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
>
>
>
>
>
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>
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Received on Tue Jul 07 2015 - 12:00:02 PDT
