<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Dear All,</span></div><div><span></span> </div><div><span>For fftw, I use the following configure,</span></div><div><span></span> </div><div><span>./configure --enable-threads --enable-float --enable-sse --prefix=/home/ABC/fftw</span></div><div><span></span> </div><div><span>For gromacs, I use the following configure,</span></div><div><span>./configure --with-fft=fftw3 --disable-threads --prefix=/home/ABC/GROMACS --enable-shared LDFLAGS='-L/home/ABC/fftw/lib' CPPFLAGS='-I/home/ABC/fftw/include'</span></div><div><span></span> </div><div><span>But in the make step of gromacs, I still got a series of error message.</span></div><div><span></span> </div><div><span>I am looking forward to getting some suggesrions to solve
it.</span></div><div><span></span> </div><div><span>Cheers,</span></div><div><span></span> </div><div><span>Wholly</span></div><div><span></span> </div><div><span>.......</span></div><span><font size="1"><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2489): undefined reference to `_fftwf_destroy_plan'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x249f): undefined reference to `_fftwf_destroy_plan'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x24b5): undefined reference to `_fftwf_destroy_plan'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x24cb): more undefined references to `_fftwf_destroy_plan' follow</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2506): undefined reference to `_fftwf_free'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2512): undefined reference to `_fftwf_free'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x251e): undefined reference to `_fftwf_free'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x25ce): undefined reference to `_fftwf_execute_dft'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x268e): undefined reference to `_fftwf_execute_dft'</font></div><div>
</div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2755): undefined reference to `_fftwf_execute_dft_c2r'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2770): undefined reference to `_fftwf_execute_dft_r2c'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2825): undefined reference to `_fftwf_execute_dft_c2r'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2840): undefined reference to `_fftwf_execute_dft_r2c'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x28ee): undefined reference to `_fftwf_execute_dft'</font></div><div>
</div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x29b5): undefined reference to `_fftwf_execute_dft_c2r'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x29d0): undefined reference to `_fftwf_execute_dft_r2c'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2a7e): undefined reference to `_fftwf_execute_dft'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b45): undefined reference to `_fftwf_execute_dft_c2r'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b60): undefined reference to `_fftwf_execute_dft_r2c'<var id="yui-ie-cursor"></var></font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b8a): undefined reference to `_fftwf_destroy_plan'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b9f): undefined reference to `_fftwf_destroy_plan'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefined reference to `_fftwf_destroy_plan'</font></div><div><font size="3">
</font></div><div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined reference to `_fftwf_destroy_plan'</font></div></font></span><div><span>.......</span></div><div><br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font size="2" face="Arial"> ----- Forwarded Message -----<br> <b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br> <b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Sunday, 11 March 2012 6:26 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: Fw: [gmx-users] gromacs 4.5.5 cygwin installation error message<br> </font> </div> <br><meta content="off"
http-equiv="x-dns-prefetch-control"><div id="yiv1898304523">
<div>
On 11/03/2012 7:03 PM, Wholly Peach wrote:
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 14pt; background-color: rgb(255, 255, 255);">
<div><span>Dear All,</span></div>
<div><span></span> </div>
<div><span>Fot the fftw3, I use the following configuration, and
make install success.</span></div>
<div><span></span> </div>
<div>./configure --enable-threads --enable-float --enable-sse
--prefix=/home/joe/fftw</div>
</div>
</blockquote>
<br>
Possibly not successful, because /home/joe probably doesn't exist on
your system. It's an *example* - you should install somewhere that
makes sense on your system. So /home/YOURUSERNAMEHERE/fftw would
make some sense. However, on Cygwin you have write permission
everywhere, so you may as well not get involved with --prefix.<br>
<br>
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 14pt; background-color: rgb(255, 255, 255);">
<div> </div>
<div>For the gromacs 4.5.5, I use the following configuration:</div>
<div> </div>
<div>./configure --with-fft=fftw3 --disable-threads
-prefix=/home/joe/GROMACS</div>
</div>
</blockquote>
<br>
Above, you've installed FFTW to a non-standard location, and now you
haven't told GROMACS where to look for it. The normal installation
instructions tell you how to do this.<br>
<br>
Also, "-prefix" is wrong. Use "--prefix". <br>
<br>
Mark<br>
<br>
<blockquote type="cite">
<div style="color: rgb(0, 0, 0); font-family: times new roman, new york, times, serif; font-size: 14pt; background-color: rgb(255, 255, 255);">
<div> </div>
<div>But for the make step, I still got the following errors.</div>
<div> </div>
<div>I am looking forward to getting a reply from you on how to
solve it.</div>
<div> </div>
<div>Cheers,</div>
<div> </div>
<div>Wholly</div>
<div> </div>
<div>....</div>
<div> </div>
<font size="1">
<div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb):
undefined reference to `_fftwf_destroy_plan'</font></div>
<div><font size="3">
</font></div>
<div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1):
undefined reference to `_fftwf_destroy_plan'</font></div>
<div><font size="3">
<var id="yiv1898304523yui-ie-cursor"></var></font></div>
<div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7):
more undefined references to `_fftwf_destroy_plan' follow</font></div>
<div><font size="3">
</font></div>
<div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37):
undefined reference to `_fftwf_free'</font></div>
<div><font size="3">
</font></div>
<div><font size="3">.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17):
undefined reference to `_fftwf_free'</font></div>
<div><font size="3">
</font></div>
<div><font size="3">collect2: ld returned 1 exit status</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Makefile:387: recipe for target `libmd.la'
failed</font></div>
<div><font size="3">
</font></div>
<div><font size="3">make[3]: *** [libmd.la] Error 1</font></div>
<div><font size="3">
</font></div>
<div><font size="3">make[3]: Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/mdlib'</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Makefile:302: recipe for target
`all-recursive' failed</font></div>
<div><font size="3">
</font></div>
<div><font size="3">make[2]: *** [all-recursive] Error 1</font></div>
<div><font size="3">
</font></div>
<div><font size="3">make[2]: Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Makefile:238: recipe for target `all'
failed</font></div>
<div><font size="3">
</font></div>
<div><font size="3">make[1]: *** [all] Error 2</font></div>
<div><font size="3">
</font></div>
<div><font size="3">make[1]: Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'</font></div>
<div><font size="3">
</font></div>
<div><font size="3">Makefile:347: recipe for target
`all-recursive' failed</font></div>
<div><font size="3">
</font></div>
<div><font size="3">make: *** [all-recursive] Error 1</font></div>
</font>
<div><br>
</div>
<div style="font-family: times new roman, new york, times, serif; font-size: 14pt;">
<div style="font-family: times new roman, new york, times, serif; font-size: 12pt;">
<div dir="ltr"> <font size="2" face="Arial"> -----
Forwarded Message -----<br>
<b><span style="font-weight: bold;">From:</span></b>
Peter C. Lai <a class="yiv1898304523moz-txt-link-rfc2396E" href="mailto:pcl@uab.edu" rel="nofollow" target="_blank" ymailto="mailto:pcl@uab.edu"><pcl@uab.edu></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Wholly Peach <a class="yiv1898304523moz-txt-link-rfc2396E" href="mailto:whollypeach@yahoo.com" rel="nofollow" target="_blank" ymailto="mailto:whollypeach@yahoo.com"><whollypeach@yahoo.com></a>; Discussion
list for GROMACS users <a class="yiv1898304523moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Sunday, 11 March 2012 11:54 AM<br>
<b><span style="font-weight: bold;">Subject:</span></b>
Re: [gmx-users] gromacs 4.5.5 cygwin installation error
message<br>
</font> </div>
<br>
I don't think fftw3 has that option, since disable-threads
pertains to<br>
mdrun parallelization (forces MPI-only, basically).<br>
<br>
On 2012-03-10 05:50:19PM -0800, Wholly Peach wrote:<br>
> Hi Mark,<br>
> <br>
> If for Gromacs I use disable --disable-threads, for
fftw3 show I also use --disable-threads?<br>
> <br>
> Wholley<br>
> <br>
> <br>
> ________________________________<br>
> From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" rel="nofollow" target="_blank" ymailto="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>>
<br>
> Sent: Sunday, 11 March 2012 11:43 AM<br>
> Subject: Re: [gmx-users] gromacs 4.5.5 cygwin
installation error message<br>
> <br>
> On 11/03/2012 12:20 PM, Peter C. Lai wrote:<br>
> > Is fftw3 properly installed in /usr/local/lib?<br>
> <br>
> And of the right precision, like reading the
installation guides will warn you...<br>
> <br>
> Mark<br>
> <br>
> > <br>
> > On 2012-03-10 03:51:12PM -0800, Wholly Peach
wrote:<br>
> >> Dear All,<br>
> >> For Gromacs installation, my configure
command is:<br>
> >> ./configure --enable-shared
LDFLAGS='-L/usr/local/lib' --disable-threads.<br>
> >> After make, the error message is as following.<br>
> >> I am looking forward to getting a reply from
you on how to avoid the error message.<br>
> >> Wholly<br>
> >> .....<br>
> >>
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5):
undefined reference to `_fftwf_destroy_plan'<br>
> >>
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb):
undefined reference to `_fftwf_destroy_plan'<br>
> >>
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1):
undefined reference to `_fftwf_destroy_plan'<br>
> >>
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more
undefined references to `_fftwf_destroy_plan' follow<br>
> >>
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37):
undefined reference to `_fftwf_free'<br>
> >>
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17):
undefined reference to `_fftwf_free'<br>
> >> collect2: ld returned 1 exit status<br>
> >> Makefile:387: recipe for target `libmd.la'
failed<br>
> >> make[3]: *** [libmd.la] Error 1<br>
> >> make[3]: Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/mdlib'<br>
> >> Makefile:302: recipe for target
`all-recursive' failed<br>
> >> make[2]: *** [all-recursive] Error 1<br>
> >> make[2]: Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'<br>
> >> Makefile:238: recipe for target `all' failed<br>
> >> make[1]: *** [all] Error 2<br>
> >> make[1]: Leaving directory
`/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'<br>
> >> Makefile:347: recipe for target
`all-recursive' failed<br>
> >> make: *** [all-recursive] Error 1<br>
> >> -- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> >> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" rel="nofollow" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> >> Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" rel="nofollow" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
> >> Please don't post (un)subscribe requests to
the list. Use the<br>
> >> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> >> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" rel="nofollow" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
> > <br>
> <br>
> -- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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before posting!<br>
> Please don't post (un)subscribe requests to the list.
Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
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<br>
> -- <br>
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before posting!<br>
> Please don't post (un)subscribe requests to the list.
Use the <br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" rel="nofollow" target="_blank" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
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<br>
<br>
-- <br>
==================================================================<br>
Peter C. Lai | University of Alabama-Birmingham<br>
Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South 20th Street<br>
<a href="mailto:pcl@uab.edu" rel="nofollow" target="_blank" ymailto="mailto:pcl@uab.edu">pcl@uab.edu</a> |
Birmingham AL 35294-4461<br>
(205) 690-0808 |<br>
==================================================================<br>
<br>
<br>
<br>
</div>
</div>
</div>
<br>
<fieldset class="yiv1898304523mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</div>
</div><meta content="on" http-equiv="x-dns-prefetch-control"><br>-- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br> </div> </div> </div></body></html>