.Juan:
I myself get similar error with `conda` install. So the best solution for
now is install from github
*git clone
https://github.com/pytraj/pytraj
<
https://github.com/pytraj/pytraj>cd pytrajpython ./setup.py install*
Let me know if there is any problem. thanks.
Hai
On Tue, Jul 7, 2015 at 2:33 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> Hi,
>
> I can answer question about `pytraj`.
>
> This error "undefined symbol: _ZN14MaskTokenArray13SelectedChar_E" likely
> indicates that you have old `libcpptraj.so` file somewhere.
>
> Since `pytraj` is in dev-status, it catch up with `cpptraj-dev` version
> and not work with version in official AT15.
>
> Can you try running this script from here:
> https://github.com/pytraj/pytraj/blob/master/scripts/find_libcpptraj.py
> `python find_libcpptraj.py`
>
> and let us know the output.
>
> Alternative, you can install from github (the most updated version).
>
>
>
> *git clone https://github.com/pytraj/pytraj
> <https://github.com/pytraj/pytraj>cd pytrajpython ./setup.py install*
>
> (`pytraj` will install `cpptraj-dev` from github for you. Make sure to
> read the instruction after the install finish)
>
> Hai
>
>
> On Tue, Jul 7, 2015 at 2:05 PM, Juan Eiros Zamora <
> j.eiros-zamora14.imperial.ac.uk> wrote:
>
>> Hi Amber users,
>>
>> I've recently downloaded AmberTools15 and followed all the installation
>> steps succesfully on a RHEL6. But when I try to do
>>
>> make test
>>
>> I get the following errors http://lpaste.net/42814355720372224 (copied
>> in this link)
>>
>> The python version that I currently use is 3.4.3 installed with Anaconda
>> 2.1.0 (64-bit) distribution. Also my PYTHONPATH is set to
>>
>> /usr/local/amber15/lib/python2.7/site-packages:/usr/local/amber/lib/python2.7/site-packages
>> after I source the $AMBERHOME/amber.sh script.
>>
>> So what's the python that AmberTools is trying to use? And how do I
>> manage to add python packages to the AmberTools installation?
>>
>> I've previously experienced problems with other AmberTools
>> programs, such as xparmed.py, or mdout_analyzer.py, (see errors here
>> http://lpaste.net/7336825506265825280 ) in which python modules are
>> missing; and I don't know how to add them because if I just do conda
>> install package it will install it in my regular python distribution
>> (although that the _tkinter that's missing I can't even find it using
>> conda).
>>
>> I've a second question also related to python. I've tried to install the
>> pytraj program on my conda distribution like the Amber Manual suggests:
>> conda install --force -c pytraj pytraj-dev
>>
>> And it installs it correctly in my anaconda3 folder. Now if I open the
>> python interpreter and import pytraj, I get the following error
>> http://lpaste.net/3868115149562839040 . I don't know if this might be
>> related to the problems I've reported before? Or it could be an issue
>> related to the Cython code that's in pytraj? Just a guess based on my
>> little experience with python.
>>
>> I'm pretty stuck on this so any guidance on this matter would be
>> appreciated,
>>
>> Juan Eiros
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue Jul 07 2015 - 15:00:02 PDT
