Fw: [gmx-users] gromacs 4.5.5 cygwin installation error message

Mark Abraham Mark.Abraham at anu.edu.au
Sun Mar 11 09:26:53 CET 2012 

On 11/03/2012 7:03 PM, Wholly Peach wrote:
> Dear All,
> Fot the fftw3, I use the following configuration, and make install 
> success.
> ./configure --enable-threads --enable-float --enable-sse 
> --prefix=/home/joe/fftw

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.

> For the gromacs 4.5.5, I use the following configuration:
> ./configure --with-fft=fftw3 --disable-threads -prefix=/home/joe/GROMACS

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.

Also, "-prefix" is wrong. Use "--prefix".

Mark

> But for the make step, I still got the following errors.
> I am looking forward to getting a reply from you on how to solve it.
> Cheers,
> Wholly
> ....
> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined 
> reference to `_fftwf_destroy_plan'
> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined 
> reference to `_fftwf_destroy_plan'
> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more undefined 
> references to `_fftwf_destroy_plan' follow
> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefined 
> reference to `_fftwf_free'
> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefined 
> reference to `_fftwf_free'
> collect2: ld returned 1 exit status
> Makefile:387: recipe for target `libmd.la' failed
> make[3]: *** [libmd.la] Error 1
> make[3]: Leaving directory 
> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/mdlib'
> Makefile:302: recipe for target `all-recursive' failed
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory 
> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'
> Makefile:238: recipe for target `all' failed
> make[1]: *** [all] Error 2
> make[1]: Leaving directory 
> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'
> Makefile:347: recipe for target `all-recursive' failed
> make: *** [all-recursive] Error 1
>
> ----- Forwarded Message -----
> *From:* Peter C. Lai <pcl at uab.edu>
> *To:* Wholly Peach <whollypeach at yahoo.com>; Discussion list for 
> GROMACS users <gmx-users at gromacs.org>
> *Sent:* Sunday, 11 March 2012 11:54 AM
> *Subject:* Re: [gmx-users] gromacs 4.5.5 cygwin installation error message
>
> I don't think fftw3 has that option, since disable-threads pertains to
> mdrun parallelization (forces MPI-only, basically).
>
> On 2012-03-10 05:50:19PM -0800, Wholly Peach wrote:
> > Hi Mark,
> >
> > If for Gromacs I use disable --disable-threads, for fftw3 show I 
> also use --disable-threads?
> >
> > Wholley
> >
> >
> > ________________________________
> >  From: Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
> > Sent: Sunday, 11 March 2012 11:43 AM
> > Subject: Re: [gmx-users] gromacs 4.5.5 cygwin installation error message
> >
> > On 11/03/2012 12:20 PM, Peter C. Lai wrote:
> > > Is fftw3 properly installed in /usr/local/lib?
> >
> > And of the right precision, like reading the installation guides 
> will warn you...
> >
> > Mark
> >
> > >
> > > On 2012-03-10 03:51:12PM -0800, Wholly Peach wrote:
> > >>     Dear All,
> > >>   For Gromacs installation, my configure command is:
> > >>   ./configure --enable-shared LDFLAGS='-L/usr/local/lib' 
> --disable-threads.
> > >> After make, the error message is as following.
> > >> I am looking forward to getting a reply from you on how to avoid 
> the error message.
> > >> Wholly
> > >>     .....
> > >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bb5): undefined 
> reference to `_fftwf_destroy_plan'
> > >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bcb): undefined 
> reference to `_fftwf_destroy_plan'
> > >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2be1): undefined 
> reference to `_fftwf_destroy_plan'
> > >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2bf7): more 
> undefined references to `_fftwf_destroy_plan' follow
> > >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2c37): undefined 
> reference to `_fftwf_free'
> > >> .libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2d17): undefined 
> reference to `_fftwf_free'
> > >> collect2: ld returned 1 exit status
> > >> Makefile:387: recipe for target `libmd.la' failed
> > >> make[3]: *** [libmd.la] Error 1
> > >> make[3]: Leaving directory 
> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src/mdlib'
> > >> Makefile:302: recipe for target `all-recursive' failed
> > >> make[2]: *** [all-recursive] Error 1
> > >> make[2]: Leaving directory 
> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'
> > >> Makefile:238: recipe for target `all' failed
> > >> make[1]: *** [all] Error 2
> > >> make[1]: Leaving directory 
> `/cygdrive/d/GROMACSNEW/GROMACS455/gromacs-4.5.5/src'
> > >> Makefile:347: recipe for target `all-recursive' failed
> > >> make: *** [all-recursive] Error 1
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> >
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> -- 
> ==================================================================
> Peter C. Lai            | University of Alabama-Birmingham
> Programmer/Analyst        | KAUL 752A
> Genetics, Div. of Research    | 705 South 20th Street
> pcl at uab.edu <mailto:pcl at uab.edu>            | Birmingham AL 35294-4461
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