AMBER Archive (2006)

Subject: Re: AMBER: Another Installation Problem

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Fri Jun 02 2006 - 11:21:09 CDT

Seth,

I have the same setup and ran into the same problem. I posted a very
similiar message to yours on the amber reflector a few months ago. From
talking to others on the amber reflector at the time I found there was no
solution to this problem directly. You should be able to compile and run
all programs except for xleap on your box. I found that a static opteron
compiled version of xleap will work on an AMD 64 box without problems. If
you have further problems, drop me an email.

Scott

On 6/1/06, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> 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:
>
> xorg-x11-devel-6.8.2-1.EL.13.25.1.i386
> xorg-x11-devel-6.8.2-1.EL.13.25.1.x86_64
>
> 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
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | 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.
>
>
>

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