On Thu, Jun 7, 2012 at 10:32 PM, Adam Jion <adamjion.yahoo.com> wrote:
> Hi Jason,
>
> I managed to install Amber12Tools on my Ubuntu 11.1 machine
> Here's what I did:
>
> 1. logged in as a superuser
> 2. Used a version of Python stored on a local folder instead of the root
> directory
>
Given your permission issues, I would probably guess that #1 was the key,
which was weird since you appeared to be trying to install Amber in your
home directory... The problem is that py_setup.sh suppresses any error
output from the compilation of the Python modules, so I couldn't see the
actual error message (my next step would have been to have you remove that).
That said, the system python HAS to be working, or many common OS
applications would not work, either.
Ultimately, I would suggest changing ownership of your amber12 directory
recursively (did you extract your AmberTools12.tar.bz2 file as root?) and
then installing it *not* as superuser so there's no chance you'll bork your
system. You can change ownership like this:
chown -R adam /home/adam/amber12
> I'm not sure if 1 or 2 did the trick, but I'm not complaining :-)
>
> Anyway, thanks for your help.
>
> Adam
>
> ps. It could be that the previous Python versions had problems relating to
> 32/64 bit architecture or single/double precision compatibility with
> Openmm/fftw. But this is highly speculative.
>
FWIW, Python has no concept of single and double precision. All floats are
C "double"s. If performance is critical enough to use "float" over
"double", Python is the wrong language for you, anyway :).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 08 2012 - 04:30:03 PDT
