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

Wholly Peach whollypeach at yahoo.com
Sun Mar 11 09:03:21 CET 2012 

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