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On 12/03/2012 8:14 AM, Wholly Peach wrote:
<blockquote
cite="mid:1331500440.41866.YahooMailNeo@web121303.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); 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>
</blockquote>
<br>
If /home/ABC exists, and you then did "make" and "make install" and
they both succeeded then you will be able to see that /home/ABC/fftw
exists and has stuff in it. You will have built non-shared libraries
however.<br>
<br>
<blockquote
cite="mid:1331500440.41866.YahooMailNeo@web121303.mail.ne1.yahoo.com"
type="cite">
<div style="color: rgb(0, 0, 0); background-color: rgb(255, 255,
255); font-family: times new roman,new york,times,serif;
font-size: 12pt;">
<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>
</blockquote>
<br>
If the FFTW installation worked, then this should work. Possibly you
will need to choose --enable-shared for both, or --disable-shared
for both - I'm not sure.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1331500440.41866.YahooMailNeo@web121303.mail.ne1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:times
new roman, new york, times, serif;font-size:12pt">
<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 <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><Mark.Abraham@anu.edu.au></a><br>
<b><span style="font-weight: bold;">To:</span></b>
Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> <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 moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org"
rel="nofollow" target="_blank"
ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> >> <a moz-do-not-send="true"
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
moz-do-not-send="true"
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
moz-do-not-send="true"
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
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> > <br>
> <br>
> -- gmx-users mailing list <a
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href="mailto:gmx-users@gromacs.org"
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ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
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> Please search the archive at <a
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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
moz-do-not-send="true"
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 moz-do-not-send="true"
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<br>
> -- <br>
> gmx-users mailing list <a
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ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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> Please search the archive at <a
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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
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