AMBER: Compiling Amber 7

From: David J. Powers <>
Date: Thu, 08 Feb 2007 10:13:00 -0500

I'm getting some errors when doing a "make install" for amber 7. My
configuration is the
                Linux Distribution: Fedora Core 5: x86_64 version
                Compiler: gcc-4.1.0 g77-3.2.3
                MPI library: mpich2-1.0.4p1
                MACHINE file: Machine.g77_mpich (from amber 7 distribution)
                        I have removed the options: -m486 and -malign-double from the
                        L1, L2 and L3 environment variables since these options are deprecated.
                        This allowed the "make install" to partially proceed. I've attached a
                        copy of the MACHINE I'm using.

I set the environment variables, AMBERHOME and MPICH_HOME. During the
"make install"
I got an error making sander. The errors were specifically:
                undefined reference to 'pthread_getspecific'
        and undefined reference to 'pthread_getspecific'

These errors occurred when accessing modules in the "libmpich.a" library
file. I assume there
are some changes I need to make to the MACHINE file. Any help would be

Prof. Dave Powers
Northern Michigan University

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Received on Sun Feb 11 2007 - 06:07:21 PST
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