[gmx-users] cannot compile parallel version

Thu Jul 8 18:48:35 CEST 2004

Hi David,

I just did as you pointed me out: added /usr/local/fftw and
/usr/local/lam to /etc/ld.so.conf, ran ldconfig e then ran
mpirun -np2 mdrun_mpi ... but I stil get the error message:

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
-----------------------------------------------------------------------------
It seems that [at least] one of the processes that was started with
mpirun did not invoke MPI_INIT before quitting (it is possible that
more than one process did not invoke MPI_INIT -- mpirun was only
notified of the first one, which was on node n0).

mpirun can *only* be used with MPI programs (i.e., programs that
invoke MPI_INIT and MPI_FINALIZE).  You can use the "lamexec" program
to run non-MPI programs over the lambooted nodes.
-----------------------------------------------------------------------------

any other clue? as I said, I had previouly version 3.1.4 running
in parallel on the same machine/OS. I just cannot figure out what
could be wrong now.

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 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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> --
> 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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