On Mon, Jan 14, 2013 at 5:39 PM, David Dubins <d.dubins.utoronto.ca> wrote:
> Hi everyone,
>
> Many moons ago, I posted a script on how to install Amber in Ubuntu 10.
>
> Well, against my better judgement, I upgraded Ubuntu last week to 12.04. I
> noticed my AmberTools no longer "worked". I followed Jason Swail's wiki on
> installing ambertools12 because I figured it was time to upgrade anyway,
> and that didn't work either. I also tried doing this from the Gnome desktop
> interface on 12.04, just in case it was a compatibility issue with Unity.
>
> When I installed AmberTools 12, the tests seem to run successfully, and I
> was thinking it was somehow my environment variables, even though I
> followed Jason Swail's instructions. I am specifically interested in
> getting nab to work, and it wouldn't even work when I copied my nuc.nab
> file directly into the bin directory where nab lives.
>
> I noticed gromacs stopped working as well, although I realize this isn't
> exactly the place to complain about that.
>
> Has anyone shared this experience? How do I go about fixing this?
>
It sounds like it's time to wipe out your installation of AmberTools 12
(and gromacs, as well as everything else that no longer works), and
recompile them from the beginning.
I know that AmberTools (and Amber) 12 compile just fine on Ubuntu 10.04 as
well as 12.04 just following the instructions on my Wiki. If it does not
work for you, then something went wrong in the upgrade process. You should
try making sure that all of your packages are up-to-date as much as
possible. You can try the commands:
sudo apt-get update
sudo apt-get upgrade
The first command should update the software repositories, while the second
should upgrade the installed packages, if I recall correctly. The apt-get
man page should be able to confirm this.
If after doing this, you are still getting errors, we would only be able to
help if we got the exact error messages you were getting (and even then,
the dist-upgrade process may have introduced errors we can't predict or
explain). As a last-ditch option, you could consider installing 12.04
fresh onto your disc (it should give you the option of not removing
existing files).
HTH,
Jason
P.S. Since this advice won't help now, I'll include it as a postscript for
future consideration. The approach I use on my Linux machines is to set up
three partitions on my hard drive (separate physical drives would also
work). The first partition is the root partition, mounted on / -- this is
where the operating system is installed. The second is the swap partition
(typically RAM to RAM x 2 in size), and the third is mounted on /home.
This way, all of your documents and settings are stored on a different
drive (or partition) than your operating system. When your system is set
up this way, you can wipe your OS and reinstall a brand new one (it doesn't
even have to be the same distro), and keep all of your old settings and
files.
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jan 14 2013 - 16:30:03 PST
