[gmx-users] How to install GROMACS in 64-bit?

Mark Abraham Mark.Abraham at anu.edu.au
Tue May 29 10:48:15 CEST 2012


On 29/05/2012 6:37 PM, a a wrote:
> Dear Sir/Madam,
>
> Thanks for the insightful comments from the experts.    Follows the 
> steps, I found the source of error:
>
> This what I have done:
>
> ====================================================
> In the following directory /home/softwares/fftw-3.0.1:
> ./configure --enable-shared --prefix=/home/softwares/fftw301
> make
> make install
>
> In the .bash file:
> export CPPFLAGS="-I/home/softwares/fftw301/include"
> export LDFLAGS="-L/home/softwares/fftw301/lib"
>
> go to the following directory /home/softwares/gromacs-4.5.5:
> ./configure --enable-shared --prefix=/home/softwares/g455
> make
> ============================================= ==============
>
> In the middle of the make, I found this error message:
>
> ==========================================================
>
> /usr/bin/ld: /usr/local/lib/libfftw3f.a(alloc.o): relocation 
> R_X86_64_32 against `.rodata.str1.1' can not be used when making a 
> shared object; recompile with -fPIC
> /usr/local/lib/libfftw3f.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[3]: *** [libmd.la] Error 1
> make[3]: Leaving directory `/home/softwares/gromacs-4.5.5/src/mdlib'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/home/softwares/gromacs-4.5.5/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/home/softwares/gromacs-4.5.5/src'
> make: *** [all-recursive] Error 1
>
> ============================================================
>
> It seems to be a problem of 64 and 32 bit, my workstation is a 64 bit 
> machine and the OS is also 64 bit, what should I do to make sure both 
> the fftw-3.0.1 library and GROMACS are compiled with 64 bit settings?

I would start by observing that those error messages pertain to an 
installation of FFTW that configure found in /usr/local/lib, and not the 
one in /home/softwares. You have to sort that out first, since this 
error messages indicates the need to use FFTW configured with 
--enable-shared, per the link I gave last time.

Mark
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