<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:14pt"><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> </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> </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="yui-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 <pcl@uab.edu><br> <b><span style="font-weight: bold;">To:</span></b> Wholly Peach <whollypeach@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <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" 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" 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" 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>> <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 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"
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<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" 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></body></html>