[gmx-developers] difficluties in compiling gromacs

[Mark Abraham]

David van der Spoel wrote:
> On 1/12/10 9:31 PM, Jin Wu wrote:
>> I get the following error message when I install gromacsv4.0.7. the 
>> commands I run are as follows:
>> /home/jinwu/swinstall/gromacs/v4.0.7/fftw-3.2.2 /configure 
>> --enable-threads --enable-float --enable-sse
> don't use the --enable-threads

The installation instructions have for years recommended compiling FFTW 
with threads, and GROMACS without.

>> make
>> make install
>> /home/jinwu/swinstall/gromacs/v4.0.7/gromacs-4.0.7/configure 
>> --with-fft=fftw3 --without-x --enable-shared
>> make
>> /usr/bin/ld: /usr/local/lib/libfftw3f.a(plan-dft-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/libfftw3f.a: could not read symbols: Bad value

That looks like a problem with linking. If FFTW built only static 
libraries, then GROMACS may struggle to generate shared ones. I suggest 
  --enable-shared on both configure lines, or neither.

Mark

>> collect2: ld returned 1 exit status
>> make[3]: *** [libmd.la] Error 1
>> make[3]: Leaving directory 
>> `/home/jinwu/swinstall/v4.0.7/gromacs-4.0.7/src/mdlib'
>> make[2]: *** [all-recursive] Error 1
>> make[2]: Leaving directory 
>> `/home/jinwu/swinstall/v4.0.7/gromacs-4.0.7/src'
>> make[1]: *** [all] Error 2
>> make[1]: Leaving directory 
>> `/home/jinwu/swinstall/v4.0.7/gromacs-4.0.7/src'
>> make: *** [all-recursive] Error 1
>>
> 
>