AMBER Archive (2005)

Subject: AMBER: Installation problem. .

From: Sukjoon Yoon (yoonsj_at_sookmyung.ac.kr)
Date: Wed Jun 15 2005 - 01:08:51 CDT

Thanks, Don and Chris.

Please let me ask one more question.

2.6 Linux kernel is already installed in my PC.

My intel fortran compiler for linux is version 8.1. Was this the
critical problem in installing AMBER 8?
Version 9.0 will be available for free from Auguest based on anouncement
in Intel website.

Is there any other method to install AMBER 8 in my 64bit machine right
now? Adding rpm library of i386 version for 32bit compile did not solve
the problem.

I would really appreciate if anybody give me an advice to intall AMBER 8
in a 64bit machine with FC3 x86_64 or FC4 x86_64. I don't want to buy a
compiler just to install AMBER...

Thanks.

Sukjoon

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Don.Bashford_at_stjude.org
Sent: Tuesday, June 14, 2005 2:57 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: Installation problem. .

>>>>> "Sukjoon" == Sukjoon Yoon <yoonsj_at_sookmyung.ac.kr> writes:

    Sukjoon> I try to install AMBER 8 on the Fedore Core 3 platform
    Sukjoon> (Xeon dual CPUs). The installation failed with the
    Sukjoon> following message: Could anybody let me know how to
    Sukjoon> overcome this "-lm" related error? I already updated
    Sukjoon> Fedora libraries before the compilation...
    Sukjoon>
    Sukjoon> [....]
    Sukjoon>
    Sukjoon> ld: skipping incompatible /usr/lib64/libm.so when searching
for -lm
    Sukjoon> ld: skipping incompatible /usr/lib64/libm.a when searching
for -lm
    Sukjoon> ld: cannot find -lm

We had similar problems on Linux/Xeon using ifort, and we even had the
Intel engineers on the case for a while. It turns out that the cure is
to upgrade to a Linux distro that uses the 2.6 Linux kernel, which has
better 64-bit support. For us this was the latest Red Hat Enterprise,
which is not free. I think Fedora Core 4, which is free, has this
kernel.

A bit more: The older Xeons, from, say, 2 years ago, are just running in
32-bit mode and are fine with the older 2.4 kernel. The Itanium chips,
which are fully 64-bit are also okay with 2.4. But the current Xeon
chips are some kind of hybrid of 32 and 64, which somehow leads to
confusion with the older kernel.

Don Bashford
Molecular Biotechnology
St. Jude Children's Research Hospital

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