[gmx-users] cannot compile parallel version
David
spoel at xray.bmc.uu.se
Thu Jul 8 21:40:34 CEST 2004
On Thu, 2004-07-08 at 18:48, Andre Farias de Moura wrote:
> 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:
OK, try this first
ldd mdrun_mpi
and see which libraries it needs.
Then, you need to add /usr/local/lib to the /etc/ld.so.conf file
and run ldconfig. Rerun the ldd command to see if that solves the
problem.
>
> 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
> > > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > >
> > > > _______________________________________________
> > > > gmx-users mailing list
> > > > gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-request at gromacs.org.
> > > >
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > --
> > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users
mailing list