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On 5/01/2012 3:37 AM, Rashek Kazi wrote:
<blockquote
cite="mid:CANvv1W60LzWX9DfmMKuzfTE3foRMeBcKO6Mo05Gf45YEkeeS1A@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
I rather suspect there is no significant difference in how to build
FFTW 3.3 or 3.2 on any platform.<br>
<br>
<blockquote
cite="mid:CANvv1W60LzWX9DfmMKuzfTE3foRMeBcKO6Mo05Gf45YEkeeS1A@mail.gmail.com"
type="cite">
<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>
</div>
</blockquote>
<br>
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...<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CANvv1W60LzWX9DfmMKuzfTE3foRMeBcKO6Mo05Gf45YEkeeS1A@mail.gmail.com"
type="cite">
<div>
<br>
<div class="gmail_quote">On Tue, Jan 3, 2012 at 5:53 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
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
moz-do-not-send="true"
href="http://libmd.la" target="_blank">libmd.la</a>'
failed</div>
<div>make[3]: *** [<a moz-do-not-send="true"
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>
<br>
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
Rashek Kazi<br>
GS 2<br>
MSTP Candidate<br>
</div>
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