Re: [AMBER] update Ambertools 12 to 13 fails

From: Robert Wohlhueter <>
Date: Mon, 08 Jul 2013 11:46:44 -0400

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", with Firefox, on the
same machine and at roughly the same time, I can connect perfectly well.
Why would wget (or whatever mechanism the 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 <
>> 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

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Received on Mon Jul 08 2013 - 09:00:02 PDT
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