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

[Qinghua Liao]

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