Re: [AMBER-Developers] Python issues...

From: Ross Walker <>
Date: Thu, 18 Feb 2016 11:03:50 -0800

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/

So it looks like it's the check that is perhaps overly sensitive?

Also any suggestions on how to make sure / 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 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:


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:

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 was sourced? and print an error? Or have the error at the build stage say this is likely because you did not source $AMBERHOME/

I think this would pre-empt a lot of install questions we might otherwise get later on the Amber mailing list.

All the best

> On Feb 18, 2016, at 10:28 AM, Ross Walker <> 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 |
> | <> | <> |
> | Tel: +1 858 822 0854 | EMail:- <> |
> ---------------------------------------------------------
> 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.

AMBER-Developers mailing list
Received on Thu Feb 18 2016 - 11:30:04 PST
Custom Search