Are you using Python 3 for your main work?
probably you need to activate the python 2 kernel
# in bash terminal
amber.python -m ipykernel install --user
# then open the notebook
amber.jupyter notebook your_notebook.ipynb
# choose Python 2 kernel
https://codingnetworker.com/wp-content/uploads/2015/11/jupyter_about_notebook_kernel-web-1024x370.png
*Note*: as stated in manual, amber use python 2 as default version because
amber can be used with phenix or rosetta, which only support py2.
If you want to use python 3, it's fine. You can try:
cd $AMBERHOME
bash ./AmberTools/src/configure_python -v 3
# and do normal installation
PS: The above "complicated" step only happens if users have different
Python versions.
Hai
On Sat, Jul 30, 2016 at 4:35 AM, Albert <mailmd2011.gmail.com> wrote:
> BTW
>
> When I open the Jupter notebook 3, I only found Python 3, instead of
> Python 2 (which is shown in the tutorial)
>
> May I ask how to evoke Jupter notebook with Python 2?
>
> Thanks again.
>
>
>
> On 07/30/2016 10:11 AM, Hai Nguyen wrote:
> > On Sat, Jul 30, 2016 at 3:59 AM, Albert <mailmd2011.gmail.com> wrote:
> >
> >> Hi:
> >>
> >> thanks a lot for the comments.
> >>
> >> I went through the manual on page 26, and I installed miniconda in
> >>
> >> /home/albert/install/amber16/lib/python2.7/site-packages/
> >
> > before I compile Amber and made links at:
> >> /home/albert/install/amber16/miniconda
> >>
> > This is not a correct way to install miniconda.
> > Normally if user's Python does not have some Python package requirement
> > (e.g numpy, matplotlib ...), amber will ask you to install miniconda and
> > amber will *automatically* do that for you (if you say YES). if your
> Python
> > distribution have all the requirements, amber does not need to install
> > miniconda.
> >
> >
> >> However, after make install Amber, I still cannot find amber.conda or
> >> amber.jupyter....
> >>
> >>
> > Can you try to manually install miniconda by following:
> >
> > cd $AMBERHOME
> >
> > # below will properly set correct namespace for you. Please look at very
> > end of this configure_python file
> > # you will see something like: ln -sf ../miniconda/bin/jupyter
> amber.jupyter
> > || error "Linking Amber's Miniconda jupyter"
> >
> > bash ./AmberTools/src/configure_python
> >
> > # reconfigure
> > ./configure gnu
> >
> > make install
> >
> > Hai
> >
> >
> >> Do you have any other idea?
> >>
> >> thx again
> >>
> >>
> >>
> >> On 07/30/2016 09:26 AM, Hai Nguyen wrote:
> >>> hi,
> >>>
> >>> you only have amber.jupyter or amber.conda if you let amber install
> >>> miniconda in $AMBERHOME.
> >>>
> >>> Please see Amber16 manual, page 26 (Python in AMBER)
> >>> If you don't have miniconda in $AMBERHOME, just replace `amber.jupyter`
> >> by
> >>> `jupyter`.
> >>>
> >>> Per conda, we recommend users to install it to handle Python extension
> >>> (written by C/Fortran, ...).
> >>> Further info:http://conda.pydata.org/docs/intro.html
> >>>
> >>> We make the namespace `amber.pip`, `amber.jupyter` or `amber.conda` to
> >> make
> >>> sure that users use the recommended Python distribution.
> >>>
> >>> Let us know if you're not clear so we can make better doc + tutorial.
> >>> thanks.
> >>>
> >>> Hai
> >>
> >> _______________________________________________
> >> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jul 30 2016 - 02:00:03 PDT
