Dear Mark (and all),<div><br></div><div>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.</div>
<div><br></div><div>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.</div><div><br></div><div>Thanks for all the help, I will try and contribute this information to be put up on the Gromacs site/wiki.<br>
<br><div class="gmail_quote">On Tue, Jan 3, 2012 at 5:53 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF"><div><div class="h5">
On 4/01/2012 5:04 AM, Rashek Kazi wrote:
<blockquote type="cite">Hi Mark (and all)
<div><br>
</div>
<div>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:</div>
<div><br>
</div>
<div>
<div>Creating library file: .libs/libmd.dll.a</div>
<div>.libs/fft5d.o:fft5d.c:(.text+0x140f): undefined reference
to `_fftwf_plan_guru_d
ft'</div>
<div>.libs/fft5d.o:fft5d.c:(.text+0x18d1): undefined reference
to `_fftwf_plan_guru_d
ft_r2c'</div>
<div>.libs/fft5d.o:fft5d.c:(.text+0x194b): undefined reference
to `_fftwf_plan_guru_d
ft_c2r'</div>
<div>.libs/fft5d.o:fft5d.c:(.text+0x1aef): undefined reference
to `_fftwf_execute'</div>
<div>.libs/fft5d.o:fft5d.c:(.text+0x2133): undefined reference
to `_fftwf_execute'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x4a):
undefined reference to `_fft
wf_malloc'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x67):
undefined reference to `_fft
wf_malloc'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x84):
undefined reference to `_fft
wf_malloc'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0xf4):
undefined reference to `_fft
wf_plan_many_dft'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x14e):
undefined reference to `_ff
twf_plan_many_dft'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x1a5):
undefined reference to `_ff
twf_plan_many_dft'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x1fc):
undefined reference to `_ff
twf_plan_many_dft'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x253):
undefined reference to `_ff
twf_plan_many_dft'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2aa): more
undefined references t
o `_fftwf_plan_many_dft' follow</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3b1):
undefined reference to `_ff
twf_free'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3bd):
undefined reference to `_ff
twf_free'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3e7):
undefined reference to `_ff
twf_free'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x3ef):
undefined reference to `_ff
twf_free'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x461):
undefined reference to `_ff
twf_destroy_plan'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x476):
undefined reference to `_ff
twf_destroy_plan'</div>
<div><br>
</div>
<div>this continues for a long time and then I get the error at
the bottom:</div>
<div><br>
</div>
<div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1):
undefined reference to `_f
ftwf_destroy_plan'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7):
more undefined references
to `_fftwf_destroy_plan' follow</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37):
undefined reference to `_f
ftwf_free'</div>
<div>.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17):
undefined reference to `_f
ftwf_free'</div>
<div>collect2: ld returned 1 exit status</div>
<div>Makefile:387: recipe for target `<a href="http://libmd.la" target="_blank">libmd.la</a>'
failed</div>
<div>make[3]: *** [<a href="http://libmd.la" target="_blank">libmd.la</a>] Error 1</div>
<div>make[3]: Leaving directory
`/home/MPrieto/gromacs-4.5.5/src/mdlib'</div>
<div>Makefile:302: recipe for target `all-recursive' failed</div>
<div>make[2]: *** [all-recursive] Error 1</div>
<div>make[2]: Leaving directory
`/home/MPrieto/gromacs-4.5.5/src'</div>
<div>Makefile:238: recipe for target `all' failed</div>
<div>make[1]: *** [all] Error 2</div>
<div> make[1]: Leaving directory
`/home/MPrieto/gromacs-4.5.5/src'</div>
<div>Makefile:347: recipe for target `all-recursive' failed</div>
<div>make: *** [all-recursive] Error 1</div>
</div>
<div><br>
</div>
<div>looks like a different set of errors here. Do you think it
might have to do with using FFTW-3.3?</div>
</div>
</blockquote>
<br></div></div>
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.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark<br>
<br>
</font></span></div>
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GS 2<br>MSTP Candidate<br>
</div>