dolfin team mailing list archive

[Murtazo Nazarov <murtazo@xxxxxxxxxx>]

On 09/09/2010 05:21 PM, Anders Logg wrote:
> Question #124644 on DOLFIN changed:
> https://answers.launchpad.net/dolfin/+question/124644
>
>      Status: Open =>  Answered
>
> Anders Logg proposed the following answer:
> On Thu, Sep 09, 2010 at 05:18:42PM +0200, Murtazo Nazarov wrote:
>    
> > On 09/09/2010 12:30 AM, Anders Logg wrote:
> >      
> > > Question #124644 on DOLFIN changed:
> > > https://answers.launchpad.net/dolfin/+question/124644
> > >
> > >      Status: Open =>   Answered
> > >
> > > Anders Logg proposed the following answer:
> > > On Wed, Sep 08, 2010 at 09:57:24PM -0000, Murtazo Nazarov wrote:
> > >        
> > > > Question #124644 on DOLFIN changed:
> > > > https://answers.launchpad.net/dolfin/+question/124644
> > > >
> > > > Murtazo Nazarov gave more information on the question:
> > > > Murtazo Nazarov wrote:
> > > >          
> > > > > Question #124644 on DOLFIN changed:
> > > > > https://answers.launchpad.net/dolfin/+question/124644
> > > > >
> > > > >      Status: Answered =>   Open
> > > > >
> > > > > Murtazo Nazarov is still having a problem:
> > > > > Anders Logg wrote:
> > > > >
> > > > >            
> > > > > > Question #124644 on DOLFIN changed:
> > > > > > https://answers.launchpad.net/dolfin/+question/124644
> > > > > >
> > > > > >      Status: Open =>   Answered
> > > > > >
> > > > > > Anders Logg proposed the following answer:
> > > > > > On Wed, Sep 08, 2010 at 05:50:29PM -0000, Murtazo Nazarov wrote:
> > > > > >
> > > > > >
> > > > > >              
> > > > > > > Question #124644 on DOLFIN changed:
> > > > > > > https://answers.launchpad.net/dolfin/+question/124644
> > > > > > >
> > > > > > >      Status: Answered =>   Open
> > > > > > >
> > > > > > > Murtazo Nazarov is still having a problem:
> > > > > > > There was some problem with dolfin.pc. Actually I modified the file. It
> > > > > > > looks like the following:
> > > > > > >
> > > > > > > # pkg-config configuration for DOLFIN
> > > > > > > prefix=/NOBACKUP/murtazo/fenics
> > > > > > > exec_prefix=/NOBACKUP/murtazo/fenics
> > > > > > > libdir=${exec_prefix}/lib
> > > > > > > includedir=${prefix}/include
> > > > > > > compiler=/usr/bin/mpicxx
> > > > > > > definitions= -DBOOST_UBLAS_NDEBUG -DHAS_PETSC -DHAS_UMFPACK -DHAS_CHOLMOD -DHAS_SCOTCH -DHAS_PARMETIS -DHAS_CGAL -DHAS_ZLIB -DHAS_CPPUNIT -DHAS_MPI -DMPICH_IGNORE_CXX_SEEK
> > > > > > > swigcflags=
> > > > > > > extlibs=
> > > > > > >
> > > > > > > Name: DOLFIN
> > > > > > > Description: Dynamic Object-oriented Library for FINite element computation
> > > > > > > Version: 0.9.9
> > > > > > > Requires: ufc-1 libxml-2.0
> > > > > > > Conflicts:
> > > > > > > Libs:  -L${libdir} -ldolfin
> > > > > > > Cflags:  -DBOOST_UBLAS_NDEBUG -DHAS_PETSC -DHAS_UMFPACK -DHAS_CHOLMOD -DHAS_SCOTCH -DHAS_PARMETIS -DHAS_CGAL -DHAS_ZLIB -DHAS_CPPUNIT -DHAS_MPI -DMPICH_IGNORE_CXX_SEEK  -DBOOST_UBLAS_NDEBUG -DHAS_PETSC -DHAS_UMFPACK -DHAS_CHOLMOD -DHAS_SCOTCH -DHAS_PARMETIS -DHAS_CGAL -DHAS_ZLIB -DHAS_CPPUNIT -DHAS_MPI -DMPICH_IGNORE_CXX_SEEK  -frounding-math -I/usr/lib/openmpi/include/openmpi -I/usr/include/cppunit -I/usr/include/suitesparse -I/usr/lib/openmpi/lib -I/usr/lib/openmpi/include -I/NOBACKUP/murtazo/fenics/src/petsc-3.1-p4/include -I/NOBACKUP/murtazo/fenics/src/petsc-3.1-p4/linux-gnu-cxx-opt/include -I/usr/include -I/NOBACKUP/murtazo/fenics/include -I/usr/include/libxml2 -I/NOBACKUP/murtazo/fenics/src/dolfin-0.9.9  -I${includedir}
> > > > > > >
> > > > > > >
> > > > > > >                
> > > > > > Keep modifying it. Looks like you are missing some flags like -lpetsc.
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >              
> > > > > I tried to include -lpetsc and even more:
> > > > >
> > > > > Libs:  -L${libdir} -lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat
> > > > > -lpetscvec -lpetsc -lX11 -ldolfin
> > > > >
> > > > > Still there is the same error.
> > > > >
> > > > > murtazo
> > > > >
> > > > >
> > > > >            
> > > > I have to say that despite my solver all demos work perfectly even
> > > > without adding this petsc links.
> > > >          
> > > I think that is because the demos are compiled using CMake, and the
> > > generated DOLFIN CMake file is correct while the DOLFIN pkg-config
> > > file is missing some important flags.
> > >
> > >        
> > Then, is CMake the only way for the fenics-apps or is there
> > generality for make and scons for example?
> >
> > murtazo
> >      
> Johannes pushed a fix for the pkg-config problem today. Try to pull
> the latest version and see if it solves your problem.
>
> --
> Anders
>
>    

I installed again the latest unstable dolfin, but the problem is still 
there:
...
g_entropy/unicorn/EntRes_2_2D.o -L/NOBACKUP/murtazo/unicorn/local/lib 
-L/usr/local/lib -L/NOBACKUP/murtazo/fenics_latest/src/lib 
-L/usr/lib/atlas -L/usr/lib/gcc/x86_64-linux-gnu/4.4.3 
-L/NOBACKUP/murtazo/fenics_latest/src/petsc-3.1-p4/linux-gnu-cxx-opt/lib 
-L/NOBACKUP/murtazo/fenics_latest/src/slepc-3.1-p2/linux-gnu-cxx-opt/lib 
-lunicorn -lopen-pal -lopen-rte -lmpi -lmpi_cxx -lcppunit -lz 
-lboost_thread-mt -lgmp -lmpfr -lgmpxx -lCGAL -lptscotcherr -lptscotch 
-llapack -lccolamd -lcolamd -lcamd -lcholmod -latlas -lamd -lumfpack 
-ldl -lpthread -lgcc_s -lutil -lnsl -lstdc++ -lm -lgfortran -lmpi_f77 
-lmpi_f90 -lblas -lHYPRE -lblacs -lscalapack -lmetis -lparmetis -lpord 
-lmumps_common -lzmumps -lsmumps -ldmumps -lcmumps -lX11 -lpetsc -lslepc 
-lboost_system -lboost_program_options -lboost_filesystem -larmadillo 
-ldolfin -lxml2
scons: done building targets.
na09:run > ./demo
./demo: symbol lookup error: 
/NOBACKUP/murtazo/fenics_latest/src/lib/libdolfin.so.0: undefined 
symbol: _Z26KSPMonitorTrueResidualNormP6_p_KSPidPv

It seems to me there all links there. Dolfin demos work without any problem.

murtazo