RE: AMBER: Another Installation Problem

From: Ross Walker <>
Date: Thu, 1 Jun 2006 22:02:03 -0700

Hi Seth,

> I appologize for asking this question a second or third time
> but I have not
> been able to find a solution.
> I am running RedHat Enterprise 4 on an AMD 64 platform. I do
> a "./configure
> -static ifort" or a "./configure -athlon -static ifort" then
> a make serial
> and the compilation process fails when trying to install
> leap. I get a
> "cannot find /usr/bin/ld -lXt".
> What is missing and what is the best way to go about trying
> to solve this
> problem?

Do you have the X11 development libraries installed? These are required to
build Xleap. Try:

up2date --showall | grep xorg-x11-devel

and see if it finds anything. Here is the list from my machine:


Note I have both the 32 bit and 64 bit versions installed. If you don't find
anything as root do:

up2date --install xorg-x11-devel

If these are both installed then I suspect the problem is the following
error message:

>/usr/bin/ld: skipping incompatible /usr/X11R6/lib/libXt.a when searching
for -lXt
>/usr/bin/ld: cannot find -lXt

This is a function of using gcc or icc in 64 bit mode with amber8 which was
released before all these x86_64 bit machines appeared and so doesn't setup
config.h correctly - you can edit the config.h file to force gcc to work in
32 bit mode - change the CC=gcc line of config.h to CC=gcc -m32. Then cd
$AMBERHOME/src/leap; make clean; make install. Note Amber 9 should not
suffer from this problem.

I have also attached the config.h file I used to compile amber 9 in 64 bit
mode on my Pentium-D with ifort - this is the same instruction set as AMD64
so should work fine. There is also a config.h.amber8 for amber8 if you are
using this.

Both compile fine with ifort v9.0.033 on my RHEL AS4 machine.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
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Received on Sun Jun 04 2006 - 06:07:13 PDT
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