On 5/01/2012 3:37 AM, Rashek Kazi wrote:
Dear Mark (and all),

Yes the issue for me turned out to be the version of FFTW I was using. The installation instructions must be different for the most recent FFTW-3.3 build but I lack the programming knowledge to know how to make this work.

I rather suspect there is no significant difference in how to build FFTW 3.3 or 3.2 on any platform.


In summary: I was unable to install Gromacs-4.5.5 using FFTW-3.3 so I downgraded back to FFTW-3.2.2 and everything installed smoothly on Cygwin.

Thanks for all the help, I will try and contribute this information to be put up on the Gromacs site/wiki.

Thanks for the thought, but I'd be amazed if your observations were consistent with an actual FFTW-on-Cygwin issue rather than some inconsistency in how your build processes were working. Occam's razor applied to new users...

Mark


On Tue, Jan 3, 2012 at 5:53 PM, Mark Abraham <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:

    On 4/01/2012 5:04 AM, Rashek Kazi wrote:
    Hi Mark (and all)

    Thanks for the response. I ran ./configure --disable-threads this
    time. ./configure went fine but again upon doing Make I have
    received a new error:

    Creating library file: .libs/libmd.dll.a
    .libs/fft5d.o:fft5d.c:(.text+0x140f): undefined reference to
`_fftwf_plan_guru_d ft'
    .libs/fft5d.o:fft5d.c:(.text+0x18d1): undefined reference to
`_fftwf_plan_guru_d ft_r2c'
    .libs/fft5d.o:fft5d.c:(.text+0x194b): undefined reference to
`_fftwf_plan_guru_d ft_c2r'
    .libs/fft5d.o:fft5d.c:(.text+0x1aef): undefined reference to
    `_fftwf_execute'
    .libs/fft5d.o:fft5d.c:(.text+0x2133): undefined reference to
    `_fftwf_execute'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x4a): undefined
reference to `_fft wf_malloc'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x67): undefined
reference to `_fft wf_malloc'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x84): undefined
reference to `_fft wf_malloc'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0xf4): undefined
reference to `_fft wf_plan_many_dft'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x14e): undefined
reference to `_ff twf_plan_many_dft'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x1a5): undefined
reference to `_ff twf_plan_many_dft'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x1fc): undefined
reference to `_ff twf_plan_many_dft'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x253): undefined
reference to `_ff twf_plan_many_dft'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2aa): more
undefined references t o `_fftwf_plan_many_dft' follow
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3b1): undefined
reference to `_ff twf_free'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3bd): undefined
reference to `_ff twf_free'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3e7): undefined
reference to `_ff twf_free'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3ef): undefined
reference to `_ff twf_free'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x461): undefined
reference to `_ff twf_destroy_plan'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x476): undefined
reference to `_ff twf_destroy_plan'

    this continues for a long time and then I get the error at the
    bottom:

    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined
reference to `_f ftwf_destroy_plan'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more
undefined references to `_fftwf_destroy_plan' follow
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefined
reference to `_f ftwf_free'
    .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefined
reference to `_f ftwf_free'
    collect2: ld returned 1 exit status
    Makefile:387: recipe for target `libmd.la <http://libmd.la>' failed
    make[3]: *** [libmd.la <http://libmd.la>] Error 1
    make[3]: Leaving directory `/home/MPrieto/gromacs-4.5.5/src/mdlib'
    Makefile:302: recipe for target `all-recursive' failed
    make[2]: *** [all-recursive] Error 1
    make[2]: Leaving directory `/home/MPrieto/gromacs-4.5.5/src'
    Makefile:238: recipe for target `all' failed
    make[1]: *** [all] Error 2
    make[1]: Leaving directory `/home/MPrieto/gromacs-4.5.5/src'
    Makefile:347: recipe for target `all-recursive' failed
    make: *** [all-recursive] Error 1

    looks like a different set of errors here. Do you think it might
    have to do with using FFTW-3.3?

    Yes. Configure thought it found FFTW3, but now you can't link to
    it. See the general installation instructions for the right kind
    of approach.

    Mark


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--
Rashek Kazi
GS 2
MSTP Candidate



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