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

From: B. Lachele Foley <>
Date: Wed, 8 Jun 2011 22:03:41 +0000

"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. However, it would be even better if there were a brief top-level readme to go with the script. After many minutes of compiler spew, it's hard to remember that bit at the end of the configure.

Something like this, and feel free to edit:

cat AT15_Amber11.README
To install Amber 11 with AmberTools1.5, you need to run the script found in the $AMBERHOME directory.

To run it, simply type:


Run this before each "make x" in the $AMBERHOME/src directory. That is, run it after configuring serial and then again after configuring parallel, but just before "make serial" and "make parallel".

Also, for maximum user-friendliness,

- echo " cd $AMBERHOME; ./; make $installtype"
+ echo " cd $AMBERHOME; ./; cd $AMBERHOME/src; make $installtype"

:-) Lachele

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

From: David A. Case []
Sent: Wednesday, June 08, 2011 5:33 PM
To: AMBER Developers Mailing List
Subject: Re: [AMBER-Developers] Intel and At1.5/Amber11 combo (on rhel 4)

On Wed, Jun 08, 2011, B. Lachele Foley wrote:
> When we try to build the AT1.5/Amber11 combo on RHEL4/Intel, there are
> errors. Building from a recent git repo is good (except the make clean
> thing in the earlier email). Building with AT1.4/Amber11 is good.
> The complaint concerns constants.f,

> cpp -traditional constants.f > _constants.f
> mpif90 -c -ip -O3 -xHost -o constants.o _constants.f
> : error #5149: Illegal character in statement label field [m]

The -FR (freeformat) flag is not being passed to the compiler. This should be
coming in through the FFLAGS field, which in turn should be picking up the
LOCALFLAGS variable in the amber11/src/sander/Makefile.

The error has nothing to do with constants.f; that is just the first file the
Makefile tries to compile. Nothing in sander will compile without the
free-format flag.

This *is* hard to debug, since no one else seems to be able to reproduce
it. Is it related to the parallel build? (That is, can you build sander
in serial mode?) I suppose you could edit amber11/src/sander/depend,
and in the rule to compile constants.f, have the Makefile echo FFLAGS,
LOCALFLAGS, etc. Note that there are lots of other things in LOCALFLAGS
that are not being picked up. Are you sure that you are running the script after every invocation of configure? Basically,
each time you re-run configure, you also need to re-run the python script.


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