Great, thank you Jason!
Regards,
Sharon
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Thursday, April 19, 2012 2:25 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Amber 12 - Check for updates failed
Ah, I had not considered this. Once you download them, you can apply them
one-by-one using patch_amber.py. So do this:
cd $AMBERHOME
./patch_amber.py --apply path/to/bugfix.1
./patch_amber.py --apply path/to/bugfix.2
./patch_amber.py --apply path/to/bugfix.1
./patch_amber.py --apply path/to/bugfix.2
(Where bugfix.1 and bugfix.2 are from AmberTools 12 and Amber 12,
respectively).
However, applying patches in this manner won't track them. If you want
them to be tracked, you will have to manually move them to the
$AMBERHOME/.patches/AmberTools_Applied_Patches/ and
$AMBERHOME/.patches/Amber_Applied_Patches/ directories. The only thing
this will do is make the "./patch_amber.py --patch-level" give the correct
behavior (and it's a good way of keeping track of which bugfixes you've
applied already).
I suppose the behavior that I would change in this respect is to
automatically move the applied patches from --apply <patch> into the
corresponding directory.
HTH,
Jason
P.S. You can also set up a mirroring type of thing, where you have a local
URL in which you store the Amber/AmberTools bug fixes in those folders.
Then, you should modify patch_amber.py so that the URLs point to your
mirrors rather than
http://ambermd.org/bugfixes/12.0 and
http://ambermd.org/bugfixes/AmberTools/12.0
If you do this, then you'll just have to keep your mirror up-to-date with
our bugfixes and patch_amber.py should work just fine.
On Thu, Apr 19, 2012 at 3:08 PM, Shaw, Sharon <sharon.shaw.hp.com> wrote:
> Hi,
> I am trying to build Amber 12 on Linux x86_64 with Intel 12.1
> compiler+libs.
> I am having problems with the installation when it tries
> to go to the Amber website to download patches. I work
> behind a corporate firewall, so the downloading of patches fails:
>
> % cd $AMBERHOME
> % ./configure intel
> Checking for updates...
> Error: Could not connect to http://ambermd.org in 10.00 seconds
> Check for updates failed.
>
> I went to the Amber website to see if I could download the AmberTools12
> and Amber12 patches myself. Each currently has 2 bugfixes, but I do not
> know how to apply these patches.
>
> I would appreciate someone telling me how to do this.
>
> Regards,
>
> Sharon Shaw
> Hewlett-Packard Co.
> High Performance Computing
> 972-605-4603
> sharon.shaw.hp.com
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 19 2012 - 13:00:03 PDT
