[gmx-users] cannot compile parallel version

[Andre Farias de Moura]

Hi David,

indeed /usr/local is not on ld.so.conf, what should I do:
add it to this file or run all those scripts again?

about the nodes OS, it's just one dual box, so it's the same
OS for both processors.

thanks again,

andre'

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
    Dr. Andre' Farias de Moura
  Laboratorio de Quimica Teorica
Universidade Federal de Sao Carlos
     Sao Carlos - SP - Brasil
/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

On Thu, 8 Jul 2004, David wrote:

> 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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