AMBER Archive (2005)

Subject: Re: AMBER: Installation problem. .

From: Don.Bashford_at_stjude.org
Date: Mon Jun 13 2005 - 12:56:46 CDT

>>>>> "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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