I looked in the config.h in my amber directory, and I did not see the
PYTHON_INSTALL variable in there. The PYTHON path in config.h is
#Python interpreter we are using
PYTHON=/usr/bin/python2.6
I was running the install as root.
These Exxact machines (or at least the ones I bought) come with an
auto-update/configure script with these contents
cd $AMBERHOME
make clean
./update_amber
./configure gnu
make -j8 install
make clean
./configure -mpi gnu
make -j8 install
make clean
./configure -cuda gnu
make -j8 install
make clean
./configure -cuda -mpi gnu
make -j8 install
make clean
echo ""
echo "Update Complete"
So I just execute that as root and it runs ./update_amber and the
./configure script and make commands to compile everything. I still had to
do the manual make_install inside of the MMPBSA directory to get that to
update. I checked with ls -l in my amber/bin directory before I did that
and the MMPBSA.py script had an old date on it corresponding to my last
update before I did the manual install, but then after manual install the
date in the bin directory was updated.
Joe
On Wed, Feb 3, 2016 at 3:17 PM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Feb 03, 2016, Josh Berryman wrote:
> >
> > I found that I had to install parmed as root. ubuntu 14.04, python
> 2.7.6
> > installed via the usual apt-get python.
>
> Hi Josh: As Jason says, this shouldn't be the case, and it's not obvious
> what
> is happening. What is the value of $PYTHON_INSTALL in your config.h file?
> Maybe you (and others) are requesting a global python install, which in
> turn
> could require root permissions.
>
> If it's the latter, we should probably fix something here: we really want
> to
> discourage people from installing all or parts of Amber as root.
>
> ...dac
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Feb 04 2016 - 14:00:03 PST
