[gmx-users] cannot compile parallel version

[David]

On Thu, 2004-07-08 at 17:38, Andre Farias de Moura wrote:
> dear Oliver,
> 
> I have tried your scripts with minor changes, as follows:
> 
> (1) script to install lam-mpi latest version:
> 
> export  LAM_D=/usr/local/lam/;
> export FFTW_D=/usr/local/fftw/;
> 
> tar -jxvf lam-7.0.6.tar.bz2
> cd lam-7.0.6
> ./configure --prefix=${LAM_D} --with-tcp-short=524288 --with-rpi=usysv
> --with-rsh=ssh
> make
> make install
> 
> 
> (2) script to install fftw:
> 
> wget --passive ftp://ftp.fftw.org/pub/fftw/fftw-2.1.5.tar.gz
> tar -zxvf fftw-2.1.5.tar.gz
> cd fftw-2.1.5
> 
> export  LAM_D=/usr/local/lam/;
> export FFTW_D=/usr/local/fftw/;
> export PATH=${LAM_D}/bin:${PATH}   # so mpicc gets found
> 
> CPPFLAGS="-I${LAM_D}/include" \
>   LDFLAGS="-L${LAM_D}/lib" \
>   ./configure --prefix=${FFTW_D} --enable-type-prefix --enable-mpi
> make
> make install
> 
> 
> (3) script ot install mdrun parallel version:
> 
> export  LAM_D=/usr/local/lam/;
> export FFTW_D=/usr/local/fftw/;
> 
> CPPFLAGS="-I${LAM_D}/include -I${FFTW_D}/include" \
>   LDFLAGS="-L${LAM_D}/lib -L${FFTW_D}/lib" \
>   ./configure --prefix=/opt/gromacs/3.2.1 --without-x \
>       --enable-mpi --program-suffix=_mpi
> make mdrun
> make install-mdrun
> 
> after half an hour running these script I ran mdrun parallel
> version as follows:
> 
> grompp -f bpcdi -c bpcdi -p bpcdi -po out -o bpcdi -np 2
> mpirun -np 2 mdrun_mpi -s bpcdi -o bpcdi -c out -e out -g out -x bpcdi -v
> -np 2
> 
> then I got these error messages:
> 
> mdrun_mpi: relocation error: /usr/local/lib/libsfftw_mpi.so.2: symbol
> errno, version GLIBC_2.0 not defined in file libc.so.6 with link time
> reference
> mdrun_mpi: relocation error: /usr/local/lib/libsfftw_mpi.so.2: symbol
> errno, version GLIBC_2.0 not defined in file libc.so.6 with link time
> reference

Are you sure that the /usr/local is available to all processors?
If so, is /usr/local in the library search path (check /etc/ld.so.conf)

Do you have different linux versions on the different nodes?

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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