[gmx-users] Compiling GROMACS 4.5.6 in Cluster

Agnivo Gosai agnivogromacs14 at gmail.com
Fri Sep 12 20:28:12 CEST 2014

Dear Users

I am facing a problem while compiling the GROMACS source code in my
university cluster. I am laying down my installation procedure step by step

1. Downloaded fftw 3.3.4
2. exported paths of C-compiler and Fortran-compiler
3. Used the following command line to configure FFTW
*./configure --prefix=/home/agosai/GROMACS/fftw-3.3.4-double
--enable-threads --with-pic=-fPIC*
There were no errors.
Proceeded with make and then make install.

4.  Downloaded and unzipped GROMACS 4.5.6 source code
5. exported c++ compiler paths.
6. Defined path to FFTW compilation as follows :-

*export CPPFLAGS="-I/home/agosai/GROMACS/fftw-3.3.4-double/include"export
7. Tried compiling GROMACS as follows :-
*./configure --prefix=/home/agosai/GROMACS/gromacs-4.5.6-double
--disable-float --program-suffix=-4.5.6-double --with-fft=fftw3*

There were no errors.
8. Then used "make"
 Following messages came :-

*ld: /home/agosai/GROMACS/fftw-3.3.4-double/lib/libfftw3.a(mapflags.o):
relocation R_X86_64_32S against `.rodata' can not be used when making a
shared object; recompile with
-fPIC/home/agosai/GROMACS/fftw-3.3.4-double/lib/libfftw3.a: could not read
symbols: Bad valuemake[3]: *** [libmd_d.la <http://libmd_d.la>] Error
1make[3]: Leaving directory
`/home/agosai/GROMACS/gromacs-4.5.6/src/mdlib'make[2]: *** [all-recursive]
Error 1make[2]: Leaving directory
`/home/agosai/GROMACS/gromacs-4.5.6/src'make[1]: *** [all] Error 2make[1]:
Leaving directory `/home/agosai/GROMACS/gromacs-4.5.6/src'make: ***
[all-recursive] Error 1*

I can not proceed to "make install".

I would be highly obliged if my mistake be pointed out and next course of
action is highlighted.

Thanks & Regards

Grad Student

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