[gmx-users] Re: compilation of gromacs-4.5.4 with fftw-3.3 for double precision versition

Christoph Junghans junghans at votca.org
Wed Mar 27 16:15:20 CET 2013 

> Date: Wed, 27 Mar 2013 15:14:19 +0100
> From: Mark Abraham <mark.j.abraham at gmail.com>
> Subject: Re: [gmx-users] compilation of gromacs-4.5.4 with fftw-3.3
>         for double      precision versition
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <CAMNuMATT-1hbT1jR8BwpfnXHXmCDTEGsZLVP4wk-18CqgfSCvQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Yes, --enable-long-double is useless for FFTW+GROMACS.
Actually long-double is, like single precision, a different library - libffwl.
Same is true for fftw's quad precision

>
> Mark
>
> On Wed, Mar 27, 2013 at 3:03 PM, Qinghua Liao <fantasticqhl at gmail.com>wrote:
>
>> Hi all,
>>
>> Finally I compiled it successfully when I used the following commands:
>>
>> 1077  ./configure --prefix=/usr/users/iff_th2/liao/fftw-3.3
>> --enable-threads --enable-shared --enable-mpi CC=gcc
>>  1078  make
>>  1079  make install
>>  1080  history | grep export
>>  1081  export CPPFLAGS=-I/usr/users/iff_th2/liao/fftw-3.3/include
>>  1082  export LDFLAGS=-L/usr/users/iff_th2/liao/fftw-3.3/lib
>>  1083  cd ../gromacs454/
>>  1084  history | grep configure
>>  1085  ./configure --prefix=/usr/users/iff_th2/liao/gromacs454/
>> --enable-double --enable-threads CC=gcc --disable-gcc41-check --enable-mpi
>> --program-suffix=_d --enable-shared
>>  1086  make
>>  1087  make install
>>
>> The only difference is that I delete the option of --enable-long-double for
>> compiling fftw and add the option of --enable-shared for compiling gromacs.
>>
>> Thanks all for the suggestions.
>>
>> All the best.
>> Qinghua Liao
>>
>>
>> On Wed, Mar 27, 2013 at 2:04 PM, Ahmet yıldırım <ahmedo047 at gmail.com>
>> wrote:
>>
>> > cd
>> > mkdir fftw3.3
>> > cd Desktop
>> > wget http://www.fftw.org/fftw-3.3.tar.gz
>> > tar xzvf fftw-3.3.tar.gz
>> > cd fftw-3.3
>> > ./configure --prefix=/home/manchu/fftw3.3 --enable-threads --enable-sse2
>> > --enable-shared
>> > make
>> > make install
>> >
>> > cd
>> > mkdir gromacs_install
>> > cd Desktop
>> > wget ftp://ftp.gromacs.org/pub/gromacs/gromac­s-4.5.5.tar.gz
>> > tar xzvf gromacs-4.5.5.tar.gz
>> > cd gromacs-4.5.5
>> > ./configure --prefix=/home/manchu/gromacs_install
>> > LDFLAGS=-L/home/manchu/fftw3.3/lib
>> CPPFLAGS=-I/home/manchu/fftw3.3/include
>> > --disable-float
>> > make
>> > make install
>> >
>> > Executables are in /home/manchu/gromacs/bin
>> > Reference:http://www.youtube.com/watch?v=bxWjWmdf6xw
>> >
>> > 2013/3/27 Qinghua Liao <fantasticqhl at gmail.com>
>> >
>> > > Dear Justin,
>> > >
>> > > Thanks very much for your reply! Yeah, I did not add the option of
>> > > --enable-shared for compilation of gromacs 4.5.4, but it still failed
>> > after
>> > > I added this option for the compilation.
>> > > For the compilations I posted in the last e-mail, I do add the option
>> of
>> > > --enable-shared in compilation of fftw 3.3, but not for compilation of
>> > > gromacs 4.5.4. Problem remains unsolved.
>> > >
>> > > I choose this  old version is to keep the simulations consistent with
>> > > previous simulations. Thanks for the suggestion!
>> > >
>> > > All the best,
>> > > Qinghua Liao
>> > >
>> > >
>> > > On Wed, Mar 27, 2013 at 12:59 PM, Justin Lemkul <jalemkul at vt.edu>
>> wrote:
>> > >
>> > > >
>> > > >
>> > > > On 3/27/13 6:57 AM, Qinghua Liao wrote:
>> > > >
>> > > >> Dear gmx users,
>> > > >>
>> > > >> I tried to compile gromacs 4.5.4 with double precision, but it
>> failed.
>> > > The
>> > > >> reason was a little wired.
>> > > >>
>> > > >> Firstly, I used the following commands to compile gromacs 4.5.4
>> > together
>> > > >> with fftw 3.3 for serial and parallel version with single precision,
>> > > and I
>> > > >> made it successfully.
>> > > >>
>> > > >>
>> > > >>   1014  ./configure --prefix=/usr/users/iff_th2/**liao/fftw-3.3
>> > > >> --enable-sse
>> > > >> --enable-threads --enable-float --enable-shared CC=gcc
>> > > >>   1015  make
>> > > >>   1016  make install
>> > > >>   1017  make distclean
>> > > >>   1018  export CPPFLAGS=-I/usr/users/iff_th2/**liao/fftw-3.3/include
>> > > >>   1019  export LDFLAGS=-L/usr/users/iff_th2/**liao/fftw-3.3/lib
>> > > >>
>> > > >>   1022  mv gromacs-4.5.4 gromacs454
>> > > >>   1023  cd gromacs454/
>> > > >>
>> > > >>   1026  ./configure --prefix=/usr/users/iff_th2/**liao/gromacs454/
>> > > >> --enable-float --enable-threads CC=gcc --disable-gcc41-check
>> > > >>   1027  make
>> > > >>   1028  make install
>> > > >>
>> > > >>   1031  make distclean
>> > > >>   1032  cd ../fftw-3.3
>> > > >>   1034  ./configure --prefix=/usr/users/iff_th2/**liao/fftw-3.3
>> > > >> --enable-sse
>> > > >> --enable-threads --enable-float --enable-shared --enable-mpi CC=gcc
>> > > >>   1035  make
>> > > >>   1036  make install
>> > > >>   1037  make distclean
>> > > >>   1038  cd ../gromacs454/
>> > > >>   1039  ls
>> > > >>   1040  make distclean
>> > > >>   1041  ./configure --prefix=/usr/users/iff_th2/**liao/gromacs454/
>> > > >> --enable-float --enable-threads CC=gcc --disable-gcc41-check
>> > > --enable-mpi
>> > > >> --program-suffix=_mpi
>> > > >>   1042  make
>> > > >>   1043  make install
>> > > >>   1044  make distclean
>> > > >>
>> > > >> But when I used these similar commands to compile for the double
>> > > >> precision,
>> > > >> it failed.
>> > > >>
>> > > >>
>> > > >>   1049  ./configure --prefix=/usr/users/iff_th2/**liao/fftw-3.3
>> > > >> --enable-long-double --enable-threads --enable-shared --enable-mpi
>> > > CC=gcc
>> > > >>   1050  make
>> > > >>   1051  make install
>> > > >>   1052  make distclean
>> > > >>   1053  cd ../gromacs454/
>> > > >>   1054  make distclean
>> > > >>   1055  ./configure --prefix=/usr/users/iff_th2/**liao/gromacs454/
>> > > >> --enable-double --enable-threads CC=gcc --disable-gcc41-check
>> > > --enable-mpi
>> > > >> --program-suffix=_d
>> > > >>   1056  make
>> > > >>
>> > > >> The error showed to me was:
>> > > >>
>> > > >> /usr/bin/ld: /usr/local/lib/libfftw3.a(**plan-dft-c2r-2d.o):
>> > relocation
>> > > >> R_X86_64_32 against `a local symbol' can not be used when making a
>> > > shared
>> > > >> object; recompile with -fPIC /usr/local/lib/libfftw3.a: could not
>> read
>> > > >> symbols: Bad value
>> > > >>
>> > > >> I added the option of --with-fPIC, but it was not recognized, and
>> > then I
>> > > >> changed it to --with-pic, but the error was still the same.
>> > > >>
>> > > >> I don't know why gromacs can recognize the fftw library when doing
>> the
>> > > >> single float compilation, but not for the double float compilation,
>> I
>> > > >> already used the shared option. Could someone give me some
>> suggestions
>> > > to
>> > > >> help me this out? Any reply will be appreciated.
>> > > >>
>> > > >>
>> > > > In your last step, you're not using --enable-shared like you did in
>> > every
>> > > > preceding step.  Adding that flag should fix it.
>> > > >
>> > > > http://www.gromacs.org/**Documentation/Installation_**
>> > > > Instructions_4.5#Details_for_**building_the_FFTW_prerequisite<
>> > >
>> >
>> http://www.gromacs.org/Documentation/Installation_Instructions_4.5#Details_for_building_the_FFTW_prerequisite
>> > > >
>> > > >
>> > > > Gromacs 4.5.4 is pretty old; is there any reason you're not using a
>> new
>> > > > version?  You'll get much better performance from 4.6.1.
>> > > >
>> > > > -Justin
>> > > >
>> > > > --
>> > > > ==============================**==========
>> > > >
>> > > > Justin A. Lemkul, Ph.D.
>> > > > Research Scientist
>> > > > Department of Biochemistry
>> > > > Virginia Tech
>> > > > Blacksburg, VA
>> > > > jalemkul[at]vt.edu | (540) 231-9080
>> > > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> > > >
>> > > > ==============================**==========
>> > > > --
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>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > Best Regards,
>> > >
>> > > Qinghua
>> > > --
>> > > gmx-users mailing list    gmx-users at gromacs.org
>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> > >
>> >
>> >
>> >
>> > --
>> > Ahmet Yıldırım
>> > --
>> > gmx-users mailing list    gmx-users at gromacs.org
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>> >
>>
>>
>>
>> --
>> Best Regards,
>>
>> Qinghua
>> --
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>
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--
Christoph Junghans
Web: http://www.compphys.de

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