I did use su and not su - . So I guess my path is not the root path in that
case. I'll try again doing that. Thanks, Ross.
On Fri, Feb 5, 2016 at 7:46 PM Ross Walker <ross.rosswalker.co.uk> wrote:
> I cannot see the problem here.
>
> su -
> cd /usr/local/amber14
>
> ./update_amber --update
>
> ./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
>
> Is PERFECTLY valid. If it does not work then someone broke the AMBER
> install process and it should be fixed.
>
> Nothing wrong with doing this as root if it is going in a global directory
> (/usr/local - that is owned by root). Sure one can do it as a nonroot user
> that has write permission etc and make sure world permissions are right
> etc. But that just complicates things for an end user and doesn't really
> gain anything if one implicitly trusts the AMBER installer.
>
> Joe did you do 'su' and not 'su -' per chance?
>
> All the best
> Ross
>
> > On Feb 5, 2016, at 5:13 AM, Jason Swails <jason.swails.gmail.com> wrote:
> >
> > On Fri, Feb 5, 2016 at 6:51 AM, Joseph Baker <bakerj.tcnj.edu> wrote:
> >
> >> Hi Jason,
> >>
> >> Thanks for the info. I actually do run as root by first using su to
> become
> >> root and not with sudo. This must be specific to the Exxact setup for my
> >> particular machine configuration then (one main fileserver machine that
> >> exports its amber install directories to my other machines), as the
> >> update_amber_installation.x script that I pasted in the previous email
> that
> >> is used to run update_amber, configure and make has these instructions
> >>
> >> #This script will update the Exxact AMBER 14 installation for the latest
> >> patches.
> >>
> >> #It needs to be run as root.
> >>
> >
> > This is poor advice IMO. If you *can* chown the directory (permissions
> > are not as straightforward on shared filesystems), I would highly
> recommend
> > doing that and then never running their update_amber_installation.x
> script
> > as root again. I would also recommend putting "set -e" at the top of
> that
> > script so that it exits as soon as it hits a command that "fails".
> Because
> > as it's written now, if any of those commands fail, it will happily move
> on
> > to the next one and pretend like everything's fine (and unless you comb
> > through the output of that script, you may be hard-pressed to even
> notice).
> >
> > As a general rule, I avoid sudo like the plague with precious few
> > exceptions. In fact, I chown /usr/local to my own username (or to a
> > separate "installer" user if I don't want to risk breaking anything there
> > in my main user account) specifically to avoid needing to use sudo to
> > install *anything* that I'm compiling by hand. Or I install it to a
> > separate directory that I'll create with root and immediately chown to
> the
> > installing user. The only installations I ever do as root come from the
> > package manager -- apt-get, yum, port, or in my case, emerge. "sudo" can
> > be an easy band-aid, but it's nearly impossible to break or corrupt your
> OS
> > with a command that doesn't use it.
> >
> > But even so, as long as $AMBERHOME/lib/python2.6 contains the MMPBSA_mods
> > package (with the same contents as are in
> > $AMBERHOME/AmberTools/src/mmpbsa_py/MMPBSA_mods + some .pyc files), and
> > amber.sh is sourced and puts $AMBERHOME/lib/python2.6 into $PYTHONPATH,
> > everything should work fine.
> >
> > If the standard install *doesn't* work, and those modules are not in that
> > directory, then more investigation is required to determine what happened
> > to it. Did the installation fail somewhere before MMPBSA.py and the
> > setup.py script never get executed? Did some environment variables get
> > bungled and the setup.py script accidentally dump the package somewhere
> > else like /lib/python2.6/site-packages?
> >
> > Since you have a workaround that seems to work for you, that may be good
> > enough, but in the interest of making future upgrades easier and
> > alleviating these issues for future users, it would be nice to figure out
> > what was going wrong in the first place.
> >
> > All the best,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Feb 05 2016 - 18:00:03 PST
