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
>
>
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Received on Sat Jul 30 2016 - 01:30:03 PDT
