[gmx-users] gromacs 4.5.5 cygwin installation error message
Wholly Peach
whollypeach at yahoo.com
Sun Mar 11 22:14:00 CET 2012
Dear All,
For fftw, I use the following configure,
./configure --enable-threads --enable-float --enable-sse --prefix=/home/ABC/fftw
For gromacs, I use the following configure,
./configure --with-fft=fftw3 --disable-threads --prefix=/home/ABC/GROMACS --enable-shared LDFLAGS='-L/home/ABC/fftw/lib' CPPFLAGS='-I/home/ABC/fftw/include'
But in the make step of gromacs, I still got a series of error message.
I am looking forward to getting some suggesrions to solve it.
Cheers,
Wholly
........libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2489): undefined reference to `_fftwf_destroy_plan'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x249f): undefined reference to `_fftwf_destroy_plan'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x24b5): undefined reference to `_fftwf_destroy_plan'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x24cb): more undefined references to `_fftwf_destroy_plan' follow
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2506): undefined reference to `_fftwf_free'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2512): undefined reference to `_fftwf_free'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x251e): undefined reference to `_fftwf_free'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x25ce): undefined reference to `_fftwf_execute_dft'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x268e): undefined reference to `_fftwf_execute_dft'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2755): undefined reference to `_fftwf_execute_dft_c2r'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2770): undefined reference to `_fftwf_execute_dft_r2c'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2825): undefined reference to `_fftwf_execute_dft_c2r'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2840): undefined reference to `_fftwf_execute_dft_r2c'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x28ee): undefined reference to `_fftwf_execute_dft'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x29b5): undefined reference to `_fftwf_execute_dft_c2r'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x29d0): undefined reference to `_fftwf_execute_dft_r2c'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2a7e): undefined reference to `_fftwf_execute_dft'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b45): undefined reference to `_fftwf_execute_dft_c2r'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b60): undefined reference to `_fftwf_execute_dft_r2c'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b8a): undefined reference to `_fftwf_destroy_plan'
.libs/gmx_fft_fftw3.o:gmx_fft_fftw3.c:(.text+0x2b9f): undefined reference to `_fftwf_destroy_plan'
.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'
.......
----- Forwarded Message -----
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 6:26 PM
Subject: Re: Fw: [gmx-users] gromacs 4.5.5 cygwin installation error message
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>
>> 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
>> >> -- gmx-users mailing list gmx-users at gromacs.org
>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> >
>>
>> -- gmx-users mailing list gmx-users at gromacs.org
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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 | Birmingham AL 35294-4461
>(205) 690-0808 |
>==================================================================
>
>
>
>
>
>
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