[gmx-users] make error "Makefile:347: recipe for target `all-recursive' failed" for Gromacs-4.5.5

[Rashek Kazi]

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.

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.

On Tue, Jan 3, 2012 at 5:53 PM, Mark Abraham <Mark.Abraham at 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' failed
> make[3]: *** [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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