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
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Received on Fri Feb 05 2016 - 17:00:03 PST
