On Wed, Jun 8, 2016 at 1:45 PM, Claudia Ramírez <
claudia.lilian.ramirez.gmail.com> wrote:
> Exactly, I'm using my python (python 2.7.6). And there is no
> $AMBERHOME/lib/python2.7/site-packages/pytraj folder, and there is no
> ''build'' in pytraj to remove. I went ahead and did the make pytraj anyhow,
> and it tells me that I don't have cython (which I do).
>
I guess you have "old" cython version. pytraj requires cython >= 0.21 (only
for development)
I am a bit surprised that there is no *exit 1 *if pytraj is not built.
*python -c 'import cython; print(cython.__version__)'*
Using miniconda should fix the issue.
Hai
>
> I will install miniconda, and let you know what happens.
>
> Thanks
>
> 2016-06-08 14:40 GMT-03:00 Hai Nguyen <nhai.qn.gmail.com>:
>
> > Looking at the log, I think Claudia used system python:
> >
> > > /usr/bin/python test.py
> >
> > I agree that we should always suggest users to install miniconda (with
> Y/N)
> > I will go ahead make that change. If anyone has strong objection, please
> > reply here. thanks.
> >
> > Hai
> >
> > On Wed, Jun 8, 2016 at 1:33 PM, David A Case <david.case.rutgers.edu>
> > wrote:
> >
> > > On Wed, Jun 08, 2016, Claudia Ramírez wrote:
> > > >
> > > > I did a git pull on Monday (June 6), with gnu 4.8 compilers and doing
> > > just
> > > > ./configure gnu (serial for now) in Ubuntu 14.04 LTS. And it has 4
> > tests
> > > on
> > > > AmberTools that aren't working (this is without my modifications),
> and
> > I
> > > > don't know why. I'm attaching the log file to see if anyone could
> help
> > me
> > > > make it work.
> > >
> > > All the problems are python-related problems, related either to pytraj
> or
> > > to the sander api interface.
> > >
> > > What is the PYTHON variable in your config.h? If you are not already
> > > using a miniconda python, try going to $AMBERHOME/AmberTools/src and
> > > running
> > > configure_python. Then go back to AMBERHOME and re-run configure.
> > >
> > > [I still am pushing the (so-far, minority) viewpoint that all users
> > should
> > > be offered the choice to install the miniconda python. Users that have
> > > both
> > > experience with python, and the desire/need to use a different
> > interpreter,
> > > are welcome to decline the offer. But configure2 is still prone to
> > > deciding
> > > that the python in a user's path is OK when it is in fact not OK. So,
> > > letting
> > > us know which python your Amber installation is using would be a help
> > > here.]
> > >
> > > ....dac
> > >
> > >
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> > >
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Received on Wed Jun 08 2016 - 11:30:02 PDT
