[gmx-users] fftw library problem in gromacs installation

Mark Abraham mark.abraham at anu.edu.au
Sun May 30 22:17:25 CEST 2010

----- Original Message -----
From: jagannath mondal <jmondal2004 at yahoo.co.in>
Date: Monday, May 31, 2010 5:44
Subject: [gmx-users] fftw library problem in gromacs installation
To: gmx-users at gromacs.org

Thanks for the detailed post.

| > Hi ,  I am having a problem in installing gromacs-4  in a suse linux in a powerpc ibm machine. The problem is that > 
> 1.  I first  installed fftw in the following way :> for single precision> ./configure --enable-float --enable-threads --prefix=/N/u/tg-jmondal/BigRed/UTIL/fftw> make> make install> 
> Then for double precision> make distclean> ./configure  --enable-threads --prefix=/N/u/tg-jmondal/BigRed/UTIL/fftw> make> make install> 
> 2. It installed both of them :> 
> 3. Now, when I tried to install gromacs4> 
> ./configure --prefix=/N/u/tg-jmondal/BigRed/UTIL/gromacs_mod_4_gcc/ --enable-mpi --program-suffix=mod_4mpi
 CPPFLAGS=-I/N/u/tg-jmondal/BigRed/UTIL/fftw/include LDFLAGS=-L/N/u/tg-jmondal/BigRed/UTIL/fftw/lib --without-x> 
> Here the mpi version is openmpi> 
> I get following error:> configure: error: Cannot find fftw3f library> But, as you may see I have specified the fftw library in configure script> 
> So, I went inside config.log file and found the following error:> 
> mpicc -o conftest  -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -maltivec -mabi=altivec -std=gnu99 -mcpu=7450 -mtune=970 -I/N/u/tg-jmondal/BigRed/UTIL/fftw/include -maltivec -mabi=altivec -L/N/u/tg-jmondal/BigRed/UTIL/fftw/lib  conftest.c -lfftw3f  -lm  >&5> /usr/bin/ld: skipping incompatible /N/u/tg-jmondal/BigRed/UTIL/fftw/lib/libfftw3f.a when searching for -lfftw3f> /usr/bin/ld: cannot find
> Looks like there is an incompatibility of mpicc with the fftw library and it may cause some problem. But , I do not know how to resolve this incompatibiilty.> 

Yes. For some reason mpicc (which is normally a wrapper for some other compiler) is finding but not liking the libfftw3f.a. You could try installing FFTW with --enable-shared, in case your linker will only do shared libraries, or something. Alternatively, find out whether the compiler will ever link to static libraries, and if not, probably get a new compiler. The problem could also be with a broken MPI library. Talk to your system admins - this problem looks like it is not specific to GROMACS.


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