Can you try your upgrade again? It seems you were just a victim of
unfortunate timing (hopefully)...
All the best,
Jason
On Mon, Jul 8, 2013 at 11:46 AM, Robert Wohlhueter <
bobwohlhueter.earthlink.net> wrote:
> Thanks, Jason,
>
> Your point on installing as root is well taken: a bad habit left over
> from the days when I was the greatest threat to systemsoftware.
>
> It's clearly a web-access problem, which is to say mine, not yours. Even
> with longer time-outs, it's still hit-and-miss, with many stalls, some
> eternal. Granted, my dsl connection is always a little flakey after long
> rains in Atlanta. But I'm puzzled that even when the update script
> tells me "cannot connect to http://ambermd.org", with Firefox, on the
> same machine and at roughly the same time, I can connect perfectly well.
> Why would wget (or whatever mechanism the patch-amber.py script uses)
> fail, when Firefox hasn't a problem?
>
> Well, that's a rhetorical question to which I don't oblige you to
> answer. (But you might know of some clever tests to diagnosis the
> situation, please let me know.)
>
> In many case, I'll keep fiddling, maybe just move the installation to a
> better internet connection.
>
> Bob Wohlhueter
>
>
> On 7/6/13 5:28 PM, Jason Swails wrote:
> > On Sat, Jul 6, 2013 at 5:08 PM, Robert Wohlhueter <
> > bobwohlhueter.earthlink.net> 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 http://ambermd.org/AmberTools-get.html
> >>
> >> 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
> >
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jul 09 2013 - 11:30:04 PDT
