RE: AMBER: Which install compiler and flags?

From: Ross Walker <>
Date: Fri, 8 Feb 2008 08:52:24 -0800

Hi Sam,

> I am migrating to a new machine and trying to reinstall
> Amber9 but I'm
> unclear on which combination of flags and compiler to give the
> ./configure script. I'm running Ubuntu 7.10 on a Intel Core 2 quad
> system (64bit). Has anyone successfully set up something similar? (I
> should also mention I'm unable to install the ifort64 compiler at the
> moment, awaiting help from intel).

I do this compilation all the time without problems, all be it on a system
running RHEL 5.0 but that shouldn't cause problems. For the Intel compiler
you have to make sure you use the ones entitled fce and cce. That is the so
called EM64T versions. Intel Core 2 is actually x86_64 not strictly 64 bit
(which would refer to Itaniums). The Core 2's support 64 bit ints and 64 bit
doubles as well as 64 bit pointers however the pointers is a bit of a con
since actually they are only 48 bits long and the chip manually pads them
out to look like 64 bits. Hence the maximum address space is 2^48 and not
2^64. The key point being that you want EM64T(x86_64) versions of the
compilers and other libraries such as MKL etc.

For ifort 10.1.008 the file you want to source in your bashrc after
installation is /opt/intel/fce/10.1.008/bin/

You can also install g95 if you want - see and select the Linux
x86_64/EMT64 (32 bit D.I.) version.

For ifort in serial the options you want for configure are:

./configure -static ifort_x86_64

for g95 you would use:

./configure -static g95

You can also try gfortran which may already be installed on your machine -
whether this works depends on how new your gfortran is:

./configure -static gfortran

If this is just for small experimental runs / learning etc then using g95 or
gfortran is fine but for optimum performance you probably want to use the
Intel compilers.

For parallel with gfortran it may well just work with the default installed
copy of LAM:

./configure -static -lam gfortran

(assuming lamboot / mpif77 etc are in your path).

For Intel mpi I would suggest getting a copy of something like mpich2.
Download this and build it using the Intel compiler. Make sure it is in your
path BEFORE the lam stuff such that which mpirun etc gives you the mpich2
executables. Then do

./configure -static -mpich2 ifort

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Feb 10 2008 - 06:07:31 PST
Custom Search