Gromacs

Cygwin

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    Table of contents
    1. 1. GROMACS 4.0.5

    Installation should follow the normal instructions, except for the following considerations:

    • an installation of FFTW3 should be used. The Cygwin package of FFTW3 called fftw3 is in double precision, which can't combine with single-precision GROMACS, so you'll have to build a single-precision version yourself following the above instructions. If you've installed the fftw3 package, it'll be best to uninstall it using the Cygwin Setup program (to prevent it downloading and installing other updated packages while you do this, choose "Install from Local Directory" in the Cygwin Setup program).
    • GROMACS 4.5.5 is broken for threading under Cygwin. You must configure GROMACS with --disable-threads.
    • At some point in the GROMACS 4.5-4.5.5 development cycle, the ability of GROMACS to link shared libraries with an autoconf build got broken. It is unlikely to be fixed. Static linking still works, if all prerequisite libraries are available in static form, by configing GROMACS with --enable-all-static. You will probably find --without-xml useful also.
    • If you experience errors duing make resembling
    ../../../libtool: fork: retry: Resource temporarily unavailable
    ../../../libtool: fork: retry: Resource temporarily unavailable
    ../../../libtool: fork: retry: Resource temporarily unavailable
    ../../../libtool: fork: retry: Resource temporarily unavailable
    ../../../libtool: fork: Resource temporarily unavailable
    

    then you are probably suffering from problems like those described here. Continuing to invoke make should eventually succeed, or you could fix the underlying problem as described on that link.

     

    GROMACS 4.0.5

    A procedure for installing GROMACS 4.0.5 has been posted to the gmx-users list.  Please see here for that procedure. Otherwise, follow the instructions above.

    Page last modified 04:39, 21 Mar 2012 by mabraham