[gmx-users] cannot compile parallel version

[David]

On Thu, 2004-07-08 at 18:34, Andre Farias de Moura wrote:
> 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?
No,
add it to the file and run ldconfig
then try mdrun 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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> 
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-- 
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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