[gmx-users] MPI compilation without shared FFTW libraries

Hans Martin Senn senn at chem.gla.ac.uk
Wed Feb 27 21:36:01 CET 2008

Dear all

I am trying to compile a parallel executable of GROMACS using gcc and  
the SCore MPI implementation on a Linux/Opteron cluster.  
(Essentially, SCore is a highly efficient MPICH incarnation that  
circumvents the TCP/IP stack; see: http://www.pccluster.org/.)

SCore MPI requires linking to some extra libraries that exist only as  
static libraries. Hence, compiling GROMACS with --enable-shared fails  
with the expected complaints along the lines of "relocation  
R_X86_64_32 against `a local symbol' can not be used when making a  
shared object; recompile with -fPIC".

So I switched to --disable-shared to make a static executable.  
However, this fails as well because the GROMACS build procedure still  
tries to link explicitly to the shared version of the FFTW libraries  

mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused - 
funroll-all-loops -o mdrun glaasje.o gctio.o init_sh.o ionize.o  
do_gct.o relax_sh.o repl_ex.o xutils.o compute_io.o md.o mdrun.o  
genalg.o  -L/usr/local/lib ../mdlib/.libs/libmd_d.a -L/usr/X11R6/ 
lib64 ../gmxlib/.libs/libgmx_d.a -lnsl /usr/local/lib/libfftw3.so - 
lm /usr/X11R6/lib64/libXm.so -lXmu -lXext -lXp -lXt -lSM -lICE -lX11

Of course, the linker falls over, complaining that:
ld: attempted static link of dynamic object `/usr/local/lib/libfftw3.so'

So my question is if and how I can convince the make procedure to use  
the static version of the FFTW library, which is available on the  
Maybe somebody could also comment on why the FFTW lib needs to be  
linked against explicitly at all, rather than using -lfftw3 and  
letting the linker figure out whether to use the static or the shared  

Any hints would be greatly appreciated!


Dr. Hans Martin Senn
Lord Kelvin/Adam Smith Research Fellow
University of Glasgow
Department of Chemistry
Joseph Black Building, University Avenue, Glasgow G12 8QQ, Scotland/UK
E-mail: senn at chem.gla.ac.uk, phone: +44 141 330 6574, fax: +44 141  
330 4888

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