On Thu, Feb 18, 2016 at 2:03 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> To add to this:
>
> If I respond no to the No compatible Python question make install still
> works fine (as long as I have sourced $AMBERHOME/bin/amber.sh).
>
ah, this is the trick. Python packages in amber do not need listed packages
at install time but require them at run time. We feel that asking
individual users to manually install numpy, matplotlib, ... whenever they
got ImportError is too much. So it's better to suggest them install
(automatically) from the beginning if their current Python distribution
does not offer enough.
>
> So it looks like it's the check that is perhaps overly sensitive?
>
> Also any suggestions on how to make sure amber.sh / amber.csh has been
> sourced before one tries to build? - I know it's at the end of the
> configure step but I always forget to read that and I am sure others do
> too. The error one gets if you don't source it is:
>
> ---------
> make[2]: Entering directory `/home/rcw/working/amber/AmberTools/src'
> (cd parmed && /bin/python setup.py install -f
> --prefix=/home/rcw/working/amber
> --install-scripts=/home/rcw/working/amber/bin)
> running install
> Checking .pth file support in
> /home/rcw/working/amber/lib64/python2.7/site-packages/
> /bin/python -E -c pass
> TEST FAILED: /home/rcw/working/amber/lib64/python2.7/site-packages/ does
> NOT support .pth files
> error: bad install directory or PYTHONPATH
>
> You are attempting to install a package to a directory that is not
> on PYTHONPATH and which Python does not read ".pth" files from. The
> installation directory you specified (via --install-dir, --prefix, or
> the distutils default setting) was:
>
> /home/rcw/working/amber/lib64/python2.7/site-packages/
>
> and your PYTHONPATH environment variable currently contains:
>
> ''
>
> Here are some of your options for correcting the problem:
>
> * You can choose a different installation directory, i.e., one that is
> on PYTHONPATH or supports .pth files
>
> * You can add the installation directory to the PYTHONPATH environment
> variable. (It must then also be on PYTHONPATH whenever you run
> Python and want to use the package(s) you are installing.)
>
> * You can set up the installation directory to support ".pth" files by
> using one of the approaches described here:
>
>
> https://pythonhosted.org/setuptools/easy_install.html#custom-installation-locations
>
> Please make the appropriate changes for your system and try again.
> make[2]: *** [parmed] Error 1
> make[2]: Leaving directory `/home/rcw/working/amber/AmberTools/src'
> make[1]: *** [serial] Error 2
> make[1]: Leaving directory `/home/rcw/working/amber/AmberTools/src'
> make: *** [install] Error 2
> -------
>
> Which doesn't make it obvious why the error is occurring. Could we
> potentially have the Make step check if amber.sh/csh was sourced? and
> print an error? Or have the error at the build stage say this is likely
> because you did not source $AMBERHOME/amber.sh?
>
> I think this would pre-empt a lot of install questions we might otherwise
> get later on the Amber mailing list.
>
>
This is due to new change in ParmEd. Jason is working on it now.
Hai
> All the best
> Ross
>
> > On Feb 18, 2016, at 10:28 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> >
> > Enterprise system
> >
> > Redhat 7.0 - Default Developer Install - Fully up to date.
> >
> > >which Python
> > /usr/bin/python
> >
> > >python -V
> > Python 2.7.5
> >
> > And yet AMBER ./configure gnu gives:
> >
> > No compatible Python installation found. I can download one from
> Continuum
> > via Miniconda with all prerequisites. This will only need to be done
> once.
> > This may take several minutes and will require Internet access.
> > Should I do that? [y/n]
> >
> > Is the check just not working properly?
> >
> > Can this be fixed please?
> >
> > In my opinion AMBER should build without issue on a Redhat default
> install given this represents >90% of commercial Linux installs so we
> should do our best to support this type of environment. We should only need
> to download a big third party python package on weird systems like OSX,
> ancient Linux OS's etc.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > ---------------------------------------------------------
> > | Associate Research Professor |
> > | San Diego Supercomputer Center |
> > | Adjunct Associate Professor |
> > | Dept. of Chemistry and Biochemistry |
> > | University of California San Diego |
> > | NVIDIA Fellow |
> > | http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> |
> http://www.wmd-lab.org <http://www.wmd-lab.org/> |
> > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk <mailto:
> ross.rosswalker.co.uk> |
> > ---------------------------------------------------------
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> not be read every day, and should not be used for urgent or sensitive
> issues.
> >
>
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Received on Thu Feb 18 2016 - 11:30:06 PST
