Re: [AMBER] update Ambertools 12 to 13 fails

From: Jason Swails <>
Date: Sat, 6 Jul 2013 17:28:45 -0400

On Sat, Jul 6, 2013 at 5:08 PM, Robert Wohlhueter <> wrote:

> I do have AmberTools 12 installed (on an Ubuntu 12.04 AMD 64-bit
> machine), and just now patched through bugfix.37 (successfully, I think,
> but I haven't try to rebuild yet.)
> The problem is that when I try the quick-and-easy `update_amber
> --upgrade` I get some fairly opaque error messages (copied below), which
> I take to mean AmberTools 12 is not really upgraded to 13, and therefore
> not ready to rebuild.
> Any advice? I haven't made custom changes to the Amber Tools 12 source
> code, but should I follow the script's advice and download the
> AmberTools13tarball?
> Bob Wohlhueter
> *****************************************************************
> root.winter-linux: ...lib/amber12 (337%)# ./update_amber --upgrade
> ./update_amber --upgrade

Please reconsider running this as root. I strongly recommend against it.
 You should change the ownership to some standard user and perform the
installation that way. This is generally good advice, since you have no
reason to trust that scripts like this are bug-free (whether malicious or
not), and you don't want one of those mistakes to ruin your computer. It's
happened before (albeit not with amber to my knowledge).

> You are about to perform a major upgrade. This is NOT reversible.
> Do you wish to continue? (y/N) y
> Reversing Amber 12/bugfix.18
> Reversing Amber 12/bugfix.17
> Reversing Amber 12/bugfix.16
> If the upgrade attempt fails, or you have made any custom changes
> to the AmberTools source code, please download the AmberTools13
> tarball from
> NOTE: This upgrade cannot be reversed!
> Downloading upgrade.patch.bz2 (23.88 MB)
> Downloading: [ ] 1.9%Traceback (most recent call last):
> [snip traceback]
> socket.timeout: timed out

Looks like the download timed out. Did you lose internet connection part
way through downloading the update? The file is downloaded in chunks of 4
KB, and if any of these take longer than the default timeout (10
seconds), then this error will occur.

If you know you just have a slow connection, then you can explicitly set
your timeout value using:

./update_amber --timeout 60 --upgrade

This will use a 60-second timeout for online queries. Since update_amber
did not make any attempt to upgrade from AmberTools 12 to AmberTools 13 (it
just rolled back some updates to prepare), you can simply try again.

Good luck,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Sat Jul 06 2013 - 15:00:02 PDT
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