dolfin team mailing list archive

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Re: _PETSC_COMM_WORLD and _MPI_COMM_WORLD

To: Discussion of DOLFIN development <dolfin-dev@xxxxxxxxxx>
From: "Garth N. Wells" <g.n.wells@xxxxxxxxxx>
Date: Fri, 16 Jun 2006 14:51:50 +0200
In-reply-to: <36969.129.240.228.53.1150457790.squirrel@webmail.uio.no>
Reply-to: Discussion of DOLFIN development <dolfin-dev@xxxxxxxxxx>

I tried linking against PETSc without any add-on solvers (no Hypre,
Spooles, etc) and received the same error, so it doesn't seem related to
the external PETSc packages.

Garth



On Fri, 2006-06-16 at 13:36 +0200, arvenk@xxxxxxxxx wrote:
> It seems like libtool is difficult to integrate with non-libtoolized
> dependencies (e.g. PETSc) :| I'll try and inquire with someone who knows
> libtool better than I do. Is there any way to determine which of the PETSc
> libraries are static btw?
> 
> Arve
> 
> > I rolled back to what we had before. Arve, tell me if you find another
> > solution.
> >
> > /Anders
> >
> >
> > On Fri, Jun 16, 2006 at 10:06:42AM +0200, Garth N. Wells wrote:
> >> On Fri, 2006-06-16 at 09:26 +0200, Anders Logg wrote:
> >> > 	On Thu, Jun 15, 2006 at 05:51:20PM +0200, Beni Stamm wrote:
> >> > > In src/lib/Makefile.am on the below mentioned line there is already
> >> > >
> >> > > libdolfin_la_LIBADD  = @DOLFIN_LTLIBOBJS@
> >> >
> >> > src/lib/Makefile.am should look as follows:
> >> >
> >> >   INCLUDES             = @KERNEL_CFLAGS@
> >> >   lib_LTLIBRARIES      = libdolfin.la
> >> >   libdolfin_la_SOURCES =
> >> >   libdolfin_la_LIBADD  = @DOLFIN_LTLIBOBJS@ @DOLFIN_EXT_LIBS@
> >> >   libdolfin_la_DEPENDENCIES = @DOLFIN_LTLIBOBJS@
> >> >
> >> > The change I made yesterday was to add @DOLFIN_EXT_LIBS@ to fix
> >> > some compilation problems related to linking of PETSc libraries.
> >> >
> >> > If this does not work for everyone, we'll just roll back the fix and
> >> > find another solution. Can anyone else confirm this problem?
> >> >
> >> > Garth, did you do a configure + make clean + make install and it still
> >> > doesn't work?
> >>
> >> I cloned a new version and it doesn't work.Deep in the output when
> >> compiling DOLFIN I do get the warning message
> >>
> >>
> >> *** Warning: Linking the shared library libdolfin.la against the
> >> *** static
> >> library
> >> /usr/local/lib/petsc-2.3.1-p14/externalpackages/spooles-2.2/linux-gnu-c-real-debug/MPI/src/spoolesMPI.a
> >> is not portable!
> >>
> >> *** Warning: Linking the shared library libdolfin.la against the
> >> *** static
> >> library
> >> /usr/local/lib/petsc-2.3.1-p14/externalpackages/spooles-2.2/linux-gnu-c-real-debug/spooles.a
> >> is not portable!
> >>
> >>
> >> I didn't configure Spooles by hand. I just let PETSc download and
> >> configure it. This could be the problem.
> >>
> >> Garth
> >>
> >>
> >>
> >> >
> >> > > (without @DOLFIN_EXT_LIBS@)
> >> > > So, I just added the @DOLFIN_EXT_LIBS@ to check the other
> >> possibility. but
> >> > > while
> >> > > running ./scripts/preconfigure the following error occurs
> >> >
> >> > This is a known bug in the script preconfigure. You need to run
> >> >
> >> >     scripts/preconfigure
> >> >
> >> > without the ./ or otherwise it will break... It's a stupid test to see
> >> > from where the script is run. I didn't have time to find a better
> >> > solution when I wrote it:
> >> >
> >> > CHECK=`echo $0 | cut -d'/' -f1`
> >> > if [ "$CHECK" != "scripts" ]; then
> >> >         echo "This script must be run from the top level directory."
> >> >         exit 1
> >> > fi
> >> >
> >> > If anyone has a better solution, just name it.
> >> >
> >> > /Anders
> >> >
> >> >
> >> > > iacspc79:/Users/stamm/Documents/dolfin-0.6.1 stamm#
> >> ./scripts/preconfigure
> >> > > This script must be run from the top level directory.
> >> > >
> >> > > Although I running this command from the dolfin-0.6.1-level.
> >> > > And I tested with only (without scripts/preconfigure):
> >> > > configure
> >> > > make
> >> > > make install
> >> > > make demo
> >> > >
> >> > > and it doesn't solve the problem.
> >> > >
> >> > > ben
> >> > >
> >> > >
> >> > > On Jun 15, 2006, at 5:30 PM, Anders Logg wrote:
> >> > >
> >> > >
> >> > >     Strange... works for me. I checked it before committing.
> >> > >
> >> > >     Does it work if you change in src/lib/Makefile.am on the line
> >> > >
> >> > >     libdolfin_la_LIBADD  = @DOLFIN_LTLIBOBJS@ @DOLFIN_EXT_LIBS@
> >> > >
> >> > >     Remove @DOLFIN_EXT_LIBS@ and then run scripts/preconfigure and
> >> > >     configure.
> >> > >
> >> > >     Does it work then?
> >> > >
> >> > >     /Anders
> >> > >
> >> > >     On Thu, Jun 15, 2006 at 05:02:46PM +0200, Garth N. Wells wrote:
> >> > >
> >> > >         Looks like something got messed up with the changes (made
> >> today) to how
> >> > >         libraries are linked. I can't link anything, and get the
> >> error
> >> > >
> >> > >         . . . . /libdolfin.so: undefined reference to `MAIN__'
> >> > >         collect2: ld returned 1 exit status
> >> > >         make: *** [dolfin-poisson] Error 1
> >> > >
> >> > >
> >> > >         Garth
> >> > >
> >> > >         On Thu, 2006-06-15 at 15:39 +0200, Beni Stamm wrote:
> >> > >
> >> > >             Hello,
> >> > >             I've just successfully compiled dolfin on my mac osx
> >> 10.5
> >> > >             (intel-based). everything worked fine.
> >> > >             I also did successfully "make demo" but while executing
> >> for example
> >> > >             "dolfin-poisson" the
> >> > >             following error occurs:
> >> > >
> >> > >
> >> > >             iacspc79:/Users/stamm/Documents/dolfin-0.6.1/src/demo/pde/poisson
> >> > >             root# ./dolfin-poisson
> >> > >             dyld: Symbol not found: _PETSC_COMM_WORLD
> >> > >               Referenced from: /usr/local/lib/libdolfin.0.dylib
> >> > >               Expected in: flat namespace
> >> > >
> >> > >
> >> > >             Trace/BPT trap
> >> > >
> >> > >
> >> > >             Is there a conflict between _PETSC_COMM_WORLD  and
> >> > >             _MPI_COMM_WORLD?
> >> > >             Do I have
> >> > >             to change something in my petsc/mpi installation? Does
> >> anyone knows
> >> > >             how to handle this
> >> > >             problem?
> >> > >
> >> > >
> >> > >             thanks for your answer
> >> > >
> >> > >
> >> > >             benjamin stamm
> >> > >
> >> > >
> >> > >             p.s.  I had to downgrade the gcc compiler from 4.2 to
> >> 4.0.1 as the
> >> > >             4.2
> >> > >             seems to be more strict than the older versions
> >> > >             (I had some errors during compilation).
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >             _________________________________________________________
> >> > >
> >> > >
> >> > >             Benjamin Stamm
> >> > >             Modeling and Scientific Computing
> >> > >             CMCS-IACS-EPFL
> >> > >             Station 8
> >> > >             CH-1015 Lausanne
> >> > >             Switzerland
> >> > >
> >> > >
> >> > >             Tel: +41 21 693 55 09,
> >> > >             http://iacs.epfl.ch/~stamm/
> >> > >             _________________________________________________________
> >> > >
> >> > >
> >> > >
> >> > >
> >> > >             _______________________________________________
> >> > >             DOLFIN-dev mailing list
> >> > >             DOLFIN-dev@xxxxxxxxxx
> >> > >             http://www.fenics.org/cgi-bin/mailman/listinfo/dolfin-dev
> >> > >
> >> > >
> >> > >
> >> > >         _______________________________________________
> >> > >         DOLFIN-dev mailing list
> >> > >         DOLFIN-dev@xxxxxxxxxx
> >> > >         http://www.fenics.org/cgi-bin/mailman/listinfo/dolfin-dev
> >> > >
> >> > >
> >> > >     _______________________________________________
> >> > >     DOLFIN-dev mailing list
> >> > >     DOLFIN-dev@xxxxxxxxxx
> >> > >     http://www.fenics.org/cgi-bin/mailman/listinfo/dolfin-dev
> >> > >
> >> > >
> >> > > _________________________________________________________
> >> > >
> >> > > Benjamin Stamm
> >> > > Modeling and Scientific Computing
> >> > > CMCS-IACS-EPFL
> >> > > Station 8
> >> > > CH-1015 Lausanne
> >> > > Switzerland
> >> > >
> >> > > Tel: +41 21 693 55 09,
> >> > > http://iacs.epfl.ch/~stamm/
> >> > > _________________________________________________________
> >> > >
> >> > >
> >> >
> >> > > _______________________________________________
> >> > > DOLFIN-dev mailing list
> >> > > DOLFIN-dev@xxxxxxxxxx
> >> > > http://www.fenics.org/cgi-bin/mailman/listinfo/dolfin-dev
> >> >
> >> >
> >> > _______________________________________________
> >> > DOLFIN-dev mailing list
> >> > DOLFIN-dev@xxxxxxxxxx
> >> > http://www.fenics.org/cgi-bin/mailman/listinfo/dolfin-dev
> >>
> >>
> >> _______________________________________________
> >> DOLFIN-dev mailing list
> >> DOLFIN-dev@xxxxxxxxxx
> >> http://www.fenics.org/cgi-bin/mailman/listinfo/dolfin-dev
> >
> 
> 
> 
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References

_PETSC_COMM_WORLD and _MPI_COMM_WORLD
From: Beni Stamm, 2006-06-15
Re: _PETSC_COMM_WORLD and _MPI_COMM_WORLD
From: Garth N. Wells, 2006-06-15
Re: _PETSC_COMM_WORLD and _MPI_COMM_WORLD
From: Anders Logg, 2006-06-15
Re: _PETSC_COMM_WORLD and _MPI_COMM_WORLD
From: Beni Stamm, 2006-06-15
Re: _PETSC_COMM_WORLD and _MPI_COMM_WORLD
From: Anders Logg, 2006-06-16
Re: _PETSC_COMM_WORLD and _MPI_COMM_WORLD
From: Garth N. Wells, 2006-06-16
Re: _PETSC_COMM_WORLD and _MPI_COMM_WORLD
From: Anders Logg, 2006-06-16
Re: _PETSC_COMM_WORLD and _MPI_COMM_WORLD
From: arvenk, 2006-06-16