[gmx-users] gromacs 4.5.5 cygwin installation error message
Peter C. Lai
pcl at uab.edu
Mon Mar 12 03:18:54 CET 2012
Oops I just saw this. Yeah it could be --enable-shared is broken on this
for cygwin, since the build is breaking during linking.
In an unrelated note, is running gromacs in cygwin supposed to be faster
than running it in a unix/linux virtual machine with paravirt I/O?
On 2012-03-12 11:21:26AM +1100, Mark Abraham wrote:
> 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
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> >> <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
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> >> <mailto:gmx-users-request 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 <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
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> > <mailto:gmx-users-request 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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