[gmx-users] cannot compile parallel version

[David]

On Thu, 2004-07-08 at 19:27, Andre Farias de Moura wrote:
> Hi David and Oliver,
> 
> I'm still getting the same error message as before...
> this is getting a little messy for me: indeed, as Oliver
> suggested, there are old fftw versions on /usr/local/lib
> (these came from rpm files I downloaded from gromacs
> homepage). Using these old libraries I was not being
> able to run the gromacs configure script (the mpicc
> error I reported at the begining of this discussion).
> following Oliver suggestion, I downloaded both fftw
> and lam-mpi latest versions and compiled again, this
> time using his scripts. I put lam and fftw on /usr/local
> just because I did not know exactly where they should
> be... anyway, this time I was able to go through the
> whole compilation without any error message, but now
> I'm stuck here.
> 
> shouldn't I begin it from the very begining? I mean:
> isn't easier to remove all the fftw and lam stuff
> from my computer and then begin from a fresh start?
> if so, how can I manage to remove all these libs and
> related stuff?
you can start by removing any rpm leftovers:
rpm -e `rpm -qa | grep fftw`
and see whether mdrun works. if not do recompile.
> 
> 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, Oliver Beckstein wrote:
> 
> > > 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
> >
> > Are your libraries living in /usr/local/fftw (eg
> > /usr/local/fftw/libsrfftw_mpi.so) or are they really in
> > /usr/local/fftw/lib? If the latter is true you would need to ad the
> > .../lib path to /etc/ld.so.config
> >
> > ... and see David's email.
> >
> > > 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
> >
> > Actually, this looks as if you have old fftws in /usr/local/lib---they get
> > picked up instead of the newly compiled ones in /usr/local/fftw/lib. I
> > think putting /usr/local/fftw/lib in ld.so.config before /usr/local/lib
> > should solve the problem.
> >
> >
> > Btw, I remember that I actually compiled my Gromacs with the
> > --enable-all-static option, so no worries about shared libs ;-)
> >
> > oli
> >
> > --
> > Oliver Beckstein * oliver at biop.ox.ac.uk
> >  http://sansom.biop.ox.ac.uk/oliver/
> >
> >
> >
> >
> > _______________________________________________
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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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