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
Received on Sat Jul 30 2016 - 02:00:03 PDT
