Re: [AMBER-Developers] Having to run configure multiple times

From: Jason Swails <>
Date: Mon, 2 Jul 2012 12:17:44 -0400

On Mon, Jul 2, 2012 at 11:51 AM, Ross Walker <> wrote:

> Hi Dave and Jason,
> I'm not sure I follow here. I thought that could 'detect'
> that a patch was already applied by looking in the applied patches
> directory. Thus my original suggestion which was to make a bugfix either
> for
> configure 'or' ship AMBERTools with bugfix.3 already applied. If it is done
> correctly then it should be automatically detected that the patch is
> already
> applied should it not?

> Indeed, why don't we just do the following:
> 1) create a new bugfix for configure and release it on the website - just
> the changes needed for running multiple times, don't update
> anything else.
> 2) Apply all the other bugfixes for AMBERTools.
> 3) Make a tar file called AmberTools12.13.tar.bz2 (the .13 referring to the
> 13 bugfixes applied). Add this to the download section on the website and
> link it to AmberTools12.tar.bz2 so we don't have to update the
> instructions.
> This way anyone who downloads the original AmberTools12.tar.bz2 file and
> applies bugfixes 1 to 13 should get exactly the same distribution as if
> they
> download the new tar file.

This is the exact proposal. I'm making the tarball tonight (along with the
quick fix to configure, to be released as bugfix.13).

My only point of concern is whether we name the new tarball
AmberTools12.13.tar.bz2 or AmberTools12.tar.bz2 (either way, it will be
identical to *original* AmberTools12 + bugfix.1-13, and ./
--patch-level will correctly reflect the patch state).

The worry with adding the 13 is that users may mistakenly think they need
to update (is this even a problem?). The worry about not adding the 13 is
that then the download is silently changed (again, is this a problem?).

Both drawbacks are minor.

Maybe we take the time to update the manual in the doc directory (and the
> one on the website) with the errata while we are at it?

I agree with this, but Dave may want to weigh in here with the implications
with Lulu and the published version...

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Mon Jul 02 2012 - 09:30:03 PDT
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