >> if not hasattr(__builtins__.property, 'setter'):
> >> AttributeError: 'dict' object has no attribute 'property'
> >> Makefile:6 : la recette pour la cible « test » a échouée
> >> make[1]: *** [test] Erreur 1
> >> make[1] : on quitte le répertoire
> >> « /home/djipey/SOFT/amber14/AmberTools/test »
> >> Makefile:43 : la recette pour la cible « test.serial » a échouée
> >> make: *** [test.serial] Erreur 2
> >>
> >> Sorry, my error messages are in french, but you can get the error
> >> message from python. The problem seems to come from the module
> >> compat24.py, which I assume handles the compatibility for python 2.4.
> >>
> >> I'm using Manjaro Linux (which is based on Arch Linux), 64 bits system,
> >> and I have python 3.4 and python 2.7 installed.
> >>
> >> Do you have an idea about how to solve this issue ?
> >>
> >> Sincerely
> >>
> >> _______________________________________________
> >> 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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Received on Mon Jun 15 2015 - 02:00:03 PDT
