[gmx-users] gromacs 4.5.5 cygwin installation error message
Peter C. Lai
pcl at uab.edu
Mon Mar 12 03:11:50 CET 2012
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.Abraham at anu.edu.au>
> To: Discussion list for GROMACS users <gmx-users at 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.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!
> >>> >> Please don't post (un)subscribe
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> >>> >> www interface or send it to 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
> >>> 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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> >>
> >>> --
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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 |
> >>==================================================================
> >>
> >>
> >>
> >>
> >>
> >>
> >
> >--
> >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!
> >Please don't post (un)subscribe requests to the list. Use
> the
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> >Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >
> >
> >
>
> --
> gmx-users mailing list gmx-users at gromacs.org
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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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