Re: [AMBER-Developers] Intel and At1.5/Amber11 combo (on rhel 4)

From: B. Lachele Foley <>
Date: Thu, 9 Jun 2011 14:09:25 +0000

The problem isn't missing the notice. The problems are: 1. After many pages of compiler spew, it's hard to find that notice again, assuming that an hour later you remember it. 2. It's hard to tell that you need to re-run the python script after every configure. It just says it needs to be run before installin Amber 11. 3. (minor point) the notice seems to tell the user to run make $installtype from $AMBERHOME and not $AMBERHOME/src.

I think a AT15_Amber11.README file at the top level with would help with all of those.

:-) Lachele

Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA

From: Jason Swails []
Sent: Thursday, June 09, 2011 10:00 AM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] Intel and At1.5/Amber11 combo (on rhel 4)

On Thu, Jun 9, 2011 at 4:35 AM, David A. Case <>wrote:

> On Wed, Jun 08, 2011, B. Lachele Foley wrote:
> > "Basically, each time you re-run configure, you also need to re-run the
> python script."
> >
> > Ahhh.... Between serial and parallel, I thought "hmmmm..... I wonder if
> running the python thing again will be necessary.... or if doing that will
> break things even worse... hmmmmm....."
> >
> > I chose not to. Works now. Thanks!
> >
> > I suppose the only way to be truly clear is to add "re-run this every
> > time you configure" to that notice.
> Jason: didn't we(you) do something like this earlier? I know we
> encountered
> this problem with another user....

This is the message printed each time configure is run:

# For AmberTools 1.5 + Amber 11, print a message about running
if [ -d ../../src/sander ]; then
   echo ""
   echo " NOTE: after installing AmberTools, if you want to compile"
   echo " Amber11 using AmberTools 1.5, you must run the "
   echo " script first, e.g.:"
   echo " cd $AMBERHOME; ./; make $installtype"
   echo " (See the Amber11 Users' Manual for full instructions,"
   echo " and be sure to have a backup, since the"
   echo " script will modify your Amber11 files.)"

This should be displayed at the very end of your configure stage, so
hopefully it would be hard to miss. If anyone has automated builds that
automatically configure and make without any user input, it'll be very easy
to miss this...

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Thu Jun 09 2011 - 07:30:04 PDT
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