You need to learn something about how configure and make works. It puts the files into the path specified by the prefix/lib and prefix/include. You *need* to tell gromacs make where to find these files using CPPFLAGS -I and LDFLAGS -L. I gave an example of CPPFLAGS and LDFLAGS several emails ago.
Your alternatives is to *not* use --prefix, which should be installing everything into /usr/local/lib, or don't use fftw3 and use the built-in fftpack which doesn't require external libraries. On 2012-03-11 06:57:38PM -0700, Wholly Peach wrote: > Dear All, > > The FFTW installation works. ABC/fftw exists after the make install. > > But for Gromacs, the /home/ABC/GROMACS cannot be created with the make step > even with the prefix in configuration. And if I create it manually, the > Gromacs make still fail. > > Please keep in mind that the Gromacs make fail from the following step: > > ---- > -out-implib -Xlinker .libs/libmd.dll.a > Creating library file: .libs/libmd.dll.a > .libs/fft5d.o:fft5d.c:(.text+0x140f): undefined reference to > `_fftwf_plan_guru_dft' > .libs/fft5d.o:fft5d.c:(.text+0x18d1): undefined reference to > `_fftwf_plan_guru_dft_r2c' > > ---- > > In addition Mark, do you mean for "--enable-shared" for both means for both > FFTW and GROMACS? > > I am looking your reply. > > Cheers, > > Wholly > > ________________________________ > From: Mark Abraham <mark.abra...@anu.edu.au> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Sent: Monday, 12 March 2012 10:21 AM > Subject: Re: [gmx-users] gromacs 4.5.5 cygwin installation error message > > > 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.abra...@anu.edu.au> > >To: Discussion list for GROMACS users <gmx-users@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 <p...@uab.edu> > >>To: Wholly Peach <whollype...@yahoo.com>; Discussion list for GROMACS users > >><gmx-users@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.abra...@anu.edu.au> > >>> To: Discussion list for GROMACS users <gmx-users@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@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-requ...@gromacs.org. > >>> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > > >>> > >>> -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. > >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >>> -- > >>> gmx-users mailing list gmx-users@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-requ...@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 > >>p...@uab.edu | Birmingham AL 35294-4461 > >>(205) 690-0808 | > >>================================================================== > >> > >> > >> > >> > >> > >> > > > >-- > >gmx-users mailing list gmx-users@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-requ...@gromacs.org. > >Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@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-requ...@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 p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
