[gmx-users] gromacs 4.5.5 cygwin installation error message

Mark Abraham Mark.Abraham at anu.edu.au
Mon Mar 12 01:21:26 CET 2012 

On 12/03/2012 8:14 AM, Wholly Peach wrote:
> Dear All,
> For fftw, I use the following configure,
> ./configure --enable-threads --enable-float --enable-sse 
> --prefix=/home/ABC/fftw

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.

> 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'

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.

Mark

> 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> <mailto:pcl at uab.edu>
>> *To:* Wholly Peach <whollypeach at yahoo.com> 
>> <mailto:whollypeach at yahoo.com>; Discussion list for GROMACS users 
>> <gmx-users at gromacs.org> <mailto: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
>> > >> -- gmx-users mailing list gmx-users at gromacs.org 
>> <mailto: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!
>> > >> Please don't post (un)subscribe requests to the list. Use the
>> > >> www interface or send it to gmx-users-request at gromacs.org 
>> <mailto:gmx-users-request at gromacs.org>.
>> > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > >
>> >
>> > -- gmx-users mailing list gmx-users at gromacs.org 
>> <mailto: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!
>> > Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org 
>> <mailto:gmx-users-request at gromacs.org>.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> > --
>> > gmx-users mailing list gmx-users at gromacs.org 
>> <mailto: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!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-request at gromacs.org 
>> <mailto:gmx-users-request at gromacs.org>.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>> -- 
>> ==================================================================
>> 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
>> (205) 690-0808            |
>> ==================================================================
>>
>>
>>
>>
>>
>
>
> -- 
> gmx-users mailing list gmx-users at gromacs.org 
> <mailto: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!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org 
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120312/aac21332/attachment.html>

More information about the gromacs.org_gmx-users mailing list